Answers Research Journal 8 (2015):273–304. www.answersingenesis.org/arj/v8/mitochondrial_DNA_clocks_linear_speciation_rates.pdf Mitochondrial DNA Clocks Imply Linear Speciation Rates Within “Kinds”
Nathaniel T. Jeanson, Institute for Creation Research, 1806 Royal Lane, Dallas, TX 75229 currently Answers in Genesis, PO Box 510, Hebron, Kentucky 41048. Abstract The mechanism of speciation remains one of the most contested scientific questions among both evolutionists and creationists. The tight linkage between this question and the question of the timing of speciation suggests that answers to the latter may aid the investigation of the former. To date within the young-earth community, no comprehensive studies on the relationship between genetics and the timing of speciation have been performed. In this study, I show that mitochondrial DNA relationships within extant families depict linear rates of speciation, a finding consistent with a mechanism of speciation that involves an originally created heterozygous allele pool fractionated by genetic drift.
Keywords: timing, mechanism, linear speciation rate, molecular clock, mitochondrial DNA
Introduction the Flood outside the Ark. Though many individuals As the history of the origins debate demonstrates, perished in the Flood, God preserved the “kinds.” the mechanism and timing of speciation are tightly Since “kinds” are probably best approximated by linked questions, the answer to each bearing weight the taxonomic rank of family, rather than species on the other. With respect to the first question, or genus (Wood 2006), speciation within a “kind”/ Darwin’s primary answer—natural selection— family has clearly occurred post-Flood. Even before was born out of his understanding of the supposed the Flood, during the ~1700 years from the Creation millions-of-years history of life. If life was ancient Week to the Deluge, speciation likely occurred. and if species appeared slowly and gradually, then However, unlike evolution, this speciation process the slow and gradual process of natural selection had its limits. Scripture does not support the natural seemed a natural fit. biological transformation of one “kind” into another That natural selection will always act with extreme “kind,” but it does support diversification within a slowness, I fully admit . . . I do believe that natural “kind” (see also Jeanson 2013). selection will always act very slowly, often only at long Because the Bible puts the date of creation at intervals of time, and generally on only a very few of 6000–10,000 years ago (Hardy and Carter 2014; the inhabitants of the same region at the same time. McGee 2012) and the date of the Flood around 4350 I further believe, that this very slow, intermittent years ago, speciation under the YE view is much action of natural selection accords perfectly well with more rapid than speciation under the evolutionary what geology tells us of the rate and manner at which view. Hence, rather than rely solely on mutation the inhabitants of this world have changed. (Darwin and natural selection to explain the diversity of life 1859, 108–09) within “kinds,” many YE creationists have proposed Modern evolutionists have followed suit and novel mechanisms for speciation. From transposon taken Darwin’s link one step further, arguing for amplification (Shan 2009) to “variation-inducing the plausibility of evolution via natural selection by genetic elements (VIGEs)” designed within front- citing the antiquity of the earth (e.g., Dawkins 2009). loaded genomes (“baranomes”) (Terborg 2008, 2009) Conversely, the young-earth (YE) creation view to “directed genetic mutations” (Lightner 2009), connects the mechanism and timing of speciation, YE creationists have wrestled with a multitude of but in a manner very different from evolutionists. processes in order to explain how a host of species The text of Genesis sets boundaries for the YE might have arisen in the last few thousand years. answers. According to Genesis 1, God supernaturally Several specific observations within this general created different “kinds” of creatures and did not YE creation view have spawned unique proposals derive them via evolution from pre-existing life on the mechanism. Based on the similarity between forms. Subsequently, two (unclean) or seven (clean) creatures depicted in ancient cave art and modern of every land, air-breathing “kind” of creature went species, Wise (1994) suggested that speciation on board the Ark, and the rest of the “kinds” survived rates exploded following the Flood and then rapidly
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Wise analyses may reveal the answers to when and how further argued that this trajectory implied that the these species originated. mechanism was primarily intrinsic to each kind Previously, analysis of mitochondrial DNA in rather than being due to natural selection and the context of the speciation question has pointed mutation. in the direction of the explosive speciation model. Concurring with Wise, Wood (2002, 2003) Wood (2012, 2013b) analyzed ancient DNA from observed that Scripture records the very rapid post- humans and from three animal families/“kinds,” Flood appearance of modern species in at least four and he argued that rapid DNA sequence change “kinds,” adding further support to the hypothesis of was required to explain the genetic diversity among a burst of speciation. However, Wood (2002, 2003, extant and extinct individuals. Consistent with the 2013a) proposed a slightly different mechanism for explosive speciation model, Wood concluded that species’ origins, one which was transposable element- mutation rates were high around the time of the mediated but environment- and/or mutation- Flood and then decayed to their current rates. triggered. However, this conclusion rested entirely on the Which one of these many hypotheses is correct? assumption that the ancient DNA sequences were One of the limitations to understanding the timing reliable. Despite the popularity of the ancient DNA, and mechanism of speciation has been the lack they appear to be degraded, perhaps beyond utility of sufficiently large datasets. For example, after (Criswell 2009; Thomas and Tomkins 2014). examining the scope of mammalian speciation Restricting his analyses to extant mitochondrial in a more comprehensive fashion, Wood (2011) DNA sequences, Jeanson (2013) recently discovered refined the rapid-post-Flood-burst speciation model. evidence for a mitochondrial DNA clock that marks Observing that most mammal families are not time within the YE paradigm. Unlike evolutionary speciose, Wood suggested that rapid burst speciation molecular clocks that “calibrate” genetic differences was a phenomenon limited to species-rich “kinds,” with evolutionary times of origin that have been not all “kinds.” derived from the evolutionary interpretation of the In addition, with respect to the traditional scientific fossil record (e.g., see Ho 2014 as an example), this field by which the past has been interrogated— mitochondrial DNA clock was derived from empirical paleontology, lack of a comprehensive creationist measurements of mutation rates. In fact, the only model has hampered firm conclusions from being assumption that the mitochondrial DNA clock made formed on the explosive speciation model. Since was that the rates of DNA change had been constant most creationists would agree that the majority through time, a uniformitarian assumption that, in of geologic layers were deposited during the Flood, this instance, fit the YE timescale. This discovery this fact eliminates a good chunk of the record from suggested that mitochondrial DNA comparisons may usefulness to the speciation question. For those reveal a window into the past at unprecedented time layers that remain, a contentious debate stills exists resolution. as to whether the K-T boundary or the Pliocene- Furthermore, the number of published Pleistocene boundary represents the Flood/post- mitochondrial DNA genomes in metazoans has Flood boundary (Austin et al. 1994; Holt 1996; Oard increased rapidly in the last few years. As of the 2007; Ross 2014; Whitmore and Garner 2008). If the time of this writing, the entire mitochondrial DNA Flood/post-Flood boundary is at the K-T, then the sequences from nearly 5000 metazoan species were thick layers of the Cenozoic represent a very short present in the NCBI RefSeq database. Together with window of time post-Flood with a very large diversity Jeanson’s (2013) findings, these data suggested that of species, adding credence to the rapid post-Flood further investigation of mitochondrial DNA might speciation hypothesis and the mechanisms that yield insights into the timing species’ origins and follow from it (e.g., Cavanaugh, Wood, and Wise thereby help resolve the question of the mechanism. 2003; Wise 2005; Whitmore and Wise 2008). If the Flood/post-Flood boundary is higher in the geologic Materials and Methods record, then the fossil layers can answer the question Sources for species counts of the timing of species’ origins with less precision, Mammal species’ taxonomic information was and the hypothesis of rapid post-Flood speciation downloaded from the IUCN Red List of Threatened remains largely untested. Species website (http://www.iucnredlist.org/) Theoretically, the tool most relevant to the February 26, 2015 by searching for “Mammalia” (see questions of when and how species originated is Supplemental Table 1 for a listing of the common genetics. Since DNA is imperfectly inherited each names for many of the taxonomic designations used generation, extant species have within themselves in this study) and exporting the results as a .csv a record of their own past, and comparative DNA file. The file was deposited in Supplemental Table Mitochondrial DNA Clocks Imply Linear SpeciationRates Within “Kinds” 275
2. Microsoft Excel was used to sort and count the DNA genome is a circular genome, the sequences to number of species per family after excluding all be aligned were simply manually adjusted so that extinct species (those with a Red List status of all sequences shared the same position #1. After this “EX”). adjustment, the sequences were re-aligned with the Reptile species’ taxonomic information was CLUSTAL software. downloaded from the Reptile Database (http://www. reptile-database.org/db-info/news.html) on February Mitochondrial DNA clock calculations 17, 2015, and the complete list of species with The empirically determined mitochondrial DNA family names was deposited in Supplemental Table mutation rates for Homo sapiens, Caenorhabditis 3. Microsoft Excel was used to sort and count the elegans, Drosophila melanogaster, and Daphnia number of species per family. pulex were obtained from the sources described Amphibian species’ taxonomic information was previously (Jeanson 2013). For Homo sapiens, the downloaded from Amphibian Species of the World recalculated mutation rate (Table 4 in Jeanson 2013) 6.0 Online Reference (http://research.amnh.org/vz/ was used. For the other species, the single base-pair herpetology/amphibia/) on February 17, 2015, and the mutation rate (i.e., not the rate that combined single complete list of orders and families with associated base-pair changes and indels together) was extracted species numbers was deposited in Supplemental from each secular publication. Table 4. Microsoft Excel was used to sort and count The equation from which predictions were the number of species per family. made for three of the groups was identical to the Taxonomic information for species within the class divergence equation (e.g., eq. 24) in Jeanson (2013). Aves was downloaded from BirdLife International This was employed for several reasons. Because (2013) the BirdLife checklist of the birds of the the human mitochondrial DNA tree for the ethnic world (http://www.birdlife.org/datazone/userfiles/file/ groups I compared had the structure of a divergence Species/Taxonomy/BirdLife_Checklist_Version_6. event rather than a coalescence event (see Results zip) in early 2014, and the complete checklist was section below), a divergence calculation seemed most deposited in Supplemental Table 5. Microsoft Excel appropriate. For the Caenorhabditis and Drosophila was used to sort and count the number of species per calculations, since I compared separated species family. to one another rather than members of the same Taxonomic information for species within the class population (see below), a divergence calculation was Actinopterygii was downloaded from the Catalog required, by definition. of Fishes (http://researcharchive.calacademy.org/ For D. pulex, because I compared individuals within research/Ichthyology/catalog/SpeciesByFamily.asp) a single species, I employed a coalescence calculation, in early 2014, and the complete catalog with species- which is the divergence calculation divided by two per-family counts was deposited in Supplemental (e.g., d = r*t, not d = r*t*2). I also incorporated a wider Table 6. Microsoft Excel was used to sort and count range of generation times using another source (e.g., the number of species per family. http://genome.jgi-psf.org/Dappu1/Dappu1.home. For analysis of the combined species-per-family html, accessed March 4, 2015) in addition to the one counts across these vertebrate classes, I combined I listed previously (Jeanson 2013). the individual counts from each of the five classes The specifics of the computations for all four above into a single dataset and used Microsoft Excel groups were deposited in Supplemental Table 8. to sort and count the number of species per family. The actual number of differences among individuals within these four groups was obtained by Mitochondrial DNA sequence sources a variety of means. For Homo sapiens ethnic groups, I and alignment re-aligned with CLUSTALX or with CLUSTAL-MTV All sequences were downloaded from NCBI the sequences from the 32 diverse non-African ethnic Nucleotide (http://www.ncbi.nlm.nih.gov/nucleotide/) groups that were compared in Ingman et al. (2000). between March 2014 and February 2015. NCBI From the resultant alignment file, I removed all but accession numbers for all sequences were listed in the D-loop sequences, and then I stripped columns Supplemental Table 7. containing gaps with the appropriate function in All mitochondrial DNA genome alignments were BioEdit software (http://www.mbio.ncsu.edu/bioedit/ performed with CLUSTALX 2.0 (http://www.clustal. bioedit.html). I then used BioEdit to create a sequence org/) or with CLUSTAL-MTV (http://www4a.biotec. difference count matrix, from which I calculated the or.th/GI/tools/clustalw-mtv) using default settings. average pairwise difference and standard deviation. After some alignment runs, it was obvious that the (The average of 12.8 differences that I found matched NCBI sequences being compared did not share the the one published in Ingman et al. (2000); see same designated position #1. Since the mitochondrial Supplemental Table 9 for the raw numbers). 276
For the four species in the Rhabditidae family W, S, V, H, D) were replaced with gaps. From the with whole genome sequences available in the NCBI resultant file, CLUSTALX was used to create Phylip Nucleotide database (all four species happened to formatted trees after selecting the “Exclude Positions be members of the genus Caenorhabditis), I aligned with Gaps” option. MEGA4 software (http://www. their sequences with CLUSTALX or CLUSTAL-MTV megasoftware.net/mega4/mega.html) was used to after electronically creating the reverse complement draw mid-point rooted trees from the Phylip files. of the C. briggsae sequences, as per previous analyses (Jeanson 2013). The resultant alignment Tests of mid-point rooting file was loaded into BioEdit where I replaced all non- Within the order Carnivora, all available standard nucleotides (e.g., N, M, R, Y, B, W, S, V, H, mitochondrial DNA whole genome sequences D) with gaps. I then used BioEdit to strip all columns within the NCBI Nucleotide RefSeq database were containing gaps and to create a sequence difference downloaded on February 26, 2015. The sequences count matrix, from which I calculated the average were aligned with CLUSTAL-MTV, and the resulting pairwise difference and standard deviation. alignment was loaded in BioEdit where all non- For the 16 species in the Drosophilidae family standard nucleotides (e.g., N, M, R, Y, B, W, S, V, H, with whole genome sequences available in the NCBI D) were replaced with gaps. From the resultant file, Nucleotide database (all 16 species happened to be CLUSTALX was used to create a Phylip formatted members of the genus Drosophila), I aligned their tree after selecting the “Exclude Positions with Gaps” sequences with CLUSTALX or CLUSTAL-MTV. option. MEGA4 software (http://www.megasoftware. The resultant alignment file was loaded into BioEdit net/mega4/mega.html) was used to draw a mid-point where I replaced all non-standard nucleotides (e.g., rooted tree from the Phylip file. N, M, R, Y, B, W, S, V, H, D) with gaps. I then used For species within the subfamily Bovinae, BioEdit to strip all columns containing gaps and mitochondrial DNA whole genome sequences within to create a sequence difference count matrix, from the NCBI Nucleotide database were downloaded on which I calculated the average pairwise difference February 13, 2015. For species within the genus Pan, and standard deviation. mitochondrial DNA whole genome sequences within For the 28 individuals within the Daphnia pulex the NCBI Nucleotide database were downloaded on species with whole genome sequences available February 17, 2015. For species within the genus Ursus, in the NCBI Nucleotide database, I aligned their mitochondrial DNA whole genome sequences within sequences with CLUSTALX or CLUSTAL-MTV. the NCBI Nucleotide database were downloaded on The resultant alignment file was loaded into BioEdit February 17, 2015. Each of these three datasets was where I replaced all non-standard nucleotides (e.g., aligned separately with CLUSTAL-MTV, and the N, M, R, Y, B, W, S, V, H, D) with gaps. I then used resulting alignments were loaded in BioEdit where BioEdit to strip all columns containing gaps and all non-standard nucleotides (e.g., N, M, R, Y, B, to create a sequence difference count matrix, from W, S, V, H, D) were replaced with gaps. From the which I obtained the highest pairwise difference resultant files, CLUSTALX was used to create Phylip value between any two individuals. formatted trees after selecting the “Exclude Positions with Gaps” option. MEGA4 software (http://www. Test of constant rate across lineages megasoftware.net/mega4/mega.html) was used to In this subset of analyses, four different datasets draw mid-point rooted, topology-only trees from the of mitochondrial DNA whole genome sequences in Phylip files. Homo sapiens were aligned with CLUSTALX or From the Bovinae alignment file, the sequences CLUSTAL-MTV. The first set of 53 ethnic groups from individuals within Syncerus caffer and within was identical to the set analyzed in Ingman et al. Bison bison were extracted. From the resultant file, (2000). The second set of 371 sequences from various CLUSTALX was used to create a Phylip formatted ethnic groups was obtained from a related source, tree after selecting the “Exclude Positions with Gaps” the mtDB (http://www.mtdb.igp.uu.se/). The third option. MEGA4 software (http://www.megasoftware. alignment compared the 53 ethnic groups from net/mega4/mega.html) was used to draw a mid-point Ingman et al. (2000) with the three fossil human rooted, linearized tree from the Phylip file. sequences identified in Supplemental Table 7. The fourth alignment utilized 828 sequences—the 827 Testing hypotheses on the timing of speciation sequences that Carter (2007) and Carter, Criswell, All 27 metazoan families were investigated in and Sanford (2008) analyzed as well as single “Eve” the same manner as follows: Mitochondrial DNA sequence from the latter. whole genome sequences were downloaded from the The resulting alignments were loaded in BioEdit, NCBI Nucleotide RefSeq database during February and all non-standard nucleotides (e.g., N, M, R, Y, B, and March of 2015. CLUSTALX or CLUSTAL-MTV Mitochondrial DNA Clocks Imply Linear SpeciationRates Within “Kinds” 277 was used to align sequences from species within the For species within the family Hynobiidae, species same family. The resulting alignment was loaded in and genus names from the Amphibian Species of BioEdit where all non-standard nucleotides (e.g., N, the World database were reconciled with the names M, R, Y, B, W, S, V, H, D) were replaced with gaps. associated with the NCBI mitochondrial sequence Sequences from sub-species and domestic species entries. In the two cases were there was a species were also manually removed from the alignments name discrepancy, a quick search identified how the in BioEdit. From the resultant files, CLUSTALX name had changed, requiring no further actions on was used to create Phylip formatted trees after species numbers per family. selecting the “Exclude Positions with Gaps” option. Since the Catalog of Fishes did not list individual As a test of constant rates across lineages, radiation species names, no reconciliation was attempted for style trees were also created for all 27 families using fish species. Thus, the total number of species within MEGA4 software (http://www.megasoftware.net/ the family was taken from the Catalog, and all mega4/mega.html). Except for the family Camelidae, species represented by NCBI sequences were simply MEGA4 was also used to draw mid-point rooted, assumed to be present within the Catalog count. linearized trees from the Phylip files with branch Similar assumptions were made for the lengths displayed. The image of the mid-point rooted, invertebrate species. Since speciation within these linearized tree with its branch length values was families was so vast, species and genus numbers were copied into Microsoft PowerPoint, and the individual obtained from the Global Biodiversity Information branch lengths values were manually entered into Facility (http://www.gbif.org/), and all species and a Microsoft Excel file. Branch length values were genera represented by NCBI sequences were simply added cumulatively where necessary for individual assumed to be present within the GBIF count. speciation events. By taking the longest distance between two species and then dividing the distance Results into either time post-Flood (e.g., 4350 years) for on- The extent of post-Creation and Ark families, or into time post-Creation (e.g., 6000 post-Flood speciation years) for off-Ark families, the branch length values Because conclusions about the explosive were converted to years. This quotient was used to speciation model have changed dramatically once then convert all branch length values (individual large datasets were included in the analyses (e.g., and cumulative) into time points. Microsoft Excel Wood 2011), I revisited the question of the scope of was used to perform linear regression on these time speciation before analyzing the mitochondrial DNA points for each family. Cumulative species numbers of metazoan families. Similar to the results of Wood and the time points of each new speciation event (2011) who found that species within a family “follow were plotted to create the graphs in Figs. 19–44. a power-law distribution,” I found that mammal kinds (approximated by the taxonomic rank of Mitochondrial DNA species representation family) followed a very rough power distribution To calculate how many species and genera within (Fig. 1). In other words, most mammal families had each family were represented by the mitochondrial few species, and a few families had many species. In DNA analyses, species names and genus names from practical terms, if the Flood ended 4350 years ago, a the IUCN table, the Reptile Database, the Amphibian Species of the World list, and the BirdLife Checklist Total families: 151 Mammalia: (Supplemental Tables 2–5) were reconciled with 30 Speciation within Kinds the names associated with the NCBI mitochondrial sequence entries. For mammal species, reconciliation 25 -0.448 was achieved by exploring the history of the y = 8.2655× 20 R2 = 0.5918 taxonomic designation. In some cases, a species or genus name had changed between the lists, despite 15
being the same creature. In these cases, no further Frequency 10 action was taken. If a name was not shared between the two, the creature under consideration was simply 5 incorporated into a larger, combined list of species or 0 genera within the family. 0 200 400 600 800 For species within the family Crocodylidae, Species/Family Fig. 1. Power curve distribution of mammalian species species and genus names from the Reptile Database per family. The amount of species per family in the class matched the names associated with the NCBI Mammalia was quantified and arrayed in a histogram mitochondrial sequence entries, and no further format. The thin black trendline and equation were derived taxonomic reconciliation was needed. from the raw data with standard tools in Microsoft Excel. 278 N. T. Jeanson modest speciation rate of one speciation event every Total families: 200 years would produce about 21 species by today. 198 Aves: 20 Nearly three-fourths of all mammal families had 21 Speciation within Kinds species or less. Conversely, just 27% of the mammal 18 16 families contained 86% of all mammal species. These 14 -0.412 results suggested that speciation was explosive for y = 7.599× 12 R2 = 0.5899 just a few mammal kinds. 10 The same lopsided pattern held true in other 8 vertebrate classes, regardless of whether the class Frequency 6 consisted almost entirely of on-Ark kinds (e.g., birds) 4 and or entirely of off-Ark kinds (e.g., bony fish). 2 0 Reptiles (class Reptilia, Fig. 2), amphibians (class 0 100 200 300 400 500 Amphibia, Fig. 3), birds (class Aves, Fig. 4), and Species/Family bony fish (class Actinopterygii, Fig. 5) all possessed Fig. 4. Power curve distribution of bird species per family. many families with few species and few families with The amount of species per family in the class Aves was many species (see Supplemental Table 1 for a listing quantified and arrayed in a histogram format. The thin of the common names for many of the taxonomic black trendline and equation were derived from the raw designations used in this study). Just like the data data with standard tools in Microsoft Excel. for the class Mammalia, a power distribution seemed Total families: the best approximation for each dataset. 491 Actinopterygii: 60 Speciation within Kinds Total families: 88 Reptilia: 50 Speciation within Kinds -0.549 14 y = 21.029× 40 R2 = 0.6633 12
-0.218 30 10 y = 3.026× R2 = 0.4851 8 Frequency 20
6 10 Frequency 4 0 0 500 1000 1500 2500 3000 3500 2 2000 Species/Family 0 0 500 1000 1500 2000 Fig. 5. Power curve distribution of bony fish species Species/Family per family. The amount of species per family in the class Actinopterygii was quantified and arrayed in Fig. 2. Power curve distribution of reptile species per a histogram format. The thin black trendline and family. The amount of species per family in the former class equation were derived from the raw data with standard Reptilia was quantified and arrayed in a histogram format. tools in Microsoft Excel. The thin black trendline and equation were derived from the raw data with standard tools in Microsoft Excel. Furthermore, when the species per family Total families: 73 counts from all five classes were combined into one Amphibia: 8 dataset, a power distribution matched the data even Speciation within Kinds better. The correlation coefficient for this combined 7 dataset was higher than the coefficient for any of 6 -0.174 y = 2.4498× the individual datasets (Fig. 6; Table 1). Overall, 5 R2 = 0.3946 the higher the n (number of families) was, the 4 better the fit was to a power law distribution (table 3
Frequency 1). Together with Wood’s (2011) results, these data 2 indicate that explosive post-Flood and post-Creation 1 speciation was limited to a select subset of kinds, and 0 it raised the question of whether unusual speciation 0 200 400 600 800 1000 mechanisms were needed to explain the majority of Species/Family speciation events in the YE model. Fig. 3. Power curve distribution of amphibian species per family. The amount of species per family in the class Amphibia was quantified and arrayed in a histogram Assessing the utility of mitochondrial DNA clocks format. The thin black trendline and equation were derived To investigate the timing of post-Flood and post- from the raw data with standard tools in Microsoft Excel. Creation speciation, I explored the possibility of using Mitochondrial DNA Clocks Imply Linear SpeciationRates Within “Kinds” 279
Total families: reasons following from the discoveries I made below, Vertebrate Summary: 1001 Speciation within Kinds I left them out of my analyses. 140 In each of the four extant species or groups 120 of species that I examined, the conclusions from 100 my previously published results (Jeanson 2013) y = 54.672×-0.69 remained the same. For example, in humans, the 80 R2 = 0.7571 predicted mitochondrial DNA diversity in the D-loop 60 of non-Africans overlapped the standard deviation Frequency 40 in current DNA diversity among non-African ethnic groups (Fig. 7). Also, the predicted mitochondrial 20 DNA diversity in the entire genomes of the three 0 animal groups captured or overlapped existing DNA 0 500 1000 1500 2000 2500 3000 3500 diversity (Figs. 8–10). Since these four independent Species/Family Fig. 6. Power curve distribution of vertebrate species data points represented three different phyla as well per family. The amount of species per family among the as both on-Ark and off-Ark creatures, I assumed five combined vertebrate classes (Mammalia, Reptilia, that mitochondrial DNA clocks existed for the rest Amphibia, Aves, Actinopterygii) was quantified and of the animal kinds, and I assumed that these clocks arrayed in a histogram format. The thin black trendline “ticked” at a constant rate through time in a manner and equation were derived from the raw data with consistent with the YE timescale. standard tools in Microsoft Excel. Homo sapiens mtDNA: Table 1. Correlation between number of families and fit 18 Molecular Clock Confirmed to a power curve. 16 14 Group Total Family # R2 to Power Curve 12 Amphibia 73 0.39 10 Reptilia 88 0.49 8 Mammalia 151 0.59 6 Aves 198 0.59 DNA Differences DNA 4 Actinopterygii 491 0.66 2 Vertebrates 1001 0.76 0 After 6000 years Actual the mitochondrial DNA clock discovered previously Fig. 7. Human mitochondrial DNA clock. Using the (Jeanson 2013). In these previously published results, empirically-derived mitochondrial DNA mutation rate for the amount of mitochondrial DNA diversity matched the D-loop in non-African individuals, the predicted amount the expectations of mutation change that had been of DNA differences after 6000 years of mutation at a constant occurring for 10,000 years or less, and it relied on the rate was compared to the average D-loop difference among mitochondrial DNA sequences published at that time. non-African ethnic groups. The height of each colored bar Since then, more genomes have been published for represented the average DNA difference, and the thick black more species within these groups, and I reinvestigated lines represented the 95% confidence interval (“After 6000 years” bar) or standard deviation (“Actual” bar). whether the results would still hold true. Furthermore, since 6000 years and not 10,000 years is generally To date, no further mitochondrial DNA mutation preferred as the date of creation (Hardy and Carter rates have been measured in additional animal 2014), I explored whether the results would stand for species. Nevertheless, for those species with a the more recent date or whether an acceleration in published mitochondrial DNA whole genome mutation rates was required, as suggested previously sequence, comparative DNA analysis was still (Wood 2012, 2013b). possible, and the resultant patterns might be Like my previous study (Jeanson 2013), I omitted informative. Hence, I proceeded to interrogate the from consideration mitochondrial DNA sequences question of the timing of speciation by restricting from fossil or extinct species. Because DNA is such my investigation to analysis of comparative a labile molecule, it seems unlikely that reliable mitochondrial DNA sequence patterns under a set of sequences will ever be obtained from samples older simplifying assumptions. than just a few years or decades, unless remarkable First, in addition to assuming that a mitochondrial care is taken to preserve them. Since the published DNA clock exists for each “kind” and that the sequences from extinct species represent samples mitochondrial DNA mutation rate was constant that have been sitting on or in the ground for through time, I assumed that the mitochondrial hundreds to thousands of years, and for additional DNA mutation rate was constant across lineages. 280
2500 Caenorhabditis mtDNA: 300 Daphnia pulex mtDNA: Molecular Clock Confirmed Molecular Clock Confirmed 250 2000 200 1500 150 1000 100 DNA Differences DNA DNA Differences DNA 500 50
0 0 After 6000 years Actual After 6000 years Actual Fig. 8. Roundworm mitochondrial DNA clock. Using the Fig. 10. Water flea mitochondrial DNA clock. Using the empirically-derived mitochondrial DNA whole genome empirically-derived mitochondrial DNA whole genome mutation rate for Caenorhabditis elegans, the predicted mutation rate for Daphnia pulex, the predicted amount amount of DNA differences after 6000 years of mutation of DNA differences after 6000 years of mutation at a at a constant rate was compared to the average difference constant rate was compared to the maximum difference among Caenorhabditis species. The height of each colored between Daphnia pulex individuals. The height of each bar represented the average DNA difference, and the thick colored bar represented the average (predicted) or black lines represented the 95% confidence interval (“After maximum (actual) DNA difference, and the thick black 6000 years” bar) or standard deviation (“Actual” bar). line represented the 95% confidence interval. Furthermore, this history would likely have been 2000 Drosophila mtDNA: Molecular Clock Confirmed recorded in the mitochondrial DNA patterns around 1800 the world. Since mitochondrial DNA is inherited 1600 maternally, the fact of the Flood and the fact of 1400 the tower of Babel led to very specific expectations 1200 about the comparative DNA patterns observable 1000 today. Because four women survived the Flood, no 800 more than four major ancestral mitochondrial DNA 600 DNA Differences DNA lineages could have given rise to the modern ethnic 400 groups. In fact, no more than three should have been 200 present (Carter 2010). Though Noah’s wife passed 0 After 6000 years Actual on her mitochondrial DNA to her three sons, her Fig. 9. Fruit fly mitochondrial DNA clock. Using the lineage then ceased since men do not pass on their empirically-derived mitochondrial DNA whole genome mitochondrial DNA to their offspring. Instead, all mutation rate for Drosophila melanogaster, the predicted modern mitochondrial DNA lineages should trace amount of DNA differences after 6000 years of mutation back to the three wives of Noah’s sons. at a constant rate was compared to the average difference Remarkably, upon visual inspection of the human among Drosophila species. The height of each colored bar mitochondrial DNA tree of various modern ethnic represented the average DNA difference, and the thick black lines represented the 95% confidence interval (“After groups, three nodes were visually apparent (Figs. 6000 years” bar) or standard deviation (“Actual” bar). 11A–B). In addition, most of the ethnic lineages stemming from these three nodes sprayed out almost This assumption was partially testable based on immediately rather than staggering out (Fig. 11A), the presence or absence of signature patterns in the as if they arose from a divergence event rather than mitochondrial DNA trees for the kinds I investigated. a coalescence event, a finding consistent with the These signature patterns derived from an analysis of description and timing of the Tower of Babel incident the human mitochondrial DNA tree for the various in Genesis 11. ethnic groups and from an analysis of the text of This fact of the three nodes in the human Genesis. According to Genesis 9:18–19, “Now the sons mitochondrial DNA tree had ramifications for the of Noah who went out of the ark were Shem, Ham, constancy of the rates of genetic change across and Japheth. And Ham was the father of Canaan. lineages. If the three nodes did indeed represent the These three were the sons of Noah, and from these sequences in the wives of Noah’s sons, then those the whole earth was populated” (NKJV). Thus, since nodes represented an identical point in time, which there are more than three different ethnic groups in means that all their descendants had been mutating existence today, our modern ethnic groups must have for an identical length of time. For non-Africans arisen post-Flood, likely as a result of the confusion of lineages (e.g., two of the three major nodes in the languages at Babel (Genesis 11). tree), the current and empirically measured rate of Mitochondrial DNA Clocks Imply Linear SpeciationRates Within “Kinds” 281
PNG Coast 41 Evenki 17
Aborigine 3
Warao 50 A B Warao 51 Buriat 8 Khirgiz 29 Yoruba 52
Indian 4 Chinese 10
Taiwan Aborigine 163
Siberian Inuit 48 Japanese 27 Bougainville Aita 254
Central Italy 301 Bamileke 5 Ewondo 18
Mkamba 38 Somalia 334 Bougainville Aita 255 Italy Sardinia 297
Italy Sardinia 303 Guarani 22 Evenki 112
Taiwan Aborigine 164 Japanese 28 Yoruba 53 Ethiopia 335 Greece Crete 313 Eth Eiotphiiao p Jiae w J e 3w0 6307 Iraq Jew 315 Effik 14 EEgEgypygpty tpS tS i wCiwaoa p 2t 29 398090 Tofalar 187 Ethiopia 328 Egypt Copt 324 Israel Druze 316 EEvveennkki i1 7170
Mansi 183
Morocco Muslim 332 Nganasan 175 IIttIataallyyly S SSaaarrdrddiinniniiaaia 3 33000542 Aborigine 3 Ethiopia 310
Ethiopia 312 Effik 15 Ethiopia 329 Southern Italy 318 Mauritania 336 Bougainville Simeku 253 Tuvli 185 Tuvan 184 Central Italy 319 Lisongo 32 Siberian Inuit 48 Chinese Han 234 Egypt Copt 327 Morocco Berber Asni 325 Jordan 69
Guarani 22 Italy 323 Ethiopia 322 Ethiopia 321 Native American 116 Japanese 27 U K dKoe BorgKyrueayhriak iir ak 1g t 12 i z8123 70229 Gre eE ctE hE eAti hto mhLipoieoipampri ia icaOn a o3 rn3os0 1m 83 131o17 4 309 Mandenka 33 ESthEoiotmhpiaioalpi a i3a 3 3 03313 Canary Islands 82 Filipino 85 Ul'chi 188
Morocco BerbMero rAoscnci o3 2507 SIsoruatehle rBne Idtaolyu i3n3 7338 Aboriginal Malay Temuan 244 Iraq 346 Ul'chi 181 Vanuatu 278 Majuro Atoll 271 Morocco Berber Bouhria 341 Nganasan 186 Warao 510 Aborigine 1 Central Italy 343 Ulchi Nanaj-Negidal 137Japanese 28 Central Italy 344 Morocco Berber Bouhria 345 Volga-Ural region 283 Southern Italy 326 Southern Italy 342
Ce Cnetrnatlr Iatal lIyta 3ly3 3940 SCaomoko Iasnla n2d8e0r 279
GGrereaat tA Annaaddaammaanneessee 2 22258 Ul'chi 182 Mbuti Pygmy 36 Volga-Ural region 28452
Mbuti Pygmy 37 Nasioi 158 Georgia 114 Aborigine 2 Tofalar 178 Kannada 154 New Britain Marabu 232 Koryak 118 New Ireland 231 Espiritu Santo 274 Native American 110 New Britain Uasilau 230
Nganasan 176 PNG Coast 41
VEasnpuiraitutu S 2a7n7to 275 Finland 127
Chinese 11 Korean 117 Aboriginal Malay Semelai 242
OOnOngngege e 2 2 220241
Indian 86 Indian 4 Georgia 113 Three nodes Koraga 155 Negidal'tsy 174 Canary Islands 83 Koryak 119 Melayu 243 Mansi 173 Spain Leon 80 Semang Jahai 238 Chinese Tujia 236 Onge 223 Chukchi 9 Filipino 153 Jordan 72 Chinese 10
Semang Batek 245 Italy 247 Chukchi 9 Ket 171 Aborigine 2 Semang Batek 237 Mullukurun 157 GOrnegaet A 2n2a2damanese 22796 Hausa 23 Mixteca - Baja133 Three nodes Navajo 134 PNG Highlands 42 Aboriginal Malay Temuan 239 Morocco 59 Bamileke 5 Spain Maragato 74 Yoruba 52 Ulchi Nanaj-Negidal 139 Morocco 58 Spain Maragato 76
Spain Leon 79 Yoruba 53 Mkamba 38 Effik 15 Ewondo 18 Mauritania 64
South African 129 German 21 Aborigine 1 Lisongo 32 San 135 Morocco 60 Jordan 71 Georgia 20 Effik 14 South African 125 Native American 111 Aboriginal Malay Semelai 241 Nicobarese 219 Mandenka 33 Nicobarese 21576 South African 131 South African 132 PNG Highlands 43 Mauritania 54 Finland 124 Piman 39 South African 121
PNG Coast 40 Buriat 169
Adygei 202 Tubalar 179
France 19 PNG Trobriand Islands 2657 Koraga 156 Hausa 23 South African 128 Italy 26 Uzbek 49 PNG Highlands 43 Morocco 61 English 16 PNG Highlands 42 PNG Coast 40 Crimean Tatar 12 Palestine 261 Mbuti Pygmy 376 Israel Druze 256
Spain 201 San 46 Ugandan 246 Cherkes 260 Spain Leon 78
San 46 Israel Druze 2589 Dutch 13 Crimean Tatar 12 Dutch 13 Georgia 20 Israel Druze 257 SauLdei bAarnaobnia 2623 Abkhazian 96 San 47 German 21 Syria 264 Daghestan Tabasaran 105 Iraqi-Israeli 115 Saudi Arabia 251 North Ossetia 95 Khwe 126
Biaka Pygmy 6 SSenpeagina l G Waloicloiaf 1423 Daghestan Dargin 989 Saami 44 Jordan 73 TDuargkheeys t1a0n3 Lezgin 102 Daghestan Lezgin 104 Daghestan Dargin 97 Pakistan 191 Pakistan 189 Mbenzele Pygmy 35 Jordan 68 Spain 192 Turkey 100 San 136 Abazin 109 Jordan 70 France 19 Spain Leon 77 English 16 Mauritania 66 Jordan 107 San 47 Pakistan 190 Turkey 108 Vietnam 291 Canary IsSlapnadins 321714041 Spain Andalusia 84 Ethiopia 198 Samoan 45 Pakistan 200
Korean 31 Pakistan 252 Spain Maragato 75 Morocco BItearlyb e Sr iAcsilyn i 337712 Ibo 25 MBibaeknaz Peyleg mPyyg 7my 34 Morocco Berber 140 Ethiopia Jew 373 Pakistan 199 Morocco 56 Spain 196 Adygei 194 Piman 39 Adygei 197 Canary Islands 55 Nigeria Songhai 354 Georgia Mingrelian 106 Yemen 195 InIdnodnoenAseibsaoi a rS ig SuTinmuhamal itM ar 2atar9 alPa4 Pay da2al9en3mg b 2a8n8g Yemen 193 Ethiopia 213 Uzbek 49 Saami 44
Mauritania 148 Mauritania 65 Central Italy 352 B METouosagnpeagiwriaintounv iS l2l12ea768 n6 812to3 5273 Ibo 24 Kikuyu 30 PNGT a T iTKwa Krai awoMpanbaiap nrnAjiguna bSAargnomabd rmo AiIagsrtroailngaarlliena n2 gdne9 74isg 28A5 i 29Ato6tl6ol l2l 72069 Iraq 357 SoMutohreorcnc Iota ly1 43749 Morocco Berber 63 Mauritania 67 Morocco Berber Asni 355
CSaonuatrhye Irsnla Intadlys 317540 Cook Islander 152 Thai 166 San 130 Indonesia Sulawesi Manado 28 Armenia 101 AboriginaVl iMetanlaym S 2e9m2elai 240 Indonesia Java Tengger 286 PNG Trobriand Islands 268 Vietnam 290 Samoan 159 Central Italy 358 Algeria 351
Morocco Berber 149 Cook Islander 151 Italy 348 Samoan 160 Taiwan Aborigine 90 Biaka Pygmy 6 Tofala rT-Nuveagnid a1l8 0122
Morocco Berber Asni 356 Central Italy 359 Korean 31 Nigeria 360 Thai 167 TaTiawiwana nA bAobroigriignien e9 188 Southern Italy 350 Italy 26
Ethiopia 353 TaiwTainw Aanb oArbigoinrieg i9n4e 93
France 369 Italy Sicily 362 Taiwan Aborigine 87 MYoSSraoaFkacauacmltmb o ei2 i B0 227e00r895ber 62 Tofalar 177 Tunisia 361 Spain MaItraaSlSygo ao uSMtutoahta hre uLderreinrninto iaIa tnInat a il13ayly46 3 513646746
Morocco Berber Asni 364 Mbenzele Pygmy 35 Adygei 203
Morocco Berber Asni 347
CanaryM Iosrloacncdos 18416
Saami 206 Southern Italy 368 Primarily Taiwan Aborigine 161
BeSrbpearin 2 21004 Tunisia 363
Berber 211 ViVeitentanmam 2 92695
Spain 212
Biaka Pygmy 7 Mbenzele Pygmy 34 Camb Tohdaiai n 1 62533 African
Taiwan Aborigine 162
Ibo 25 Nicobarese 2M1a8lay 138
Chinese 11 Exclusively Ibo 24 branch African (1 sequence from
branch Kikuyu 30 a Jordanian)
C Chinese 11
Chukchi 9 Piman 39
Mkamba 38 Samoan 45 Italy 26 Korean 31 Aborigine 2
Uzbek 49 Crimean Tat aDru 1tc2h 13 Guarani 22 Aborigine 1
France 19
English 16 Saami 44 Siberian Inuit 48 Japanese 28 PNG Coast 40 Japanese 27 PNG Highlands 43
PNG Highlands 42 Homo sapiens ssp. Denisova Warao 51 Warao 50
Georgia 20 Evenki 17 German 21 Khirgiz 29
Buriat 8
Chinese 10 Indian 4 Three nodes Ewondo 18 Lisongo 32
Yoruba 53 Bamileke 5 PNG Coast 41 Aborigine 3
Homo heidelbergensis
Yoruba 52
Mbuti Pygmy 36 Mbuti Pygmy 37
Effik 14 Hausa 23
Homo sapiens neanderthalensis Effik 15
Mandenka 33
San 46
Biaka Pygmy 6 San 47
Mbenzele Pygmy 35 Ibo 24
Ibo 25 Biaka Pygmy 7 Mbenzele Pygmy 34
Kikuyu 30 Fossil Exclusively sequences African branch Fig. 11. Three-node structure of the human mitochondrial DNA tree. A Whole genome alignment and resultant phylogenetic tree of 53 human ethnic groups. Upon visual inspection, three major subgroups or nodes were visible. One of the nodes was exclusively African lineages, and some of the branches stemming from this node were about twice as long as the other branches. B Whole genome alignment and resultant phylogenetic tree of 371 human individuals from various human ethnic groups. Similar to A, visual inspection demonstrated the existence of three major subgroups or nodes. Again, like A one of the nodes was almost exclusively African lineages, and some of the branches stemming from this node were about twice as long as the other branches. C Same data as A but with three fossil human sequences included. Similar to A visual inspection demonstrated the existence of three major subgroups or nodes. Again, like A one of the nodes was exclusively African lineages, and some of the branches stemming from this node were about twice as long as the other branches. Surprisingly, all three fossil human individuals branched off from the exclusively African lineage, and their branch lengths were much longer than those of the extant human individuals. change in the D-loop matches the predictions of the analyses within animal families, I created a radiation hypothesis that the rate of change has been constant style tree for each family, visually inspected the with time (Fig. 7). trees for obvious roots, and visually compared the By contrast, the section of the tree containing branch lengths about the proposed root to assess the exclusively African lineages had a maximum branch possibility of rate heterogeneity across species within length about twice as long as the non-African branches a family (Supplemental Figs. 1–24, 49–51). (Fig. 11). Presumably, some of the lineages in the The branch length patterns among the three African branch had been mutating twice as fast as the nodes in the human tree lent further support to the non-African branches, giving rise to the discrepancy exclusion of fossil sequences from consideration in the in branch lengths. This hypothesis had preliminary present analyses. When the Homo heidelbergensis, support in the discovery that another form of genetic Homo sp. Altai, and Homo sapiens neanderthalensis change, recombination, occurs faster in African than mitochondrial genomes were included in the in non-Africans (Hinch et al. 2011). Together, these analysis, two facts were immediately apparent. facts suggested that visual examination of radiation First, these sequences were indeed quite divergent style trees with visually obvious roots might identify from the mitochondrial DNA sequences of extant lineages with faster or slower rates than the overall human ethnic groups (Fig. 11C). Second, all three rate. Hence, before performing species’ time of origin fossil sequences branched off from the exclusively 282 N. T. Jeanson
African lineage (Fig. 11C). This suggested that, the mitochondrial genome, and since the node upon if the fossil sequences were indeed reliable, they which “Eve” is centered represents three-fourths represented a subsection of the African lineage with of the sequence samples, the parameters of their an unusually high mutation rate. In fact, the high methods almost guaranteed that Eve would land rate may have caused the extinction of these ancient exactly at the node most represented. Alternatively, human populations. Alternatively, these sequences since so few generations passed between Adam and may still be degraded. Regardless of which of these Noah according to Genesis 5, one of the wives of two explanations was true, fossil sequences clearly Noah’s sons may have inherited her DNA sequence represented an unusual set of data, and these data with little to no mutations from Eve’s original created did not contradict the assumption in modern lineages sequence. Regardless of the explanation, the results of constant rates of mitochondrial DNA mutation and inferences of the present study were reconcilable through time. with previously published YE creationist data on Since these results implied that the three nodes mitochondrial “Eve.” represented the sequences of the three wives of Noah’s Speciation rate analyses required a second sons, the data further implied that the sequence of assumption besides the assumption of rate mitochondrial “Eve” was located somewhere between homogeneity. Since species have formed post-Creation them. Previous YE creationist studies (Carter, and post-Flood, there obviously existed a point in time Criswell, and Sanford 2008) of mitochondrial “Eve” when speciation commenced. Since we currently lack placed her sequence, not between these three nodes, measured mitochondrial DNA mutation rates for the but exactly centered on one of them (Fig. 12). This vast majority of animal families, absolute rooting of finding may have been an artifact of the methodology each family’s mitochondrial DNA tree was impossible used, a possibility the authors readily acknowledged. at present. Since Carter, Criswell, and Sanford inferred the “Eve” However, the majority of families appeared to sequence from the majority allele at each position in pass the visual rate homogeneity test (Supplemental
Eve
gi|51451330|gb|AY714050.1| Homo sapiens isolate A174 mitochondrion complete genome
gi|51451288|gb|AY714047.1| Homo sapiens isolate C31 mitochondrion complete genome
gi|32891746|gb|AY255180.1| Homo sapiens isolate QD8147 mitochondrion complete genome
gi|50295416|gb|AY519489.2| Homo sapiens isolate NegidalB5 mitochondrion complete genome
gi|32348170|gb|AY289064.1| Homo sapiens isolate E9 mitochondrion complete genome
gi|61743586|gb|AY972053.1| Homo sapiens isolate QJ383 mitochondrion complete genome
gi|51450966|gb|AY714024.1| Homo sapiens isolate C35 mitochondrion complete genome gi|57903982|gb|AY882396.1| Homo sapiens isolate 18 U1a Tor9 mitochondrion complete genome gi|51451218|gb|AY714042.1| Homo sapiens isolate R196 mitochondrion complete genome
gi|40848531|gb|AY49g5i|233283.418| H01o6m|gob s|AaYp2ie8n9s0 i5s3o.l1a|t eH Jo4m-o0 8s ampitioecnhso isnodlraioten A cuosm15p lmetieto gcehnoonmdreion complete genome
gi|75905882|gb|AY963584.2| Homo sapiens isolate 13 R21 Tor64 mitochondrion complete genome
gi|32348296|gb|AY289073.1| Homo sapiens isolate K4b mitochondrion complete genome gi|51451022|gb|AY714028.1| Homo sapiens isolate A163 mitochondrion complete genome gi|51451316|gb|AY714049.1| Homo sapiens isolate T108 mitochondrion complete genome gi|51451050|gb|AY714030.1| Homo sapiens isolate T1 mitochondrion complete genome gi|40848503|gb|AY495236.1| Homo sapiens isolate J4-06 mitochondrion complete genome gi|32891732|gb|AY255179.1| Homo sapiens isolate WH6973 mitochondrion complete genome
gi|51451162|gb|AY714038.1| Homo sapiens isolate C132 mitochondrion complete genome gi|40848447|gb|AY495232.1| Homo sapiens isolate J4-02 mitochondrion complete genome
gi|51451078|gb|AY714032.1| Homo sapiens isolate C60 mitochondrion complete genome
gi|40848433|gb|AY495231.1| Homo sapiens isolate J4-01 mitochondrion complete genome gi|57903996|gb|AY882397.1| Homo sapiens isolate 19 U1b Tor133 mitochondrion complete genome
gi|29690658|gb|AY195764.1| Homo sapiens haplotype E19U mitochondrion complete genome gi|113706994|gb|DQ404444.3| Homo sapiens isolate AUR17 mitochondrion complete genome gi|51450896|gb|AY714019.1| Homo sapiens isolate T130 mitochondrion complete genome gi|32348072|gb|AY289057.1| Homo sapiens isolate Aus21 mitochondrion complete genome
gi|48596193|gb|AY195778.2| Homo sapiens haplotype E8J mitochondrion complete genome gi|75905877|gb|AY963579.3| Homo sapiens isolate 8 R9b Tor56 mitochondrion complete genome gi|51450924|gb|AY714021.1| Homo sapiens isolate C110 mitochondrion complete genome
gi|51451092|gb|AY714033.1| Homo sapiens isolate R80 mitochondrion complete genome gi|32891704|gb|AY255177.1| Homo sapiens isolate QD8167 mitochondrion complete genome gi|395764489|gb|AY275533.2| Homo sapiens isolate 236 mitochondrion complete genome gi|166362175|gb|DQ272125.2| Homo sapiens isolate YK38 mitochondrion complete genome ggigi||54i|14g040i8|g4584i0|148818044248807494|58|gg6|5bgb11|b|A|Ag7|YAYb|g7Y4|Ab149Y|49A5405Y29324353952.45.113.2|1| 3 H3H| .H17oo|.mo 1mHm|o ooH o smso asaompap soipieea isnenpasnsiep s iisnis eiosonlo laisaslta teoiest el BaoJ 3Jtl4ea04- tJe 0-m04 5Ji4-t 4om0 m-c3i0thoi tm7oc cimnhtohdoictornhincododhnrniro idconrond i omc r cnioopo m nlcem po tceplmeo lgetpmeetel epng gtloeeemn tgenoee ogmnmeeonemoeme gi|51450658|gb|AY714002.1| Homo sapiens isolate B46 mitochondrion complete genome gi|51451190|gb|AY714040.1| Homo sapiens isolate T115 mitochondrion complete genome
gi|32348044|gb|AY289055.1| Homo sapiens isolate Aus17 mitochondrion complete genome gi|32891565|gb|AY255167.1| Homo sapiens isolate XJ8451 mitochondrion complete genome gi|51451134|gb|AY714036.1| Homo sapiens isolate C21 mitochondrion complete genome gi|32891676|gb|AY255175.1| Homo sapiens isolate GD7824 mitochondrion complete genome gi|113706998|gb|DQ404446.3| Homo sapiens isolate AUD32 mitochondrion complete genome
gi|32348030|gb|AY289054.1| Homo sapiens isolate Aus16 mitochondrion complete genome gi|395764488|gb|AY275532.2| Homo sapiens isolate M3 mitochondrion complete genome gi|57903758|gb|AY882380.1| Homo sapiens isolate 2 U2b Tor35 mitochondrion complete genome gi|395764494|gb|AY275537.2| Homo sapiens isolate 183 mitochondrion complete genome gi|48596g2i|62613|g9b4|A2Y1169|g5b7|A9Y19.25| 0H2o8m9o.2 s| Hapoimenos s haappielontsy piseo Alaste1 0NF4 m mitoitocchhoonnddriroionn c coommplpelteet eg egneonmome e gi|51450532|gb|AY713993.1| Homo sapiens isolate R96 mitochondrion complete genome gi|51451148|gb|AY714037.1| Homo sapiens isolate A54 mitochondrion complete genome gi|57903786|gb|AY882382.1| Homo sapiens isolate 4 U2e Tor10 mitochondrion complete genome gi|86450443|gb|DQ372869.1| Homo sapiens isolate PAI9 mitochondrion complete genome gi|48596141|gb|AY195749.2| Homo sapiens haplotype Na1B mitochondrion complete genome gi| 5g1i|5415405918000|g8b|g|AbY|A7Y1741042052.17| .H1|o Hmoom soa spaiepniesn iso islaotela Cte2 R73 m6i tmocitohcohnodnridornio cno cmopmleptele gtee gneonmoeme gi|32891606|gb|AY255170.1| Homo sapiens isolate GD7813 mitochondrion complete genome gi|51450602|gb|AY713998.1| Homo sapiens isolate T100 mitochondrion complete genome gi|51450630|gb|AY714000.1| Homo sapiens isolate A52 mitochondrion complete genome gi|40849315|gb|AY495294.1| Homo sapiens isolate T2-07 mitochondrion complete genome gi|32891g5i|7392|8g9b1|A3Y5255|g5b1|6A8Y.215| H51o5m2o.1 s| aHpoiemnos s isaopliaetnes G isDo7la8t0e9 S mDi1to0c3h5o2n mdritiocnh coonmdrpiolente c goemnpolmete genome
gi|40849147|gb|AY495282.1| Homo sapiens isgoi|l4ga0it|e48 0T4819-43199749 m4|g1itbo|g|cAbhY|Ao4Yn94d59r3i5o03n00 . 1c3o| .H1m|o pHmleootme s oga espnaieopnmiesen iso islaotela Tte3 T-033-0 m6i tmocitohcohnodnridornio cno cmopmleptele gtee gneonmoeme gi|51450994|gb|AY714026.1| Homo sapiens isolate R177 mitochondrion complete genome gi|57903772|gb|AY882381.1| Homo sapiens isolate 3 U2c Tor36 mitochondrion complete genome gi|395764487|gb|AY275531.2| Homo sapiens isolate 2041 mitochondrion complete genome gi|636528826|gb|AY275536.3| Homo sapiens isolate 167 mitochondrion complete genome gi|32348617|gb|AY289096.1| Homo sapiens isolate 513 mitochondrion complete genome gi|51451036|gb|AY714029.1| Homo sapiens isolate C169 mitochondrion complete genome gi|51450574|gb|AY713996.1| Homo sapiens isolate B53 mitochondrion complete genome gi|57904010|gb|AY882398.1| Homo sapiens isolate g2i0|5 U7950a411 T9o2r|1g3b | AmYit8o8c2h4o1nd1r.1io| nH ocmomo pslaepteie gnesn oismoelate 33 U5b1d Tor120 mitochondrion complete genome gi|40849343|gb|AY495296.1| Homo sapiens isolate T2-09 mitochondrion complete genome gi|51450728|gb|AY714007.1| Homo sapiens isolate B70 mitochondrion complete genome gi|40g8i|4490382499|2g5b9|A|gYb4|9A5Y249955.219| H0.o1m| Hoo smaop iseanpsi eisnosla isteo Tla2te-0 T82 m-0it3o cmhitooncdhroionnd r cioonm cpolemtep gleeten ogmeneome gi|51450644|gb|AY714001.1| Homo sapiens isolate T124 mitochondrion complete genome gi|57904248|gb|AY882415.1| Homo sapiens isolate 37 U5b2 Tor124 mitochondrion complete genome gi|40848377|gb|AY495227.1| Homo sapiens isolate J3-10 mitochondrion complete genome
gi|51450672|gb|AY714003.1| Homo sapiens isolate C g3i| 5m7it9o0c4h2o2n0d|rgiobn|A Yc8o8m2p4le1t3e. 1g|e Hnomoe sapiens isolate 35 U5b2 Tor77 mitochondrion complete genome gi|40849175|gb|AY495284.1| Homo sapiens isolate T1-19 mitochondrion complete genome
gi|40847929|gb|AY495195.1| Homo sapiens isolate J1-01 mitochondrion complete genome ggi|5 ig|51i|1454515040455700654|8g|8gb|bgA|bAY|Y7A71Y137391983991.91.71| H.|1 Ho| Hommomo s osa apspiaeipeninses nis siso iolsaloateltae At eA1 68A1 4m 0mit omitocitchohoconhndodrnirodionrin o c n co omcmopmplelpetelte gt eg engnoeomnmoeme e gi|40848055|gb|AY495204.1| Homo sapiens isolate J1-10 mitochondrion complete genome gi|40849063|gb|AY495276.1| Homo sapiens isolate T1-10 mitochondrion complete genome ggi|6i|312732448365559|g|gbb|A|AYY926839507929.1.1| H| Hoommoo s saappieiennss is isoolalatete 1 D FC1aH10 T0o2r m49ito mcihtoocnhdorniodnr io cno mcopmleptele gtee gneonmoeme gi|32348548|gb|AY289091.1| Homo sapiens isolate SH29 mitochondrion complete genome gi|40849469|gb|AY495305.1| Homo sapiens isolate T3-08 mitochondrion complete genome gi|40848405|gb|AY495229.1| Homo sapiens isolate J3-12 mitochondrion complete genome gi|57904206|gb|AY882412.1| Homo sapiens isolate 34 U5b1d Tor119 mitochondrion complete genome gi|32891509|gb|AY255163.1| Homo sapiens isolate QD8168 mitochondrion complete genome gi|40848363|gb|AY495226.1| Homo sapiens isolate J3-09 mitochondrion complete genome gi|636528825|gb g|Ai|5Y7297054503254.2|g| Hb|oAmY8o8 s2a3p9ie9n.1s| Hisomlaote s 2a0p3ie2n msi tioscohlaoten d2r1io Un5 cao1m Tpolre1te0 1g e mniotomcheondrion complete genome gi|40849119|gb|AY495280.1| Homo sapiens isolate T1-14 mitochondrion complete genome gi|40848209|gb|AY495215.1| Homo sapiens isolate J2-06 mitochondrion complete genome gi|51450420|gb|AY713985.1| Homo sapiens isolate A65 mitochondrion complete genome gi|57904150|gb|AY882408.1| Homo sapiens isolate 30 U5b1b Tor118 mitoc ghio|5n1d4r5io0n9 1c0om|gpbl|eAtYe7 g1e4n0o2m0e.1| Homo sapiens isolate S11 mitochondrion complete genome gi|g5i1|4405g80i4|9g493i0|3g487i0|44g1890b|4g48|A9b14Y4|3A972|Y4g7145b|4g95|0Ab5|g2Y|2Ab249Y|.9A1845Y|. 91H345|0 9oH315m0og.3g1o2mi|0i|5 .g| s14Ho41iga|0 . 4os41Hip8g|0ma5|4 io4iHe8gp|0o4m9n4ii8o| e024sgso94mn830ai 2|09is4so18p4|2a0 9g o|4iis5ges7p82bl9a|bno3ig48|e3Apt|sl|ebA97agn0Yi e |Yi3|tbRsA1ge7n45| Yob 1AigTs974l|48YbaA3 o5|i9g0s64|t-YlAe2a50b1o 94mY 8t2T1|5leA9a84i83 .t2 mY51toT.9e9-1942|c30i5 .t|HT1o 9h-4H230.c|52o1 9mHo-5h2.mn|310 m ioH9mtd.|7o1 nmo7Hro ic|mtsdi .omsH1ohracin at|moiso phH pn amconicsoeidopeh oan srcminompe diasonsoinrp eanmidi soisilnsp er pon casiontoselle opa lsncioa smtitge e oltsi oaescep n mg Rlt ionlaeTseplm9ot 2 atneTilese2m-ltpo 2ae T0otg lem-te 21elT0a tgei- en2tmTto0e o- 2gc4min0 tmTo-eh o5mi02tcneom 6m-hiotcn1o eomihdt0conorie htcmdionoohrcidntniohr d nciocordh noin ocrodm in ooncrp mind ocl ermpn ociotl emp ocn ltmgpeo clte mpegonlt epegmonlt eegmpont eglmeon egtmeeone meognmeonmeoeme gi|82792528|gb|DQ301810.1| Homo sapiens isolate D5257 mitochondrion complete genome gi|51450546|gb|AY713994.1| Homo sapiens isolate C195 mitochondrion complete genome gi|51450854|gb|AY714016.1| Homo sapiens isolate C200 mitochondrion complete genome gi|57904122|gb|AY882406. 1g|i |H57o9m0o4 s2a3p4i|egnbs|A iYs8o8la2te4 1248. 1U| 5Hbo1mbo T soar1p2ie9n ms itsooclhaoten 3d6ri oUn5 bco2m Tpolre1te3 2g e mniotomcehondrion complete genome gi|57904262|gb|AY882416.1| Homo s agpi|5ie7n9s0 i4s0o6la6te|g 3b8|A UY868a2 T4o0r24.11 |m Hitoomchoo snadpriieons c isomolpaltet e2 4g eUn5obm1eb Tor85 mitochondrion complete genome g gi|4i|802874982833898|g|gbb|A|DY4Q9350216800.10|. 1H| oHmoom soa spaiepniesn iss oislaotlea tKe3 D-0116 5m6it omcithoocnhdorniodnri o cno mcopmleptele gtee ngoemnoeme gi|32348478|gb|AY289086.1| Homo sapiens isolate NG29 mitochondrion complete genome gi|4084904g9i||g4gb0i|8|A44Y0848994959321|7g35b3.|1Ag|Yb H|4Ao9Ym542o97 5s12a.18p|1i eH.1no|s mH isoo mslaotp esi eaTnp1si-e0 ins9so m liasittoecl aTht1eo- nT0d15r- im1o5nito m ciohtomocnphdloerntieod ngr ie ocnoo m cmpoelmetpel egten goemneome gi|51451g1i0|468|g5b9|6A1Y8791|4g0b3|A4Y.1|9 H5o7m74o. 2s|a Hpoiemnos sisaoplaieten sR h1a5p4l omtyitopceh Eo1n0dJr imonito cohmonpdlertieo ng e cnoommpelete genome gi|78776059|gb|DQ272119.1| Homo sapiens isolate Mg231 mitochondrion complete genome gi|40848321|gb|AY495223.1| Homo sapiens isolate J3-06 mitochondrion complete genome gi|51451246|gb|AY714044.1| Homo sapiens isolate C40 mitochondrion complete genome gi|32348002|gb|AY289052.1| Homo sapiens isolate Aus14 mitochondrion complete genome gi|40848307|gb|AY495g2i|2420.814| H82o7m9o|g sba|ApYie4n9s5 i2s2o0la.1te| HJ3o-m0o5 smaitpoicehnosn isdoriloante cJo3m-0p3le mteit ogcehnoonmderion complete genome gi|51450770|gb|AY714010.1| Homo sapiens isolate SW4 mitochondrion complete genome ggi|4ig|40i|0848404881428317|9g|5gb|b|gA|bAY|Y4A49Y9545292151327.1.41| H.|1 Ho| Hommomo s osa apspiaeipeninses nis siso iolsaloateltae Jt eJ2 2-J0-204-8 0m 5mit omitocitchohoconhndodrnirodionrin o c n co omcmopmplelpetelte gt eg engnoeomnmoeme e gig|5i|15415405309420|6g|bg|bA|YA7Y1731938938.41.|1 H| Homomo os aspaipeinesn sis iosloaltaet eA 3A02 6m mitoitcohcohnodnrdiorino n c ocmomplpeltet eg egneonmome e gi|32891523|gb|AY255164.1| Homo sapiens isolate GD7811 mitochondrion complete genome gi|32348603|gb|AY289095.1| Homo sapiens isolate 496 mitochondrion complete genome gi|58333729|emb|AJ842744.1| Homo sapiens complete mitochondrial genome haplotype B4a1a individual Am015 gi|32891285|gb|AY255147.1| Homo sapiens isolate LN7595 mitochondrion complete genome gi|40848937|gb|AY495267.1| Homo sapiens isolate T1-01 mitochondrion complete genome gi|g4i0|4804884183292|g3b|g|AbY|A4Y9459251201.16|. 1H| oHmoom soa spaiepniesn is oislaotlea tJe2 J-20-10 m7 imtoictohcohnodnrdiornio nc o cmopmleptlee tgee gneonmoeme gi|5790409 4g|ig|5b7|A9Y0848123460|g4b.1|A| YH8o8m2o4 0s7a.p1i|e Hnosm isoo slaatep i2e6n sU i5sbo1labte T 2o9r1 U350b m1bito Tcohro7n6d mrioitonc choomndprleioten g ceonmopmlete genome gi|57904052|gb|AY882401.1| Homo sapiens isolate 23 U5b1b Tor128 mitochondrion complete genome gi|58333783|emb|AJ84 2g7i|35208.19| 1H3o1m3o|g sba|ApYie2n5s5 1c4o9m.1p|l eHteo mmoito scahpoienndsri aisl ogleanteo LmNe7 h5a5p2l omtyitopceh Bo4nad2r i oinnd icvoidmupalle Ptew g0e1n2ome gi|48596135|gb|AY195745.2| Homo sapiens haplotype E12T mitochondrion complete genome gi|32348589|gb|AY289094.1| Homo sapiens isolate S1220 mitochondrion complete genome gi|78776129|gb|DQ272124.1| Homo sapiens isolate Dong35 mitochondrion complete genome gi|58333767|emb|AJ842748.1| Homo sapiens complete mitochondrial genome haplotype B4a1a individual Am111 gi|57904178|gb|AY882410.1| Homo sapiens isolate 32 U5b1c Tor121 mitochondrion complete genome gi|32348562|gb|AY289092.1| Homo sapiens isolate SH33 mitochondrion complete genome gi|50295413|gb|AY519484.2| Homo sapiens isolate BuriatB3 mitochondrion complete genome gi|78776073|gb|DQ272120.1| Homo sapiens isolate Shui102 mitochondrion complete genome gi|40847985|gb|AY495199.1| Homo sapiens isolate J1-05 mitochondrion complete genome gi|40849812906801319375g|ig|4b0|A8Y449935825867|g356794b.1|A| YH4o9m5o2 9s9a.p1i|e Hnosm isoo slaatep iTe1n-s120 i80123s omlaitotec hTo3n-0d2ri omnit o ccohmopnlderteio gne cnoompelete genome gi|40848069|gb|AY495205.1| Homo sapiens isolate J1-11 mitochondrion complete genome gi|4g8i|45098641897901557029|g1975b|g|AbY|A1Y94597562767.2802379| .H1|o Hmoom soa spaiepniesn hsa ipsloltaytpee T E11-01246713T miittochondrriion compllette genome gig|4i|g04i80|4480748974597799|9g4|bg3|b|Ag|YAb4Y|A94Y594159925701.019.|16 H|. 1Ho| moHmoo oms asopa sipeainepsnie sins isos loiasltaoetl eaJ t1Je-1 J0-130- 6m0 m2ito imtcoihctoohcnohdnordniordinor ni oc noc mo cmpolpmelteptl eg tegene gonemonmeoeme gi|32348687|gb|AY289101.1| Homo sapiens isolate Sb29 mitochondrion complete genome gi|33465995|gb|AY275534.1| Homo sapiens isolate 2579 mitochondrion com gpi|l5e1te4 g5e0n7o0m0|egb|AY714005.1| Homo sapiens isolate R94 mitochondrion complete genome gi|40848027|gb|AY495202.1| Homo sapiens isolate J1-08 mitochondrion complete genome gi|50295420|gb|AY519492.2| Homo sapiens isolate To gfai|l3a2rB849 1m2ito5c7h|gobn|AdYri2o5n5 c1o4m5.p1le| Hteo gmeon osmapeiens isolate WH6967 mitochondrion complete genome gi|g4i0|4804874987111|g1b|g|AbY|A4Y9459159280.18|. 1H| oHmoom soa spaiepniesn is oislaotlea tJe1 J-10-41 m4 imtoictohcohnodnrdiornio nc o cmopmleptlee tgee gneonmoeme gi|66356286|gb|AY950290.1| Homo sapiens isolate N20 mitochondrion complete genome gi|32348184|gb|AY289065.1| Homo sapiens isolate F5 mitochondrion complete genome gi|48596151|gb|AY195754.2| Homo sapiens haplotype E9J mitochondrion complete genome gi|82792346|gb|DQ301797.1| Homo sapiens isolate D1520 mitochondrion complete genome gi|58333791|emb|AJ842751.1| Homo sapiens complete mitochondrial genome haplotype B4a2 individual Ya015 gi|57903954|gb|AY882394.1| Homo sapiens isolate 16 K1c Tor106 mitochondrion complete genome gi|50295422|gb|AY519494.2| Homo sapiens isolate TubalarB1 mitochondrion complete genome gi|57904164|gb|AY882409.1| Homo sapiens isolate 31 U5b1c Tor122 mitochondrion complete genome gi|40848909|gb|AY495265.1| Homo sapiens isolate K3-06 mitochondrion complete genome gi|32891187|gb|AY255140.1| Homo sapiens isolate QD8 g1i|4319 5m7it6o4c4h8o5n|dgrbio|AnY 2c7o5m5p2le7t.e2 |g Heonmomo esapiens isolate 2812 mitochondrion complete genome gi|32348673|gb|AY289100.1| Homo sapiens isolate Sb13 mitochondrion complete genome g ig|5i|75 g97i|09540704930884|01g|0bg8|bA||gYAb8Y|8A828Y428048002.341.0|1 H5| H.o1mo| Hmoo osm asopa ipseianepsni seis niossloa ilstaeot e2la 22te 5U 2U57b5 U1bb15 bT 1oTbro1 rT21o33r 19 m 1 mit o mitcoithcoohcnohdnordniordinori no c n oc mocmopmlpelptelte egt eg negonemonmoemee gi|32348492|gb|AY289087.1| Homo sapiens isolate SH10 mitochondrion complete genome
gi|82792276|gb|DQ301792.1| Homo sapiens isolate D1311 mitochondrion complete genome gi|48526883|gb|AY255136.2| Homo sapiens isolate SD10313 mitochondrion complete genome gi|82792486|gb|DQ301807.1| Homo sapiens isolate D4757 mitochondrion complete genome gi|32348450|gb|AY289084.1| Homo sapiens isolate 36 mitochondrion complete genome
gi|32348226|gb|AY g2i |g83i92|3032643884.2184|5 H07|og5mb|g|oAb Y|sA2aY8p29ie80n96s09 9i.s13o|. 1Hla| otHem oCom1 so1a 1sp2aie pmnieiston icssh oisolaontleda rtCeio 1Sn1 9c20o1 m6 pmitoleitcotehc oghneodnrodiomrinoe n c ocmomplpelteet eg egneonmomee gi|51450518|gb|AY713992.1| Homo sapiens isolate C57 mitochondrion complete genome gi| 5g8i|8363435704439|e9m|gbb|A|DJQ84327724857.31.|1 H| Homomo os aspaipeinesn sc oismoplaletete T mRiOto1c3h7o nmditroicahl goenndorimone choamplpolteytpe eg eBn4oam1ae individual Am034 gi|4g0i|48g04i8|g4g41i0|g4i82|84i05|408|g084g3b8148i||g|468A0gbi870|gY14i|g1|89Ai4g30|g4i57Y09|b|8i4g0|38|45|g40Abi8|0|9420gb8iY|4|A5804b|24A81Y2940|858A9Y2|406.8g413Y5499654b8|9429g3 5.|H18|31g9A5b|2g934|bo|52Y| g0AHb|39|mg2.40Ab1Y|5|oAb1g97oY|.4|A 1mY|g1Hb5. A419sY|4b. |2o9Y1HA|5a4 9|0H 5A4|mYs2p9 o5H329Y4oa1i5om2e.154o9mp82 2nso92m|5i.2 oe1sa H.35s218o n|. ps 1i02aoHs|. s 1ia|H.2epm5 o1 oH|api4 ni.slo|He1ma pioH.seom1n |tois ome Hnlo|isao msa HnsoJm ot oipeso a 1omisolis a oeJp-msia so1pstln1iaepo l5iasa-ep tni lJe1 psa tmniies2 sniatJpse in-oJ itsp1imso n0eisJl1 si-aocise3nis 20-toitolh nse1aoi-m7lscoas0 3tl Jieaoimshnt l2 eiao1m tlsoJdea i tcm-Joelin3r t0atJehoi3l icd-oaJt9t3 oec0-Jhrnt3 -0ecnm hi13oJ 0- 2hdo c-J1ni3m4t 1ornom31d- i im3noc0dtm- roimt 0dnih8roimoctpio7ir omct nhlioccet onhom poc ithncdt eoc lnhimceot r nho cdgocitnpmoedochrenomdln irnhepogndmri podtl neiorecoplnriden mo t nilgec oderto nme ce io nrtgomc e oi npgm oceno emcgolenoe pm oemcnp motl epmcnolemep tlogmeptleem tlpeg tngpele tegoel negte mengotene oegmno mngeoemoenememnoeomemee gi|58333759|emb|AJ842747.1| Homo sapiens complete g mi|3ito2c8h9o1n1d1r7ia|gl bg|eAnYo2m55e1 h3a5p.1lo| Htyopme oB 4sa1paie ninsd iisvoidlautael LYNa0715289 mitochondrion complete genome gi|82792360|gb|DQ301798.1| Homo sapiens isolate D1606 mitochondrion complete genome gi|82792514|gb|DQ301809.1| Homo sapiens isolate D5077 mitochondrion complete genome
g gi|6i |g6i6|363565636252868325|8g|g4bb|gA|AbYY|9A95Y5090252808628.81.17| H|. 1Ho| oHmmoom s soaa pspiaeiepnnises nis isso oilsalaotetlea N tNe1 6N m m2it oimtocicthohoconhndodrnirodionrni o c nco o mcmoppmleleptetle g tgee ngnoeomnmoeeme gi| 4g8i|509269157482|g3b|g|AbY|A1Y951797409.25| .H2|o Hmoom soa spaiepniesn hsa ipsloltaytpee T Ausv3aBn Bm4it omcithoocnhdorniodnrio cno cmopmleptele gtee gneonmoeme gi|33465911|gb|AY275528.1| Homo sapiens isolate 415 mitochondrion complete genome gi|40848797|gb|AY495257.1| Homo sapiens isolate K2-06 mitochondrion complete genome
gi|51450616|gb|AY713999.1| Homo sagpi|3ie2n3s4 i8s5o0la6te|g Cb|1A8Y02 8m9it0o8c8h.o1n| Hdroiomno csoampipelneste i sgoelnaotem SeH17 mitochondrion complete genome gi|57904276|gb|AY882417.1| Homo sapiens isolate 39 U6b Tor14 mitochondrion complete genome gi|40848755|gb|AY495254.1| Homo sapiens isolate K2-03 mitochondrion complete genome gi|3234 8g3i|89644|g5b0|A6Y1218 |g9ib|03|D8203Q.4138|7 H323o88m8|g1ob. 1s|A|a HYp2oie8mn9os0 si7sa6op.l1aie|t eHn sWo misEo1 l8sa atmep iMtioeFcn0hs2o is5no dmlraiitotenc 1 h c0oo0nm dmpriitoloencte h c gooenmndporilmeotne gceonmopmleete genome gi|40848923|gb|AY495266.1| Homo sapiens isolate K3-07 mitochondrion complete genome gi|57903940|gb|AY882393.1| Homo sapiens isolate 15 U8b Tor48 mitochondrion complete genome gi|82792430724|gb|DQ301870919.1| Homo sapiens isolate D1760216 mitochondrion complete genome gi|86450555|gb|DQ372877.1| Homo sapiens isolate MJ86 mitochondrion complete genome gi|82792640|gb|DQ301818.1| Homo sapiens isolate E1365 mitochondrion complete genome gi|5 g1i|455709409307|4g4b||gAbY|7A1Y38989203.719| H.1o| Hmoom soa psiaepnise nisso ilsaotela Cte5 13 Um2itoac Tho gori n3|g8d4i 2|g8r 7im 2|og89 7ingit2|2o89 i7 |2c8293ho27424om7915n|92g6p7d23b|lg0er41|iDb|toge538|nQDb 80|g | 3QDegcb0nob|3QD1om|0D3Q7m1p0Q838el1e930t8.e0121 17|g. 13H89e|. 105onH|53.om 1oH.m1|om oH|e somHoa sompa msoiepao sniep sanieap issnpie oisisenl aoinsstls eaois tliDeaso tol1Deal1 at1De2t8e 5D32 6D 1m9743 im7t26o im609cto27 himcto omhictnoihtdocnorchdinohordnionor nd nicodr o nicrom io ncpmn o cl epm cotlepom tlmgepe tplgenle tgeonte mgon gemoenemnoeommee gi|40848783|gb|AY495256.1| Homo sapiens isolate K2-05 mitochondrion complete genome gi|51450868|gb|AY714017.1| Homo sapiens isolate T150 mitochondrion complete genome gi|51894476|gb|AY738940.1| Homo sapiens isolate Tor1 #43 mitochondrion complete genome gi|82792584|gb|DQ301814.1| Homo sapiens isolate D5908 mitochondrion complete genome
gi|4084878624951|gb|AY49525593.1| Homo sapiens isolate K2-0482 mitochondrion complete genome g ig|4 gi|8 4gi|540i|9408608418474863869|709g1|bg3||gbA|gb|YAb|1AY|9AY45Y497495695252.240253.|1 H1.1| .Ho1| Hm|o Homoom osmo aso psa isapeapinepiseni enshns aiss piso lioslatolyatelpate Kete K1 E K1-11-302-K15 m 3 mi tmoiitocitcohhcoohnnoddnrirdoiiornino c n co ocmmopmplelpleteltee gt ege egnneoonmmoemee gi|40848629|gb|AY495245.1| Homo sapiens isolate K1-07 mitochondrion complete genome gi|82792332|gb|DQ3017 g9i|67.414| H75o8m4o0 s|gabp|DieQns2 0is0o8la0t5e. 1D| 1H4o3m5o m sitaopciheonnsd isrioolna t ec o7m67p lmetieto gcehnoonmdreion complete genome gi|40848867|gb|AY495262.1| Homo sapiens isolate K3-03 mitochondrion complete genome gi|82792598|gb|DQ301815.1| Homo sapiens isolate D5939 mitochondrion complete genome gi|82792545464|gb|DQ30181024.1| Homo sapiens isolate D54525312 mitochondrion complete genome gi|40848811|gb|AY495258.1| Hgio|8m2o7 9s2a2p9ie0n|gsb is|DoQla3te0 K127-9037.1 m| Hitoocmho nsdarpioienn sc oismoplaletete D g1e3n2o0m meitochondrion cgoi|4m0p8le4t8e6 g4e3n|gobm|AeY495246.1| Homo sapiens isolate K1-08 mitochondrion complete genome gi|40848685|gb|AY495249.1| Homo sapiens isolate K1-11 mitochondrion complete genome gi|74475826|gb|DQ200804.1| Homo sapiens isolate 24 mitochondrion complete genome gi|40848727|gb|AY495252.1| Homo sapiens isolate K1-14 mitochondrion complete genome gi|8279261226|gb|DQ3018167.1| Homo sapiens isolate E1028291 mitochondrion complete genome gi|74475798|gb|DQ200802.1| Homo sapiens isolate 30 mitochondrion complete genome gi|82792472|gb|DQ30 g1i8|40068.14|8 H65o75841m13759|og bs|aApYi4e9n5s2 is43o8172904l.a1t|e H Do4m4o8 s1a mpiiteoncsh oisnodlaritoen K 1c-o10m0394126p mleittoec gheonnodmrieon complete genome gi|57903870|gb|AY882388.1| Homo sapiens isolate 10 U4b Tor12 mitochondrion complete genome ggi|7i|85 69g 40ig|8 5gi|6 508gi| 438g5 7ig| 523i6g2|i 3|g0839i||g28i634|2|g8b36837b6| 4Ag1354|48D5iY|7518|g5840972|Qbe063565|0|gm354D613|1eb725b|3Q5g|m|2g70A|7Abg38b|4bYg4J|b7A|7|2Ab.8|28YD18Y|J4D8|.2| 91Q2gH828Q0|8b47 36oH9793|247D.m017o17628Q|o.m02 4.18H13 283s9|o7| .o H1.7a.H 41sm|52po .||oaH1 H.8oim1emp|o 7 Ho|snoi oemH1mas o sn.so1p moiassa m|is e posHspisaoni aliesoaeop spsnamtnli eaiiispeso tnp3 eino ie csis selBsPnao ai n4 Osmtclpeaso o3ii pts eTloiTm1aslonLe coC4topels3tahre llPm a56 eWtoi esm8t1 tinemt o EK imd tmiKlocA7taoriActhP itiotmcetoPoh1chn ci8Tcon9tho h 9Rhnd conmco odrmOdnhninrtomrdoi1ditdianoorcnp3rrli cin ohdl1oigceah nor n eotmclioe no gn m ocni dntgeomopdr enmc imlcrpoenohieolnptoemoe mn lmltnh eecg p dat ce oeg lrhpeo mneigoaltmoneepnptom pnylg le omlcopetteoymente mp goeB gemp4e nlBaeno41teoma mg1 e ieann d ionivmdideivuidaul Taal A0m83145 gi|57903926|gb|AY882392.1| Homo sapiens isolate 14 U8a Tor47 mitochondrion complete genome gi|32348156|gb|AY289063.1| Homo sapiens isolate E4 mitochondrion complete genome gi|74475812|gb|DQ200803.1| Homo sapiens isolate 47 mitochondrion complete genome gi|51451302|gb|AY714048.1| Homo sapiens isolate R63 mitochondrion complete genome gi|57903842|gb|AY882386.1| Homo sapiens isolate 8 U4a Tor60 mitochondrion complete genome
gi|8645045875|gb|DQ3728702.1| Homo sapiens isolate TRO12323 mitochondrion complete genome gi|51451274|gb|AY714046.1| Homo sapiens isolate R62 mitochondrion complete genome gi|32891089|gb|AY255133.1| Homo sapiens isolate GD7812 mitochondrion complete genome gi|8542707989042382958640859280135|gb|DAYQ843890251327896905314108.1.1| |H Hoommoo s saappieiennss i sisoolalatete 1K D3714- K02171425837a 297m T mitooritc1oh5co h mnodintordicorhinoo n cn odcmroiompnlpe clteot egm egpneleontmeo megenome gi|51450434|gb|AY713986g.1i|5| H14o5m0o4 s6a2p|giebn|AsY i7s1o3la9te8 8C.16|5 H moimtooc hsoanpdierniosn i s coolamtep lRet5e3 g menitoocmheondrion complete genome g gi|3i|33446655992359|g|gbb|A|AYY22775552390.1.1| H| Hoommoo s saappieiennss is isoolalatete 5 14706 m6i tmocitohcohnodnridornio cno cmopmleptele gtee gneonmoeme gi|74475784|gb|DQ200801.1| Homo sapiens isolate 1820 mitochondrion complete genome
gi|51450812|gb|AY71 g4i0|21536.13|1 H1o2m98o| gsba|pAiYe8n8s2 is3o9l1a.t2e| BH1o9m moit oscahpoienndsr iosno l actoem 1p3l eUte7 gTeorn3o7m me itochondrion complete genome gi|51894504|gb|AY738942.1| Homo sapiens isolate Tor3 #20 mitochondrion complete genome gi|57903898|gb|AY882390.1| Homo sa pgiie|5n1s4 i5s0o8la2te6 |1g2b |UAY9b7 1T4o0r5184 . 1m| iHtoocmhoon sdarpioien n cso imsopllaette Bg8e1n ommitoechondrion complete genome gi|441432863|gb |gAiY|5878920338850.20|| gHbo|AmYo8 s8a2p3i8e3n.s1 |i sHoolamteo 7s aUp3iebn Tso irs5o9la mtei t5o cUh3oan dTroior8n6 c momitopclehtoen gdernioonm ceomplete genome
gi|51450686|gb|AY714004.1| Homo sapien sg i|s5o1l4a5te0 C9522| gmbit|oAcYh7o1n4d0r2io3n.1 |c Hoommpole stea gpeiennosm iseolate C11 mitochondrion complete genome gi|51450448|gb|AY713987.1| Homo sapiens isolate T26 mitochondrion complete genome gi|57903884|gb|AY882389.1| Homo sapiens isolate 11 U9a Tor40 mitochondrion complete genome
gi|51894518|gb|AY738943.1| Homo sapiens isolate Tor4 ZE2030 mitochondrion complete genome gi|57903814|gb|AY882384.1| Homo sapiens isolate 6 U3b Tor11 mitochondrion complete genome gi|57903856|gb|AY882387.1| Homo sapiens isolate 9 U4a Tor78 mitochondrion complete genome
gi|51450364|gb|AY713981.1| Homo sapiens isolate R98 mitochondrion complete genome gi|51450784|gb|AY714011.1| Homo sapiens isolate S4 mitochondrion complete genome gi|48596154|gb|AY195756.2| Homo sapiens haplotype E23N1B mitochondrion complete genome gi|51450756|gb|AY714009.1| Homo sapiens isolate A190 mitochondrion complete genome gi|51450798|gb|AY714012.1| Homo sapiens isolate A165 mitochondrion complete genome
gi|51894532|gb|AY738944.1| Homo sapiens isolate Tor5 #112 mitochondrion complete genome gi|82792350442|gb|DQ301789141.1| Homo sapiens isolate D1535647 mitochondrion complete genome gi|78776087|gb|DQ272121.1| Homo sapiens isolate QJ185 mitochondrion complete genome gi|51450714|gb|AY714006.1| Homo sapiens isolate R43 mitochondrion complete genome
gi|51451232|gb|AY714043.1| Homo sapiens isolate C118 mitochondrion complete genome gi|51894490|gb|AY738941.1| Homo sapiens isolate Tor2 ZE1043 mitochondrion complete genome gi|75905878|gb|AY963580.2| Homo sapiens isolate 9 N21 Tor57 mitochondrion complete genome gi|48596177|gb|AY195769.2| Homo sapiens haplotype E22i mitochondrion complete genome gi|51451204|gb|AY714041.1| Homo sapiens isolate C124 mitochondrion complete genome gi|86450695|gb|DQ372887.1| Homo sapiens isolate TRI65 mitochondrion complete genome gi|51894546|gb|AY738945.1| Homo sapiens isolate Tor6 #113 mitochondrion complete genome gi|32891159|gb|AY255138.1| Homo sapiens isolate XJ8426 mitochondrion complete genome gi|48596176|gb|AY195768.2| Homo sapiens haplotype E15W mitochondrion complete genome gi|40849789119|gb|AY49532380.1| Homo sapiens isolate V1-235 mitochondrion complete genome gi|242308759|gb|AY963586.3| Homo sapiens isolate I3a Tor21 mitochondrion complete genome gi|51450882|gb|AY714018.1| Homo sapiens isolate B59 mitochondrion complete genome gi|40847803|gb|AY495186.1| Homo sapiens isolate H6-10 mitochondrion complete genome gi|51451176|gb|AY714039.1| Homo sapiens isolate B23 mitochondrion complete genome gi|48596223|gb|AY195792.2| Homo sapiens haplotype As9Y mitochondrion complete genome gi|48596195|gb|AY195779.2| Homo sapiens haplotype E14W mitochondrion complete genome
gi|40847775|gb|AY495184.1| Homo sapiens isolate H6-08 mitochondrion complete genome gi|113706988|gb|DQ404441.3| Homo sapiens isolate AUD3 mitochondrion complete genome gi|51450742|gb|AY714008.1| Homo sapiens isolate R132 mitochondrion complete genome gi|113706986|gb|DQ404440.3| Homo sapiens isolate AUR1 mitochondrion complete genome gi|40849735|gb|AY495324.1| Homo sapiens isolate V1-19 mitochondrion complete genome gi|84682446|gb|DQ341066.1| Homo sapiens isolate 9 L3x Tor72 mitochondrion complete genome gi|69938883|gb|AY495123.2| Homo sapiens isolate H2-03 mitochondrion complete genome
gi|51894616|gb|AY738950.1| Homo sapiens isolate Tor11 ZEus mitochogni|d5r1io8n9 4 c6o3m0p|glebte|A gYe7n3o8m9e51.1| Homo sapiens isolate Tor12 ZE1090 mitochondrion complete genome gi|51g8i|49048546905|g6b7|A|gYb7|A3Y84994563.11| 2H.1o|m Hoo smaop sieanpsie isnosl aisteo lTaoter 7V 1#-1077 mmitiotocchhoonnddrrioionn c coommppleletete g geennoommee gi|408467576259034693157|gb|AY495019178518923.1| Homo sapiens isolate H16-0262357 mitochondrion complete genome gi|51450294|gb|AY713976.1| Homo sapiens isolate R89 mitochondrion complete genome
gi|48596196|gb|AY195781.2| Homo sapiens haplotype E16V mitochondrion complete genome
gi|48596155|gb|AY195758.2| Homo sapiens haplotype E5H mitochondrion complete genome gi|51894770|gb|AY738961.1| Homo sapiens isolate Tor22 #117 mitochondrion complete genome gi|408496732071|gb|AY495312732.1| Homo sapiens isolate V1-1287 mitochondrion complete genome Eve1.0 gi|84682642|gb|DQ341080.1| Homo sapiens isolate 23 L3h Tor67 mitochondrion complete genome gi|51g8i|9541688964|7g0b0|A|gYb7|3A8Y975358.915| H6.o1m| Hoo smaop iseanpsi eisnosla isteo Tlaotre1 T6o #r9157 #m9it3o c mhiotoncdhroionnd rcioonm pcloemtep gleetneo gmeenome gi|40849693|gb|AY495321.1| Homo sapiens isolate V1-16 mitochondrion complete genome gi|84682628|gb|DQ341079.1| Homo sapiens isolate 22 L3h Tor31 mitochondrion complete genome gi|51894714|gb|AY738957.1| Homo sapiens isolate Tor18 #109 mitochondrion complete genome gi|84682460|gb|DQ341067.1| Homo sapiens isolate 10 L3x Tor82 mitochondrion complete genome gi|40847075|gb|AY495134.1| Homo sapiens isolate H2-14 mitochondrion complete genome gi|51894588|gb|AY738948.1| Homo sapiens isolate Tor9 #96 mitochondrion complete genome gi|51894602|gb|AY738949.1| Homo sapiens isolagtei|5 T1o4r5103 Z2E21|5g6b3|A Ym7ito1c3h9o7n8d.1r|i oHno cmoom spalepteie gnesn isoomlaete B49 mitochondrion complete genome gi|29690560|gb|AY195757.1| Homo sapiens haplotype E6H mitochondrion complete genome gi|51895190|gb|AY738991.1| Homo sapiens isolate Tor52 #98 mitochondrion complete genome gi|84682362|gb|DQ341060.1| Homo sapiens isolate 3 L5 Tor74 mitochondrion complete genome gi|29690476|gb|AY195751.1| Homo sapiens haplotype E2H mitochondrion complete genome gi|51894742|gb|AY738959.1| Homo sapiens isolate Tor20 #103 mitochondrion complete genome gi|51894728|gb|AY738958.1| Homo sapiens isolate Tor19 ZE2181 mitochondrion complete genome gi|40847243|gb|AY495146.1| Homo sapiens isolate H3-01 mitochondrion complete gengoi|5m1eg8i9|g2g4i9i|5|4g4670i09|45880|14g4476b965678|576482A03251675092384|Yg3751137957b3||g3g|6Ab8b|Yg|9|AA1b4YY9|7A445.Y919775|5 H1303701o021.19248m867150493|7. .1Ho19| | os. H1Hma|o opHommi eosoonma sspoa aii esppnoaiieeslpann ihtesesan iTispsol oirsllat8ayot tepZlea eE HtVe1 E15 9B1-320172031265948V miiitttoocchhoonnddrrrioiionn c coommpplelletette g geennomomee gi|51450560|gb|AY713995.1| Homo sapiens isolate B15 mitgoic|5h1o8n9d4r7io5n6 |cgobm|ApYl7e3te8 g9e6n0o.1m| He omo sapiens isolate Tor21 ZE620 mitochondrion complete genomeggi|5gi|51gi|518i|5189g1895gi|89504i|953746851238095160|89g324|436gb4|6781gb|A|62387045gb|AY176845093b|AY7319875|gAY73|gbY738b|739A|380AY8903Y1981.491892.951| 7.H571| .H104|o H0458392167|om H18560247.om2o.om12|o sHm|o saHo sapom sapiemoapieno pisen isaen isapns isopis eisoli aenisolatnseolats e hlTat e iaToste pTor 4lTorloa64ortty52 erZp403 ZEHe8 #E113625 #123E-049110328704H2301456 miiitttoocchhoonnndddrrriioioonnn c ccooommmpppleleletetete g g geenenonomommeee ggi|4gi|40gi|608i|g6984i9g47|49i3g71|0438ig03|8048gi61|48048i1|g|g648086|igb7|640854|gb|39684A|0gb|9654AY8b||3A564Yg|A|7Y489b7gY|4795|1bgA493|51|bgYA95|139|gb4YA51g38|b|i9g4YA|14i3.|15b94AY623.01|59Y4 A8.8H2|1549 .YH42|o02 9534H7|om. 695081H9g3omg.7098o|51i2 o|miH5.928o |1|7s4m H1o.2 4|1sa0 go8 H.|m0os1|gap8 b 9Hs.mao|bpi41 |e5HAapmo|i6 |oAens 0YpHiom6 eonYsa54im2eon s4 pa0s9i7snmso 9ip|asi5egs|o 5goipsa1nebsol 1bai iap5sn|oelAa0|tpi2Ae oaslneiYat6sie. Ylp sen1Hait7.ose 24i nsH|te3i 2leo s|H9as n8i2H- los5tHa o1es29i-lso1ta1m8 2e-8Hiolm0s2ta3 - 1eomHl210o3at o. em 1Hsi.-8l2 t 1ame so2|Hia - 1t|mtH oac 1e0iHpt-1ocph i6o0imtH1-eochio m80e-nmic2hont 03noomsh-iondt2 sco m onsidri t sh0comindairostoa hcoidmrpiontlpnoihcaroin lie aidtnochteon en trdnhocen i sHorcdon mshH i ncorindm3 ospii1 sonmdr- noplci-e0om nrod pl1ocaiet7l oneaprl 7moect ien mtlo gemtocpe nT gei tmcotHlep oie goetn om clpc1tgernoemco4lph-etnom eh1gm2plonotem eo3g lnopZmet en egdmlEte donegrsiet ritmeongoaio moenc g mnno he coim ntecomnoeocmdmehproepiloenlentdet er cigo goenemn ncopomlemeteep lgeeten goemneome gi|40847565|gb|AY495169.1| Homo sapiens isolate H5-05 mitochondrion complete genomegi|5g1i|849048948608|3g7b||gAbY|7A3Y84997561.17| H.1o| Hmom soa psiaepnise nisso ilsaotela Tteo rH317- Z2E86 m72ito mchitoocnhdorniodnr i ocno m copmleptele gtee ngoenmoeme gi|51g8i|49048647726|g2b1|A|gYb7|A3Y84995541.17| 3H.1o|m Hoo smaop sieanpsie isnosl aisteo lTaoter 1H55 Z-0E92 2m1i3to cmhitoncdhorinodnr icoonm cpolmetpel egten goemnoeme gi|51894658|gb|AY738953g.i1|5| 1H8o9m4o6 4s4a|pgibe|nAsY 7is3o8la9t5e2 T.1o|r H14o mZEo1 s7a4p2i e mnisto icshoolantder Tioonr 1 c3o ZmEp2le2te1 0g e mnitoomcheondrion complete genome gi|48596197|gb|AY195782.2| Homo sapiens haplotype A7NL mitochondrion complete genome gii|408475923|gb|AY49517616.1| Homo sapiiens iisollate H5-072 miitochondriion compllete genome gi|84682418|gb|DQ341064.1| Homo sapiens isolate 7 L7 Tor66 mitochondrion complete genome gi|84682488|gb|DQ341069.1| Homo sapiens isolate 12 L3i Tor69 mitochondrion complete genome gi|48596203|gb|AY195783.2| Homo sapiens haplotype A4L1B2 mitochondrion complete genome gi|84682502|gb|DQ341070.1| Homo sapiens isolate 13 L3e5 Tor79 mitochondrion complete genome gi|84682530|gb|DQ341072.1| Homo sapiens isolate 15 L3d1 Tor4 mitochondrion complete genome gi|40847579|gb|AY495170.1| Homo sapiens isolate H5-06 mitochondrion complete genome gi|229470343|gb|DQ341068.2| Homo sapiens isolate 11 L3i Tor70 mitochondrion complete genome gi|84682376|gb|DQ341061.1| Homo sapiens isolate 4 L5 Tor68 mitochondrion complete genome gi|84682544|gb|DQ341073.1| Homo sapiens isolate 16 L3b g Ti|o8r466 m82ito5c5h8o|gnbd|DrioQn3 4c1om07p4le.1te| Hgeonmoom seapiens isolate 17 L3c Tor84 mitochondrion complete genome gi|85541074|gb|DQ341063.1| Homo sapiens isolate 6 L6 Tor39 mitochondrion complete genome gi|48596217|gb|AY195789.2| Homo sapiens haplotype A3L1B1 mitochondrion complete genome gi|84682432|gb|DQ341065.1| Homo sapiens isolate 8 L4 Tor71 mitochondrion complete genome gi|40847649|gb|AY495175.1| Homo sapiens isolate H5-11 mitochondrion complete genome gi|40846571|gb|AY495098.1| Homo sapiens isolate H1-09 mitochondrion complete genome gi|84682656|gb|DQ341081.1| Homo sapiens isolate 24 L3a Tor73 mitochondrion complete genome gi|84682348|gb|DQ341059.1| Homo sapiens isolate 2 L1c2a Tor7 mitochondrion complete genome gi|84682516|gb|DQ341071.1| Homo sapiens isolate 14 L3e Tor5 mitochondrion complete genome gi|51894840|gb|AY738966.1| Homo sapiens isolate Tor27 ZE327 mitochondrion complete genome gi|48596205|gb|AY195784.2| Homo sapiens haplotype A8NL mitochondrion complete genome gi|40846823|gb|AY495116.1g|i |H40o8m4o7 s1a8p7i|egnbs|A iYs4o9la5te1 4H21.1-2| H7 ommitooc shaopniednriso nis ocloamtep Hle2te-2 g2e mnoitomcehondrion complete genome gi|40846893|gb|AY495121.1| Homo sapiens isolate H2-01 mitochondrion complete genome gi|51g8i|9450286406|6g9b7|A|gYb7|3A8Yg94i9|95651.180|9 H75.o31m1| H6o|o gsmba|opA iYse7an3ps9i eis0no0sl0a i.st1eo| THlaooterm5 H7o1 #s-9a12p8 i emniitso cishoolnadtderr iTiooonnr 6 cc1oo m#m9pp0lele tmete igt ogecenhnoomnmederion complete genome gi|5g1i|5819859251283|g2b|g|AbY|A7Y3783989939.14| .H1|o Hmoom soa spaiepniesn iso islaotela Tteo Tr5o4r5 Z5E #2120482 miittochondrion compllettee ggeennoommee gi|51894826|gb|AY738965.1g| iH|5o1m89o5 s1a0p6ie|gnbs|A isYo7la3t8e9 T8o5r.216| H ZoEmsgo smaitopciehnosn idsroiolant e c Toomrp4l6e tZeE g1e0n0o meitochondrion complete genome gi|29690840|gb|AY195777.1| Homo sapiens haplotype A10L1A2 mitochondrion complete genome gi|51895288|gb|AY738998.1| Homo sapiens isolate Tor59 ZEft mitogcih|6o9n9d3ri8o8n8 c7o|gmbp|AleYte4 9g5en1o4m5.e2| Homo sapiens isolate H2-25 mitochondrion complete genome gi|51450350|gb|AY71398g0i.|14|0 H8o4m96o2 s3a|gpbie|AnYs4 is9o5l3a1te6 R.19| H1 ommitoc shaopniednriso nis ocloamtep Vle1t-e1 g1e mniotomcehondrion complete genome gi|40847089|gb|AY495135.1| Homo sapiens isolate H2-15 mitochondrion complete genome gi|40846949|gb|AY495125.1| Homo sapiens isolate H2-05 mitochondrion complete genome gggii|i|4|44000888444777100113793||g|ggbbb||A|AAYYY444999555111333701..1.11|| | H Hooommooo s ssaaapppiieieennnsss i isissooollalaattetee H H222---111701 m miititotooccchhhooonnndddrrriioioonnn c ccooommppplleleettetee g ggeeennnooommeee gi|40g8i|4571248550|3g7b8|A|gYb4|A9Y5174193.918| H2.o1m| Hoo smaogp iis|e5an1ps8i e9isn5os3la 0ist2eo| gHlab3te|A- 0BY647 3m8it9o9c9h.o1n| Hdroiomno csoampipelneste i sgoelnaotem Teor60 ZE975 mitochondrion complete genome gi|29690882|gb|AY195780.1| Homo sapiens haplotype A2L1 mitochondrion complete genome gi|40847103|gb|AYgg4i|i49|40508184347673.121|9 3H9|go|gbmb|Ao|AY sY4a49p95i5e11n55s10 .i1s.1|o |H lHaotoemm Hoo 2s s-a1ap6pie imennistos ic sishoolalnatedte rH iHo3n3- -0 c06o5 m miptiotloecctheho gonendndrorioimonne c coommppleletete g geennoommee gi|40846515|gb|AY495094.1| Homo sapiens isolate H1-05 mitochondrion complete genome gi|84682334|gb|DQ341058.1| Homo sapiens isolate 1 L0a2a Tor29 mitochondrion complete genome gi|40847173|gb|AY495141.1| Homo sapiens isolate H2-21 mitochondrion complete genome gi|40847789|gb|gAgiY|4i|g40gi9g0|8i4g|5i84g|0i4g1|407i4g8|0i847g8|10i48|508i48|704.81075148704784|784g 8H7|434g17b2479o1b|457gA94|m1|g6|A3bY5g5|b7ogY9||4b3Ag| b47Ags9||YbAg|9Yba5Ag4|YbA54|p1Yb9A4|Y1A9i34|5Ye9A48Y591n45Y9741.56s9145.9613 5|9i 150sH5|.19 516H1.o816o.1|416 l.o|Ha2m15 .|1H mt.|H7oe1 .|H1o o.m |Ho1H s|mHo ms|Hoa 6mHoa pmos- mops0i maeos ima9osepn aosp anoimsp easips ea isnipeatsi nopeiasinspoescinp esoilne shasin lesianot sseino stlnioea sliHo adsl itoaH selitro2aselto iae6Hol-to aelH1t -aneHl4t 1ae9Ht4 e- H41tc e-0Hm4 - H0o4m 7-0H4i4mt-04 o3im-0t4 2o-mpc0 8m-0i ctlh6m0ioe t5mhio t1ctmio etocmnio htcm ionhgtdciohtcdioerhtncoihrcnodhnicohdonrodhnorim don roicd nori nedocnoridno rinod mor cin o mricn op cin o cpnml o ecnm ol cme pto cem potclmpeo lmgpoel mtpegelmtpeltep negltp enlgot eglt oemgtn egmtn eogen egone mognemonmeonmeonmeomeomemeee gi|g5i1g|48ig|049i8|054g8106i48|6576941855|8g1909b|9g35|A|b6g0Y||bAg27|Yb2A34|YAg894Yb959|78A1532Y118.713093|. 018H8.|01 9oH.|17m Ho|9 omHo.1 smo| a mHosp aosiep masnipeaosinp es isisnea osinpsl siaoes tlineoass ltoTae liot aseHrto e4H1l3 a-T12 tZoe-41Er T 41m2o1 2mirt o0Z4it0cEo h6 c #mo0h1i3nto o dmn cmrdhiitiotroicnonch nd hco ro oicnonmodndmrp r icoilopeonnltem ct cepgoo leegmnteeppon lglmeoettmen eogmeneome ggig|i4g|i4|0i4|04808048487474979718085813|7g|1g|bg|bg|bA|bA|YA|YA4Y4Y94945959151591914938.21.81.|1 .|H1 |H |Ho Homomomomo os os as aspapaipeipeineinesnsn si si sio siogsloalioa|lt4aeltae0t eHt 8e Hg H74 Hi7|-647-0750-7-0860 5m4 1m |6mig tmio6tbiotci4o|tcAoh1chYco|hgo4hnobn9odn|d5nArdri0dYorio9r4inoin9o n c.n5 1 c o 1c| o cmH0omo3mpomp.lm1pelpe|lto elHte t segto ega emg epgneonieoen onsmnomoasmempe iesieonlast eis Hol1a-te1 0H m1-it1o4c hmoitnodcrhion d croiomnp cleotem gpelenteo mgeenome gi|51894896|gb|AY738970.1| Homo sapiens isolate Tor31 ZE1584 mitochondrion complete genome gi|40847677|gb|AY495177.1| Homo sapiens isolate H6-01 mitochondrion complete genome gi|29690686|gb|AY195766.1| Homo sapiens haplotype A11L2b mitochondrion complete genome gi|75905883|gb|AY963585.2| Homo sapiens isolate 14 L0f Tor65 mitochondrion complete genome gi|40846501|gb|AY495093.1| Homo sapiens isolate H1-04 mitochondrion complete genome gi|48596208|gb|AY195785.2| Homo sapiens haplotype A6L2C mitochondrion complete genome gi|51894812|gb|AY738964.1| Homo sapiens isolate Tor25 ZE1209 mitochondrion complete genome ggi|i4|400884476291355|g|gbb|A|AYY449955114244.1.1| |H Hoommoo s saappieiennss i sisoolalatete H H22--2044 m mitiotocchhoonnddrrioionn c coommppleletete g geennoommee gi|51895246|gb|AY738995.1| Homo sapiens isolate Tor56 #87 mitochondrion complete genome gi|51895092|gb|AY738984.1| Homo sapiens isolate Tor45 #99g mi|5it1o8c9h4o7n8d4ri|ognb | AcYom73p8le9te6 2g.e1n| Homome o sapiens isolate Tor23 #94 mitochondrion complete genome gi|40846711|gb|AY495108.1| Homo sapiens isolate Hg1i|-51198 m95ito1c4h8o|gnbd|AriYo7n3 c8o9m88p.l1e|t eH goemnoo smaepiens isolate Tor49 ZE820 mitochondrion complete genome gi|48596191|gb|AY195776.2| Homo sapiens haplotype A9L2a mitochondrion complete genome gi|40847005|gb|AY495129.1| Homo sapiens isolate H2-09 mitochondrion complete genome gi|51895120|gb|AY738986.1| Homo sagpi|i4e8n5s9 i6s1o4la3te|g Tbo|Ar4Y71 9Z5E725127.62 | m Hitoomchoo snadprioen s c hoampplloettyep gee En7oHme mitochondrion complete genome gi|84682390|gb|DQ341062.1| Homo sapiens isolate 5 L2d Tor38 mitochondrion complete genome gi|51895274|gb|AY738997.1| Homo sapiens isolate Tor58 ZE730 mitochondrion complete genome
gi|51450308|gb|AY713977.1| Homo sapiens isolate R99 mitochondrion complete genome gi|69938884|gb|AY495127.2| Homo sapiens isolate H2-07 mitochondrion complete gengoi|m51eg8i9|541g98i3|94g840i||g948b904|486A|47Yg67b873|A6|8gY59b7|7g|3A3b8Y.|1A94|7Y9 H745o.911m51| H12o1. o1s9m|a .H1po|oi esHmnaoospm isiesoano spslaai eitspenoi esTlan oistsre3o iTs4lao #terl1a3 H1t8e1 #H - 1m2113i-to63 mc 0 mih tmoiotcointohcdchorhonioondnndr ircdoiorninmo c n pco l oecmmtoepmp lgelpeteltne got egem egneneoonmmoeeme gi|48596215|gb|AY195788.2| Homo sapiens haplotype A5L2A1 mitochondrion complete genome
gi|40846907|gb|AY495122.1| Homo sapiens isolate H2-02 mitochondrion complete genome gi|32348254|gb|AY289070.1| Homo sapiens isolate g Ci|3A2M8 m91ito3c6h9o|gnbd|AriYo2n5 c5o1m53p.l1e|t eH goemnoo smaepiens isolate XJ8420 mitochondrion complete genome gi|51895176|gb|AY738990.1| Homo sapiens isolate Tor51 ZE623 mitochondrion complete gggie|i5|n51o18m899e44886882|g|gbb|A|AYY773388996689.1.1| |H Hoommoo s saappieiennss i sisoolalatete T Toor2r390 Z #E111004 4 m mitoitcohcohnodnrdiorinon c coommppleletete g geennoommee
gi|78775961|gb|DQ272112.1| Homo sapiens isolate Hui45 mitochondrion complete genome ggi|4i|400884477887539|g|gbb|A|AYY449955119910.1.1| H| Hoommoo s saappieiennss is isoolalatete H H77-0-043 m mitoitocchhoonnddriroionn c coommppleletete g geennoommee gi|40847257|gb|AY495147.1| Homo sapiens isolate H3-02 mitochondrion complete genome gi|29690434|gb|AY195748.1| Homo sapiens haplotype Na2D mitochondrion complete genome gi|32891537|gb|AY255165.1| Homo sapiens isolate GD7830 mitochondrion complete genome gi|51895008|gb|AY738978.1| Homo sapiens isolate Tor39 #107 mitochondrion complete genome gi|75905871|gb|AY963573.2| Homo sapiens isolate 2 D4b2b Tor50 mitochondrion complete genome gi|48596219|gb|AY195790.2| Homo sapiens haplotype As8D mitochondrion complete genome gi|78775975|gb|DQ272113.1| Homo sapiens iso glai|t5e0 E2W95K441 m9i|tgobc|hAoYn5d1r9io4n9 1 c.2o|m Hpolemteo gseanpoiemnes isolate NganasanD4 mitochondrion complete genome gi|113200490|gb|J01415.2|HUMMTCG Homo sapiens mitochondrion complete genome gi|48526882|gb|AY255134.2| Homo sapiens isolate LN7550 mitochondrion complete genome gi|51894854|gb|AY738967.1| Homo sapiens isolate Tor28 ZE573 mitochondrion complete genome gi|51894798|gb|AY738963.1g|i |H40o8m4o7 s3a5p5i|egnbs|A iYs4o9la5te1 5T4o.r12| 4H #o1m0o2 s maiptoiecnhso nisdorliaotne cHo3m-0p9le mtei tgoecnhoomnderion complete genome gi|78775891|gb|DQ272107.1| Homo sapiens isolate QH9505 mitochondrion complete genome gi|51894952|gb|AY738974.1| Homo sapiens isolate Tor35 ZE1852 mitochondrion complete genome gi|40847845|gb|AY495189.1| Homo sapiens isolate H7-02 mitochondrion complete genome gi|48596136|gb|AY195746.2| Homo sapiens haplotype E3H mitochondrion complete genome gi|32891467|gb|AY255160.1| Homo sapiens isolate QD8166 mitochondrion complete genome gi|40846543|gb|AY495096.1| Homo sapiens isolate H1-07 mitochondrion complete genome gi|32891341|gb|AY255151.1| Homo sapiens isolate GD7829 mitochondrion complete genome
gi|51894924|gb|AY738972.1| Homo sapiens isolate Tor33 ZE2147 mitochondrion complete genome
gi|51894910|gb|AY738971.1| Homo sapiens isgoi|l4a8te5 T9o6r13920 #|g1b1|5A Y m1i9to5c7h7o5n.2d|r Hioonm coo msappleieten gse hnaopmloetype E1H mitochondrion complete genome gi|32891495|gb|AY255162.1| Homo sapiens isolate GD7837n mitochondrion complete genome gi|40847341|gb|AY495153.1| Homo sapiens isolate H3-08 mitochondrion complete genome gi|50295412|gb|AY570525.2| Homo sapiens isolate TuvanD5 mitochondrion complete genome gi|71373158|gb|DQ137400.1| Homo sapiens isolate UV241 mitochondrion complete genome gi|46242454|gb|AY570524.1| Homo sapiens isolate Mansi10512 mitochondrion complete genome gi|32891592|gb|AY255169.1| Homo sapiens isolate YN289 mitochondrion complete genome gi|78775905|gb|DQ272108.1| Homo sapiens isolate Hani10 mitochondrion complete genome gi|86450583|gb|DQ372879.1| Homo sapiens isolate PO332 mitochondrion complete genome gi|86450639|gb|DQ372883.1| Homo sapiens isolate T726 mitochondrion complete genome gi|60257630|gb|AY922298.1| Homo sapiens isolate SW23 mitochondri ogni|7 c1o3m73p1le7te2 |gebn|DoQm1e37401.1| Homo sapiens isolate UV364 mitochondrion complete genome gi|71373144|gb|DQ137399.1| Homo sapiens isolate UV144 mitochondrion complete genome
gi|78775919 |gib|7|D87Q7257924170|g9b.1|D| HQo2m7o2 1s1a1p.i1e|n Hso ismoola stea pQieHn9s6 i6s1o lmatieto UchZoBn6d mriiotonc hcoonmdpriloente cgoemnopmleete genome gi|71373130|gb|DQ137398.1| Homo sapiens isolate Kol17 mitochondrion complete genome gi|78775933|gb|DQ272110.1| Homo sapiens isolate PK36 mitochondrion complete genome gi|60257014|gb|AY922254.1| Homo sapiens isolate R64 mitochondrion complete genome gi|32891173|gb|AY255139.1| Homo sapiens isolat eg iE|9W32K82085 m4i0to|gcbh|oDnQd4ri0o8n6 c7o7m.2p| Hleotem goe snaopmiens clone P31 mitochondrion complete genome gi|60 2g5i|372032488|g2b8|A2Y|g9b2|A2Y225859.10| 7H2o.1m| oH soampoie snasp iseonlsa ties oTl8a tme iKto1c1hbo mnditoricohno cnodmripolne t ec ogmenpolemtee genome gi|60257602|gb|AY922296.1| Homo sapiens isolate R56 mitochondrion complete genome gi|60257042|gb|AY922256.1| Homo sapiens isolate A47 mitochondrion complete genome gi|48596153|gb|AY195755.2| Homo sapiens haplotype As11G mitochondrion complete genome gi|48596164|gb|AY195762.2| Homo sapiens haplotype As7G mitochondrion complete genome gi|75905874|gb|AY963576.2| Homo sapiens isolate 5 M21a Tor53 mitochondrion complete genome
gi|32891145|gb|AY255137.1| Homo sapiens isolate SD10368 mitochondrion complete genome gi|32891425|gb|AY255157.1| Homo sapiens isolate XJ8416 mitochondrion complete genome gi|60257112|gb|AY92 g2i2|66012.15|7 H0o7m0|og bs|aApYi9e2n2s2 is5o8l.a1t|e H Co5m1o m siatopciehnosn disroiolant e c Bo1m5p6le mteit ogcehnonmderion complete genome
gi|78775989|gb|DQ272114.1| Homo sapiens isolate Miao239 mitochondrion complete genome gi|60257756|gb|AY922307.1| Homo sapiens isolate R65 mitochondrion complete genome gi|60257056|gb|AY922257.1| Homo sapiens isolate T14 mitochondrion complete genome gi|32891229|gb|AY255143.1| Homo sapiens isolate DW48 mitochondrion complete genome gi|32891383|gb|AY255154.1| Homo sapiens isolate SD10334 mitochondrion complete genome
gi|60257168|gb|AY922265.1| Homo sapiens isolate R45 mitochondrion complete genome gi|60257126|gb|AY922262.1| Homo sapiens isolate R110 mitochondrion complete genome gi|78776017|gb|DQ272116.1| Homo sapiens isolate Shui10 mitochondrion complete genome gi|60257000|gb|AY922253.1| Homo sapiens isolate A57 mitochondrion complete genome gi|51894966|gb|AY738975.1| Homo sapiens isolate Tor36 ZE657 mitochondrion complete genome gi|60257140|gb|AY922263.1| Homo sapiens isolate A68 mitochondrion complete genome gi|78776003|gb|DQ272115.1| Homo sapiens isolate Mg50 mitochondrion complete genome gi|32347988|gb|AY289051.1| Homo sapiens isolate Aus13 mitochondrion complete genome gi|93280542|gb|DQ408679.2| Homo sapiens clone T12 mitochondrion complete genome gi|60257224|gb|AY922269.1| Ho gmi|o9 4s4a4p9ie8n3s6 i|sgobl|aAtYe9 T57072 m9i9to.2c|h Hoonmdroio sna pcioemnpsl eisteo lgaeten GomA1e3 mitochondrion complete genome
gi|60257210|gb|AY922268.1| Homo sapiens isolate B107 mitochondrion complete genome gi|9444982730|gb|AY95029521.2| Homo sapiens isolate O421209 mitochondrion complete genome gi|60257154|gb|AY922264.1| Homo sapiens isolate R134 mitochondrion complete genome gi|93280541|gb|DQ408678.2| Homo sapiens clone R1 mitochondrion complete genome gi|75905875|gb|AY963577.2| Homo sapiens isolate 6 M21b Tor54 mitochondrion complete genome gi|60257336|gb|AY922277.1| Homo sapiens isolate T153 mitochondrion complete genome
gi|32348142|gb|AY289062.1| Homo sapiens isolate B6 mitochondrion complete genome gi|32891215|gb|AY255142.1| Homo sapiens isolate Miao271 mitochondrion complete genome gi|75905880|gb|AY963582.2| Homo sapiens isolate 11 M9* Tor62 mitochondrion complete genome gi|60257182|gb|AY922266.1| Homo sapiens isolate T21 mitochondrion complete genome gi|32348268|gb|AY289071.1| Homo sapiens isolate T1331 mitoch ogni|9d4ri4o4n9 c8o3m0p|glebt|eA Yg9e5n0o2m9e6.2| Homo sapiens isolate GA8 mitochondrion complete genome gi|60257238|gb|AY922270.1| Homo sapiens isolate C64 mitochondrion complete genome
gi|75905876|gb|AY963578.2| Homo sapiens isolate 7 N22 Tor55 mitochondrion complete genome g ig|6i|06205275079088|4g|bg|bA|YA9Y2922226205.91.|1 H| Homomo os aspaipeinesn sis iosloaltaet eB 4B76 6m mitoitcohcohnodnrdiorino n c ocmomplpeltet eg egneonmome e gi|60257476|gb|AY922287.1| Hom goi| 6s0a2p5ie7n3s0 i8s|oglba|tAeY T9123252 m75ito.1c| hHoonmdori osna pcioemnsp liestoel agteen To6m9e mitochondrion complete genome gi|48131404|gb|AY255178.2| Homo sapiens isolate YN163 mitochondrion complete genome
gi|32891299|gb|AY255148.1| Homo sapiens isolate GD7817 mitochondrion complete genome gi|60257490|gb|AY922288.1| Homo sapiens isolate A46 mitochondrion complete genome gi|60257434|gb|AY922284.1| Homo sapiens isolate T20 mitochondrion complete genome gi|32891411|gb|AY255156.1| Homo sapiens isolate SD10324 mitochondrion complete genome gi|60257196|gb|AY922267.1| Homo sapiens isolate C26 mitochondrion complete genome gi|32348086|gb|AY289058.1| Homo sapiens isolate Aus22 mitochondrion complete genome
gi|29690784|gb|AY195773.1| Homo sapiens haplotype E18X mitochondrion complete genome gi|94315510|gb|DQ513522.1| Homo sapiens isolate PJ10 mitochondrion complete genome gi|60257560|gb|AY922293.1| Homo sapiens isolate R37 mitochondrion complete genome gi|60257532|gb |gAiY|6902225279315.10|| gHbo|AmYo9 s2a2p2i7e8n.s1 |i sHoolamteo Ts2a3p imenitosc ihsonladteri oRn4 4c ommitopclehteo ngednriomn e complete genome gi|60257518|gb|AY922290.1| Homo sapiens isolate T72 mitochondrion complete genome
gi|60257462|gb|AY922286.1| Homo sapiens isolate A24 mitochondrion complete genome gi|32891243|gb|AY255144.1| Homo sapiens isolate WH6954 mitochondrion complete genome
gi|32348128|gb|AY289061.1| Homo sapiens isolate B4 mitochondrion complete genome gi|93280538|gb|DQ408675.2| Homo sapiens clone OR89 mitochondrion complete genome gi|93280537|gb|DQ408674.2| Homo sapiens clone OR82 mitochondrion complete genome
gi|32891201|gb|AY255141.1| Homo sapiens isolate GD7834 mitochondrion complete genome gi|60257616|gb|AY922297.1| Homo sapiens isolate T12 mitochondrion complete genome
gi|40795190|gb|AY519486.1| Homo sapiens is goi|l3a2te3 K4e8t03538A|1g bm|AitoYc2h8o9n0d5r6io.1n| H coomop lseatep gieennso imsoelate Aus20 mitochondrion complete genome gi|32348310|gb|AY289074.1| Homo sapiens isolate M306 mitochondrion complete genome gi|94315496|gb|DQ513521.1| Homo sapiens isolate PS38 mitochondrion complete genome gi|60257252|gb|AY922271.1| Homo sapiens isolate R59 mitochondrion complete genome gi|32348114|gb|AY289060.1| Homo sapiens isolate B2 mitochondrion complete genome gi|60257280|gb|AY922273.1| Homo sapiens isolate C48 mitochondrion complete genome
gi|6 g0i|265072256763|6g4b||gAbY|9A2Y292722.719| H.1o| Hmoom soa psiaepnise nisso ilsaotela Tte1 7R m11ito4c mhiotoncdhroionnd criomn p cleotme pgleenteo gmeenome gi|60257378|gb|AY922280.1| Homo sapiens isolate T159 mitochondrion complete genome gi|50295424|gb|AY519496.2| Homo sapiens isolate UlchiC1a mitochondr igoin|7 5c9o0m5p8le7t9e| ggbe|nAoYm96e3581.2| Homo sapiens isolate 10 M21c Tor61 mitochondrion complete genome
gi|60257294|gb|AY922274.1| Homo sapiens isolate C56 mitochondrion complete genome gi|7137328740|gb|DQ1374098.1| Homo sapiens isolate UV15282 mitochondrion complete genome gi|84682586|gb|DQ341076.1| Homo sapiens isolate 19 L3f Tor83 mitochondrion complete genome
gi|78776115|gb|DQ272123.1| Homo sapiens isolate Kor70 mitochondrion complete genome gi|113707000|gb|DQ404447.3| Homo sapiens isolate AUD38 mitochondrion complete genome gi|75905873|gb|A gYi|946835597651.527| H|gobm|AoY 1s9a5p7ie6n0s.2 is| Holoamteo 4 s Aa4p Tieonrs5 2h a mpiltotcyhpoen Adsri1oAn m ciotomcphloented grieonno mcoemplete genome gi|93280543|gb|DQ408680.2| Homo sapiens clone T9 mitochondrion complete genome gi|51451064|gb|AY714031.1| Homo sapiens isolate R148 mitochondrion complete genome gi|47717682|gb|AY615359.1| Homo sapiens isolate NganasanM10320HgC mitochondrion complete genome gi|4 g6i2|448254 9g86i2|541|g08b250|9|Ag56Yb415|A167Y5801|5g92b56|A7.1Y7|512 H19.2o95| m47H86oo73 ms.2ao|p Hsieaonpmsieo ins ssoa lhapatiep nTlosUt yihVspaLoepIl a mlAotesittyo 5KpcCoehr omiAansiktdo4CrcCio2h nbmo n mictodoitcromihocponhln eo cdtneord igmoreinpon ln eco t omecm oegmpelnpeoltemt ege egneonmome e gi|60257448|gb|AY922285.1| Homo sapiens isolate C8 mitochondrion complete genome
gi|60257546|gb|AY922292.1| Homo sapiens isolate T13 mitochondrion com gpi|l9e3te2 g8e0n5o3m9e|gb|DQ408676.2| Homo sapiens clone P12 mitochondrion complete genome gi|86450541|gb|DQ372876.1| Homo sapiens isolate MJ22 mitochondrion complete genome gi|48596214|gb|AY195786.2| Homo sapiens haplotype Na5A mitochondrion complete genome gi|71373256|gb|DQ137407.1| Homo sapiens isolate UV361 mitochondrion complete genome gi|84682600|gb|DQ341077.1| Homo sapiens isolate 20 L3f1 Tor75 mitochondrion complete genome gi|40795218|gb|AY519488.1| Homo sapiens isolate Mansi1A1 mitochondrion complete genome gi|7 g8i7|47767014757|g1b0||DgbQ|A2Y7621151386.11| .H1|o Hmoom soa spaiepniesn iso islaotela gYteiK| 5U003lc2 mh9i5i3to42c1Hh7go|gCnbd m|AriiYoto5nc1 hc9o4nm9d0pr.li2eo|tn eH gcoeomnmoop smleaetpei egnesn oismoelate Ngana gsi|a6n0C2527b6 m8i6to|gcbh|oAnYd9r2io2n3 0 c2o.1m| pHleotme og esnaopmieens isolate R188 mitochondrion complete genome
gi|32891551|gb|AY255166.1| Homo sapiens isolate WH6980 mitochondrion complete genome gi |g6i0|6205275470369|g2b|g|AbY|A9Y2922228228.11|. 1H| oHmoom soa spaiepniesn is oislaotlea tBe2 A66 m4 imtoictohcohnodnrdiornio nc o cmopmleptlee tgee gneonmoeme
gi|50295421|gb|AY519493.2| Homo sapiens igsio|4la8t5e9 T6o1fa5l6a|rgZb m|AitYo1c9h5o7n5d9rio.2n| H comop lestaep gienso mheaplotype Na4C mitochondrion complete genome
Three gi|29690616|gb|AY195761.1| Homo sapiens haplotype As12Z mitochondrion complete genome gi|60257322|gb|AY922276.1| Homo sapiens isolate C182 mitochondrion complete genome
gi|60257504|gb|AY922289.1| Homo sapiens isolate R61 mitochondrion complete genome gi|50295425|gb|AY519497.2| Homo sapiens isolate UlchiS mitochondrion complete genome gi|86450429|gb|DQ372868.1| Homo sapiens isolate AMI15 mitochondrion complete genome gi|75905881|gb|AY963583.2| Homo sapiens isolate 12 M22 Tor63 mitochondrion complete genome gi|60257420|gb|AY922283.1| Homo sapiens isolate R81 mitochondrion complete genome gi|78776101|gb|DQ272122.1| Homo sapiens isolate Oro 38 mitochondrion complete genome gi|60257658|gb|AY922300.1| Homo sapiens isolate C4 mitochondrion complete genome gi|60257588|gb|AY922295.1| Homo sapiens isolate T6 mitochondrion complete genome gi|29690980|gb|AY195787.1| Homo sapiens haplotype Na3X mitochondrion complete genome gi|71373228|gb|DQ137405.1| Homo sapiens isolate 1111F mitochondrion complete genome gi|32891271|gb|AY255146.1| Homo sapiens isolate Mg246 mitochondrion complete genome gi|32891662|gb|AY25517 g4i|.610| H25o7m7o0 s0a|gpbie|AnYs9 i2s2o3la0te3 .X1J| H84o3m5o m siatopciehnosn disroiolant e c Rom10p2le mtei tgoecnhoomnderion complete genome
gi|g9i4|94g44i|499489 43g849i|39|g548b|43g|A4bY9||gA98bY52|9A045Y3|g090b250|9A0.28Y2|. 92H57| oH0.2m2o| o9Hm 3so.a2m sp| oaHie psoniaemspn oiise s onisalsaop tileisae otGnelsa AG t1iesA5 oG1 ml1aA it9mteo micOtohi2tcoo1hcn omhdnoritdionorcdniohr inco on cmd ocrpmioolempntle pe c ltgeoet megn epgonlemeontemo gmeeenome gi|60257574|gb|AY922294.1| Homo sapiens isolate T71 mitochondrion complete genome gi|60257728|gb|AY922305.1| Homo sapiens isolate T3 mitochondrion complete genome
nodes gi|32891397|gb|AY255155.1| Homo sapiens isolate WH6979 mitochondrion complete genome gi|50295414|gb|AY519485.2| Homo sapiens isolate EvenkiC2a mitochondrion complete genome gi|60257742|gb|AY922306.1| Homo sapiens isolate T11 mitochondrion complete genome
gi|32891481|gb|AY255161.1| Homo sapiens isolate QD8159 mitochondrion complete genome gi|84682614|gb|DQ341078.1| Homo sapiens isolate 21 L3f1 Tor81 mitochondrion complete genome gi|60257644|gb|AY922299.1| Homo sapiens isolate R58 mitochondrion complete genome gi|48596144|gb|AY195753.2| Homo sapiens haplotype As6C mitochondrion complete genome gi|78776031|gb|DQ272117.1| Homo sapiens isolate Bouyei18 mitochondrion complete genome gi|71373242|gb|DQ137406.1| Homo sapiens isolate UV772 mitochondrion complete genome gi|60257770|gb|AY922308.1| Homo sapiens isolate T27 mitochondrion complete genome gi|32891690|gb|AY255176.1| Homo sapiens isolate LN7710 mitochondrion complete genome gi|29690756|gb|AY195771.1| Homo sapiens haplotype As2A mitochondrion complete genome gi|32891439|gb|AY255158.1| Homo sapiens isolate LN7711 mitochondrion complete genome
gi|50295411|gb|AY615360.2| Homo sapiens isolate TofalarM10448HgC mitochondrion complete genome gi|93280536|gb|DQ408672.2| Homo sapiens clone M42 mitochondrion complete genome gi|32891327|gb|AY255150.1| Homo sapiens isolate WH6958 mitochondrion complete genome g ig|3i|23324384281129|8g|bg|bA|YA2Y8298096076.61.|1 H| Homomo os aspaipeinesn sis iosloaltaet eY 7Y 6m mitoitcohcohnodnrdiorino n c ocmomplpeltet eg egneonmome e
gi|32348534|gb|AY289090.1| Homo sapiens isolate SH23 mitochondrion complete genome
gi |g9i3|9141474397842|g5b|g|Db|QAY490580627934.2.2| H| Hoommoo s saappieiennss c ilsoonlea tOe 9O m23ito mcihtoocnhdorniodnr i ocno m cpolmetpel egten goemneome
gi|32348100|gb|AY289059.1| Homo sapiens isolate Aus23 mitochondrion complete genome gi|32348464|gb|AY289085.1| Homo sapiens isolate NG12 mitochondrion complete genome gi|60257672|gb|AY922301.1| Homo sapiens isolate B177 mitochondrion complete genome gi|113706996|gb|DQ404445.3| Homo sapiens isolate AUR25 mitochondrion complete genome
gi|60257714|gb|AY922304.1| Homo sapiens isolate C39 mitochondrion complete genome
gi|32348366|gb|AY289078.1| Homo sapiens isolate GP4 mitochondrion complete genome
gi|51451260|gb|AY714045.1| Homo sapiens isolate C134 mitochondrion complete genome
gi| 8g6i|846540560259|g7b|g|DbQ|D3Q73278 2g88i2|38.120|3 .H14|o 8Hm4o0om8 so|ga sbpa|iAepnYies2n 8iss9o 0isla8ot1ela. 1Mte| OH P3oO0m34o9 m 2s iamtopictioehcnohsno disnrodiolraniot e nc W o cmEop2ml3ep tmle itgteoe cgnheoonmnoedmreion complete genome
gi|32891453|gb|AY255159.1| Homo sapiens isolate Miao248 mitochondrion complete genome
gi|61393479|gb|AY956412.1| Homo sapiens isolate UasiQ2a001 mitochondrion complete genome gi|113706990|gb|DQ404442.3| Homo sapiens isolate AUR6 mitochondrion complete genome gi|84682670|gb|DQ341082.1| Homo sapiens isolate 25 M1 Tor196 mitochondrion complete genome
gi|256946672|gb|AY956413.2| Homo sapiens isolate MadkQ2b001 mitochondrion complete genome
gi|61393513|gb|AY956414.1| Homo sapiens isolate MaraQ2c001 mitochondrion complete genome gi|32348324|gb|AY289075.1| Homo sapiens isolate 961 mitochondrion complete genome gi| 8g6i|8465405606675|g3b|g|DbQ|D3Q7327828858.14| .H1|o Hmoom soa spaiepniesn isso islaotela Wte SC7I125 m3i tmocitohcohnodnridornio cno cmopmleptele gtee gneonmoeme
gi|32348520|gb|AY289089.1| Homo sapiens isolate SH19 mitochondrion complete genome gi|32891620|gb|AY255171.1| Homo sapiens isolate SD10362 mitochondrion complete genome
gi|32891634|gb|AY255172.1| Homo sapiens isolate GD7825 mitochondrion complete genome
gi|113706992|gb|DQ404443.3| Homo sapiens isolate AUR7 mitochondrion complete genome
gi|32891648|gb|AY255173.1| Homo sapiens isolate XJ8450 mitochondrion complete genome
gi|32348380|gb|AY289079.1| Homo sapiens isolate WE16 mitochondrion complete genome
gi|32348422|gb|AY289082.1| Homo sapiens isolate WE4 mitochondrion complete genome
gi|71373312|gb|DQ137411.1| Homo sapiens isolate Aita7942 mitochondrion complete geno gmi|e32348645|gb|AY289098.1| Homo sapiens isolate 600 mitochondrion complete genome
gi |g7i1| 7g31i|77331723072031|1g48b|g6|Db|g|QDb1Q|D31Q73417034370.410|. 1H2| .oH1m|o Homo soma sopa isepaniepsni eissn oislao istleao tUela VUte1V U718V7 9m19 imt omictoithocochnhodonrndiodrniroi o ncn o c mcoopmmlepptlele tgete g ngeoenmnooemmee
gi|84682572|gb|DQ341075.1| Homo sapiens isolate 18 L3f Tor80 mitochondrion complete genome gi|78776157|gb|DQ272126.1| Homo sapiens isolate She54 mitochondrion complete genome
gi|71373298|gb|DQ137410.1| Homo sapiens isolate Aita7876 mitochondrion complete genome
gi|32348631|gb|AY289097.1| Homo sapiens isolate 526 mitochondrion complete genome Fig. 12. Location of mitochondrial “Eve” within the three-node structure of the human mitochondrial DNA tree. Whole genome alignment and resultant phylogenetic tree of 828 human individuals plus the previously derived mitochondrial “Eve” sequence. Similar to Fig. 11, three major nodes were visible, and “Eve” was located at one of the nodes which happened to be the node containing the most individuals in the dataset. Mitochondrial DNA Clocks Imply Linear SpeciationRates Within “Kinds” 283
Ailuridae Mustela kathiah voucher YP6126 Mephitidae Mustela nivalis voucher YP1 Neovison vison voucher ROM1024 Mustela altaica Herpestidae Mustela frenata voucher ROM10M1artes ma Mrteasrtes zibellina Mustela sibirica voucher YP613 Mustela erminea Martes melampus Spilogale putorius Ailurus fulgens Mustela putorius voucher ROM11 Martes americana voucher ROM11 Mephitis mephitis voucher YP29 Mustela nigripes Martes foina voucher YP6135 Mustelidae Martes flavigula Herpestes javanicus Hyaenidae Hyaena hyaena isolate Cerza Gulo gulo1 Crocuta crocuta isolate CC8 Martes pennanti isolate MP41 Nandiniidae Lutra lutra
Enhydra lutris Prionodon pardicolor isolate T Nandinia binotata isolate GLC8 Melogale moschata voucher YP61
Viverridae Genetta servalina isolate GLC9 Meles meles
Viverricula indica Meles anakuma
Arctonyx collaris voucher YP60 Lynx rufus Procyonidae
Acinonyx jubatus Taxidea taxus voucher ROM11145 Nasua nasua voucher ROM108237 Felidae Puma concolor
Procyon lotor Prionailurus bengalensis eupti
Felis catus
Arctocephalus forsteri Neofelis nebulosa Arctocephalus townsendi Panthera tigris Neophoca cinerea
Uncia uncia Phocarctos hookeri
Panthera onca Arctocephalus pusillus Otariidae
Panthera pardus Eumetopias jubatus
Panthera leo persica Zalophus californianus
Callorhinus ursinus
Nyctereutes procyonoides
Odobenus rosmarus rosmarus Vulpes corsac Pusa caspica Pusa sibirica Vulpes vulpes Canidae Halichoerus grypus Vulpes zerda Pusa hispida Odobenidae
Chrysocyon brachyurus Phoca vitulina Phoca largha
Cuon alpinus Canis lupus Phoca groenlandica Phoca fasciata Canis latrans Cystophora cristata Hydrurga leptonyx Lobodon car cLienpotpohnaygcahotes weddellii Erignathus barbatus Monachus schauinsMlairnoduinga leonina Ailuropoda melanoleucTaremarctos ornatus Melursus ursinus Phocidae Ursus arctos Ursus maritimus Ursus thibetanus Ursidae Helarctos malayUarnsuuss americanus
Fig. 13. Mitochondrial DNA differences among species within Carnivora. Whole genome alignment and resultant DNA differences depicted as branch lengths on a tree. Species within a family were highlighted with different colors. Colored circles represented the deepest root for each family. As the black arrows highlighted, the DNA differences separating the roots of different families were short relative to the DNA differences separating the species within a family.
Figs. 1–24, 49–51). Twenty-four of the families all would have raised concerns that mutations had been displayed an easily identifiable root from which ongoing long before speciation commenced. Since species radiated with roughly equal branch lengths relatively few DNA differences separated unrelated (Supplemental Figs. 1, 3–12, 14, 16–24). Only Ursidae (i.e., separately created) families, the assumption (Supplemental Fig. 2), Gruidae (Supplemental that the midpoint approximated the start of the Fig. 13), and Crocodylidae (Supplemental Fig. 15) speciation process gained further credibility. had radiation style trees resembling the human Hence, for each family I created linearized trees, mitochondrial DNA tree. These three animal rooted the trees on the midpoint, and assumed that families had visually identifiable roots from which speciation began at the midpoint (Supplemental Figs. most species in the family had roughly equivalent 25–48, 52–53). For on-Ark “kinds,” I assumed that branch lengths, but from which a few species had the midpoint represented the first year immediately unusually long branch lengths. Thus, for most of the post-Flood (e.g., 4350 years ago). For off-Ark “kinds,” families, rooting the tree on the midpoint seemed I assumed that the midpoint represented the first a reasonable approximation of the start of the year immediately post-Creation (e.g., 6000 years speciation process. ago). If some “kinds” did not form a single new species Furthermore, mitochondrial DNA sequence until late post-Creation or late post-Flood, this alignments above the taxonomic rank of family methodology would miss this fact. However, since indicated that, between some families, relatively few rapid speciation early post-Flood was the prevailing DNA differences existed (Fig. 13). If large numbers hypothesis, I effectively set up this experiment to be of DNA differences had separated families, this fact overly generous towards the early speciation view. 284
I also made a third assumption in these genetic part of the speciation event itself, and though the analyses, namely, that the branch point between actual event may have been slightly before or after two species represented the actual speciation event. the time represented by the branch point, using the This hypothesis was partially tested by aligning the branch point as a surrogate for the time of speciation sequences from multiple individuals within each appeared to be a reasonable first approximation. species. For the families Bovidae, Ursidae, and Hominidae, species existed for which sequences Speciation hypotheses from multiple individuals were present in the With these methodological parameters in mind, I NCBI databases. If branch points on the tree did derived several expectations in light of the prevailing not represent speciation events, then this analysis YE hypotheses on the timing of speciation. These should have resulted in crossing and mixing up of hypotheses and their predictions can be divided into the branches from multiple individuals in separate four general categories. As Wise (1994) and Wood species. In other words, there should have been (2002, 2003) have previously speculated, speciation no obvious single branch point separating all the post-Flood and even post-Creation may have been individuals within a species from all the other early and rapid followed by a long period of little individuals in a separate species. speciation (the “Early episode” hypothesis, Fig. 18). After aligning sequences from individuals within Alternatively, it is possible that this timeline was each of these families and then drawing trees flipped—a long period of little speciation followed by a reflecting only the topology of the relationships, a rapid burst in the recent past (the “Late” hypothesis, single branch point still separated species from one Fig. 18). As Wise (1994) and Wood (2002, 2003) another. No overlapping branches were found, and have pointed out previously, this hypothesis seems no branches from separate species crossed (Figs. unlikely since recent history records hardly any 14–16). Thus, the assumption that the branch point speciation events. Nonetheless, it was worth testing. represents a speciation event seemed reasonable. Finally, speciation may have occurred at a constant Conversely, when a tree was drawn to reflect the rate (“Linear,” Fig. 18), or it may have involved a actual DNA differences rather than just the topology series of bursts (“Episodic,” Fig. 18). of the relationships, the branch lengths appeared to reflect recent historical events. From recorded Genetic patterns fit the linear history, the American bison (Bison bison) and African speciation hypothesis buffalo (Syncerus caffer) appear to have undergone I tested these four hypotheses by aligning the population bottlenecks of different sizes. From mitochondrial DNA sequences for species within a population estimates of millions to tens of millions family, creating a tree to reflect the DNA differences, of individuals worldwide, the American bison was and then linearizing the tree and rooting it on the hunted to less than 1000 individuals globally in midpoint, as per the assumptions I articulated above. the late 1800s/early 1900s—a >99.9% reduction in I then used the branch lengths between each branch population size (Gates et al. 2010). Currently, the point as a surrogate for time between speciation numbers have recovered to only ~530,000 individuals events and created a timeline from these DNA (Gates and Aune 2008). By contrast, the African differences. buffalo population lost only 80–90% of its individuals These analyses were limited by the fact that not (Mack 1970) in the late 1800s, and its current all species within a family were represented by worldwide population size is closer to 1,000,000 than DNA sequences in the curated public databases. For 500,000 (IUCN SSC Antelope Specialist Group 2008). example, among the most speciose mammal families Since the mitochondrial DNA branch lengths (e.g., those with 60 or more species), only the family reflect the time to a common ancestor, and since Bovidae had 75% of its species represented in the this time is a function of effective population size NCBI RefSeq database (Table 2). The remainder (Futuyma 2009), population genetics would predict of these speciose families lacked 50% species a shorter coalescence time (branch length) for the representation, and most lacked even 10% species American bison population than for the African representation (Table 2). buffalo population. In fact, actual branch lengths Nevertheless, in the family Bovidae, the pattern matched this prediction (Fig. 17). Hence, branch of speciation was abundantly clear. The trajectory of lengths appeared to record real historical events speciation was a very tight fit (R2 = 0.997) with the within species. linear speciation hypothesis (Fig. 19). In addition, Given this precedence within species, it seemed since 48 of 52 (92%) genera within Bovidae were plausible to assume that branch points represented or represented in these data, eventual publication at least approximated real speciation events between of the mitochondrial DNA sequences from the species. Though multiple individuals may have been remaining species within Bovidae seemed unlikely to Mitochondrial DNA Clocks Imply Linear SpeciationRates Within “Kinds” 285
Tragelaphus spekii 1 Tragelaphus spekii 2 Tragelaphus eurycerus SUN8 1 Tragelaphus eurycerus SUN8 2 Tragelaphus scriptus PhC17 1 Tragelaphus scriptus PhC17 2 Tragelaphus scriptus MBP11 Taurotragus derbianus1 Taurotragus derbianus2 Tragelaphus oryx PHC13 1 Tragelaphus oryx PHC13 2 Tragelaphus strepsiceros 1 PH Tragelaphus strepsiceros 2 PH Tragelaphus angasii MBP15 1 Tragelaphus angasii MBP15 2 Tragelaphus scriptus CAR31 Tragelaphus imberbis1 Tragelaphus imberbis2 Tetracerus quadricornis1 Tetracerus quadricornis2 Boselaphus tragocamelus1 Boselaphus tragocamelus2 Syncerus caffer 3485 Syncerus caffer 3487 Syncerus caffer 3481 Syncerus caffer 3489 Syncerus caffer 3480 Syncerus caffer 660 Syncerus caffer 654 Syncerus caffer 3478 Syncerus caffer 3475 Syncerus caffer 3490 Syncerus caffer 3488 Syncerus caffer1 Syncerus caffer2 Syncerus caffer 394 Syncerus caffer 9083 Syncerus caffer 391 Syncerus caffer 393 Syncerus caffer 411 Syncerus caffer 671 Syncerus caffer 649 Syncerus caffer 9102 Syncerus caffer 9092 Syncerus Syncerus caffer 9080 Syncerus caffer 3483 caffer Syncerus caffer 3482 individuals Syncerus caffer 3479 Syncerus caffer 9084 Syncerus caffer 9081 Syncerus caffer 3486 Syncerus caffer 668 Syncerus caffer 3484 Syncerus caffer 388 Syncerus caffer 426 Syncerus caffer 412 Syncerus caffer 655 Syncerus caffer 410 Syncerus caffer 9079 Syncerus caffer 398 Syncerus caffer 425 Branch point Syncerus caffer 423 Syncerus caffer 409 defining the Syncerus caffer 385 Syncerus caffer 396 separation between Syncerus caffer 428 Syncerus caffer 421 Syncerus Bubalus depressicornis1 Bubalus depressicornis2 and Bison individuals Bos mutus1 Bos mutus2 Bison bison1 Bison bison2 Bison bison BYNP1586 Bison bison B929 Bison bison B1051 Bison bison B790 Bison bison B1029 Bison bison BNBR1 Bison bison B1050 Bison bison B880 Bison bison B959 Bison bison B925 Bison bison B853 Bison bison B854 Bison bison BFN5 Bison bison B973 Bison Bison bison B1005 Bison bison B985 bison Bison bison B1031 individuals Bison bison VZ Bison bison wElkIsland14 Bison bison B1091 Bison bison B979 Bison bison B897 Bison bison BTSBH1005 Bison bison BTSBH1001 Bison bison B1428 Bison bison wElkIsland1 Bison bison B1018 Bison bison B855 Bison bison B1191 Bison bison B935 Bison bison B877 Bison bison B961 Bos gaurus Mondulkiri1 Bos gaurus Mondulkiri2 Bos javanicus CERZA Bos javanicus Card4 Bison bonasus1 Bison bonasus2 Bison bonasus CYTO Bison bonasus Bos javanicus1 Bos javanicus2 Pseudoryx nghetinhensis1 Pseudoryx nghetinhensis2 Fig. 14. Topology-only tree of Bovinae individuals and species. Whole genome alignment and resultant branching relationships depicted in a topology-only diagram. Lengths of the branches did not correspond exactly to actual DNA differences but did depict branching relationships. As was apparent upon visual inspection, neither the Syncerus caffer individuals nor the Bison bison individuals ever had branches intermixed with branches from other species, consistent with the hypothesis that branch points correspond to actual speciation events. 286 N. T. Jeanson
Pan paniscus 166Kosana Pan paniscus PP06 Pan paniscus PP55 Pan paniscus 55Catherine Pan paniscus PP23 Pan paniscus 167Mubikisi Pan paniscus PP57 Pan paniscus PP75 Pan paniscus Semendwa Pan paniscus 88Hermien Pan paniscus PP60 Pan paniscus Keza Pan paniscus PP11 Pan paniscus PP14 Pan paniscus 260Kumbuka Pan paniscus 67Dzeeta Pan paniscus PP20 Pan paniscus Api Pan paniscus Kubulu Pan paniscus Pan paniscus Bolobo Pan paniscus Likasi Pan paniscus PP30 Pan paniscus Fizi Pan paniscus Matadi Pan Pan paniscus PP58 Pan paniscus PP10 Pan paniscus Isiro paniscus Pan paniscus 168Zorba Pan paniscus PP61 Pan paniscus PP68 individuals Pan paniscus 54Masikini Pan paniscus Kisantu Pan paniscus Lipopo Pan paniscus Tshilomba Pan paniscus Lomami Pan paniscus Malou L Pan paniscus Bandundu Pan paniscus Lodja Pan paniscus PP35 Pan paniscus Kikwit Pan paniscus Max Pan paniscus PP05 Pan paniscus Billi L Pan paniscus PP18 Pan paniscus 46Natalie Pan paniscus Boende Pan paniscus PP03 Pan paniscus 91Hortense Pan paniscus PP54 Pan paniscus PP25 Pan paniscus 57Desmond Pan paniscus PP69 Pan paniscus PP56 Pan trog verus 10794Marco Pan trog verus Marco Pan trog verus 10986Totie Pan trog verus YK3 Pan trog isolate Jenny Pan trog verus King-Louis Pan trog verus Robert Pan trog verus 11112Regina Pan trog verus Wubbo Pan trog Pan trog verus 10795Liesbeth Branch point Pan trog verus Liesbeth Pan trog verus TA24 Pan trog verus Cookie defining the Pan trog verus Oscar Pan trog verus 11251Sherry Pan trog verus 12122Linda separation Pan trog verus Regina Pan trog verus ISIS #2216 Pan trog verus ISIS #2435 Pan trog verus 11051Carolina Pan trog verus 12295Carl Pan trog verus studbook #341 Pan trog verus Annaclara Pan trog verus 11210Pearl Pan trog verus 12315Yoran Pan trog verus 11057Renee Pan trog verus Hilko Pan trog verus Ricky Pan trog verus Frits Pan trog verus Louise Pan trog verus ISIS #2738 Pan trog ellioti Emma Pan trog ellioti VC3 Pan trog ellioti WE449 Pan trog ellioti WE451 Pan trog ellioti VC2 Pan trog vellerosus ISIS #2412 Pan trog ellioti SA163 Pan trog ellioti Pan trog ellioti SA159 Pan trog ellioti VC1 Pan trog trog 10887Brigitte Pan trog trog Dzeke Pan trog trog Mvadi Pan trog trog Morphee Pan trog trog Mpassa Pan trog trog Amelie Pan trog trog CP466 Pan trog trog Vaillant Pan trog trog Makata Pan trog schweinf Asega Pan trog schweinf BD10 Pan trog schweinf Megan Pan trog Akim Pan trog schweinf Mawa Pan trog schweinf Okech Pan trog schweinf Kisembo Pan trog Christophe Pan trog Flo Pan trog schweinf Sunday Pan trog schweinf Robbie Pan trog schweinf Sally Pan trog schweinf WK8 Pan Pan trog Cherie Pan trog schweinf Kazahukire Pan trog schweinf Nakuu troglodytes Pan trog schweinf Becky Pan trog schweinf 11785Exota Pan trog schweinf Bahati individuals Pan trog schweinf WK7 Pan trog schweinf Eddy Pan trog schweinf ISIS #925 Pan trog schweinf Ikuru Pan trog schweinf Nani Pan trog schweinf NY16 Pan trog schweinf Cindy Pan trog schweinf Mika Pan trog schweinf Umutama Pan trog schweinf 11784Paula Pan trog schweinf 12231Noach Pan trog schweinf BU203 Pan trog schweinf Kidogo Pan trog schweinf 12232Niko Pan trog schweinf ISIS #3020 Pan trog schweinf Mgbadolite Pan trog schweinf GM188 Pan trog schweinf Indi Pan trog trog Bakoumba Pan trog trog Judy Pan trog trog Julie Pan trog trog BB236 Pan trog trog BQ404 Pan trog trog Grand-Maitre Pan trog trog GT714 Pan trog trog Masuku Pan trog trog Aboume Pan trog trog ISIS #4441 Pan trog trog Agnagui Pan trog trog GT305 Pan trog trog MT117 Pan trog trog Clara Pan trog trog Lalala Pan trog trog WE464 Pan trog trog Bailele Pan trog trog 11525Cindy Pan trog trog Bimangou Pan trog trog Botsomi Pan trog trog Ayrton Pan trog trog Chinoc Pan trog trog Doris Pan trog trog Brigitte Pan trog trog LP14 Pan trog trog LP20 Pan trog trog Fifi Pan trog trog Golfi Pan trog trog GT311 Pan trog trog 10892Victoria Pan trog trog Lufino Pan trog trog Castro Pan trog trog Makokou Pan trog trog Noemie Pan trog trog 11043Susi Pan trog trog Benefice Pan trog trog Marcelle Pan trog trog Chiqiuta Pan trog trog Moanda Pan trog trog Moka Pan trog trog Loufoumbou Pan trog trog DP108 Pan trog trog Fan-Tueck Pan trog trog Gao Pan trog trog LP9 Fig. 15. Topology-only tree of Pan individuals and species. Whole genome alignment and resultant branching relationships depicted in a topology-only diagram. Lengths of the branches did not correspond exactly to actual DNA differences but did depict branching relationships. As was apparent upon visual inspection, none of the individuals within Pan paniscus and Pan troglodytes ever had branches intermixed with branches from the other species, consistent with the hypothesis that branch points correspond to actual speciation events. Mitochondrial DNA Clocks Imply Linear SpeciationRates Within “Kinds” 287
Ursus americanus Ursus americanus isolate BLK01 Ursus thibetanus Ursus thibetanus ussuricus Ursus thibetanus thibetanus Ursus thibetanus formosanus Ursus thibetanus mupinensis Ursus arctos isolate 12WH Ursus arctos isolate A91-05 Ursus Ursus arctos isolate ABC1-0517 Ursus arctos isolate 14KB arctos Branch point Ursus arctos isolate ABC2-Luck individuals Ursus maritimus isolate PB12-N defining the Ursus maritimus isolate PB1-N2 Ursus maritimus isolate PB4-N2 separation Ursus maritimus Ursus maritimus isolate PB13-N Ursus maritimus isolate PB5-N2 Ursus maritimus isolate PB14-N Ursus maritimus isolate PB3-N2 Ursus maritimus isolate PB8-N7 Ursus maritimus isolate PB16-N Ursus maritimus isolate PB7-N7 Ursus maritimus isolate PB9-N2 Ursus maritimus isolate PB18-N Ursus maritimus isolate AK1-54 Ursus Ursus maritimus isolate 2629 maritimus Ursus maritimus isolate AK2-56 Ursus maritimus isolate PB2-N2 individuals Ursus maritimus isolate PB6-N2 Ursus maritimus isolate PB11-N Ursus maritimus isolate PB17-N Ursus maritimus isolate AK3-57 Ursus maritimus isolate AK5-65 Ursus maritimus isolate AK4-23 Ursus maritimus isolate PB15-N Ursus maritimus isolate PB10-N Ursus maritimus isolate 495 Ursus arctos Ursus arctos isolate 76824 Ursus arctos isolate KEN10-UAR Ursus arctos isolate 34 Ursus arctos isolate 38 Ursus arctos isolate 29 Ursus arctos isolate 31 Ursus arctos isolate 40 Ursus arctos isolate 45 Ursus arctos isolate 1 Ursus arctos isolate 14 Ursus arctos isolate 2 Ursus arctos isolate 10 Ursus arctos isolate 6 Ursus arctos isolate 4 Ursus arctos isolate 8 Ursus arctos isolate 5 Ursus arctos isolate 11 Ursus arctos isolate 7 Ursus arctos isolate 13 Ursus arctos isolate 54 Ursus arctos isolate 9 Ursus arctos isolate 23 Ursus arctos isolate 15 Ursus arctos isolate 25 Ursus arctos isolate 16 Ursus arctos isolate 19 Ursus arctos isolate 22 Ursus arctos isolate 49 Ursus arctos isolate 20 Ursus arctos isolate 33 Ursus arctos isolate 42 Ursus arctos isolate 12 Ursus Ursus arctos isolate 3 Ursus arctos isolate 18 arctos Ursus arctos isolate 24 Ursus arctos isolate 17 individuals Ursus arctos isolate 21 Ursus arctos isolate 26 Ursus arctos isolate 58 Ursus arctos isolate 61 Ursus arctos isolate 57 Ursus arctos isolate 47 Ursus arctos isolate 51 Ursus arctos isolate 48 Ursus arctos isolate 52 Ursus arctos isolate 50 Ursus arctos isolate 53 Ursus arctos isolate 55 Ursus arctos isolate 59 Ursus arctos isolate 56 Ursus arctos isolate 60 Ursus arctos isolate 63 Ursus arctos isolate 62 Ursus arctos isolate 41 Ursus arctos isolate 46 Ursus arctos isolate 27 Ursus arctos isolate 35 Ursus arctos isolate 36 Ursus arctos isolate 39 Ursus arctos isolate 37 Ursus arctos isolate 44 Ursus arctos isolate 28 Ursus arctos isolate 43 Ursus arctos isolate 30 Ursus arctos isolate 32 Ursus arctos isolate 64 Fig. 16. Topology-only tree of Ursus individuals and species. Whole genome alignment and resultant branching relationships depicted in a topology-only diagram. Lengths of the branches did not correspond exactly to actual DNA differences but did depict branching relationships. As was apparent upon visual inspection, neither the Ursus arctos individuals nor the Ursus maritimus individuals ever had branches intermixed with branches from other species, consistent with the hypothesis that branch points correspond to actual speciation events. Though the Ursus arctos individuals appeared to stem from two different populations, the individuals from Ursus maritimus were still clearly distinct from Ursus arctos individuals. 288 N. T. Jeanson
Bison bison1 Bison bison2 Bison bison BYNP1586 Bison bison B929 Bison bison B1051 Bison bison B790 Bison bison B1029 Bison bison BNBR1 Bison bison B1050 Bison bison B880 Bison bison B959 Bison bison B925 Bison bison B854 Bison bison B853 Bison bison BFN5 Bison bison B973 American bison Bison bison B1005 Bison bison B985 (Bison bison) Bison bison B1031 Bison bison VZ individuals Bison bison wElkIsland14 Bison bison B1091 Bison bison B979 Bison bison B897 Bison bison BTSBH1005 Bison bison BTSBH1001 Bison bison B1428 Bison bison wElkIsland1 Longer branch Bison bison B1018 Bison bison B855 length/coalescence time Bison bison B1191 Bison bison B935 for African buffalo than Bison bison B877 Bison bison B961 for American bison Syncerus caffer 655 Syncerus caffer 410 Syncerus caffer 9079 Syncerus caffer 398 Syncerus caffer 425 Syncerus caffer 423 Syncerus caffer 409 Syncerus caffer 385 Syncerus caffer 428 Syncerus caffer 396 Syncerus caffer 421 Syncerus caffer 668 Syncerus caffer 3484 Syncerus caffer 388 Syncerus caffer 426 Syncerus caffer 412 Syncerus caffer1 Syncerus caffer2 Syncerus caffer 394 Syncerus caffer 9083 Syncerus caffer 391 Syncerus caffer 393 African buffalo Syncerus caffer 411 Syncerus caffer 671 (Syncerus caffer) Syncerus caffer 649 Syncerus caffer 9102 individuals Syncerus caffer 9092 Syncerus caffer 9080 Syncerus caffer 3483 Syncerus caffer 3482 Syncerus caffer 3479 Syncerus caffer 9084 Syncerus caffer 9081 Syncerus caffer 3486 Syncerus caffer 3490 Syncerus caffer 3488 Syncerus caffer 3478 Syncerus caffer 3475 Syncerus caffer 3489 Syncerus caffer 3487 Syncerus caffer 3480 Syncerus caffer 660 Syncerus caffer 3485 Syncerus caffer 3481 Syncerus caffer 654
Fig. 17. Different coalescent times within Bovinae. Whole genome alignment and resultant DNA differences depicted as branch lengths on a tree. To magnify the differences in branch lengths among Syncerus caffer and Bison bison individuals, the middle section of the tree was omitted, as indicated by the dashed lines. Upon visual inspection, it was apparent that the branch lengths connecting the most distant Syncerus caffer individuals were longer than the branch lengths connecting the most distant Bison bison individuals. Hence, the coalescence time for Syncerus caffer was longer than for Bison bison, consistent with the recent and more dramatic population bottleneck experienced by Bison bison.
Fig. 18 (left). Hypotheses on the timing of speciation Hypotheses on the Timing of Speciation within biblical parameters. Using the family Muridae (712 total species) as an example of a speciose family, Early episode Episodic Linear Late contrasting hypotheses on the timing of speciation 800 post-Flood were depicted visually. The “Early episode” 700 hypothesis represented one in which speciation 600 happened in a rapid burst and then quickly tapered off. 500 The “Episodic” hypothesis represented a proposal that 400 speciation happened in several short bursts over time. 300 The “Linear” hypothesis represented a guess that the
Total Species Total 200 speciation rate has been constant with time, while the 100 “Late” hypothesis represented the mirror image of the 0 “Early episode”—that speciation rates were virtually 0 1000 2000 3000 4000 zero for several thousand years and then recently and Years Post-Flood rapidly increased to high levels. Mitochondrial DNA Clocks Imply Linear SpeciationRates Within “Kinds” 289
Table 2. Mammalian species representation per family in NCBI RefSeq database. Species with % Species with Order Family Species# mtDNA sequences in mtDNA sequence NCBI RefSeq represented Rodentia Muridae 716 32 4 Rodentia Cricetidae 699 11 2 Chiroptera Vespertilionidae 421 10 2 Eulipotyphla Soricidae 376 6 2 Rodentia Sciuridae 279 6 2 Chiroptera Pteropodidae 187 4 2 Chiroptera Phyllostomidae 174 12 7 Cetartiodactyla Bovidae 141 106 75 Primates Cercopithecidae 125 56 45 Chiroptera Molossidae 100 0 0 Didelphimorphia Didelphidae 99 4 4 Rodentia Echimyidae 90 2 2 Chiroptera Hipposideridae 84 0 0 Chiroptera Rhinolophidae 74 7 9 Dasyuromorphia Dasyuridae 72 5 7 Diprotodontia Macropodidae 67 3 4 Lagomorpha Leporidae 62 7 11 Rodentia Heteromyidae 62 0 0 Rodentia Ctenomyidae 60 2 3 Rodentia Nesomyidae 60 0 0
change the match between linear speciation 48 of 52 Bovidae (Chordata, 106 of 141 hypothesis and the actual speciation timeline. genera Mammalia, Ruminantia): species I also assessed several mammal families whose (92%) Speciation Rate (75%) species were completely represented in the NCBI 120 RefSeq database. Though several families with four or 100 fewer species were completely represented, under the assumptions I made for these analyses, tree-drawing 80 and curve-fitting for these families would have been 60 statistically uninformative. For mammals, this 40 y = 0.0266x − 1.7549 effectively eliminated 38% (58 of 151) of the families Total Species Total R2 = 0.9973 from consideration. Of the remaining 62%, three 20 were fully represented in the NCBI RefSeq database: 0 0 1000 2000 3000 4000 Ursidae, Rhinocerotidae, and Balaenopteridae. All Years Post-Flood three of these families fit the linear speciation rate hypothesis (Figs. 20–22). Fig. 19. Speciation rate within the family Bovidae. Though the correlation coefficient for each of Whole genome alignments for extant, wild (non- these families was lower than the coefficient for domestic) species in the family Bovidae were performed. the Bovidae family, this result may have been an A phylogenetic tree was created from which branch artifact of small number statistics. Since Ursidae, lengths between branch points were extracted, converted Rhinocerotidae, and Balaenopteridae had only to years, and used to plot the timeline of branching/ eight, five, and nine species total, respectively, small speciation within the family. The results were a tight fit deviations from the mean would have had higher to a linear function, which was represented by the thin statistical consequence than deviations in a family black line and the equation, both of which were derived via linear regression of the raw data in Microsoft Excel. with over 100 data points. Furthermore, since Representation of genera and species within the family the radiation style tree for Ursidae suggested the were depicted in the upper left and right corners, possibility of different rates of change for at least two respectively. of the Ursid species (Supplemental Fig. 2), the lower 290 N. T. Jeanson
5 of 5 Ursidae (Chordata, 8 of 8 2 of 2 Balaenopteridae (Chordata, 9 of 9 genera Mammalia, Carnivora): species genera Mammalia, Cetacea): species (100%) Speciation Rate (100%) (100%) Speciation Rate (100%) 9 10 8 7 8 6 6 5 4 4 y = 0.0015x + 2.692 3 2 Total Species Total
Total Species Total R = 0.9479 2 y = 0.0016x + 2.0883 2 1 R2 = 0.8669 0 0 0 1000 2000 3000 4000 0 1000 2000 3000 4000 5000 6000 Years Post-Flood Years Post-Flood Fig. 22. Speciation rate within the family Fig. 20. Speciation rate within the family Ursidae. Balaenopteridae. Whole genome alignments for extant Whole genome alignments for extant species in the species in the family Balaenopteridae were performed. family Ursidae were performed. A phylogenetic tree A phylogenetic tree was created from which branch was created from which branch lengths between branch lengths between branch points were extracted, converted points were extracted, converted to years, and used to plot to years, and used to plot the timeline of branching/ the timeline of branching/speciation within the family. speciation within the family. The results were a fairly The results were a good fit to a linear function, which tight fit to a linear function, which was represented was represented by the thin black line and the equation, by the thin black line and the equation, both of which both of which were derived via linear regression of the were derived via linear regression of the raw data in raw data in Microsoft Excel. Representation of genera Microsoft Excel. Representation of genera and species and species within the family were depicted in the upper within the family were depicted in the upper left and left and right corners, respectively. right corners, respectively. 1 of 1 Equidae (Chordata, 6 of 7 4 of 4 Rhinocerotidae (Chordata, 5 of 5 genera Mammalia, Perissodactyla): species genera Mammalia, Perissodactyla): species (100%) Speciation Rate (86%) (100%) Speciation Rate (100%) 7 6 6 5 5 4 4 3 3 2 y = 0.0009x + 2.405 2 Species Total 2 Total Species Total y = 0.0012x + 2.4506 R = 0.8842 1 1 R2 = 0.8595 0 0 0 1000 2000 3000 4000 0 1000 2000 3000 4000 Years Post-Flood Years Post-Flood Fig. 23. Speciation rate within the family Equidae. Fig. 21. Speciation rate within the family Rhinocerotidae. Whole genome alignments for extant, wild (non- Whole genome alignments for extant species in the domestic) species in the family Equidae were performed. family Rhinocerotidae were performed. A phylogenetic A phylogenetic tree was created from which branch tree was created from which branch lengths between lengths between branch points were extracted, converted branch points were extracted, converted to years, and to years, and used to plot the timeline of branching/ used to plot the timeline of branching/speciation within speciation within the family. The results were a good fit the family. The results were a good fit to a linear to a linear function, which was represented by the thin function, which was represented by the thin black black line and the equation, both of which were derived line and the equation, both of which were derived via via linear regression of the raw data in Microsoft Excel. linear regression of the raw data in Microsoft Excel. Representation of genera and species within the family Representation of genera and species within the family were depicted in the upper left and right corners, were depicted in the upper left and right corners, respectively. respectively. For mammal families with incomplete species correlation coefficient may have been a consequence representation in the NCBI RefSeq database but of non-identical mutation rates across species within higher representation than Bovidae, a match the Ursidae family. Hence, these data from three on- between the linear speciation rate hypothesis and Ark families (Bovidae, Ursidae, Rhinocerotidae) and the data was the rule. Equidae (Fig. 23), Hominidae one off-Ark family (Balaenopteridae) all depicted the (Fig. 24), and Phocidae (Fig. 25) all fit the linear rate same result: A linear timeline of speciation. hypothesis well. Mitochondrial DNA Clocks Imply Linear SpeciationRates Within “Kinds” 291
3 of 3 Hominidae (Chordata, 5 of 6 18 of 18 Cervidae (Chordata, 34 of 56 genera Mammalia, Primates): species genera Mammalia, Ruminantia): species (100%) Speciation Rate (83%) (100%) Speciation Rate (61%) 6 45 40 5 35 4 30 3 25 20 2 y = 0.0009x + 1.8999 15 y = 0.0093x − 0.104 2 2 Total Species Total
R = 0.9861 Species Total R = 0.9382 1 10 5 0 0 0 1000 2000 3000 4000 0 1000 2000 3000 4000 Years Post-Flood Years Post-Flood Fig. 24. Speciation rate within the family Hominidae. Fig. 26. Speciation rate within the family Cervidae. Whole genome alignments for extant species in the Whole genome alignments for extant species in the family Hominidae were performed. A phylogenetic tree family Cervidae were performed. A phylogenetic tree was was created from which branch lengths between branch created from which branch lengths between branch points points were extracted, converted to years, and used to plot were extracted, converted to years, and used to plot the the timeline of branching/speciation within the family. timeline of branching/speciation within the family. The The results were a tight fit to a linear function, which results were a fairly tight fit to a linear function, which was represented by the thin black line and the equation, was represented by the thin black line and the equation, both of which were derived via linear regression of the both of which were derived via linear regression of the raw data in Microsoft Excel. Representation of genera raw data in Microsoft Excel. Representation of genera and species within the family were depicted in the upper and species within the family were depicted in the upper left and right corners, respectively. left and right corners, respectively.
12 of 13 Phocidae (Chordata, 15 of 19 19 of 21 Cercopithicidae (Chordata, 56 of 125 genera Mammalia, Carnivora): species genera Mammalia, Primates): species (92%) Speciation Rate (79%) 90%) Speciation Rate (45%) 16 60 14 50 12 10 40 8 30 6 y = 0.0024x + 1.839 20
Total Species Total 2
4 R = 0.9783 Species Total y = 0.0147x − 8.3859 2 10 R2 = 0.976 0 0 0 1000 2000 3000 4000 5000 6000 0 1000 2000 3000 4000 Years Post-Flood Years Post-Flood Fig. 25. Speciation rate within the family Phocidae. Fig. 27. Speciation rate within the family Cercopithecidae. Whole genome alignments for extant species in the Whole genome alignments for extant species in the family family Phocidae were performed. A phylogenetic tree Cercopithecidae were performed. A phylogenetic tree was created from which branch lengths between branch was created from which branch lengths between branch points were extracted, converted to years, and used to plot points were extracted, converted to years, and used to plot the timeline of branching/speciation within the family. the timeline of branching/speciation within the family. The results were a tight fit to a linear function, which The results were a tight fit to a linear function, which was represented by the thin black line and the equation, was represented by the thin black line and the equation, both of which were derived via linear regression of the both of which were derived via linear regression of the raw data in Microsoft Excel. Representation of genera raw data in Microsoft Excel. Representation of genera and species within the family were depicted in the upper and species within the family were depicted in the upper left and right corners, respectively. left and right corners, respectively.
Even mammal families that were moderately to all fit a linear speciation rate with little to any evidence intensely speciose but less well-represented with of a burst of speciation immediately post-Flood or post- mitochondrial DNA sequences displayed a linear Creation. Thus, independent of Ark status (e.g., on- or off- pattern. Cervidae (61% species representation, Fig. Ark), mammalian order (e.g., Ruminantia, Carnivora, 26), Cercopithecidae (45% species representation, Fig. Perissodactyla, Cetacea, Primates, and Rodentia), and 27), Mustelidae (42% species representation, Fig. 28), species DNA sequence representation (e.g., 100% to Delphinidae (49% species representation, Fig. 29), 4%), mammal families showed a linear rate of speciation and even Muridae (4% species representation, Fig. 30) since the Flood or since Creation (Figs. 19–30). 292 N. T. Jeanson
10 of 21 Mustelidae (Chordata, 25 of 59 9 of 148 Muridae (Chordata, 32 of 716 genera Mammalia, Carnivora): species genera Mammalia, Rodentia): species 48%) Speciation Rate (42%) 6%) Speciation Rate (4%) 30 35 25 30 25 20 20 15 15 10 10 Total Species Total Total Species Total y = 0.0054x + 3.6156 y = 0.0091x − 5.2738 2 5 R = 0.9755 5 R2 = 0.9308 0 0 0 1000 2000 3000 4000 0 1000 2000 3000 4000 Years Post-Flood Years Post-Flood Fig. 28. Speciation rate within the family Mustelidae. Fig. 30. Speciation rate within the family Muridae. Whole genome alignments for extant species in the Whole genome alignments for extant species in the family Mustelidae were performed. A phylogenetic tree family Muridae were performed. A phylogenetic tree was created from which branch lengths between branch was created from which branch lengths between branch points were extracted, converted to years, and used to plot points were extracted, converted to years, and used to the timeline of branching/speciation within the family. plot the timeline of branching/speciation within the The results were a tight fit to a linear function, which family. The results were a fairly tight fit to a linear was represented by the thin black line and the equation, function, which was represented by the thin black both of which were derived via linear regression of the line and the equation, both of which were derived via raw data in Microsoft Excel. Representation of genera linear regression of the raw data in Microsoft Excel. and species within the family were depicted in the upper Representation of genera and species within the family left and right corners, respectively. were depicted in the upper left and right corners, respectively.
13 of 17 Delphinidae (Chordata, 18 of 37 5 of 5 Gruidae (Chordata, 15 of 15 genera Mammalia, Cetacea): species genera Aves, Gruiformes): species 76%) Speciation Rate (49%) (100%) Speciation Rate (100%) 20 16 14 15 12 10 10 8 y = 0.0032x + 2.3011 6
Total Species Total 5 2
R = 0.9587 Species Total 4 y = 0.0033x − 0.5932 2 R2 = 0.864 0 0 0 1000 2000 3000 4000 5000 6000 0 1000 2000 3000 4000 Years Post-Flood Years Post-Flood Fig. 29. Speciation rate within the family Delphinidae. Fig. 31. Speciation rate within the family Gruidae. Whole genome alignments for extant species in the Whole genome alignments for extant species in the family Delphinidae were performed. A phylogenetic family Gruidae were performed. A phylogenetic tree tree was created from which branch lengths between was created from which branch lengths between branch branch points were extracted, converted to years, and points were extracted, converted to years, and used to plot used to plot the timeline of branching/speciation within the timeline of branching/speciation within the family. the family. The results were a fairly tight fit to a linear The results were a good fit to a linear function, which function, which was represented by the thin black was represented by the thin black line and the equation, line and the equation, both of which were derived via both of which were derived via linear regression of the linear regression of the raw data in Microsoft Excel. raw data in Microsoft Excel. Representation of genera Representation of genera and species within the family and species within the family were depicted in the upper were depicted in the upper left and right corners, left and right corners, respectively. respectively. visual rate homogeneity test (Supplemental Fig. This linear pattern was true across vertebrate 13), lineages within Gruidae may have undergone classes. Within Aves, both well-represented unequal rates of mutation change. Hence, if this (Gruidae, 100% species representation, Fig. 31) unequal mutation rate hypothesis was indeed true, and poorly represented (Phasianidae, 26% species then the correlation coefficient for Gruidae might representation, Fig. 32) families generally matched have been even higher had mutation rates been the linear speciation rate hypothesis. As per the identical across lineages. Mitochondrial DNA Clocks Imply Linear SpeciationRates Within “Kinds” 293
25 of 45 Phasianidae (Chordata, Aves, 49 of 187 10 of 10 Hynobiidae (Chordata, 28 of 66 genera Galliformes): species genera Amphibia, Caudata): species (56%) Speciation Rate (26%) (100%) Speciation Rate (42%) 60 35 50 30 40 25 20 30 15 20
Total Species Total 10 y = 0.0109x + 3.1334 Species Total y = 0.0073x − 1.0897 10 R2 = 0.9851 5 R2 = 0.9346 0 0 0 1000 2000 3000 4000 0 1000 2000 3000 4000 Years Post-Flood Years Post-Flood Fig. 32. Speciation rate within the family Phasianidae. Fig. 34. Speciation rate within the family Hynobiidae. Whole genome alignments for extant species in the Whole genome alignments for extant species in the family family Phasianidae were performed. A phylogenetic tree Hynobiidae were performed. A phylogenetic tree was was created from which branch lengths between branch created from which branch lengths between branch points points were extracted, converted to years, and used to plot were extracted, converted to years, and used to plot the the timeline of branching/speciation within the family. timeline of branching/speciation within the family. The The results were a tight fit to a linear function, which results were a fairly tight fit to a linear function, which was represented by the thin black line and the equation, was represented by the thin black line and the equation, both of which were derived via linear regression of the both of which were derived via linear regression of the raw data in Microsoft Excel. Representation of genera raw data in Microsoft Excel. Representation of genera and species within the family were depicted in the upper and species within the family were depicted in the upper left and right corners, respectively. left and right corners, respectively.
3 of 4 Crocodylidae (Chordata, 13 of 16 the family (Supplemental Fig. 15). Thus, if this genera Reptilia, Crocodylia): species unequal mutation rate hypothesis was indeed true, (75%) Speciation Rate (81%) the correlation coefficient for Crocodylidae might 60 have been even higher had rates been identical 50 across lineages. Regardless, the existing results still 40 matched the linear speciation rate hypothesis. 30 Among fish families, whether the species representation by DNA sequences was high 20
Total Species Total y = 0.002x + 0.9192 (Anguillidae, 89%), intermediate (Scombridae, 10 R2 = 0.9068 47%), or low (Tetraodontidae, 31%), linear rates 0 of speciation were the rule (Figs. 35–37). Even the 0 1000 2000 3000 4000 5000 6000 most species-rich family across all vertebrate classes Years Post-Flood (Cyprinidae, 2935 extant species) showed a strongly Fig. 33. Speciation rate within the family Crocodylidae. linear speciation rate, despite having only 10% of its Whole genome alignments for extant species in the species represented by mitochondrial DNA sequences family Crocodylidae were performed. A phylogenetic (Fig. 38). Thus, linear rates were independent of Ark tree was created from which branch lengths between branch points were extracted, converted to years, and status, species representation, and mammalian order, used to plot the timeline of branching/speciation within and they were also independent of vertebrate class. the family. The results were a good fit to a linear Linear rates were also independent of phylum. function, which was represented by the thin black Among arthropods, linear rates described crustacean line and the equation, both of which were derived via (Fig. 39) and insect speciation alike (Figs. 40–41). linear regression of the raw data in Microsoft Excel. Among cnidarians, only a single family was analyzed, Representation of genera and species within the family and it deviated from linear speciation hypothesis, were depicted in the upper left and right corners, showing evidence in favor of the late speciation respectively. hypothesis instead (Fig. 42). However, since two- In addition, some of the best-represented reptile thirds of the species in this analysis came from (Crocodylidae, 81% species representation, Fig. 33) only one of the 14 Acroporidae genera, the match and amphibian (Hynobiidae, 42% species between the data and the late speciation hypothesis representation, Fig. 34) families also matched the may have been an artifact of species representation. linear speciation hypothesis. Again, the visual rate Hence, linear speciation rates described the timing homogeneity test for Crocodylidae suggested that of speciation within families almost entirely mutation rates were unequal across lineages within independent of the biology of each family. 294 N. T. Jeanson
Anguillidae (Chordata, 17 of 19 Tetraodontidae (Chordata, 59 of 193 Actinopterytii, Anguilliformes): species Actinopterygii, Tetraodontiformes): species Speciation Rate (89%) Speciation Rate (31%) 25 70 60 20 50 15 40 10 30 y = 0.003x + 3.9695
Total Species Total 20 2 Species Total 5 R = 0.8904 y = 0.0096x + 0.6412 10 R2 = 0.9893 0 0 0 1000 2000 3000 4000 5000 6000 0 1000 2000 3000 4000 5000 6000 Years Post-Flood Years Post-Flood Fig. 35. Speciation rate within the family Anguillidae. Fig. 37. Speciation rate within the family Tetraodontidae. Whole genome alignments for extant species in the Whole genome alignments for extant species in the family Anguillidae were performed. A phylogenetic tree family Tetraodontidae were performed. A phylogenetic was created from which branch lengths between branch tree was created from which branch lengths between points were extracted, converted to years, and used to plot branch points were extracted, converted to years, and the timeline of branching/speciation within the family. used to plot the timeline of branching/speciation within The results were a good fit to a linear function, which the family. The results were a tight fit to a linear was represented by the thin black line and the equation, function, which was represented by the thin black both of which were derived via linear regression of the line and the equation, both of which were derived via raw data in Microsoft Excel. Representation of species linear regression of the raw data in Microsoft Excel. within the family was depicted in the upper right corner. Representation of species within the family was depicted in the upper right corner. Scombridae (Chordata, 25 of 53 Actinopterygii, Scombriformes): species Cyprinidae (Chordata, 293 of 2935 Speciation Rate (47%) Actinopterygii, Cypriniformes): species 30 Speciation Rate (10%) 350 25 300 20 250 15 200 10 150 Total Species Total y = 0.0035x + 1.1158 5 2 Total Species Total 100 R = 0.9565 y = 0.0607x − 77.9 0 50 R2 = 0.9692 0 1000 2000 3000 4000 5000 6000 0 Years Post-Flood 0 1000 2000 3000 4000 5000 6000 Fig. 36. Speciation rate within the family Scombridae. Years Post-Flood Whole genome alignments for extant species in the Fig. 38. Speciation rate within the family Cyprinidae. family Scombridae were performed. A phylogenetic Whole genome alignments for extant species in the tree was created from which branch lengths between family Cyprinidae were performed. A phylogenetic tree branch points were extracted, converted to years, and was created from which branch lengths between branch used to plot the timeline of branching/speciation within points were extracted, converted to years, and used to plot the family. The results were a fairly tight fit to a linear the timeline of branching/speciation within the family. function, which was represented by the thin black The results were a tight fit to a linear function, which line and the equation, both of which were derived via was represented by the thin black line and the equation, linear regression of the raw data in Microsoft Excel. both of which were derived via linear regression of the Representation of species within the family was depicted raw data in Microsoft Excel. Representation of species in the upper right corner. within the family was depicted in the upper right corner. Even the families that were mentioned in Scripture and which were previously used to argue of speciation from being drawn, yet the wild camel (Wood 2002) for the early episode hypothesis showed (Camelus ferus) branched immediately from the speciation patterns that did not contradict the linear putative root and did not show a nested hierarchical speciation rate hypothesis. As described above, the pattern with the remaining species or any other family Equidae showed a linear speciation rate (Fig. such pattern suggestive of a later speciation event 23), and the wild horse (Equus przewalskii) branched (Supplemental Fig. 49). off first from the Equid family tree (Supplemental In families Felidae and Canidae, species Fig. 29). The family Camelidae had only three representation was low, but the data still correlated species total, preventing a strict graph on the timing well with the linear speciation rate hypothesis (Figs. Mitochondrial DNA Clocks Imply Linear SpeciationRates Within “Kinds” 295
8 of 23 Parastacidae (Arthropoda, 26 of 215 49 of 691 Nymphalidae (Arthropoda, 102 of 24,595 genera Malacostraca, Decapoda): species genera Insecta, Lepidoptera): species (35%) Speciation Rate (12%) (7%) Speciation Rate (0.4%) 35 140 30 120 25 100 20 80 15 60 10 y = 0.0057x + 0.6099 Total Species Total
Total Species Total 40 2 y = 0.0211x − 4.0316 5 R = 0.9584 20 R2 = 0.9579 0 0 0 1000 2000 3000 4000 5000 6000 0 1000 2000 3000 4000 5000 6000 Years Post-Flood Years Post-Flood Fig. 39. Speciation rate within the family Parastacidae. Fig. 41. Speciation rate within the family Nymphalidae. Whole genome alignments for extant species in the Whole genome alignments for extant species in the family Parastacidae were performed. A phylogenetic family Nymphalidae were performed. A phylogenetic tree was created from which branch lengths between tree was created from which branch lengths between branch points were extracted, converted to years, and branch points were extracted, converted to years, and used to plot the timeline of branching/speciation within used to plot the timeline of branching/speciation within the family. The results were a fairly tight fit to a linear the family. The results were a fairly tight fit to a linear function, which was represented by the thin black function, which was represented by the thin black line and the equation, both of which were derived via line and the equation, both of which were derived via linear regression of the raw data in Microsoft Excel. linear regression of the raw data in Microsoft Excel. Representation of genera and species within the family Representation of genera and species within the family were depicted in the upper left and right corners, were depicted in the upper left and right corners, respectively. respectively.
26 of 1472 Acrididae (Arthropoda, 30 of 6615 5 of 14 Acroporidae (Cnidaria, 18 of 423 genera Insecta, Orthoptera): species genera Anthozoa, Scleractinia): species (2%) Speciation Rate (0.5%) (36%) Speciation Rate (4%) 40 20 35 y = 0.0015x + 0.9842 30 15 R2 = 0.4546 25 20 10 15
Total Species Total 5 Total Species Total 10 y = 0.0054x + 2.5598 5 R2 = 0.8803 0 0 0 1000 2000 3000 4000 5000 6000 0 1000 2000 3000 4000 5000 6000 Years Post-Flood Years Post-Flood Fig. 42. Speciation rate within the family Acroporidae. Fig. 40. Speciation rate within the family Acrididae. Whole genome alignments for extant species in the Whole genome alignments for extant species in the family Acroporidae were performed. A phylogenetic tree family Acrididae were performed. A phylogenetic tree was created from which branch lengths between branch was created from which branch lengths between branch points were extracted, converted to years, and used to points were extracted, converted to years, and used to plot plot the timeline of branching/speciation within the the timeline of branching/speciation within the family. family. The results were a poor fit to a linear function The results were a good fit to a linear function, which (represented by the thin black line and the equation, was represented by the thin black line and the equation, both of which were derived via linear regression of the both of which were derived via linear regression of the raw data in Microsoft Excel) and seemed a better fit the raw data in Microsoft Excel. Representation of genera “Late” hypothesis (Fig. 18). Representation of genera and species within the family were depicted in the upper and species within the family were depicted in the upper left and right corners, respectively. left and right corners, respectively. 43–44).Though the wolf and lion appeared to become (Wood 2002). Also, in general for every speciation separate species within their respective families event, a new species splits off from a parent species, midway through or late in the post-Flood period, and the identity of the parental species in the wolf their lineages branched off early. Furthermore, it’s and lion lineages is unknown. It may have been the unclear whether the modern wolf and lion species wolf or lion, respectively, all along. Thus, the findings are the same species to which Scripture refers in the of this study were not in conflict with the biblical passages used to argue for an early speciation event account of the natural history of these families. 296 N. T. Jeanson
6 of 14 Felidae (Chordata, 10 of 37 Implications genera Mammalia, Carnivora): species (43%) Speciation Rate (27%) A B Extant on-Ark “kinds” Extant off-Ark “kinds” 12 Rate of Extant species Rate of Extant species 10 = = speciation ~4350 years speciation ~6000 years 8 6 C D Speciation rate per family 4 y = 0.0035x + 1.7512 (constant with time) More species
Total Species Total R2 = 0.9459 Species per family yet to come? 2 (increasing with time) 120 0 100 80 0 1000 2000 3000 4000 60
40 y = 0.0266× −1.7549 Total Species Total R2 = 0.9973 Years Post-Flood Speciation rate per species 20 0 is declining 0 1000 2000 3000 4000 Fig. 43. Speciation rate within the family Felidae. Whole Years Post-Flood genome alignments for extant species in the family Felidae were performed. A phylogenetic tree was created Fig. 45. Implications of the discovery of linear speciation from which branch lengths between branch points were rates within diverse families. A. If speciation rates extracted, converted to years, and used to plot the are linear for all “kinds” taken on board the Ark, then timeline of branching/speciation within the family. The the rate of speciation can be predicted by dividing the results were a fairly tight fit to a linear function, which number of extant species by the date of the Flood (~4350 was represented by the thin black line and the equation, years ago). B. If speciation rates are linear for all “kinds” both of which were derived via linear regression of the not taken on board the Ark, then the rate of speciation raw data in Microsoft Excel. Representation of genera can be predicted by dividing the number of extant and species within the family were depicted in the upper species by the date of Creation (~6000 years ago). C. left and right corners, respectively. If speciation rates are linear for all “kinds,” this means that the speciation rate per family is constant with 6 of 13 Canidae (Chordata, 9 of 36 time. However, since speciation is happening, the total genera Mammalia, Carnivora): species number of species within the family is increasing with (46%) Speciation Rate (25%) 10 time. A constant numerator divided by an increasing denominator results in a quotient that is decreasing 8 with time. Hence, if speciation rates are linear for all “kinds,” then the speciation rate per species is declining. 6 D. If speciation rates are linear for all “kinds,” then 4 the graphs imply that more speciation is yet to come— that speciation is still on-going and has not ceased
Total Species Total y = 0.0019x + 2.2218 2 R2 = 0.9649 permanently. 0 species within the family divided by ~4350 years. For 0 1000 2000 3000 4000 off-Ark families, the per-year rate of speciation is the Years Post-Flood number of extant species within the family divided Fig. 44. Speciation rate within the family Canidae. by ~6000 years (Fig. 45A–B). Whole genome alignments for extant species in the This was well illustrated in the mammalian family Canidae were performed. A phylogenetic tree families for whom all of their species were represented was created from which branch lengths between branch points were extracted, converted to years, and used to plot in the mitochondrial DNA databases. For example, the timeline of branching/speciation within the family. in Balaenopteridae, the predicted rate of speciation The results were a tight fit to a linear function, which (9/6000 = 0.0015) exactly matched the slope derived was represented by the thin black line and the equation, from linear regression of the mitochondrial DNA both of which were derived via linear regression of the data (Fig. 22). Also, in the family Ursidae, the raw data in Microsoft Excel. Representation of genera predicted rate of speciation (8/4350 = 0.0018) closely and species within the family were depicted in the upper matched the slope derived from linear regression of left and right corners, respectively. the mitochondrial DNA data (0.0016; see Fig. 20). Since linear speciation rates were found across Finally, in the family Rhinocerotidae, the predicted such a diversity of taxa, the major findings of this rate of speciation (5/4350 = 0.0011) closely matched study were generalizable into a single, testable the slope derived from linear regression of the equation: The absolute rate of speciation for extant mitochondrial DNA data (0.0012; see Fig. 21). species within a family is the division of the number To clarify, this equation makes predictions about of extant species within a family by the Ark- the timing of speciation only for extant species. The appropriate value. That is, for on-Ark families, the total number of species within a family at any point per-year rate of speciation is the number of extant in time includes both the still-extant species that had Mitochondrial DNA Clocks Imply Linear SpeciationRates Within “Kinds” 297
Pan troglodytes
Pan trog trog GT714 Pan trog trog GT305
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Fig. 46. Possible evidence for ongoing speciation within Pan. The same raw alignment data from which the trees in Fig. 15 were derived was used to create a mid-point rooted phylogenetic tree of members of the genus Pan. As was depicted in Fig. 15, the individuals within Pan paniscus species clearly segregated as a group from the individuals within the Pan troglodytes species. Within the latter, several subgroups were visible, corresponding to Pan troglodytes subspecies, and these subgroups may be the precursors to new Pan species. formed then, plus now-extinct species which were several subspecies exist, a fact which is immediately alive at the time. The equations in Fig. 45A–B make visible in genetics (Fig. 46, derived from the same data no predictions for the total number of species within as Fig. 15 but rooted on the midpoint and without a family at any point in time because the equations selecting the topology-only option in MEGA4). If the do not include data on now-extinct species. current geographic restriction (Humle et al. 2008; A second implication of these results was that the Oates et al. 2008; Tutin et al. 2008; Wilson et al. 2008) per species speciation rates were (and are) declining. of these Pan troglodytes subpopulations continues, Since the speciation rates per family were constant and if interbreeding among these subspecies fails to with time but the number of species within each occur, new Pan species may soon emerge. family was increasing with time, this effectively meant that speciation rate of each species was Discussion becoming smaller with the passage of time (Fig. 45C). Ramifications for the timing of speciation A third implication of these results was that high The results of this study highlight the unique rates of speciation continue to this day (Fig. 45D). advantages of genetics over the fossil record on the In contrast, the evolutionary model postulates that question of the timing of speciation. Since only a few individual species arise over hundreds of thousands select time points are represented in the fossil record, to millions of years (Futuyma 2009), implying that the history that can be inferred from paleontology is speciation is a rarely seen event. The equations in rather imprecise temporally. (This is true regardless Fig. 45A–B estimate ongoing speciation at much of where the Flood/post-Flood boundary is placed in faster rates. For example, within Bovidae, the the fossil record.) Conversely, in speciose “kinds,” predicted rate of speciation is 0.03 species per year genetics theoretically offers many more time points. (141/4350 = 0.03) or one new species every 31 years. In addition, some categories of “kinds” (e.g., insects) Currently, the African buffalo (Syncerus fossilize poorly, limiting the broad taxonomic caffer) contains several subspecies, including the utility of paleontology. In contrast, DNA sequence morphologically distinct African forest buffalo information can be obtained freely in theory from (Syncerus caffer nanus). If these subspecies become nearly any species alive today. Hence, the findings of geographically (and, therefore, reproductively) this study represent the first high resolution window isolated, they might eventually be classified as in the relative timing of speciation for extant species. separate species, consistent with the conclusion that Observing the past through this window revealed speciation is ongoing and observable. abundant evidence consistent with the linear As another example, the family Hominidae has a speciation rate hypothesis. Nearly every family that predicted rate of speciation of 0.001 (6/4350 = 0.001), was studied matched the expectations of the constant or one new species every 725 years. Within the rate model. Although the entire dataset represented common chimpanzee species (Pan troglodytes), less than 30 metazoan families, the linear speciation 298 N. T. Jeanson rate results were true regardless of the classes and Under the assumption that molecular clocks phyla to which these families belonged, suggesting do indeed exist, the results of this study found no that constant speciation rates would generally be evidence in support of the early episode hypothesis found across most taxa. Furthermore, the results (Fig. 18) of Wise (1994) and Wood (2002, 2003). The were so consistent that they led to a predictive model fact that most vertebrate families are not highly for the timing of speciation (Fig. 45A–B), one that can speciose (Figs. 1–6) and that fact that nearly every be tested with addition families in the future. family showed a linear rate of species accumulation These results can be reconciled with the previous regardless of within-family species richness (Figs. data used to argue for an early episode of speciation. 19–44) together argued against the hypothesis that As described in the Results section, the four families modern species arose immediately post-Flood in a alluded to in Scripture (Wood 2002) did not contradict burst of speciation. the linear speciation rate hypothesis. Also, even Hence, it appears that speciation is not “rapid” in if the Flood/post-Flood boundary is at the K-T, the the sense of the early episode hypothesis (Fig. 18), high number of species formed then may not have but speciation does seem to happen much faster than been the ancestors of modern extant species, which the evolutionary community has maintained. would alleviate any apparent contradiction between All of these results are dependent upon the the paleontological findings and the present genetic assumption that the taxonomic rank of family is findings. Finally, fossil DNA (Wood 2012, 2013b) equivalent to the biblical designation of “kind,” as per appears to be degraded, or it may represent a group previous data (Wood 2006). If “kinds” turn out to be of individuals with unique and unusually high higher or lower than the rank of family, then these mutation rates (Fig. 11C). Neither of these scenarios results would be called into question. For highly undermine the foundational assumption of this speciose families, the possibility is especially real study—that rates of mitochondrial DNA change in that the “kind” boundary may not be equivalent to extant species have been constant through time. the rank of family. Nevertheless, this assumption of constant Nevertheless, the preliminary results in this mitochondrial DNA mutation rates could be falsified study suggest that the conclusion of linear rates of in the future by one of at least two different methods. speciation would remain intact. For example, in If ancient DNA could be demonstrated to be reliable, several of the speciose families, mitochondrial DNA and if it could be demonstrated that these fossil DNA representation was poor. Hence, these groups could sequences found immediately post-Flood were too be viewed as an approximation of a “kind” boundary genetically diverse to be explained by a constant rate lower than the rank of family. Even in these groups, of mutation, then the major undergirding assumption linear speciation rates were still seen (e.g., Figs. 30, of the present study would be in error. 38, 40–41), suggesting that linear rates of speciation Alternatively, since the prospect of finding non- were the rule even if the “kind” boundary were shifted degraded DNA from fossils seems unlikely at present, slightly from the family rank. the assumption of a constant rate of mutation could be tested with living species. By measuring the mutation Remaining questions on the timing of speciation rates in additional species within a family; making Several aspects of the timing of speciation were genetic diversity predictions from these rates under inaccessible by the methods employed in this study. the assumption that rates have been constant; and First, because I assumed that the start of the then comparing the predictions to actual diversity, speciation process was approximated by the midpoint the utility of the constant rate assumption could be root of each tree, it is difficult to make firm conclusions evaluated. If the predictions from these additional about the absolute timing of speciation. It is entirely rates underestimate actual diversity within the possible that species within on-Ark “kinds” coalesce family, then the assumption of constant rates would sooner than 4350 years ago and that species within be falsified, and it would appear that mutation rates off-Ark “kinds” coalesce sooner than 6000 years ago. were higher in the past, as per Wood’s conclusions If these hypotheses are true, a linear pattern (2012, 2013b). This result would also imply that early would still be present within these families, but only episode (Fig. 18) speciation hypothesis was correct. for the length of time that speciation was happening. Instead, if the predictions overestimated actual In a sense, this result would be a fusion of the linear diversity in the family, then it would appear that and late hypotheses. Under this scenario, speciation either mutation rates were slower in the past or that events would begin late post-Flood, but, once they species within a family coalesced sooner than 4350 began, they would follow a linear pattern. Hence, years ago (on-Ark families)/6000 years ago (off-Ark anchoring the linear patterns discovered in this families). This result would imply that a version of study to absolute dates on the YE timescale will the late hypothesis (Fig. 18) was correct. require further study. Mitochondrial DNA Clocks Imply Linear SpeciationRates Within “Kinds” 299
Evaluation might begin by comparing the the family may have encountered during its history. predictions from the equations in Fig. 45A–B to This suggests that speciation may not be a process recorded history. In addition, mitochondrial DNA of directed mutation in response to environmental mutation rates could be measured for several species challenges. within each family to see if the predictions from Furthermore, since the rate of speciation appears these rates overestimate or accurately describe the to be constant, rather than an exponential function genetic diversity within the family. If the predictions which eventually trails off with time, the need for matched the actual diversity, this would support the creative mechanisms of speciation appears to be assumptions made in this study and the timestamps obviated. Since some of the most inventive mechanistic assigned to the various speciation events. hypotheses were created to explain the early episode Despite these concerns, the preliminary results hypothesis of speciation (Fig. 18), the fact of linear of this study suggest that, for several “kinds,” the speciation rates implies that novel proposals are timelines I depicted (Figs. 19–44) were not too far no longer required. Specifically, this would suggest off the absolute timescale. For example, among the that transposon-mediated mechanisms (e.g., Terborg on-Ark carnivores (Fig. 13), the various families were 2008, 2009; Shan 2009; Wood 2002, 2003) are not separated from one another by few DNA differences. needed for speciation. In contrast, species within families were sometimes Nevertheless, the fact of chromosomal differences separated by large DNA differences. Had speciation among species may still necessitate unique proposals commenced late post-Flood, then I would have on genetic change (Wood 2013a). expected the DNA differences between species to By contrast, the linear speciation rate results have been less than the DNA differences between in the present study implicate a mechanism that families. has existed in the creationist community for Second, the timing of speciation for extinct families decades (e.g., Parker 1980)—a hypothesis termed is also inaccessible by this study. Since I limited my “heterozygous fractionation” (Wood 2002). Under analyses to extant species, these results say nothing this hypothesis, God created the first individuals about the timing of speciation for “kinds” which did within each “kind” with heterozygosity in their not survive to today. nuclear DNA compartment. This genetic diversity Third, these results are silent on the question represents the raw material to be reshuffled each of the rates of speciation for now-extinct species in generation, and the process of recombination still-extant families. Presumably, if DNA data were ultimately leads to morphologically distinct available for these extinct species, the fact of linear individuals that form populations which we would rates would remain, and only the slopes/absolute label separate “species.” values for the rates of speciation would need to be Though the focus in this study was mitochondrial modified. In a sense, the speciose-families with poor DNA, the principles about the timing of speciation DNA sequence representation (Figs. 30, 38, 40–41) that were inferred from these data were consistent are already a model of this scenario. I anticipate that with several expectations of the heterozygous the addition of more DNA sequences from extant fractionation hypothesis for nuclear DNA. First, species to these family calculations will simply under this hypothesis, fractionating the originally change the slope and not the linear structure of the diverse pool of nuclear alleles would likely dilute graph. the potential for speciation within each new species. Finally, these studies do not directly address Since each new species would contain a fraction of the why some families became very speciose and others original nuclear allele pool, the number of available remained/are species-poor. The power distribution nuclear alleles for recombination would become seems to approximate the species per family in a smaller with each new speciation event. This would variety of taxonomic groups, but the reason why this effectively lower the speciation potential with each function fits the data best remains unknown. new speciation event, consistent with the results of this study that indicate that the rate of speciation per Ramifications for the mechanism of speciation species is declining (Fig. 45C). The results of this study put several of the Second, on the flip side, under the heterozygous prevailing hypotheses on the mechanism of speciation fractionation hypothesis, speciation would be ongoing. in a new light. The equations in Fig. 45A–B indicate Since it’s not driven by any unique environmental that the rate of speciation is predictable from the trigger or by one-time historical events, new species total number of species within a family. Since species could form, theoretically, at any time so long as within a family occupy diverse environments, it would sufficient alleles are present for recombination to appear that the rate of speciation within a family is produce new varieties. The results of this study not predictable from the type of environments that suggest that speciation is ongoing (Fig. 45D). 300 N. T. Jeanson
Third, independent of the results of this study, Furthermore, it suggested that the mechanism of precise accounting for the current set of alleles in speciation was shared across diverse “kinds” and the human population nearly requires an initially that this mechanism might be genetic drift of created heterozygous pair (Carter 2011). If humans were heterozygosity. created heterozygous, perhaps the animals “kinds” were as well. Acknowledgments Fractionation of a heterozygous allele pool is Jason Lisle was instrumental in deriving the also a feasible explanation. Population genetics conclusion that speciation rates per species are has identified the conditions required to prevent declining, and he was a key consultant on many fractionation of heterozygosity—conditions termed other facets of this undertaking. Rob Carter always “the Hardy-Weinberg principle” (Futuyma 2009). If a provided unique and invaluable feedback on the population of individuals is infinite in size, if mating many genetic aspects of this study, particularly on among individuals occurs randomly and without the details of population genetics. A preliminary inbreeding, if the species is not broken up into version of this work was presented at the 2014 different isolated subpopulations (migration and gene Creation Research Society meeting, and feedback flow reduce boundaries between subpopulations), if from the attendees there was helpful in refining the mutation does not occur, and if natural selection does conclusions. Special thanks to the reviewers who also not happen, then heterozygosity will be maintained, helped refine the conclusions in this paper. and no change in the frequency of alleles in the population will occur. Obviously, these conditions do References not exist anywhere on earth, which means that all Austin, S. A., J. R. Baumgardner, D. R. Humphreys, A. 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Supplemental Files file was used to create a radiation style tree. Supplemental Fig. 1. Radiation style tree of species within Supplemental Fig. 16. Radiation style tree of species within the family Bovidae. Mitochondrial DNA whole genome the family Hynobiidae. Mitochondrial DNA whole genome alignments were performed, and the resultant alignment alignments were performed, and the resultant alignment file was used to create a radiation style tree. file was used to create a radiation style tree. Supplemental Fig. 2. Radiation style tree of species within Supplemental Fig. 17. Radiation style tree of species within the family Ursidae. Mitochondrial DNA whole genome the family Anguillidae. Mitochondrial DNA whole genome alignments were performed, and the resultant alignment alignments were performed, and the resultant alignment file was used to create a radiation style tree. file was used to create a radiation style tree. Supplemental Fig. 3. Radiation style tree of species within the Supplemental Fig. 18. Radiation style tree of species within family Rhinocerotidae. Mitochondrial DNA whole genome the family Scombridae. Mitochondrial DNA whole genome alignments were performed, and the resultant alignment alignments were performed, and the resultant alignment file was used to create a radiation style tree. file was used to create a radiation style tree. Rather than Supplemental Fig. 4. Radiation style tree of species within the genus-species names, the NCBI accession information was family Balaenopteridae. Mitochondrial DNA whole genome displayed for each species. alignments were performed, and the resultant alignment Supplemental Fig. 19. Radiation style tree of species within the file was used to create a radiation style tree. family Tetraodontidae. Mitochondrial DNA whole genome Supplemental Fig. 5. Radiation style tree of species within alignments were performed, and the resultant alignment the family Equidae. Mitochondrial DNA whole genome file was used to create a radiation style tree. alignments were performed, and the resultant alignment Supplemental Fig. 20. Radiation style tree of species within file was used to create a radiation style tree. the family Cyprinidae. Mitochondrial DNA whole genome Supplemental Fig. 6. Radiation style tree of species within alignments were performed, and the resultant alignment the family Hominidae. Mitochondrial DNA whole genome file was used to create a radiation style tree. alignments were performed, and the resultant alignment Supplemental Fig. 21. Radiation style tree of species within file was used to create a radiation style tree. the family Parastacidae. Mitochondrial DNA whole genome Supplemental Fig. 7. Radiation style tree of species within alignments were performed, and the resultant alignment the family Phocidae. Mitochondrial DNA whole genome file was used to create a radiation style tree. Rather than alignments were performed, and the resultant alignment genus-species names, the NCBI accession information was file was used to create a radiation style tree. displayed for each species. Supplemental Fig. 8. Radiation style tree of species within Supplemental Fig. 22. Radiation style tree of species within the family Cervidae. Mitochondrial DNA whole genome the family Acrididae. Mitochondrial DNA whole genome alignments were performed, and the resultant alignment alignments were performed, and the resultant alignment file was used to create a radiation style tree. file was used to create a radiation style tree. Rather than Supplemental Fig. 9. Radiation style tree of species within the genus-species names, the NCBI accession information was family Cercopithecidae. Mitochondrial DNA whole genome displayed for each species. alignments were performed, and the resultant alignment Supplemental Fig. 23. Radiation style tree of species within the file was used to create a radiation style tree. family Nymphalidae. Mitochondrial DNA whole genome Supplemental Fig. 10. Radiation style tree of species within alignments were performed, and the resultant alignment the family Mustelidae. Mitochondrial DNA whole genome file was used to create a radiation style tree. Rather than alignments were performed, and the resultant alignment genus-species names, the NCBI accession information was file was used to create a radiation style tree. displayed for each species. Supplemental Fig. 11. Radiation style tree of species within Supplemental Fig. 24. Radiation style tree of species within the family Delphinidae. Mitochondrial DNA whole genome the family Acroporidae. Mitochondrial DNA whole genome alignments were performed, and the resultant alignment alignments were performed, and the resultant alignment file was used to create a radiation style tree. file was used to create a radiation style tree. Rather than Supplemental Fig. 12. Radiation style tree of species within genus-species names, the NCBI accession information was the family Muridae. Mitochondrial DNA whole genome displayed for each species. alignments were performed, and the resultant alignment Supplemental Fig. 25. Linearized and mid-point rooted file was used to create a radiation style tree. tree of species within the family Bovidae. Mitochondrial Supplemental Fig. 13. Radiation style tree of species within DNA whole genome alignments were performed, and the the family Gruidae. Mitochondrial DNA whole genome resultant alignment file was used to create a linearized, alignments were performed, and the resultant alignment mid-point rooted tree with branch lengths displayed. The file was used to create a radiation style tree. mid-point root was assumed to represent the start of the Supplemental Fig. 14. Radiation style tree of species within speciation process. the family Phasianidae. Mitochondrial DNA whole genome Supplemental Fig. 26. Linearized and mid-point rooted alignments were performed, and the resultant alignment tree of species within the family Ursidae. Mitochondrial file was used to create a radiation style tree. Rather than DNA whole genome alignments were performed, and the genus-species names, the NCBI accession information was resultant alignment file was used to create a linearized, displayed for each species. mid-point rooted tree with branch lengths displayed. The Supplemental Fig. 15. Radiation style tree of species within mid-point root was assumed to represent the start of the the family Crocodylidae. Mitochondrial DNA whole genome speciation process. alignments were performed, and the resultant alignment Supplemental Fig. 27. Linearized and mid-point rooted tree Mitochondrial DNA Clocks Imply Linear SpeciationRates Within “Kinds” 303
of species within the family Rhinocerotidae. Mitochondrial Supplemental Fig. 36. Linearized and mid-point rooted tree DNA whole genome alignments were performed, and the of species within the family Muridae. Mitochondrial resultant alignment file was used to create a linearized, DNA whole genome alignments were performed, and the mid-point rooted tree with branch lengths displayed. The resultant alignment file was used to create a linearized, mid-point root was assumed to represent the start of the mid-point rooted tree with branch lengths displayed. The speciation process. mid-point root was assumed to represent the start of the Supplemental Fig. 28. Linearized and mid-point rooted tree of speciation process. species within the family Balaenopteridae. Mitochondrial Supplemental Fig. 37. Linearized and mid-point rooted DNA whole genome alignments were performed, and the tree of species within the family Gruidae. Mitochondrial resultant alignment file was used to create a linearized, DNA whole genome alignments were performed, and the mid-point rooted tree with branch lengths displayed. The resultant alignment file was used to create a linearized, mid-point root was assumed to represent the start of the mid-point rooted tree with branch lengths displayed. The speciation process. mid-point root was assumed to represent the start of the Supplemental Fig. 29. Linearized and mid-point rooted speciation process. tree of species within the family Equidae. Mitochondrial Supplemental Fig. 38. Linearized and mid-point rooted tree DNA whole genome alignments were performed, and the of species within the family Phasianidae. Mitochondrial resultant alignment file was used to create a linearized, DNA whole genome alignments were performed, and the mid-point rooted tree with branch lengths displayed. The resultant alignment file was used to create a linearized, mid-point root was assumed to represent the start of the mid-point rooted tree with branch lengths displayed. The speciation process. mid-point root was assumed to represent the start of the Supplemental Fig. 30. Linearized and mid-point rooted tree speciation process. Rather than genus-species names, the of species within the family Hominidae. Mitochondrial NCBI accession information was displayed for each species. DNA whole genome alignments were performed, and the Supplemental Fig. 39. Linearized and mid-point rooted tree resultant alignment file was used to create a linearized, of species within the family Crocodylidae. Mitochondrial mid-point rooted tree with branch lengths displayed. The DNA whole genome alignments were performed, and the mid-point root was assumed to represent the start of the resultant alignment file was used to create a linearized, speciation process. mid-point rooted tree with branch lengths displayed. The Supplemental Fig. 31. Linearized and mid-point rooted tree mid-point root was assumed to represent the start of the of species within the family Phocidae. Mitochondrial speciation process. DNA whole genome alignments were performed, and the Supplemental Fig. 40. Linearized and mid-point rooted tree resultant alignment file was used to create a linearized, of species within the family Hynobiidae. Mitochondrial mid-point rooted tree with branch lengths displayed. The DNA whole genome alignments were performed, and the mid-point root was assumed to represent the start of the resultant alignment file was used to create a linearized, speciation process. mid-point rooted tree with branch lengths displayed. The Supplemental Fig. 32. Linearized and mid-point rooted tree mid-point root was assumed to represent the start of the of species within the family Cervidae. Mitochondrial speciation process. DNA whole genome alignments were performed, and the Supplemental Fig. 41. Linearized and mid-point rooted tree resultant alignment file was used to create a linearized, of species within the family Anguillidae. Mitochondrial mid-point rooted tree with branch lengths displayed. The DNA whole genome alignments were performed, and the mid-point root was assumed to represent the start of the resultant alignment file was used to create a linearized, speciation process. mid-point rooted tree with branch lengths displayed. The Supplemental Fig. 33. Linearized and mid-point rooted tree mid-point root was assumed to represent the start of the of species within the family Cercopithecidae. Mitochondrial speciation process. DNA whole genome alignments were performed, and the Supplemental Fig. 42. Linearized and mid-point rooted tree resultant alignment file was used to create a linearized, of species within the family Scombridae. Mitochondrial mid-point rooted tree with branch lengths displayed. The DNA whole genome alignments were performed, and the mid-point root was assumed to represent the start of the resultant alignment file was used to create a linearized, speciation process. mid-point rooted tree with branch lengths displayed. The Supplemental Fig. 34. Linearized and mid-point rooted tree mid-point root was assumed to represent the start of the of species within the family Mustelidae. Mitochondrial speciation process. Rather than genus-species names, the DNA whole genome alignments were performed, and the NCBI accession information was displayed for each species. resultant alignment file was used to create a linearized, Supplemental Fig. 43. Linearized and mid-point rooted tree mid-point rooted tree with branch lengths displayed. The of species within the family Tetraodontidae. Mitochondrial mid-point root was assumed to represent the start of the DNA whole genome alignments were performed, and the speciation process. resultant alignment file was used to create a linearized, Supplemental Fig. 35. Linearized and mid-point rooted tree mid-point rooted tree with branch lengths displayed. The of species within the family Delphinidae. Mitochondrial mid-point root was assumed to represent the start of the DNA whole genome alignments were performed, and the speciation process. resultant alignment file was used to create a linearized, Supplemental Fig. 44. Linearized and mid-point rooted tree mid-point rooted tree with branch lengths displayed. The of species within the family Cyprinidae. Mitochondrial mid-point root was assumed to represent the start of the DNA whole genome alignments were performed, and the speciation process. resultant alignment file was used to create a linearized, 304 N. T. Jeanson
mid-point rooted tree with branch lengths displayed. The Supplemental Fig. 51. Radiation style tree of species within mid-point root was assumed to represent the start of the the family Canidae. Mitochondrial DNA whole genome speciation process. alignments were performed, and the resultant alignment Supplemental Fig. 45. Linearized and mid-point rooted tree file was used to create a radiation style tree. of species within the family Parastacidae. Mitochondrial Supplemental Fig. 52. Linearized and mid-point rooted DNA whole genome alignments were performed, and the tree of species within the family Felidae. Mitochondrial resultant alignment file was used to create a linearized, DNA whole genome alignments were performed, and the mid-point rooted tree with branch lengths displayed. The resultant alignment file was used to create a linearized, mid-point root was assumed to represent the start of the mid-point rooted tree with branch lengths displayed. The speciation process. Rather than genus-species names, the mid-point root was assumed to represent the start of the NCBI accession information was displayed for each species. speciation process. Supplemental Fig. 46. Linearized and mid-point rooted tree Supplemental Fig. 53. Linearized and mid-point rooted of species within the family Acrididae. Mitochondrial tree of species within the family Canidae. Mitochondrial DNA whole genome alignments were performed, and the DNA whole genome alignments were performed, and the resultant alignment file was used to create a linearized, resultant alignment file was used to create a linearized, mid-point rooted tree with branch lengths displayed. The mid-point rooted tree with branch lengths displayed. The mid-point root was assumed to represent the start of the mid-point root was assumed to represent the start of the speciation process. Rather than genus-species names, the speciation process. NCBI accession information was displayed for each species. Supplemental Table 1. Common names for taxonomic groups Supplemental Fig. 47. Linearized and mid-point rooted tree and species used in this study. of species within the family Nymphalidae. Mitochondrial Supplemental Table 2. Taxonomic information from IUCN for DNA whole genome alignments were performed, and the species within Mammalia. resultant alignment file was used to create a linearized, Supplemental Table 3. Taxonomic information from the mid-point rooted tree with branch lengths displayed. The Reptile Database for species within Reptilia. mid-point root was assumed to represent the start of the Supplemental Table 4. Taxonomic information from the speciation process. Rather than genus-species names, the Amphibian Species of the World list for species within NCBI accession information was displayed for each species. Amphibia. Supplemental Fig. 48. Linearized and mid-point rooted tree Supplemental Table 5. Taxonomic information from the of species within the family Acroporidae. Mitochondrial BirdLife Checklist for species within Aves. DNA whole genome alignments were performed, and the Supplemental Table 6. Taxonomic information from the resultant alignment file was used to create a linearized, Catalog of Fishes for members of Actinopterygii. mid-point rooted tree with branch lengths displayed. The Supplemental Table 7. NCBI accession numbers for all mid-point root was assumed to represent the start of the sequences used in this paper. speciation process. Rather than genus-species names, the Supplemental Table 8. Raw calculations for mitochondrial NCBI accession information was displayed for each species. DNA clock predictions. Supplemental Fig. 49. Radiation style tree of species within Supplemental Table 9. D-loop sequence differences among the family Camelidae. Mitochondrial DNA whole genome human non-African ethnic groups. alignments were performed, and the resultant alignment file was used to create a radiation style tree. Supplemental Fig. 50. Radiation style tree of species within the family Felidae. Mitochondrial DNA whole genome alignments were performed, and the resultant alignment file was used to create a radiation style tree.