Genomes of the extinct Bachman’s warbler show high divergence and no evidence of admixture with other extant Vermivora warblers
Genomes of the extinct Bachman’s warbler show high divergence and no evidence of admixture with other extant Vermivora warblers
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DOI：
10.1016/j.cub.2023.05.058
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发表时间：
2023-06
期刊：
影响因子：
9.2
通讯作者：
Andrew W. Wood;Zachary A. Szpiech;I. Lovette;Brian Tilston Smith;D. P. Toews
中科院分区：
文献类型：
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作者：
Andrew W. Wood;Zachary A. Szpiech;I. Lovette;Brian Tilston Smith;D. P. Toews
巴赫曼莺 1（Vermivora bachmanii）——最后一次被发现是在 1988 年——是最近灭绝的北美雀形目鸟类之一。2,3,4考虑到它的两种现存同源——蓝翅莺 (V. cyanoptera) 和金翅莺 (V. chrysoptera)5,6,7,8 正在进行广泛的杂交，并且共享模式由于巴赫曼莺与这些现存物种之间的杂交之间的羽毛变异，有人认为巴赫曼莺可能也具有杂交祖先的成分。在这里，我们使用 20 世纪之交收集的历史 DNA (hDNA) 和巴赫曼莺的整个基因组来解决这个问题。我们将这些数据与两个现存的蠕虫物种结合起来，检查种群分化、近亲繁殖和基因流的模式。与混合假说相反，基因组证据与 V 一致。 bachmanii是一个高度分化、生殖隔离的物种，没有基因渗入的证据。我们表明，这三个物种具有相似的纯合性运行（ROH）水平，与较小的长期有效种群规模或种群瓶颈的影响一致，具有 oneV。 bachmanii 离群值显示大量长 ROH 和 FROH 大于 5%。我们还使用种群分支统计估计发现了先前未记录的 V 谱系特异性进化的证据。 金翅目有一个候选色素基因 CORIN，它是 ASIP 的已知修饰因子，而 ASIP 反过来又参与该鸟类家族的黑喉和面具着色。总之，这些基因组结果还凸显了自然历史收藏品如何成为现存和灭绝物种信息的无价宝库。
Bachman's warbler1(Vermivora bachmanii)—last sighted in 1988—is one of the only North American passerines to recently go extinct.2,3,4Given extensive ongoing hybridization of its two extant congeners—the blue-winged warbler (V. cyanoptera) and golden-winged warbler (V. chrysoptera)5,6,7,8—and shared patterns of plumage variation between Bachman's warbler and hybrids between those extant species, it has been suggested that Bachman's warbler might have also had a component of hybrid ancestry. Here, we use historic DNA (hDNA) and whole genomes of Bachman's warblers collected at the turn of the 20thcentury to address this. We combine these data with the two extantVermivoraspecies to examine patterns of population differentiation, inbreeding, and gene flow. In contrast to the admixture hypothesis, the genomic evidence is consistent withV. bachmaniihaving been a highly divergent, reproductively isolated species, with no evidence of introgression. We show that these three species have similar levels of runs of homozygosity (ROH), consistent with effects of a small long-term effective population size or population bottlenecks, with oneV. bachmaniioutlier showing numerous long ROH and a FROHgreater than 5%. We also found—using population branch statistic estimates—previously undocumented evidence of lineage-specific evolution inV. chrysopteranear a pigmentation gene candidate,CORIN, which is a known modifier ofASIP, which is in turn involved in melanic throat and mask coloration in this family of birds. Together, these genomic results also highlight how natural history collections are such invaluable repositories of information about extant and extinct species.