Selection at linked sites in the partial selfer Caenorhabditis elegans
Selection at linked sites in the partial selfer Caenorhabditis elegans
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DOI：
10.1093/molbev/msg072
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发表时间：
2003-05-01
影响因子：
10.7
通讯作者：
Payseur, BA
中科院分区：
文献类型：
--
作者：
Cutter, AD;Payseur, BA
自然选择可以产生局部重组率和中性DNA多态性水平之间的相关性，作为遗传搭便车和背景选择的结果。理论表明，在连锁位点的选择应该影响模式的中性变化在部分销售人口更显着比在异交人口。然而，在连锁网站的选择经验调查主要集中在异交物种。为了评估选择作为中性多态性的决定因素在部分自受精的背景下的潜在作用，我们进行了多变量分析的单核苷酸多态性（SNP）密度在整个基因组的线虫秀丽隐杆线虫。我们基于已发表的SNP数据集进行分析，并将基因组划分为窗口，以计算所有六条染色体上的SNP密度、重组率和基因密度。我们的分析发现，C基因组中的重组率和中性多态性（通过非编码SNP密度估计）之间存在强正相关性。优雅的此外，我们发现在一些分析中，中性多态性的水平在基因密集区比在基因贫乏区低。分析结合当地估计的分歧之间的C。elegans和C. Briggsae指出，单独的突变解释不太可能解释观察到的模式。因此，我们将这些发现解释为自然选择塑造C.优美的我们的研究首次证明了部分自交动物的这种效应。遗传搭便车和背景选择的显式模型都可以充分描述重组率和SNP密度之间的关系，但只有当它们包含自交率时。阐明了遗传搭便车和背景选择在C.秀丽隐杆线虫等待着具体的理论预测的发展，以解释部分自花受精和有偏见的性别比例。
Natural selection can produce a correlation between local recombination rates and levels of neutral DNA polymorphism as a consequence of genetic hitchhiking and background selection. Theory suggests that selection at linked sites should affect patterns of neutral variation in partially selling populations more dramatically than in outcrossing populations. However, empirical investigations of selection at linked sites have focused primarily on outcrossing species. To assess the potential role of selection as a determinant of neutral polymorphism in the context of partial self-fertilization, we conducted a multivariate analysis of single-nucleotide polymorphism (SNP) density throughout the genome of the nematode Caenorhabditis elegans. We based the analysis on a published SNP data set and partitioned the genome into windows to calculate SNP densities, recombination rates, and gene densities across all six chromosomes. Our analyses identify a strong, positive correlation between recombination rate and neutral polymorphism (as estimated by noncoding SNP density) across the genome of C. elegans. Furthermore, we find that levels of neutral polymorphism are lower in gene-dense regions than in gene-poor regions in some analyses. Analyses incorporating local estimates of divergence between C. elegans and C. briggsae indicate that a mutational explanation alone is unlikely to explain the observed patterns. Consequently, we interpret these findings as evidence that natural selection shapes genome-wide patterns of neutral polymorphism in C. elegans. Our study provides the first demonstration of such an effect in a partially selfing animal. Explicit models of genetic hitchhiking and background selection can each adequately describe the relationship between recombination rate and SNP density, but only when they incorporate selfing rate. Clarification of the relative roles of genetic hitchhiking and background selection in C. elegans awaits the development of specific theoretical predictions that account for partial self-fertilization and biased sex ratios.