The goal of this project is to obtain high-quality sequence for the genomes of ~150 isolates of the microcrustacean Daphnia pulex, as well as lower-coverage data for ~5000 additional geographically distributed genotypes for population-genetic analysis. The study species is a major model system employed in the research of a large international consortium of life scientists. As the assayed genotypes will be maintained indefinitely in a clonal fashion, the resultant data set will serve as a permanent resource for the research community. Innovative features of the project include the direct sequencing and assembly of haplotypes via whole-genome amplification of isolated sperm, and the application of maximum-likelihood methods for estimating patterns of within- and among-individual variation and linkage disequilibrium. The availability of direct estimates of the rate and molecular spectra of de novo mutations in all major lineages to be studied provides a level of power for the interpretation of molecular population-genetic data that has not been possible in prior work, e.g., estimation of the power of genetic drift in each study population. In addition to providing a community resource, which will leverage additional work from numerous other labs, the sampling scheme for this survey is designed to generate results bearing on several long-standing problems in evolutionary genetics. First, the study species harbors a large number of permanently asexual lineages, resulting from an unusual system of sex-limited meiosis suppression that promotes the recurrent production of novel asexual clones via backcrossing of males to the sexual species. Analyses of asexual lineages with a range of ages will provide an unprecedented opportunity to evaluate the genome-wide causes and consequences of the loss of recombination, and such analyses are further enhanced by the presence of two chromosomes that never recombine, even via male transmission. Second, D. pulex harbors substantial numbers of novel introns. Collection of hundreds of neo-introns, analysis of their molecular features, and elucidation of their genealogical distributions will set the stage for future functional work on the mechanisms of intron origin, one of the great mysteries in evolutionary genomics. Third, one extensive lineage of D. pulex has undergone a prolonged population bottleneck, and comparison of this to ~50 other populations will cover essentially the full range of effective population sizes known in metazoan species, providing a unique genome- wide analysis of the consequences of variation in the strength of random genetic drift. Finally, as only about half of the genotypes to be sequenced are capable of male production, comparative analyses will provide insight into the mechanisms of sex determination in this system, clarifying the proposed existence of a nonrecombining mating-system chromosome, and evaluating the consequences of such a genetic environment on an otherwise freely recombining genetic background.

Public Health Relevance

The central goal of this project is to develop a population-genomic database for the model invertebrate Daphnia pulex. The study species is the premier sentinel species used in the field of aquatic ecotoxicology, the dominant model for the study of the genotype-environment interaction, and the target of research of a large consortium of investigators in genetics, molecular biology, cell biology, proteomics, and developmental biology. The overall sampling scheme is also designed to yield novel insights into three unsolved problems in evolutionary and population genetics: 1) the genome-wide causes and consequences of the loss of genetic recombination;2) the impact of small population size on genomic integrity;and 3) the mechanisms by which introns become established in protein-coding genes.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Genetic Variation and Evolution Study Section (GVE)
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Eckstrand, Irene A
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Indiana University Bloomington
Schools of Arts and Sciences
United States
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Jiang, Xiaoqian; Tang, Haixu; Mohammed Ismail, Wazim et al. (2018) A Maximum-Likelihood Approach to Estimating the Insertion Frequencies of Transposable Elements from Population Sequencing Data. Mol Biol Evol 35:2560-2571
Long, Hongan; Sung, Way; Kucukyildirim, Sibel et al. (2018) Evolutionary determinants of genome-wide nucleotide composition. Nat Ecol Evol 2:237-240
Ackerman, Matthew S; Johri, Parul; Spitze, Ken et al. (2017) Estimating Seven Coefficients of Pairwise Relatedness Using Population-Genomic Data. Genetics 206:105-118
Lynch, Michael; Gutenkunst, Ryan; Ackerman, Matthew et al. (2017) Population Genomics of Daphnia pulex. Genetics 206:315-332
Jiang, Xiaoqian; Tang, Haixu; Ye, Zhiqiang et al. (2017) Insertion Polymorphisms of Mobile Genetic Elements in Sexual and Asexual Populations of Daphnia pulex. Genome Biol Evol 9:362-374
Maruki, Takahiro; Lynch, Michael (2017) Genotype Calling from Population-Genomic Sequencing Data. G3 (Bethesda) 7:1393-1404
Ye, Zhiqiang; Xu, Sen; Spitze, Ken et al. (2017) A New Reference Genome Assembly for the Microcrustacean Daphnia pulex. G3 (Bethesda) 7:1405-1416
Lynch, Michael; Ackerman, Matthew S; Gout, Jean-Francois et al. (2016) Genetic drift, selection and the evolution of the mutation rate. Nat Rev Genet 17:704-714
Keith, Nathan; Tucker, Abraham E; Jackson, Craig E et al. (2016) High mutational rates of large-scale duplication and deletion in Daphnia pulex. Genome Res 26:60-9
Raborn, R Taylor; Spitze, Ken; Brendel, Volker P et al. (2016) Promoter Architecture and Sex-Specific Gene Expression in Daphnia pulex. Genetics 204:593-612

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