Evolution of asexual Daphnia pulex in Japan: variations and covariations of the digestive, morphological and life history traits

Abstract

Background Several genetic lineages of obligate parthenogenetic Daphnia pulex , a common zooplankton species, have invaded Japan from North America. Among these, a lineage named JPN1 is thought to have started colonization as a single genotype several hundred to thousand years ago and subsequently produced many genotypes in Japan. To examine the phenotypic variations due to ecological drivers diverging the genotypes in new habitats, we measured heritability and variation in 17 traits, including life history, morphology and digestive traits, and the genetic distance among the D. pulex JPN1 genotypes in Japan. Results We found that most of the traits measured varied significantly among the genotypes and that heritability was highest in the morphological traits, followed by the digestive and life history traits. In addition, 93% of the variation in these traits was explained by the first three components in the principal component analysis, implying that variation of these heritable traits is not random but rather converged into a few directions. These relations among traits revealed the potential importance of predation pressures and food conditions as factors for diverging and selecting different genotypes. However, the magnitude of the difference in any single trait group did not correlate with the genetic distance. Conclusions Our findings show that the divergent traits evolved within D. pulex JPN1 lineage without genetic recombination, since their ancestral clone invaded Japan. Large variations and covariations of the phenotypic traits, irrespective of the genetic distance among the genotypes, support the view that the invasive success of D. pulex JPN1 was promoted by a genetic architecture that allowed for large phenotypic variations with a limited number of functionally important mutations without recombination. Electronic supplementary material The online version of this article (10.1186/s12862-019-1453-9) contains supplementary material, which is available to authorized users.

Centennial clonal stability of asexual Daphnia in Greenland lakes despite climate variability

“…For example, using 12 microsatellite loci, So et al (2015) detected only four MLGs in asexual Daphnia pulex that had invaded Japanese lakes and ponds. Interestingly, these MLGs comprised 21 mitochondrial haplotypes, indicating a higher genotype diversity than that resolved by the microsatellite loci (So et al, 2015), a finding that was later confirmed using whole-genome sequencing (Tian et al, 2019).…”

“…Interestingly, these MLGs comprised 21 mitochondrial haplotypes, indicating a higher genotype diversity than that resolved by the microsatellite loci (So et al., 2015), a finding that was later confirmed using whole‐genome sequencing (Tian et al., 2019). In particular, these authors concluded that the observed divergent traits in these closely related asexual genotypes evolved without recombination from an ancestral clone by a limited number of functionally significant mutations (Tian et al., 2019). (iii) Epigenetic modifications explain clonal adaptation and allow clones to persist …”

“…In particular, these authors concluded that the observed divergent traits in these closely related asexual genotypes evolved without recombination from an ancestral clone by a limited number of functionally significant mutations (Tian et al, 2019).…”

Centennial clonal stability of asexualDaphniain Greenland lakes despite climate variability

“…For example, using 12 microsatellite loci, So et al [61] detected only four MLGs in asexual Daphnia pulex that had invaded Japanese lakes and ponds. Interestingly, these MLGs comprised 21 mitochondrial haplotypes, indicating a higher genotype diversity than that resolved by the microsatellite loci [61], a finding that was later confirmed using whole genome sequencing [62]. In particular, these authors concluded that the observed divergent traits in these closely related asexual genotypes evolved without recombination from an ancestral clone by a limited number of functionally significant mutations [62].…”

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

“…Whole-genome sequencing was performed according to a previous study 60 . Fifty to seventy individuals of each genotype were collected for DNA extraction using a Maxwell (R) 16 instrument (Promega, Madison, WI, USA) and Maxwell (R) 16 LEV Plant DNA Kit (Promega).…”