Patterns of Variation of Mutation Rates of Mitochondrial and Nuclear Genes of Gastropods Thomas F
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Duda Jr. BMC Ecol Evo (2021) 21:13 BMC Ecology and Evolution https://doi.org/10.1186/s12862-021-01748-2 RESEARCH ARTICLE Open Access Patterns of variation of mutation rates of mitochondrial and nuclear genes of gastropods Thomas F. Duda Jr.* Abstract Background: Although mitochondrial DNA (mtDNA) of many animals tends to mutate at higher rates than nuclear DNA (nuDNA), a recent survey of mutation rates of various animal groups found that the gastropod family Bradybae- nidae (suborder Helicina) shows a nearly 40-fold diference in mutation rates of mtDNA ( µm) and nuDNA ( µn), while other gastropod taxa exhibit only two to fve-fold diferences. To determine if Bradybaenidae represents an outlier within Gastropoda, I compared estimated values of µm/µn of additional gastropod groups. In particular, I recon- structed mtDNA and nuDNA gene trees of 121 datasets that include members of various clades contained within the gastropod subclasses Caenogastropoda, Heterobranchia, Patellogastropoda, and Vetigastropoda and then used total branch length estimates of these gene trees to infer µm/µn. Results: Estimated values of µm/µn range from 1.4 to 91.9. Datasets that exhibit relatively large values of µm/µn (i.e., > 20), however, show relatively lower estimates of µn (and not elevated µm) in comparison to groups with lower val- ues. These datasets also tend to contain sequences of recently diverged species. In addition, datasets with low levels of phylogenetic breadth (i.e., contain members of single genera or families) exhibit higher values of µm/µn than those with high levels (i.e., those that contain representatives of single superfamilies or higher taxonomic ranks). Conclusions: Gastropods exhibit considerable variation in estimates of µm/µn. Large values of µm/µn that have been calculated for Bradybaenidae and other gastropod taxa may be overestimated due to possible sampling artifacts or processes that depress estimates of total molecular divergence of nuDNA in groups that recently diversifed. Keywords: Gastropoda, Mutation rates, Mitochondrial DNA, Nuclear DNA µ µ Background between m and n (~ 2 to 10-fold diference) than ver- Information concerning patterns of variation of mutation tebrates (~ 10 to 25-fold diference) [3, 4, 7–11]. A recent µ µ rates of nuclear and organellar genomes is important for comparison of estimates of the ratio m/ n of 122 animal understanding the factors that infuence these rates and taxa (one sponge, 78 vertebrates, 33 arthropods, and 10 how they impact interactions among genomes [1–4]. For molluscs) found that one mollusc group, members of µ most animal taxa, mutation rates ( m) of mitochondrial the gastropod family Bradybaenidae (subclass Hetero- DNA sequences (mtDNA) are higher than mutation rates branchia, order Stylommatophora, suborder Helicina), µ µ µ ( n) of nuclear DNA sequences (nuDNA) [5–7]. None- shows a nearly 40-fold diference in m and n, whereas theless, invertebrates tend to show smaller diferences other molluscs, including representatives of six other gas- tropod groups, exhibited only two to fve-fold diferences *Correspondence: [email protected] [4]. Is Bradybaenidae an exception within Mollusca or do Museum of Zoology & Department of Ecology of Evolutionary Biology, other gastropods (e.g., other members of the species rich University of Michigan, 1105 N. University, Ann Arbor, MI 48109-1085, USA suborder Helicina) have exceptionally large values of µ © The Author(s) 2021. 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The Creative Commons Public Domain Dedication waiver (http://creat iveco mmons .org/publi cdoma in/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Duda Jr. BMC Ecol Evo (2021) 21:13 Page 2 of 9 µ Table 1 Identity of mtDNA and nuDNA gene regions m/ n? Furthermore, what potential factors contribute to µ µ that were included in the 3692 NCBI PopSets the large values of m/ n that Bradybaenidae and possibly other gastropod groups exhibit? Gene Number To address the above questions, I estimated and com- µ µ Mitochondrial genes 2593 pared m/ n of additional gastropod groups, including 12S 120 members of four of the six subclasses of Gastropoda— 16S 784 Caenogastropoda, Heterobranchia, Patellogastropoda, cytb 79 and Vetigastropoda—and additional groups from the COI 1551 suborder Helicina. I aimed to determine if Bradybaeni- COII 13 dae is an outlier within Gastropoda or if other gastropod µ µ NADH 30 taxa also exhibit such large values of m/ n. I also evalu- µ µ Other genes 124 ated whether variation in m/ n among gastropod taxa µ µ Nuclear genes 1099 refects relative diferences in m or n among groups µ µ rRNA (5.8S, 18S, 28S, ITS1, ITS2) 639 exhibiting diferent values of m/ n. In addition, I sought µ µ Actin 19 to determine if large values of m/ n might be overes- timated due to possible inclusion of recently diverged Conotoxins 28 µ µ EF1α 12 species by comparing ratios of m/ n from datasets that include diferent levels of taxonomic breadth (i.e., those Histone (H3, H4) 215 that include members of genera, families, superfamilies, Other genes 186 or higher taxonomic categories). I largely followed the Only gene regions included in 10 or more PopSets are listed approach described in [4] of gathering published mtDNA Cytb: cytochrome b; COI: cytochrome oxidase subunit I; COII: cytochrome oxidase subunit II; NADH: nicotinamide adenine dinucleotide; ITS1: internal transcribed and nuDNA gene sequences from corresponding sets of space I; ITS2: internal transcribed space 2; EF1α : elongation factor 1-alpha individuals/species, reconstructing gene trees, and then µ µ inferring relationship between m and n by calculat- ing the ratio of the total branch lengths of mtDNA and lipoprotein (mlp) gene as well as sequences of an intron nuDNA gene trees. I estimated total branch lengths at of a gamma glutamyl carboxylase gene. third codon positions for coding regions (as implemented Five sets of sequences included data from two in [4]) and all positions of intron regions as a proxy for mtDNA genes and one nuDNA gene (N = 2; COI and neutral divergence. cytb in both cases) or from two nuDNA genes and one mtDNA gene (N = 3; H3 and H4 in two cases and H3 Results and ANT in the other). I also included datasets of the Datasets two sets of mtDNA and nuDNA that were previously Searching for the term “Gastropoda [Organism]” in the examined in [4] but not uploaded originally to NCBI NCBI PopSets database yielded 3692 datasets. More than as PopSets (i.e., COI and H3 sequences of Bradybaeni- two-thirds of the PopSets (N 2593) contained mtDNA dae and Aglajidae from [12] 12]). I divided mtDNA and = nuDNA sequences of one set of PopSets into three sets sequences and more than half of these (N = 1551) included COI sequences (Table 1). Most nuDNA of individual alignments that each contained sequences sequences included sequences of various regions of the of single superfamilies of the subclass Vetigastropoda rRNA transcription unit (i.e., 5.8S, 18S, 28S, and internal (i.e., Fissurelloidea and Lepetelloidea from the order Lepetellida, and Trochoidea from the order Trochida); transcribed spacers 1 and 2 (ITS1 and ITS2)) (N = 639) µ µ (Table 1). Otherwise, sequences of histone (mostly this was performed to enable comparison of m/ n histone H3 (H3)) comprised the next most abundant from these lower taxonomic categories. I also combined nuDNA gene region included in these PopSets (Table 1). two sets of PopSets from the same author(s) given that I identifed 118 sets of PopSets from the same the diferent PopSets included sequences from mem- author(s) that included both mtDNA and nuDNA data bers of the same family. Hence, in total I examined 121 of protein-coding regions or introns of at least three sets of mtDNA and nuDNA data. Te datasets contain species. All but four of the mtDNA sequence datasets sequences of members of four gastropod subclasses, included COI sequences; the four exceptions con- including Caenogastropoda (N = 31), Heterobranchia tained cytochrome b (cytb) sequences. All but six of the (N = 81), Patellogastropoda (N = 1), and Vetigastrop- nuDNA sequence dataset included coding regions of oda (N = 8), as well as a considerable breadth of the histone H3 (H3); these other datasets contained coding superfamilies (N = 34) contained within these clades regions of actin, adenine nucleotide translocase (ANT), (Additional fle 1: Table S1). While most datasets con- histone H4 (H4; two datasets), and a megalin-like tained representatives of single genera (N = 54), others Duda Jr. BMC Ecol Evo (2021) 21:13 Page 3 of 9 included members of single families (N = 34), super- Architaenioglossa; PopSet UID 1125137272, genus families (N = 18), or higher level ranks (N = 15). Acroloxus, family Acroloxidae, superorder Hygrophila); results from analyses of these datasets were excluded Sequence analyses µ µ from those that utilize ratios of m/ n or log-trans- I reconstructed mtDNA and nuDNA gene trees using formed values of TBL of nuDNA given that these values maximum likelihood approaches and then calculated are undefned.