Dataset Information

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.

SUBMITTER: Haag CR

PROVIDER: S-EPMC2674827 | biostudies-literature | 2009 May

REPOSITORIES: biostudies-literature

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Publications

Nucleotide polymorphism and within-gene recombination in Daphnia magna and D. pulex, two cyclical parthenogens.

Haag Christoph R CR McTaggart Seanna J SJ Didier Anaïs A Little Tom J TJ Charlesworth Deborah D

Genetics 20090318 1

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 ...[more]

PMID: 19299338

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Project description:Transposable elements (TEs) represent a major portion of most eukaryotic genomes, yet little is known about their mutation rates or how their activity is shaped by other evolutionary forces. Here, we compare short- and long-term patterns of genome-wide mutation accumulation (MA) of TEs among 9 genotypes from three populations of Daphnia magna from across a latitudinal gradient. While the overall proportion of the genome comprised of TEs is highly similar among genotypes from Finland, Germany, and Israel, populations are distinguishable based on patterns of insertion site polymorphism. Our direct rate estimates indicate TE movement is highly variable (net rates ranging from -11.98 to 12.79 x 10−5 per copy per generation among genotypes), differing both among populations and TE families. Although gains outnumber losses when selection is minimized, both types of events appear to be highly deleterious based on their low frequency in control lines where propagation is not limited to random, single-progeny descent. With rate estimates 4 orders of magnitude higher than base substitutions, TEs clearly represent a highly mutagenic force in the genome. Quantifying patterns of intra- and interspecific variation in TE mobility with and without selection provides insight into a powerful mechanism generating genetic variation in the genome. Author summary Transposable elements (TEs) are a significant portion of most eukaryotic genomes, yet our understanding of their rates of mobility and their patterns of accumulation remain very limited. Here, we estimate genome-wide rates of gain and loss of TEs in Daphnia magna, a well-studied model organism in ecology, and compare these rates of mutation to the long-term accumulation of TEs in the genome. Rates vary remarkably among genotypes and populations, and between different types of TEs within the same lineage. Despite this variation, over long time periods, TE content in the genome is extremely similar across genotypes within the species. We compare our results to the few estimates available from other taxa, and argue that TEs are an important source of mutagenesis in the genome worthy of further investigation.

Dataset Information

Nucleotide polymorphism and within-gene recombination in Daphnia magna and D. pulex, two cyclical parthenogens.

Publications

Nucleotide polymorphism and within-gene recombination in Daphnia magna and D. pulex, two cyclical parthenogens.

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