Population Genomics of Daphnia pulex

描述（由申请人提供）： 该项目的目标是获得约150个微甲壳动物蚤状水蚤分离株的基因组的高质量序列，以及约5000个地理分布基因型的低覆盖率数据，用于群体遗传分析。研究物种是一个大型国际生命科学家联盟研究中使用的主要模型系统。由于测定的基因型将以克隆方式无限期地保持，因此所得数据集将作为研究社区的永久资源。该项目的创新特点包括通过分离精子的全基因组扩增直接测序和组装单倍型，以及应用最大似然法估计个体内和个体间变异和连锁不平衡模式。在所有待研究的主要谱系中，对从头突变的速率和分子谱的直接估计的可用性为解释分子群体遗传数据提供了一定水平的能力，这在先前的工作中是不可能的，例如，估计每个研究群体中遗传漂变的能力。 除了提供一个社区资源，这将利用来自许多其他实验室的额外工作，本次调查的抽样方案旨在产生结果，对进化遗传学中的几个长期存在的问题。首先，研究物种窝藏了大量的永久无性系，导致一个不寻常的系统的性别限制减数分裂抑制，促进经常性生产的新无性克隆通过回交的男性有性物种。对不同年龄的无性系进行分析，将为评估基因组范围内重组丢失的原因和后果提供前所未有的机会，而且由于存在两条即使通过雄性传播也不会重组的染色体，这种分析得到了进一步加强。其次，D.蚤状病毒含有大量的新内含子。收集数百个新内含子，分析其分子特征，并阐明其系谱分布将为未来内含子起源机制的功能性工作奠定基础，这是进化基因组学中的一个重大谜团。第三，D.蚤类经历了一个长期的种群瓶颈期，将其与其他约50个种群进行比较，基本上涵盖了后生动物物种已知的有效种群规模的全部范围，为随机遗传漂变强度变异的后果提供了独特的全基因组分析。最后，由于只有大约一半的基因型进行测序的男性生产能力，比较分析将提供深入了解在这个系统中的性别决定的机制，澄清提出的存在一个nonrecombining交配系统染色体，并评估这样一个遗传环境的后果，否则自由重组的遗传背景。

DESCRIPTION (provided by applicant): 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.