Deleterious variation shapes the genomic landscape of introgression.
Deleterious variation shapes the genomic landscape of introgression.
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DOI：
10.1371/journal.pgen.1007741
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发表时间：
2018-10
期刊：
影响因子：
4.5
通讯作者：
Lohmueller KE
中科院分区：
文献类型：
--
作者：
Kim BY;Huber CD;Lohmueller KE
虽然人们认识到种群大小的变化会影响自然种群中有害变异的模式，但人们对基因流动如何影响有害变异以及如何受到有害变异动态的影响的关注较少。在这里，我们使用种群遗传模拟来研究在不同的人口统计情景、交配系统、优势系数和重组率下，基因流如何影响有害变异。我们的结果表明，种群之间的混合可以暂时减少较小种群的遗传负荷，并导致引入祖先的频率增加，特别是如果有害突变是隐性的。此外，当新突变的适合度效应是隐性的时，有害变异存在的位置上的种群间差异在杂交个体中创造了杂种优势。总而言之，这些因素导致了导入祖先的增加，特别是在重组率较低的时候。在某些情况下，即使在没有有益突变的情况下，导入祖先的频率也可以从最初的5%增加到30%-75%，并固定在许多基因座上。此外，有害的变异和混合可以在导入祖先的频率和重组率或外显子密度之间产生相关性，即使在没有其他类型的选择的情况下也是如此。这些相关性的方向取决于特定的人口学特征，以及突变是相加的还是隐性的。因此，在引用其他机制来解释不寻常的遗传变异模式之前，混合的零模型必须同时包括人口统计学和有害变异。来自不同种群的个体有时会产生可生育的后代，并在一种称为杂交的过程中交换遗传物质。杂交个体的基因组通常在整个基因组中显示出非随机的杂交祖先模式，其中一些地区来自第二群体的祖先频率较高，而其他地区的杂交祖先频率较低。通常，这种模式被归因于适应性渗入，即有益的遗传变异从一个种群传递到另一个种群，或者是这些不同物种之间的基因组不亲和性。然而，其他机制可能导致杂交种的这些不同的祖先模式。在这里，我们使用模拟来研究有害的突变是否会影响跨基因组的导入祖先的模式。我们发现，当较大人口的祖先与较小的人口相加时，较大人口的祖先的频率显著增加，因为它携带的有害突变较少。即使在任何一个群体中都没有有益的突变，这种情况也会发生。此外，我们还表明，性染色体进化相对于常染色体的差异，或交配系统的差异，可以以类似的方式影响导入模式。我们的研究认为，有害突变应该包括在群体遗传模型中，用于识别基因组中似乎处于选择之下的不寻常区域。
While it is appreciated that population size changes can impact patterns of deleterious variation in natural populations, less attention has been paid to how gene flow affects and is affected by the dynamics of deleterious variation. Here we use population genetic simulations to examine how gene flow impacts deleterious variation under a variety of demographic scenarios, mating systems, dominance coefficients, and recombination rates. Our results show that admixture between populations can temporarily reduce the genetic load of smaller populations and cause increases in the frequency of introgressed ancestry, especially if deleterious mutations are recessive. Additionally, when fitness effects of new mutations are recessive, between-population differences in the sites at which deleterious variants exist creates heterosis in hybrid individuals. Together, these factors lead to an increase in introgressed ancestry, particularly when recombination rates are low. Under certain scenarios, introgressed ancestry can increase from an initial frequency of 5% to 30–75% and fix at many loci, even in the absence of beneficial mutations. Further, deleterious variation and admixture can generate correlations between the frequency of introgressed ancestry and recombination rate or exon density, even in the absence of other types of selection. The direction of these correlations is determined by the specific demography and whether mutations are additive or recessive. Therefore, it is essential that null models of admixture include both demography and deleterious variation before invoking other mechanisms to explain unusual patterns of genetic variation. Individuals from distinct populations sometimes will produce fertile offspring and will exchange genetic material in a process called hybridization. Genomes of hybrid individuals often show non-random patterns of hybrid ancestry across the genome, where some regions have a high frequency of ancestry from the second population and other regions have less. Typically, this pattern has been attributed to adaptive introgression, where beneficial genetic variants are passed from one population to the other, or to genomic incompatibilities between these distinct species. However, other mechanisms could lead to these heterogeneous patterns of ancestry in hybrids. Here we use simulations to investigate whether deleterious mutations affect the patterns of introgressed ancestry across genomes. We show that when ancestry from a larger population is added to a smaller population, the ancestry from the larger population dramatically increases in frequency because it carries fewer deleterious mutations. This occurs even in the absence of beneficial mutations in either population. Additionally, we show that differences in sex chromosome evolution relative to autosomes, or differences in mating system, can affect patterns of introgression in similar ways. Our study argues that deleterious mutations should be included in population genetic models used to identify unusual regions of the genome that appear to be under selection in hybrids.
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