Population genomics of Daphnia pulex

Michael Lynch, Ryan N Gutenkunst, Matthew Ackerman, Ken Spitze, Zhiqiang Ye, Takahiro Maruki, Zhiyuan Jia

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Using data from 83 isolates from a single population, the population genomics of the microcrustacean Daphnia pulex are described and compared to current knowledge for the only other well-studied invertebrate, Drosophila melanogaster. These 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 (<100 bp) distances in D. melanogaster and at long distances in D. pulex. The 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 >0.05 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 ~ 2× higher level of selection scaled to the power of drift in D. melanogaster, but this may in part be a consequence of recent demographic changes. These results establish D. pulex as an excellent system for future work on the evolutionary genomics of natural populations.

Original languageEnglish (US)
Pages (from-to)315-332
Number of pages18
JournalGenetics
Volume206
Issue number1
DOIs
StatePublished - May 1 2017

Fingerprint

Daphnia
Metagenomics
Drosophila melanogaster
Untranslated Regions
Intergenic DNA
Linkage Disequilibrium
Mutation Rate
Invertebrates
Population Density
Codon
Genetic Recombination
Demography
Population

Keywords

  • Daphnia
  • Genetic variation
  • Linkage disequilibrium
  • Population genomics
  • Population size

ASJC Scopus subject areas

  • Genetics

Cite this

Lynch, M., Gutenkunst, R. N., Ackerman, M., Spitze, K., Ye, Z., Maruki, T., & Jia, Z. (2017). Population genomics of Daphnia pulex. Genetics, 206(1), 315-332. https://doi.org/10.1534/genetics.116.190611

Population genomics of Daphnia pulex. / Lynch, Michael; Gutenkunst, Ryan N; Ackerman, Matthew; Spitze, Ken; Ye, Zhiqiang; Maruki, Takahiro; Jia, Zhiyuan.

In: Genetics, Vol. 206, No. 1, 01.05.2017, p. 315-332.

Research output: Contribution to journalArticle

Lynch, M, Gutenkunst, RN, Ackerman, M, Spitze, K, Ye, Z, Maruki, T & Jia, Z 2017, 'Population genomics of Daphnia pulex', Genetics, vol. 206, no. 1, pp. 315-332. https://doi.org/10.1534/genetics.116.190611
Lynch M, Gutenkunst RN, Ackerman M, Spitze K, Ye Z, Maruki T et al. Population genomics of Daphnia pulex. Genetics. 2017 May 1;206(1):315-332. https://doi.org/10.1534/genetics.116.190611
Lynch, Michael ; Gutenkunst, Ryan N ; Ackerman, Matthew ; Spitze, Ken ; Ye, Zhiqiang ; Maruki, Takahiro ; Jia, Zhiyuan. / Population genomics of Daphnia pulex. In: Genetics. 2017 ; Vol. 206, No. 1. pp. 315-332.
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