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

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.

The complete mitochondrial genome of water flea Ceriodaphnia dubia (Crustacea: Cladocera) NIES strain

“…The following sequences were used to infer the tree: Daphnia pulex LC705055.1, D. pulex LC632389.1 (Ohtsuki et al. 2022 ), D. pulex AF117817.1 (Crease 1999 ), D. mitsukuri MW699926.1, D. galeata LC152879.1 (Tokishita et al. 2017 ), D. laevis MK059395.1 (Martins Ribeiro et al.…”

Lineage‐specific trait variations and plasticity of obligate parthenogenetic animals following the expansion of distribution range to a continental archipelago

“…Thus, in each lineage, we used a majority of the genotypes distributed in Japan. Moreover, the genotypes used in this study were the same as those used by Ohtsuki et al (2022), who examined the number of nonsynonymous and synonymous mutations (dN/dS ratio) within these lineages. According to that study, the dN/dS ratio within the JPN1 lineage was lower than that of the JPN2 lineage, suggesting that the former lineage was more efficiently subjected to purification selections (Ohta, 1973(Ohta, , 1992Houle et al, 1996;Bataillon, 2000).…”

“…Recently, Ohtsuki et al (2022) found that the base substitution rate estimated from whole-genome sequences was larger among the genotypes of the JPN1 lineage when compared with those of the JPN2 lineage, indicating that the divergent age of the JPN1 lineage is older than that of the JPN2. Moreover, the dN/dS ratio was significantly lower within the JPN1 than within the JPN2 lineage.…”

“…Theories suggest that at the onset of evolution, such as when an invasive organism exploits a new habitat, a variety of mutants are likely to accumulate in the population due to relaxed selection in the new habitats (Peischl et al, 2013; Bock et al, 2014). As the new mutants have nonsynonymous substitutions that are generally deleterious (Shen et al, 2022), most mutants will eventually be eliminated by negative selection in a given environment (Ohtsuki et al, 2022). From a genomic perspective, if this were the case, the ratio of nonsynonymous to synonymous mutation rates (dN/dS) within the population should eventually decrease.…”

To lose is to win: Long‐term co‐occurrence of two asexual populations realized by a dormant strategy of the inferior competitor

“…Among Daphnia species, D. cf. pulex sensu Hebert (1995), often referred to as panarctic D. pulex (Colbourne et al, 1998), has obligate asexual lineages (Innes & Hebert, 1988;Ohtsuki et al, 2022;Paland et al, 2005). These lineages were originally found in North America but have expanded their range to other continents and continental islands, including Japan (Ma et al, 2019;So et al, 2015;Ye et al, 2021).…”