Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.
Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada.
Mol Ecol. 2021 Nov;30(21):5517-5529. doi: 10.1111/mec.16128. Epub 2021 Sep 7.
Geographically connected species pairs with weakly differentiated genomes could either represent cases of genomic homogenization in progress or of incipient parapatric speciation. Discriminating between these processes is difficult because intermediate stages of either may produce weakly differentiated genomes that diverge at few locations. We used coalescent modelling applied to a genome-wide sample of SNPs to discriminate between speciation with gene flow and genomic homogenization in two phenotypically distinct but genomically weakly diverged species of elevationally replacing Ramphocelus tanagers, forming a hybrid zone in the Andean foothills. We found overwhelming support for a model of genomic homogenization following secondary contact. Simulating under this model suggested that our species pair was differentiated (F = 0.30) at secondary contact but that most of the genome has rapidly homogenized during 254 Ky of high gene flow towards the present (F = 0.02). Despite extensive genome-wide homogenization, plumage remains distinctive with a narrower than expected geographic cline width, indicating divergent selection on colour. We found two SNPs significantly associated with plumage colour, which retain moderately high F . We conclude that the majority of the genome has fused, but that divergent selection on select loci probably maintains the geographically structured colour differences between these incipient species.
地理上相互关联的物种对，基因组分化较弱，可能代表基因组同质化进程中的情况，也可能代表准地理物种形成的初期阶段。要区分这两个过程比较困难，因为这两个过程的中间阶段都可能产生基因组分化较弱的情况，这些情况只在少数几个位置发生分歧。我们使用基于全基因组 SNP 样本的合并模型，来区分具有基因流的物种形成和基因组同质化这两个过程，这两个过程分别发生在两个表型明显不同但基因组分化较弱的 Ramphocelus 唐纳雀 Elevationally 取代物种中，它们在安第斯山麓的混合区形成了一个杂交区。我们发现，强烈支持继二次接触之后的基因组同质化模型。在这个模型下进行模拟表明，我们的物种对在二次接触时已经分化（F = 0.30），但在 254 千年来高基因流的作用下，大多数基因组已经迅速同质化到现在（F = 0.02）。尽管基因组广泛同质化，但羽毛仍然具有独特性，其地理渐变宽度比预期的要窄，表明在颜色上存在分歧选择。我们发现了两个与羽毛颜色显著相关的 SNP，它们仍然保持着中等偏高的 F 。我们的结论是，大多数基因组已经融合，但在一些特定的基因座上的分歧选择可能会维持这些处于初期阶段的物种之间具有地理结构的颜色差异。
