Dataset Information

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 ([Formula: see text]_m) and nuDNA ([Formula: see text]_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 [Formula: see text]_m/[Formula: see text]_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 [Formula: see text]_m/[Formula: see text]_n.

Results

Estimated values of [Formula: see text]_m/[Formula: see text]_n range from 1.4 to 91.9. Datasets that exhibit relatively large values of [Formula: see text]_m/[Formula: see text]_n (i.e., >?20), however, show relatively lower estimates of [Formula: see text]_n (and not elevated [Formula: see text]_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 [Formula: see text]_m/[Formula: see text]_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 [Formula: see text]_m/[Formula: see text]_n. Large values of [Formula: see text]_m/[Formula: see text]_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.

SUBMITTER: Duda TF

PROVIDER: S-EPMC7853320 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Publications

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

Duda Thomas F TF

BMC ecology and evolution 20210126 1

<h4>Background</h4>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 ([Formula: see text]<sub>m</sub>) and nuDNA ([Formula: see text]<sub>n</sub>), while other gastropod taxa exhibit only two to five-fold differences. To determine if Bradybaenidae represe ...[more]

PMID: 33514316

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Project description:It has long been known that rates of synonymous substitutions are unusually low in mitochondrial genes of flowering and other land plants. Although two dramatic exceptions to this pattern have recently been reported, it is unclear how often major increases in substitution rates occur during plant mitochondrial evolution and what the overall magnitude of substitution rate variation is across plants.A broad survey was undertaken to evaluate synonymous substitution rates in mitochondrial genes of angiosperms and gymnosperms. Although most taxa conform to the generality that plant mitochondrial sequences evolve slowly, additional cases of highly accelerated rates were found. We explore in detail one of these new cases, within the genus Silene. A roughly 100-fold increase in synonymous substitution rate is estimated to have taken place within the last 5 million years and involves only one of ten species of Silene sampled in this study. Examples of unusually slow sequence evolution were also identified. Comparison of the fastest and slowest lineages shows that synonymous substitution rates vary by four orders of magnitude across seed plants. In other words, some plant mitochondrial lineages accumulate more synonymous change in 10,000 years than do others in 100 million years. Several perplexing cases of gene-to-gene variation in sequence divergence within a plant were uncovered. Some of these probably reflect interesting biological phenomena, such as horizontal gene transfer, mitochondrial-to-nucleus transfer, and intragenomic variation in mitochondrial substitution rates, whereas others are likely the result of various kinds of errors.The extremes of synonymous substitution rates measured here constitute by far the largest known range of rate variation for any group of organisms. These results highlight the utility of examining absolute substitution rates in a phylogenetic context rather than by traditional pairwise methods. Why substitution rates are generally so low in plant mitochondrial genomes yet occasionally increase dramatically remains mysterious.

Dataset Information

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

Background

Results

Conclusions

Publications

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

Similar Datasets

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