Nucleotide Polymorphism and Within-Gene Recombination in Daphnia magna and D. pulex, Two Cyclical Parthenogens

Abstract

Theory predicts that partially asexual organisms may make the ''best of both worlds'': for the most part, they avoid the costs of sexual reproduction, while still benefiting from an enhanced efficiency of selection compared to obligately asexual organisms. There is, however, little empirical data on partially asexual organisms to test this prediction. Here we examine patterns of nucleotide diversity at eight nuclear loci in continentwide samples of two species of cyclically parthenogenetic Daphnia to assess the effect of partial asexual reproduction on effective population size and amount of recombination. Both species have high nucleotide diversities and show abundant evidence for recombination, yielding large estimates of effective population sizes (300,000-600,000). This suggests that selection will act efficiently even on mutations with small selection coefficients. Divergence between the two species is less than one-tenth of previous estimates, which were derived using a mitochondrial molecular clock. As the two species investigated are among the most distantly related species of the genus, this suggests that the genus Daphnia may be considerably younger than previously thought. Daphnia has recently received increased attention because it is being developed as a model organism for ecological and evolutionary genomics. Our results confirm the attractiveness of Daphnia as a model organism, because the high nucleotide diversity and low linkage disequilibrium suggest that fine-scale mapping of genes affecting phenotypes through association studies should be feasible.

Population Genetics of Duplicated Alternatively Spliced Exons of the Dscam Gene in Daphnia and Drosophila

“…magna , array 4 has low nucleotide diversity (π) both at non-synonymous and at synonymous sites, whereas array 6 and exon 10 have moderate levels of synonymous diversity (π s ) (Table 3), similar to the average values estimated for eight housekeeping Da. magna genes in another study [34], and higher than in a sample of putative immunity genes in this species [35]. In contrast, non-synonymous diversity (π a ) in array 6 and exon 10 is about ten times higher than in other Da.…”

Mitochondrial Capture Misleads about Ecological Speciation in the Daphnia pulex Complex

“…The gene trees corresponded to the same sample size as our ND5 dataset, with the same number of gene copies sampled from each of the four species (Table 3). The estimated divergence times of the species tree were converted to the number of generations assuming a mutation rate of 10 -9 per site per generation [52], and the simulation was repeated for a range of the effective population sizes, N e , for the individual species (equal for all species), equivalent to 100 000, 500 000, 1 000 000 and 1 500 000, which encompassed the empirical estimates [10,53]. To determine if the observed mtDNA gene tree, with NAPC haplotypes in a clade with NAPX haplotypes, could have been generated under the estimated species tree, we recorded the percentage of the gene trees simulated for a given N e that had NAPC and NAPX genes as a clade.…”

The first-generation Daphnia magna linkage map

“…The divergence between D. pulex and D. magna had been estimated from mtDNA sequences to be about 200 MYA [10]. However, recent estimates of divergence time between these species, measured using nuclear genes, is reduced to 7.6 - 15.6 MYA depending on parameters [11]. …”