Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis.
Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis.
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DOI：
10.1101/gr.187237.114
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发表时间：
2015-05
期刊：
影响因子：
7
通讯作者：
Cutter AD
中科院分区：
文献类型：
--
作者：
Thomas CG;Wang W;Jovelin R;Ghosh R;Lomasko T;Trinh Q;Kruglyak L;Stein LD;Cutter AD
秀丽隐杆线虫是与秀丽隐杆线虫比较发育进化的模型。在世界范围内收集的C. briggsae暗示了由纬度或受限制的地理位置分开的遗传群体之间的有趣的分歧历史，这正在被用来剖析适应性进化和生殖不相容的遗传基础；然而，种群分化的基因组范围和时间尚不清楚。研究人员对37株秀丽隐杆线虫野生分离株进行了高覆盖全基因组测序，并对703个基因组单倍型组合采用两两序列马尔可夫聚结（PSMC）模型，推断种群历史、自然选择的基因组范围，并与40株秀丽隐杆线虫野生分离株进行了比较。我们估计，至少有6个不同的C. briggsae谱系在大约20万代以前彼此分离，包括“温带”和“热带”系统地理群，它们在全世界大多数样本中占主导地位。此外，一个大约200万代以前的古代种群在其历史上分裂，加上谱系群体之间只有罕见的基因流动，证实了这个系统是早期物种形成的模型。基因组的低重组区和高重组区给出了种群规模随时间变化的明显特征，表明由于自交受精的极端近亲繁殖，选择对高度相关的基因组部分产生了广泛影响。功能突变的分析表明，由于选择作用于长连锁块，基因组环境是比单个编码基因的功能属性更重要的种群变异驱动因素。
The nematode Caenorhabditis briggsae is a model for comparative developmental evolution with C. elegans. Worldwide collections of C. briggsae have implicated an intriguing history of divergence among genetic groups separated by latitude, or by restricted geography, that is being exploited to dissect the genetic basis to adaptive evolution and reproductive incompatibility; yet, the genomic scope and timing of population divergence is unclear. We performed high-coverage whole-genome sequencing of 37 wild isolates of the nematode C. briggsae and applied a pairwise sequentially Markovian coalescent (PSMC) model to 703 combinations of genomic haplotypes to draw inferences about population history, the genomic scope of natural selection, and to compare with 40 wild isolates of C. elegans. We estimate that a diaspora of at least six distinct C. briggsae lineages separated from one another approximately 200,000 generations ago, including the “Temperate” and “Tropical” phylogeographic groups that dominate most samples worldwide. Moreover, an ancient population split in its history approximately 2 million generations ago, coupled with only rare gene flow among lineage groups, validates this system as a model for incipient speciation. Low versus high recombination regions of the genome give distinct signatures of population size change through time, indicative of widespread effects of selection on highly linked portions of the genome owing to extreme inbreeding by self-fertilization. Analysis of functional mutations indicates that genomic context, owing to selection that acts on long linkage blocks, is a more important driver of population variation than are the functional attributes of the individually encoded genes.
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影响因子：
30.8
作者：
Andersen, Erik C.;Gerke, Justin P.;Shapiro, Joshua A.;Crissman, Jonathan R.;Ghosh, Rajarshi;Bloom, Joshua S.;Felix, Marie-Anne;Kruglyak, Leonid
通讯作者：
Kruglyak, Leonid
影响因子：
4.5
作者：
Brandvain Y;Slotte T;Hazzouri KM;Wright SI;Coop G
通讯作者：
Coop G
影响因子：
10.7
作者：
Charlesworth, B
通讯作者：
Charlesworth, B
影响因子：
3.4
作者：
Baird, SE;Davidson, CR;Bohrer, JC
通讯作者：
Bohrer, JC
影响因子：
4.9
作者：
Cutter, Asher D.;Yan, Weiang;Felix, Marie-Anne
通讯作者：
Felix, Marie-Anne