Soft selective sweeps in complex demographic scenarios.
Soft selective sweeps in complex demographic scenarios.
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DOI：
10.1534/genetics.114.165571
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发表时间：
2014-10
期刊：
影响因子：
3.3
通讯作者：
Messer PW
中科院分区：
文献类型：
--
作者：
Wilson BA;Petrov DA;Messer PW
从头突变的适应可以产生所谓的软选择扫描，其中独立突变起源的适应性等位基因同时扫描整个群体。群体遗传理论预测，如果群体规模和适应性等位基因的突变率的乘积足够大，这样在一个达到固定之前就可以建立多个适应性突变，那么这种软扫描应该是可能的；然而，目前尚不清楚人口统计过程如何影响观察到软扫描的概率。在这里，我们将软选择扫描理论扩展到允许人口规模随时间变化的现实人口情景。我们首先表明，种群瓶颈可以导致在最初的软选择扫描中，除了一个适应性谱系外，其他所有谱系都被移除。这种“硬化”软选择扫描的参数可能是由一个简单的启发式条件决定的。我们进一步发展了一个广义的分析框架，基于凝聚过程的扩展，用于计算任意人口情景下软扫描的概率。在这一分析框架中出现了两个重要的限制：在与扫描持续时间相比人口规模波动快的限制中，软扫描的可能性由扫描持续时间内估计的有效人口规模方差的调和平均值决定；在相反的慢波动极限中，软扫描的可能性由扫描开始时的瞬时方差有效种群大小决定。我们表明，作为这一发现的结果，观察到软扫描的概率成为选择强度的函数。具体来说，在种群规模剧烈波动的物种中，强选择比弱选择更有可能产生软扫。我们的研究结果强调了在短进化时间尺度上准确的人口统计估计对于理解从头突变适应的群体遗传学的重要性。
Adaptation from de novo mutation can produce so-called soft selective sweeps, where adaptive alleles of independent mutational origin sweep through the population at the same time. Population genetic theory predicts that such soft sweeps should be likely if the product of the population size and the mutation rate toward the adaptive allele is sufficiently large, such that multiple adaptive mutations can establish before one has reached fixation; however, it remains unclear how demographic processes affect the probability of observing soft sweeps. Here we extend the theory of soft selective sweeps to realistic demographic scenarios that allow for changes in population size over time. We first show that population bottlenecks can lead to the removal of all but one adaptive lineage from an initially soft selective sweep. The parameter regime under which such “hardening” of soft selective sweeps is likely is determined by a simple heuristic condition. We further develop a generalized analytical framework, based on an extension of the coalescent process, for calculating the probability of soft sweeps under arbitrary demographic scenarios. Two important limits emerge within this analytical framework: In the limit where population-size fluctuations are fast compared to the duration of the sweep, the likelihood of soft sweeps is determined by the harmonic mean of the variance effective population size estimated over the duration of the sweep; in the opposing slow fluctuation limit, the likelihood of soft sweeps is determined by the instantaneous variance effective population size at the onset of the sweep. We show that as a consequence of this finding the probability of observing soft sweeps becomes a function of the strength of selection. Specifically, in species with sharply fluctuating population size, strong selection is more likely to produce soft sweeps than weak selection. Our results highlight the importance of accurate demographic estimates over short evolutionary timescales for understanding the population genetics of adaptation from de novo mutation.
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DOI：
10.1073/pnas.0401720101
发表时间：
2004-07-20
影响因子：
11.1
作者：
Innan, H;Kim, Y
通讯作者：
Kim, Y
DOI：
10.1007/978-0-387-78168-6_1
发表时间：
2008-01-01
期刊：
PROBABILITY MODELS FOR DNA SEQUENCE EVOLUTION, SECOND EDITION
影响因子：
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作者：
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通讯作者：
Durrett, Richard
影响因子：
1.5
作者：
Engen, Steinar;Lande, Russell;Saether, Bernt-Erk
通讯作者：
Saether, Bernt-Erk
影响因子：
9.8
作者：
Bersaglieri, T;Sabeti, PC;Hirschhorn, JN
通讯作者：
Hirschhorn, JN
影响因子：
3.7
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Fischer W;Ganusov VV;Giorgi EE;Hraber PT;Keele BF;Leitner T;Han CS;Gleasner CD;Green L;Lo CC;Nag A;Wallstrom TC;Wang S;McMichael AJ;Haynes BF;Hahn BH;Perelson AS;Borrow P;Shaw GM;Bhattacharya T;Korber BT
通讯作者：
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