Genomics of adaptive divergence with chromosome-scale heterogeneity in crossover rate
Genomics of adaptive divergence with chromosome-scale heterogeneity in crossover rate
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DOI：
10.1111/mec.14373
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发表时间：
2017-11-01
影响因子：
4.9
通讯作者：
Roesti, Marius
中科院分区：
文献类型：
--
作者：
Berner, Daniel d;Roesti, Marius
不同种群之间的遗传分化通常在染色体中心比外围更大。通常被忽视的是，这种大范围的分化模式有时被归因于交叉率的异质性，从而导致染色体内的连锁选择，但其潜在的机制仍然不完全清楚。一项涉及46种生物的文献调查显示，大多数真核生物确实表现出染色体中心相对于外围的交叉率降低。通过对现有遗传变异进行分类，模拟种群分化成不同的生态生境，我们证明了这种染色体尺度的交叉率异质性，与多基因发散选择相结合，导致了更强的搭便车，特别是阻碍了基因跨染色体中心的流动。在不需要选择新的突变的情况下，这会迅速导致低交叉中心相对于高交叉外围染色体的种群分化增加(“染色体中心偏向分化”，CCBD)。利用模拟和经验数据，我们证明了种群间较强的CCBD可以提供多基因适应性分化的证据，并伴随着基因流动的阶段。我们进一步论证了交叉率中染色体尺度的异质性对种群分化以外的分析的影响，包括对种群间系统发育和并行适应进化的推断，对选择下的遗传位点的检测，以及对基因组区域选择强度的解释。总体而言，我们的结果呼吁在进化基因组学中更好地理解染色体规模的异质性在交叉率方面的作用。
Genetic differentiation between divergent populations is often greater in chromosome centres than peripheries. Commonly overlooked, this broadscale differentiation pattern is sometimes ascribed to heterogeneity in crossover rate and hence linked selection within chromosomes, but the underlying mechanisms remain incompletely understood. A literature survey across 46 organisms reveals that most eukaryotes indeed exhibit a reduced crossover rate in chromosome centres relative to the peripheries. Using simulations of populations diverging into ecologically different habitats through sorting of standing genetic variation, we demonstrate that such chromosome-scale heterogeneity in crossover rate, combined with polygenic divergent selection, causes stronger hitchhiking and especially barriers to gene flow across chromosome centres. Without requiring selection on new mutations, this rapidly leads to elevated population differentiation in the low-crossover centres relative to the high-crossover peripheries of chromosomes ("Chromosome Centre-Biased Differentiation", CCBD). Using simulated and empirical data, we then show that strong CCBD between populations can provide evidence of polygenic adaptive divergence with a phase of gene flow. We further demonstrate that chromosome-scale heterogeneity in crossover rate impacts analyses beyond that of population differentiation, including the inference of phylogenies and parallel adaptive evolution among populations, the detection of genetic loci under selection, and the interpretation of the strength of selection on genomic regions. Overall, our results call for a greater appreciation of chromosome-scale heterogeneity in crossover rate in evolutionary genomics.