Deleterious variation shapes the genomic landscape of introgression

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.

尽管学界已认识到种群大小变化可影响自然种群中的有害变异（deleterious variation）模式，但针对基因流（gene flow）如何影响有害变异动态、以及有害变异动态又如何反作用于基因流的研究却相对匮乏。本研究通过群体遗传学模拟（population genetic simulations）方法，系统探究了多种种群历史场景、交配系统、显性系数及重组率条件下，基因流对有害变异的调控作用。结果表明，种群间的遗传混合可暂时降低小型种群的遗传负荷，并提升渐渗血统的频率——尤其当有害突变为隐性时。此外，若新突变的适合度效应呈隐性，种群间有害变异所在位点的差异会使杂种个体产生杂种优势。综合而言，上述因素会推动渐渗血统占比升高，在重组率较低的情境下尤为显著。在部分特定场景中，即便不存在有益突变，初始频率仅为5%的渐渗血统占比可攀升至30%~75%，并在多个遗传位点达到固定状态。进一步研究发现，即便未引入其他类型的选择作用，有害变异与遗传混合也可使渐渗血统频率与重组率或外显子密度之间产生显著相关性。这类相关性的方向由具体的种群历史场景，以及突变是加性还是隐性所共同决定。因此，在引入其他机制以解释异常遗传变异模式前，遗传混合的零模型必须同时纳入种群历史与有害变异这两类核心因素。