Data from: The genomic consequences of adaptive divergence and reproductive isolation between species of manakins

The processes of adaptation and speciation are expected to shape genomic variation within and between diverging species. Here we analyze genomic heterogeneity of genetic differentiation and introgression in a hybrid zone between two bird species (Manacus candei and M. vitellinus) using 59 100 SNPs, a whole genome assembly, and Bayesian models. Measures of genetic differentiation (inline image) and introgression (genomic cline center [α] and rate [β]) were highly heterogeneous among loci. We identified thousands of loci with elevated parameter estimates, some of which are likely to be associated with variation in fitness in Manacus populations. To analyze the genomic organization of differentiation and introgression, we mapped SNPs onto a draft assembly of the M. vitellinus genome. Estimates of inline image, α, and β were autocorrelated at very short physical distances (< 100 bp), but much less so beyond this. In addition, average statistical associations (linkage disequilibrium) between SNPs were generally low and were not higher in admixed populations than in populations of the parental species. Although they did not occur with a constant probability across the genome, loci with elevated inline image, α, and β were not strongly co-localized in the genome. Contrary to verbal models that predict clustering of loci involved in adaptation and isolation in discrete genomic regions, these results are consistent with the hypothesis that genetic regions involved in adaptive divergence and reproductive isolation are scattered throughout the genome. We also found that many loci were characterized by both exceptional genetic differentiation and introgression, consistent with the hypothesis that loci involved in isolation are also often characterized by a history of divergent selection. However, the concordance between isolation and differentiation was only partial, indicating a complex architecture and history of loci involved in isolation.

适应性演化与物种形成过程，被认为会塑造分化物种内部及彼此间的基因组变异。本研究针对两种鸟类（白须娇鹟*Manacus candei*和黄顶娇鹟*M. vitellinus*）之间的杂交带（hybrid zone），利用59100个单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）、全基因组组装序列（whole genome assembly）以及贝叶斯模型（Bayesian models），分析了遗传分化（genetic differentiation）与基因渐渗（introgression）的基因组异质性。遗传分化的度量指标（[内嵌图像]）与基因渐渗的度量指标（基因组渐变群（genomic cline）中心[α]和速率[β]）在各基因座（locus，复数形式为loci）间呈现高度异质性。我们鉴定出数千个参数估计值升高的基因座，其中部分基因座可能与娇鹟属种群的适合度（fitness）变异相关。为分析分化与渐渗的基因组组织模式，我们将单核苷酸多态性位点定位至黄顶娇鹟的基因组草图组装序列中。[内嵌图像]、α和β的估计值在极短物理距离（<100碱基对，base pair, bp）内存在自相关特征，但超过该距离后自相关性大幅减弱。此外，单核苷酸多态性间的平均统计关联度（即连锁不平衡（Linkage Disequilibrium））整体偏低，且混合种群（admixed populations）中的关联度并未高于亲本物种（parental species）种群。尽管参数估计值升高的基因座在基因组中并非以恒定概率出现，但它们并未在基因组中发生显著共定位。与“适应性演化与生殖隔离（Reproductive Isolation）相关的基因座会聚集于离散基因组区域”的定性模型（verbal models）预测相悖，本研究结果支持“参与适应性分化（adaptive divergence）与生殖隔离的遗传区域散布于整个基因组”的假说。我们还发现，许多基因座同时表现出异常的遗传分化与基因渐渗特征，这与“参与生殖隔离的基因座通常经历过歧化选择（divergent selection）历史”的假说相符。然而，生殖隔离与遗传分化之间的一致性仅为部分性的，这表明参与生殖隔离的基因座具有复杂的遗传架构（genetic architecture）与演化历史。