An extensive candidate gene approach to speciation: diversity, divergence and linkage disequilibrium in candidate pigmentation genes across the European crow hybrid zone
An extensive candidate gene approach to speciation: diversity, divergence and linkage disequilibrium in candidate pigmentation genes across the European crow hybrid zone
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DOI：
10.1038/hdy.2013.68
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发表时间：
2013-07
期刊：
影响因子：
3.8
通讯作者：
J. Poelstra;Hans Ellegren;Jochen B. W. Wolf
中科院分区：
文献类型：
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作者：
J. Poelstra;Hans Ellegren;Jochen B. W. Wolf
颜色模式在适应和物种形成中起着重要作用。欧洲乌鸦系统就是一个突出的例子，在这个系统中，全黑的腐肉乌鸦和灰衣连帽乌鸦在一个狭窄的杂交区相遇。在没有中性遗传差异的情况下，通过分类交配维持显著的表型差异，表明存在少数主要影响色素沉着的基因。我们利用哺乳动物丰富的表型和遗传资源，鉴定了鸟类的95个候选色素沉着基因。基于功能注释，我们从37个最有希望的候选物种中选择了一个子集，并为此开发了一个跨鸟类系统发育的标记系统。在乌鸦种群样本（每个分类单元n= 23）中，我们总共测序了107个扩增子（每个基因约3个位点，总计60kb）。Tajima的D、Fu的F S、DHEW和HKA （Hudson-Kreitman-Aguade）的统计揭示了几个偏离中性的扩增子；然而，这两个分类群之间的分化都没有显著提高。因此，该系统中的颜色分化可能由未表征的色素沉着基因或基因外的调控区域介导。另外，观察到的高群体重组率（4N er ~ 0.03），整体连锁不平衡在大约100 bp的范围内迅速下降，可能会损害用附近标记检测因果位点的能力。我们的结果增加了关于候选基因方法在基因组特征和表型性状的遗传结构方面的效用的争论。
Colouration patterns have an important role in adaptation and speciation. The European crow system, in which all-black carrion crows and grey-coated hooded crows meet in a narrow hybrid zone, is a prominent example. The marked phenotypic difference is maintained by assortative mating in the absence of neutral genetic divergence, suggesting the presence of few pigmentation genes of major effect. We made use of the rich phenotypic and genetic resources in mammals and identified a comprehensive panel of 95 candidate pigmentation genes for birds. Based on functional annotation, we chose a subset of the most promising 37 candidates, for which we developed a marker system that demonstrably works across the avian phylogeny. In total, we sequenced 107 amplicons (∼ 3 loci per gene, totalling 60 kb) in population samples of crows (n= 23 for each taxon). Tajima’s D, Fu’s F S, DHEW and HKA (Hudson–Kreitman–Aguade) statistics revealed several amplicons that deviated from neutrality; however, none of these showed significantly elevated differentiation between the two taxa. Hence, colour divergence in this system may be mediated by uncharacterized pigmentation genes or regulatory regions outside genes. Alternatively, the observed high population recombination rate (4N e r∼ 0.03), with overall linkage disequilibrium dropping rapidly within the order of few 100 bp, may compromise the power to detect causal loci with nearby markers. Our results add to the debate as to the utility of candidate gene approaches in relation to genomic features and the genetic architecture of the phenotypic trait in question.