• Whale evolution (connects to material earlier in semester)-Ex of morphological tree being fixed (and what we learn then we found some fossil support) • Mammals… Ex of a tree still in process of being figured out (not in your book) • So is one kind of tree “better”? (Advantages and Disadvantages of different trees) Wrap up!! • What regions of the genome do we look at? • Molecular clocks What regions do we use to building a phylogeny with genetic data? (What different kinds of DNA are there?) o Autosomes o Sex chromosomes (Y) o Mitochondria o Chloroplasts Why are mitochondrial and chloroplast genomes circular? https://link.springer.co m/article/10.1023%2FA %3A1007564209282?LI =true What regions do we use to building a phylogeny with genetic data? (What different kinds of DNA are there?) o Autosomes o Sex chromosomes (Y) o Mitochondria o Chloroplasts Then we may choose to use… o One gene or a set of genes… o Whole genome Phylogenetic relationships are often constructed by weighing evidence from multiple genes because that is probably more accurate than looking at one gene or region! Then we also have to be aware that…. Different parts of the genome differ in their rate of evolution and therefore their utility in building trees. Slowly evolving regions or genes useful for distantly related species or species that diverged a long time ago! Rapidly evolving regions or genes useful for closely related lineages or species that diverged recently. Which of the following would be more useful in determining the relationships between very ancient lineages. (Which will change more slowly?) • Nucleotides (DNA) or Amino Acid Sequences (proteins)? • Functioning/Important Genes or Pseudogenes? • Functioning/Important Genes or Mobile genetic elements (repetitive sequences)? • Non-coding regions or coding regions? • Introns or Exons? • Synonymous mutations or Non-synonymous mutations? Synonymous do not alter the amino acid sequence of the protein and are often selectively neutral Non-synonymous mutation do alter the amino acid sequence of the protein more likely to be subject to selection What are some synonymous substitutions here? GGU, GGC, GGA will also match to Glycine mRNA Table Different parts of the genome differ in their rate of evolution and therefore their utility in building trees. You would want to choose the right region to consider. Molecular Clock Support for clock-like substitution rates comes from graphs. Lineages that diverged a long time ago would have more or fewer substitutions (or point mutations)? Molecular Clock Support for clock-like substitution rates comes from graphs. Lineages that diverged a long time ago would have more or fewer substitutions? How do we know when the last common ancestor lived? Human vs Cows Goats vs Cows Molecular Clock To look back many Millions of years would you want a slowly or rapidly evolving region? Molecular Clock Once we have “calibrated the clock for mammals” by fitting a line to these data points…how can we use this information? We can use it to extrapolate divergence dates for other mammals without a good fossil record. So lets say we do not have a good fossil record of manatees, but we count 40 substitutions between them and cows… You can extrapolate based on fit of line! Can we use a mammal clock to look at reptile divergence dates? Chapter 13:The origin of species How do we go about defining a species? How does one species become two? Ex. Bighorn sheep Which populations would you expect to be genetically different from one another? Which would be similar? Why? Topics for this Chapter • How do we define species? • How do new species form? • Fate of hybrid zones • Reproductive barriers • Problems with bacteria • Bears, bears, bears How would you go about discerning whether these two are representatives of ONE SPECIES OR TWO SPECIES? What would you want to know/measure? http://www.fws.gov/red IMPORTANT for -ESA wolf/aboutredwolf.html 1st we had Biological Species Concept (Mayr) Do they interbreed and produce fertile offspring? Advantages? Problems? 1. Asexual species… 2. Fossils 3. Geographically separated 4. Hybridizers 5. Do we really do this? Elk and red deer: two species? Morphological Species Concept Do they look the same? Advantages? Works well for fossils! Problems? How different is different? Sibling species (what are these?) Ex. Short-toed treecreeper (Certhia brachydactyla) (left) differs subtly from the common treecreeper (C. familiaris) (right) (www.mun.ca/biology/scarr/Fut_15_03_treecreepe...) Often the first thing you do…until time or $$$ to ….. Phylogenetic or Evolutionary Species Concept How long have these two groups been on separate evolutionary paths? Reconstruct evolutionary history of populations (often but not always infer through molecular genetic info) EX. Shiitake Mushrooms (Donohue and Hibbett ’96) Ranges from Japan, Thailand, Borneo, New Zealand and Tasmania Widely cultivated Threatened due to…. Researchers used all three “species concepts” •All are reproductively compatible so …. •Morphological measurements clustered in 3 groups •ribosomal RNA-4 distinct groups •Basically there are cryptic species here Lets apply our 3 concepts to our wolves Can interbreed? Yes! many Canids do! Morphology? Look different-RW is smaller, with longer ears and legs relative to body size, color different Phylogenetic (genetic) analysis examined 48,000 single nucleotide polymorphisms of red wolf, wolves from NE, our MN gray wolf, coyotes and dogs Red wolves were 76-80 % coyote and 20-24 % gray wolf…USFWS is a species Whatever it is … considered extinct in the wild by 1980. Captured individuals in ‘70s were combined with zoo populations to start a captive breeding program with 14 individuals…. Have introduced some back into wild. Today 220 in captivity but only a small number have persisted in wild….about 100? http://www.fws.gov/species/species_accounts/bio_rwol.html FYI..Mexican gray wolf is a subspecies Canis lupus baileyi Next couple slides are extra but interesting. First slide is a research paper. Second set are government reports. Show the complexity of the situation and the way the Fish and Wildlife Service struggles with that complexity when there are legal ramifications. Species definitions have real life ramifications! We found that coyote-derived ancestry is highest in individuals identified as red wolves from the southeastern United States and lowest among wolves of the Great Lakes region (for example, Minnesota, Isle Royale National Park, Wisconsin, and Algonquin Provincial Park) (Fig. 3). The south-to-north gradient of coyote ancestry (Fig. 3) is consistent with a known historical process in which wolf-like canids disappeared first from the American South and East, concurrent with early European colonization and the conversion of woodland habitat to agricultural landscape. Extirpation of wolves in the southeast followed shortly after the advent of private, state, and federal bounty beginning in the 1880s (1). As wolves became scarce, dispersing individuals would have a low probability of finding conspecific mates, resulting in an increase in coyote-wolf admixture. Only at the turn of the last century would a similar process occur in the Great Lakes region, as local gray wolf populations declined and coyotes expanded into the region (8). Coyotes and their hybrid descendants advanced eastward through Ontario, Quebec, the Maritime Provinces, and New England (8, 36). Both the timetable of wolf extirpation and its thoroughness likely explain the observed gradient in coyote–gray wolf admixture. The early and complete extermination of wolves in the American South provided opportunities for admixture, which has created a varied, dominantly coyote ancestry mosaic across the genome [for example, vonHoldt et al. (5) and Tang et al. (37)]. In contrast, the more recent entrance of coyotes into the Great Lakes region and the continued abundance of gray wolves in much of the region have maintained a higher proportion of gray wolf ancestry (Figs. 1 to 3 and Table 3).Bridgett M. vonHoldt et al. Sci Adv 2016;2:e1501714 So basically populations that had diverged and differentiated to some extent bumped into one another again and interbred…..What do we do with that? https://www.Fws.gov/southeast/pdF/Five-year-reviews/red-wolF-2018.pdf “In 2016, an expert workshop was convened to investigate and address key questions related to uncertainty surrounding hybridization and the potential increase in introgression with coyotes and challenges to survival of red wolves. The main contribution of the workshop was the evaluation of competing evolutionary origin hypotheses for the red wolf, specifically whether the red wolf is a listable entity under the ESA (Pacifi and Mills 2016, p. 13). Although the attending experts did not reach consensus on a hypothesis, they did agree that there was a logical and valid path to make a determination that the red wolf is a listable entity under the ESA either as a species (C. rufus), a subspecies or distinct population segment (DPS) of eastern wolf (C. lycaon), or a subspecies or DPS of gray wolf (C. lupus) (Pacifi and Mills 2016, p. 16). However, even with this conclusion, the Service must ensure the red wolf meets the definition of species under the ESA. The term “species” under the ESA includes any subspecies of fish or wildlife or plants, and any DPS of any species of vertebrate fish or wildlife which interbreeds when mature. “ “Genetic studies present conflicting interpretations and offer various theories on the origin of the red wolf and recommendations on the correct taxonomic status. There are three main theories on the origin of the red wolf: (1) the red wolf originated from ancient hybridization between gray wolves and coyotes, (2) the red wolf originated from recent (post European colonization) hybridization between gray wolves and coyotes, and (3) the red wolf evolved from a common ancestor with the coyote, but is of a lineage divergent from coyotes.