Department of Ecology & Evolution, University of Chicago, USA.
Genome Biol Evol. 2013;5(6):1233-45. doi: 10.1093/gbe/evt090.
Hybrid speciation appears to be rare in animals, yet characterization of possible examples offers to shed light on the genomic consequences of this unique phenomenon, as well as more general processes such as the role of adaptation in speciation. Here, we first generate transcriptome assemblies for a putative hybrid butterfly species, Papilio appalachiensis, its parental species, P. glaucus and P. canadensis, and an outgroup, P. polytes. Then, we use these data to infer genome-wide patterns of introgression and genomic mosaicism using both phylogenetic and population genetic approaches. Our results reveal that there is little genetic divergence among all three of the focal species, but the subset of gene trees that strongly support a specific tree topology suggest widespread sharing of genetic variation between P. appalachiensis and both parental species, likely as a result of hybrid speciation. We also find evidence for substantial shared genetic variation between P. glaucus and P. canadensis, which may be due to gene flow or ancestral variation. Consistent with previous work, we show that P. applachiensis is more similar to P. canadensis at Z-linked genes and more similar to P. glaucus at mitochondrial genes. We also identify a variety of targets of adaptive evolution, which appear to be enriched for traits that are likely to be important in the evolution of this butterfly system, such as pigmentation, hormone sensitivity, developmental processes, and cuticle formation. Overall, our results provide a genome-wide portrait of divergence and introgression associated with adaptation and speciation in an iconic butterfly radiation.
杂种形成似乎在动物中较为罕见，但对可能的例子进行特征描述，有助于揭示这一独特现象的基因组后果，以及更普遍的过程，如适应在物种形成中的作用。在这里，我们首先为一个假定的杂种蝴蝶物种——Papilio appalachiensis，其亲本物种 P. glaucus 和 P. canadensis，以及一个外群 P. polytes 生成转录组组装。然后，我们使用这些数据通过系统发育和群体遗传学方法推断全基因组的基因渗入和基因组镶嵌模式。我们的结果表明，所有三个焦点物种之间的遗传分化很小，但强烈支持特定树拓扑的基因树子集表明，P. appalachiensis 与两个亲本物种之间广泛共享遗传变异，这可能是杂种形成的结果。我们还发现 P. glaucus 和 P. canadensis 之间存在大量共享的遗传变异，这可能是由于基因流或祖先变异。与之前的工作一致，我们表明 P. applachiensis 在 Z 连锁基因上与 P. canadensis 更为相似，而在线粒体基因上与 P. glaucus 更为相似。我们还鉴定出了多种适应进化的靶点，这些靶点似乎富集了在这个蝴蝶系统进化中很重要的特征，如色素沉着、激素敏感性、发育过程和表皮形成。总的来说，我们的研究结果提供了一个标志性蝴蝶辐射中与适应和物种形成相关的分歧和基因渗入的全基因组图谱。
