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 (&lt; 100 bp), but much less so beyond this. In addition, average statistical associations (linkage disequilibrium) betw...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物种间的基因组变异。本研究借助59100个单核苷酸多态性位点（Single Nucleotide Polymorphism, SNPs）、全基因组组装序列以及贝叶斯模型，对两种娇鹟：白须娇鹟（*Manacus candei*）与黄顶娇鹟（*M. vitellinus*）之间的杂交带的遗传分化与基因渗入的基因组异质性展开分析。遗传分化指标（文中内嵌图像）与基因渗入指标——基因组渐变中心[α]及速率[β]——在各基因位点间呈现高度异质性。我们鉴定出数千个参数估计值升高的位点，其中部分位点极有可能与娇鹟种群的适合度变异相关。为解析分化与基因渗入的基因组组织模式，我们将SNPs比对至黄顶娇鹟（*M. vitellinus*）的基因组草图组装序列。α、β的估计值在极短物理距离内（<100 bp）存在自相关性，但超出该距离后相关性显著减弱。此外，平均统计关联（连锁不平衡）在……