Data from: Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k SNP array

With the access to draft genome sequence assemblies and whole-genome re-sequencing data from population samples, molecular ecology studies will be able to take truly genome-wide approaches. This now applies to an avian model system in ecological and evolutionary research: Old World flycatchers of the genus Ficedula, for which we recently obtained a 1.1 Gb collared flycatcher genome assembly and identified 13 million SNPs in population re-sequencing of this species and its sister species, pied flycatcher. Here we developed a custom 50K Illumina iSelect flycatcher SNP array with markers covering 30 autosomes and the Z chromosome. By using a number of selection criteria for inclusion in the array, both genotyping success rate and polymorphism information content (mean marker heterozygosity = 0.41) were high. We used the array to assess linkage disequilibrium (LD) and hybridization in flycatchers. LD declined quickly to the background level at an average distance of 17 kb but the extent of LD varied markedly within the genome and was more than 10-fold higher in ‘genomic islands’ of differentiation than in the rest of the genome. Genetic ancestry analysis identified 33 F1 hybrids but no later-generation hybrids from sympatric populations of collared flycatchers and pied flycatchers, contradicting earlier reports of backcrosses identified from much fewer number of markers. With an estimated divergence time as recently as <1 million years ago, this suggests strong selection against F1 hybrids and unusually rapid evolution of reproductive incompatibility in an avian system.

随着种群样本的草图基因组序列组装体与全基因组重测序数据的获取，分子生态学研究得以采用真正意义上的全基因组研究范式。这一范式如今可应用于生态与进化研究中的鸟类模式系统——姬鹟属（*Ficedula*）旧大陆鹟类。我们近期已为该属的斑颈姬鹟（collared flycatcher）构建了1.1 Gb的基因组组装体，并在该物种及其近缘物种斑姬鹟（pied flycatcher）的种群重测序中鉴定出1300万个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点。
本研究定制开发了一款50K因美纳（Illumina）iSelect鹟类SNP分型芯片，其标记位点覆盖30条常染色体及Z染色体。通过一系列芯片标记筛选标准，该芯片的分型成功率与多态性信息含量（平均标记杂合度=0.41）均处于较高水平。
本研究利用该芯片对鹟类的连锁不平衡（Linkage Disequilibrium, LD）与杂交现象进行评估。结果显示，连锁不平衡程度在平均间隔17 kb时快速衰减至背景水平，但基因组内的连锁不平衡程度存在显著差异：分化“基因组岛”区域的连锁不平衡程度较基因组其余区域高出10倍以上。
遗传祖先成分分析显示，在斑颈姬鹟与斑姬鹟的同域种群中，共鉴定出33例F1代杂交个体，但未发现后续世代的杂交个体，这与此前基于少量标记鉴定出回交个体的研究报道相矛盾。据估算，两个物种的分化时间距今不足100万年，这表明该鸟类系统中存在对F1代杂交个体的强烈选择，且生殖不相容性的演化速度异乎寻常地快。