title: Population Genomics ofDaphnia pulex.
abstract: Using data from 83 isolates from a single population, the population genomics of the microcrustaceanDaphnia pulexare described and compared to current knowledge for the only other well-studied invertebrate,Drosophila melanogasterThese two species are quite similar with respect to effective population sizes and mutation rates, although some features of recombination appear to be different, with linkage disequilibrium being elevated at short ([Formula: see text] bp) distances inD. melanogasterand at long distances inD. pulexThe study population adheres closely to the expectations under Hardy-Weinberg equilibrium, and reflects a past population history of no more than a twofold range of variation in effective population size. Fourfold redundant silent sites and a restricted region of intronic sites appear to evolve in a nearly neutral fashion, providing a powerful tool for population genetic analyses. Amino acid replacement sites are predominantly under strong purifying selection, as are a large fraction of sites in UTRs and intergenic regions, but the majority of SNPs at such sites that rise to frequencies [Formula: see text] appear to evolve in a nearly neutral fashion. All forms of genomic sites (including replacement sites within codons, and intergenic and UTR regions) appear to be experiencing an [Formula: see text] higher level of selection scaled to the power of drift inD. melanogaster, but this may in part be a consequence of recent demographic changes. These results establishD. pulexas an excellent system for future work on the evolutionary genomics of natural populations.
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405 milynch@indiana.edu.
authors.forename: Michael
authors.initials: M
authors.lastname: Lynch
authors.affiliation: Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721.
authors.forename: Ryan
authors.initials: R
authors.lastname: Gutenkunst
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405.
authors.forename: Matthew
authors.initials: M
authors.lastname: Ackerman
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405.
authors.forename: Ken
authors.initials: K
authors.lastname: Spitze
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405.
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Ye
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405.
authors.forename: Takahiro
authors.initials: T
authors.lastname: Maruki
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47405.
authors.forename: Zhiyuan
authors.initials: Z
authors.lastname: Jia
mesh_terms: D000818:Animals; D003621:Daphnia / Q000235:genetics*; D004331:Drosophila melanogaster / Q000235:genetics*; D019143:Evolution, Molecular; D005828:Genetics, Population; D016678:Genome; D023281:Genomics; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide
keywords: Daphnia; genetic variation; linkage disequilibrium; population genomics; population size