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Data from: Invasions of an obligate asexual daphnid species support the nearly neutral theory

Citation

Urabe, Jotaro; Ohtsuki, Hajime; Norimatsu, Hiromoto; Makino, Takashi (2022), Data from: Invasions of an obligate asexual daphnid species support the nearly neutral theory, Dryad, Dataset, https://doi.org/10.5061/dryad.n5tb2rbx6

Abstract

To verify the "nearly neutral theory (NNT)," the ratio of nonsynonymous to synonymous substitutions (dN/dS) was compared among populations of different species. To determine the validity of NNT, however, populations that are genetically isolated from each other but share the same selection agents and differ in size should be compared. Genetically different lineages of obligate asexual Daphnia pulex invading Japan from North America are an ideal example as they satisfy these prerequisites. Therefore, we analyzed the whole-genome sequences of 18 genotypes, including those of the two independently invaded D. pulex lineages (JPN1 and JPN2) and compared the dN/dS ratio between the lineages. The base substitution rate of each genotype demonstrated that the JPN1 lineage having a larger distribution range diverged earlier and thus was older than the JPN2 lineage. Comparisons of the genotypes within lineages revealed that changes in dN/dS occurred after the divergence and were larger in the younger lineage, JPN2. These results imply that the JPN1 lineage has been more effectively subjected to purification selections, while slightly deteriorating mutations are less purged in JPN2 with smaller population size. Altogether, the lineage-specific difference in the dN/dS ratio for the obligate asexual D. pulex was well explained by the NNT.

Methods

Detailed methods are described in the paper.

Usage Notes

Data set used for Fig. 1, Fig. 2 and Fig. 3 of the paper.

Funding

Japan Society for the Promotion of Science, Award: 19207003

Japan Society for the Promotion of Science, Award: 22370007

Japan Society for the Promotion of Science, Award: 25291094

Japan Society for the Promotion of Science, Award: 15H02642

Japan Society for the Promotion of Science, Award: 16H02522

Japan Society for the Promotion of Science, Award: 20H03315