Determinants of the Efficacy of Natural Selection on Coding and Noncoding Variability in Two Passerine Species.
Determinants of the Efficacy of Natural Selection on Coding and Noncoding Variability in Two Passerine Species.
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DOI：
10.1093/gbe/evx213
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发表时间：
2017-11-01
影响因子：
3.3
通讯作者：
Zeng K
中科院分区：
文献类型：
--
作者：
Corcoran P;Gossmann TI;Barton HJ;Great Tit HapMap Consortium;Slate J;Zeng K
种群遗传学理论预测，当有效种群规模(Ne)较大时，选择应该更有效，并且选择的效果应该与重组率正相关。在这里，我们分析了十个大山雀和十个斑马雀的基因组。4倍退化位点的核苷酸多样性表明斑马雀的Ne是其2.83倍。我们获得了明确的证据，表明净化选择在斑马雀身上更有效。正向选择(α)固定的0倍退化位点的替换比例在两个物种中都很高(大山雀48%；斑雀%)，斑雀的比例明显高于斑雀。当根据GC保守性变化(即A和T之间以及G和C之间)估计α时，两个物种的估计值都减少了(大山雀22%；斑雀53%)。本文提出的一个理论模型表明，未能控制GC偏向基因转换的影响可能是高估α的一个潜在因素，而且这种影响不能通过首先将人口统计模型与中性变量相匹配来缓解。我们首次在鸟类中对非翻译区域的α进行了估计，并发现了实质性适应性变化的证据。最后，尽管纯化选择在高重组区较强，但我们获得了混合证据，表明α随着重组率的增加而增加，特别是在考虑了GBGC之后。这些结果突出表明，在量化选择时考虑GBGC的潜在混杂效应是很重要的，我们对决定选择有效性的因素的理解是不完整的。
Population genetic theory predicts that selection should be more effective when the effective population size (Ne) is larger, and that the efficacy of selection should correlate positively with recombination rate. Here, we analyzed the genomes of ten great tits and ten zebra finches. Nucleotide diversity at 4-fold degenerate sites indicates that zebra finches have a 2.83-fold larger Ne. We obtained clear evidence that purifying selection is more effective in zebra finches. The proportion of substitutions at 0-fold degenerate sites fixed by positive selection (α) is high in both species (great tit 48%; zebra finch 64%) and is significantly higher in zebra finches. When α was estimated on GC-conservative changes (i.e., between A and T and between G and C), the estimates reduced in both species (great tit 22%; zebra finch 53%). A theoretical model presented herein suggests that failing to control for the effects of GC-biased gene conversion (gBGC) is potentially a contributor to the overestimation of α, and that this effect cannot be alleviated by first fitting a demographic model to neutral variants. We present the first estimates in birds for α in the untranslated regions, and found evidence for substantial adaptive changes. Finally, although purifying selection is stronger in high-recombination regions, we obtained mixed evidence for α increasing with recombination rate, especially after accounting for gBGC. These results highlight that it is important to consider the potential confounding effects of gBGC when quantifying selection and that our understanding of what determines the efficacy of selection is incomplete.
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DOI：
10.1111/evo.12673
发表时间：
2015-06
期刊：
Evolution; international journal of organic evolution
影响因子：
--
作者：
Connallon T;Clark AG
通讯作者：
Clark AG
影响因子：
10.7
作者：
Bolívar P;Mugal CF;Nater A;Ellegren H
通讯作者：
Ellegren H
影响因子：
7
作者：
Backstrom, Niclas;Forstmeier, Wolfgang;Ellegren, Hans
通讯作者：
Ellegren, Hans
影响因子：
7
作者：
Bullaughey, Kevin;Przeworski, Molly;Coop, Graham
通讯作者：
Coop, Graham
影响因子：
10.7
作者：
Castellano, David;Coronado-Zamora, Marta;Eyre-Walker, Adam
通讯作者：
Eyre-Walker, Adam