Spatial structure alters the site frequency spectrum produced by hitchhiking
Spatial structure alters the site frequency spectrum produced by hitchhiking
复制标题
空间结构改变了搭便车产生的场地频谱
DOI：
10.1093/genetics/iyac139
复制
发表时间：
2022
期刊：
影响因子：
3.3
通讯作者：
Novembre, ed., J.
中科院分区：
文献类型：
--
作者：
Min, Jiseon;Gupta, Misha;Desai, Michael M.;Weissman, Daniel B.;Novembre, ed., J.
由于遗传搭便车而导致的遗传多样性的减少被广泛用于从测序数据中发现过去的选择性扫描，但对空间结构如何影响搭便车知之甚少。我们使用数学建模和模拟，以找到未折叠的网站频谱留下的搭便车在基因组区域的扫描人口占据一个一维范围。对于这些人群，扫描以费舍尔波的形式传播，而不是逻辑上的。我们发现，这留下了一个特征的3部分网站频谱在轨迹非常接近的扫描轨迹。极低的频率主要是由最近发生的突变后，扫描和不受搭便车。在适度低的频率下，有一个过渡区，主要由等位基因组成，这些等位基因在离开波前之前短暂地在扫描波上“冲浪”，留下的光谱接近于在混合良好的人群中预期的光谱。然而，对于中高频，有一个独特的缩放制度的网站频谱产生的等位基因漂移到固定在波前，然后进行整个人口。对于稍微远离基因组上被扫过的基因座的基因座，重组在恢复1D种群的多样性方面比在混合良好的种群中有效得多。我们发现，这些签名的空间可以很强，即使在明显的混合人口与可忽略不计的空间遗传分化，这表明空间结构可能经常扭曲自然种群中的搭车签名。
The reduction of genetic diversity due to genetic hitchhiking is widely used to find past selective sweeps from sequencing data, but very little is known about how spatial structure affects hitchhiking. We use mathematical modeling and simulations to find the unfolded site frequency spectrum left by hitchhiking in the genomic region of a sweep in a population occupying a 1D range. For such populations, sweeps spread as Fisher waves, rather than logistically. We find that this leaves a characteristic 3-part site frequency spectrum at loci very close to the swept locus. Very low frequencies are dominated by recent mutations that occurred after the sweep and are unaffected by hitchhiking. At moderately low frequencies, there is a transition zone primarily composed of alleles that briefly “surfed” on the wave of the sweep before falling out of the wavefront, leaving a spectrum close to that expected in well-mixed populations. However, for moderate-to-high frequencies, there is a distinctive scaling regime of the site frequency spectrum produced by alleles that drifted to fixation in the wavefront and then were carried throughout the population. For loci slightly farther away from the swept locus on the genome, recombination is much more effective at restoring diversity in 1D populations than it is in well-mixed ones. We find that these signatures of space can be strong even in apparently well-mixed populations with negligible spatial genetic differentiation, suggesting that spatial structure may frequently distort the signatures of hitchhiking in natural populations.
登录
查看更多内容
全球适应使对局部适应的基因组扫描的解释变得复杂。
影响因子：
5
作者：
Booker TR;Yeaman S;Whitlock MC
通讯作者：
Whitlock MC
影响因子：
16.6
作者：
Fusco D;Gralka M;Kayser J;Anderson A;Hallatschek O
通讯作者：
Hallatschek O
DOI：
--
发表时间：
1971
期刊：
Genetical research
影响因子：
--
作者：
T. Maruyama
通讯作者：
T. Maruyama
细分人群中的遗传搭便车。
DOI：
10.1017/s001667239800319x
发表时间：
1998
期刊：
Genetical research
影响因子：
--
作者：
Slatkin,M;Wiehe,T
通讯作者：
Wiehe,T
影响因子：
2.4
作者：
Brunet, E;Derrida, B
通讯作者：
Derrida, B