Patterns of variation of mutation rates of mitochondrial and nuclear genes of gastropods

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 Bradybaenidae (suborder Helicina) shows a nearly 40-fold difference in mutation rates of mtDNA ($$\mu$$ μ m) and nuDNA ($$\mu$$ μ n), while other gastropod taxa exhibit only two to five-fold differences. To determine if Bradybaenidae represents an outlier within Gastropoda, I compared estimated values of $$\mu$$ μ m/$$\mu$$ μ n of additional gastropod groups. In particular, I reconstructed 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 $$\mu$$ μ m/$$\mu$$ μ n. Results Estimated values of $$\mu$$ μ m/$$\mu$$ μ n range from 1.4 to 91.9. Datasets that exhibit relatively large values of $$\mu$$ μ m/$$\mu$$ μ n (i.e., > 20), however, show relatively lower estimates of $$\mu$$ μ n (and not elevated $$\mu$$ μ m) in comparison to groups with lower values. 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 $$\mu$$ μ m/$$\mu$$ μ n 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 $$\mu$$ μ m/$$\mu$$ μ n. Large values of $$\mu$$ μ m/$$\mu$$ μ n 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 diversified.

Inter-Specific Genetic Exchange Despite Strong Divergence in Deep-Sea Hydrothermal Vent Gastropods of the Genus Alviniconcha

“…This means that d A and d XY are nearly equivalent, and the time since species split (>25 Ma according to Breusing et al [ 14 ]) has long past the time needed for allelic lineage sorting between the three species (~8 Ne). Rather, our results are consistent with the neutral ratio of mitochondrial to nuclear mutation rate observed in non-vertebrates (typically around 5 [ 17 ]), although this ratio varies widely in molluscs (from 1.4 in Fissurelloidea to 91.9 in Cristataria [ 73 ], see also Allio et al [ 74 ]). In the absence of strongly biased sex ratios, the contrast in evolutionary rate between mitochondrial and nuclear genomes could also be explained by differences in the strength of background selection.…”

Validating a molecular clock for nudibranchs—No fossils to the rescue

“…Müller & Albach, 2010 ), thereby limiting our understanding of rate variation across the genomes of most species. In fact, we uncovered significant differences in nuclear and mitochondrial substitution and mutation rates, as evidenced by an elevated μm/μn ratio, similar to findings in other gastropods (Duda, 2021 ). Given the evidence for rate variation among both taxa and loci, future work will look to reassess substitution rates using transcriptome data from recent phylogenomic studies (Layton et al., 2020 ; Moles & Giribet, 2021 ).…”

“…Müller & Albach, 2010), thereby limiting our understanding of rate variation across the genomes of most species. In fact, we uncovered significant differences in nuclear and mitochondrial substitution and mutation rates, as evidenced by an elevated μm/μn ratio, similar to findings in other gastropods (Duda, 2021).…”

“…Trees were built with a GTR + G model and 1000 bootstrap replicates with Doriprismatica atromarginata as an outgroup for the concatenated dataset, COI and 16S, and with Tyrinna evelinae as an outgroup for ANT. Total branch length (TBL) of each gene tree was summed and used to derive a mutation rate ratio for mitochondrial (μm) and nuclear loci (μn) following Duda ( 2021 ). For μm, an average TBL of both genes was used.…”