Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543; Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; Museum of Comparative Zoology, 26 Oxford Street, Cambridge, MA 02138, USA; and Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA.
Syst Biol. 2014 Mar;63(2):134-52. doi: 10.1093/sysbio/syt070. Epub 2013 Dec 4.
Genetic introgression is pervasive in nature and may lead to large-scale phenotypic assimilation and/or admixture of populations, but there is limited knowledge on whether large phenotypic changes are typically accompanied by high levels of introgression throughout the genome. Using bioacoustic, biometric, and spectrophotometric data from a flycatcher (Tyrannidae) system in the Neotropical genus Zimmerius, we document a mosaic pattern of phenotypic admixture in which a population of Zimmerius viridiflavus in northern Peru (henceforth "mosaic") is vocally and biometrically similar to conspecifics to the south but shares plumage characteristics with a different species (Zimmerius chrysops) to the north. To clarify the origins of the mosaic population, we used the RAD-seq approach to generate a data set of 37,361 genome-wide single nucleotide polymorphisms (SNPs). A range of population-genetic diagnostics shows that the genome of the mosaic population is largely indistinguishable from southern Z. viridiflavus and distinct from northern Z. chrysops, and the application of parsimony and species tree methods to the genome-wide SNP data set confirms the close affinity of the mosaic population with southern Z. viridiflavus. Even so, using a subset of 2710 SNPs found across all sampled lineages in configurations appropriate for a recently proposed statistical ("ABBA/BABA") test that distinguishes gene flow from incomplete lineage sorting, we detected low levels of gene flow from northern Z. chrysops into the mosaic population. Mapping the candidate loci for introgression from Z. chrysops into the mosaic population to the zebra finch genome reveals close linkage with genes significantly enriched in functions involving cell projection and plasma membranes. Introgression of key alleles may have led to phenotypic assimilation in the plumage of mosaic birds, suggesting that selection may have been a key factor facilitating introgression.
遗传渗入在自然界中普遍存在，可能导致大规模的表型同化和/或群体混合，但对于大型表型变化是否通常伴随着整个基因组中高水平的渗入，知之甚少。利用新热带 Zimmerius 属的一种食虫鸟（Tyrannidae）系统的生物声学、生物计量和分光光度数据，我们记录了一种表型混合的镶嵌模式，秘鲁北部的 Zimmerius viridiflavus 种群（以下简称“镶嵌”）在声音和生物计量上与南部的同物种相似，但与北部的不同物种（Zimmerius chrysops）具有羽毛特征。为了阐明镶嵌种群的起源，我们使用 RAD-seq 方法生成了一个包含 37361 个全基因组单核苷酸多态性（SNP）的数据集。一系列群体遗传学诊断表明，镶嵌种群的基因组在很大程度上与南部的 Z. viridiflavus 无法区分，与北部的 Z. chrysops 明显不同，简约法和种系发生树方法在全基因组 SNP 数据集上的应用也证实了镶嵌种群与南部的 Z. viridiflavus 密切相关。即便如此，使用在所有采样谱系中发现的 2710 个 SNP 的子集，以适合最近提出的一种用于区分基因流和不完全谱系分选的统计（“ABBA/BABA”）测试的配置，我们检测到来自北部 Z. chrysops 的低水平基因流入镶嵌种群。将 Z. chrysops 向镶嵌种群的基因渗入候选基因座映射到斑胸草雀基因组上，发现与细胞突起和质膜相关的功能显著富集的基因紧密连锁。关键等位基因的渗入可能导致了镶嵌鸟类羽毛的表型同化，这表明选择可能是促进基因渗入的关键因素。
