Museum genomics reveals the speciation history of Dendrortyx wood-partridges in the Mesoamerican highlands
Museum genomics reveals the speciation history of Dendrortyx wood-partridges in the Mesoamerican highlands
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博物馆基因组学揭示了中美洲高地 Dendrortyx 木鹧鸪的物种形成历史
DOI：
10.1016/j.ympev.2019.03.017
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发表时间：
2019
影响因子：
4.1
通讯作者：
McCormack, John E.
中科院分区：
文献类型：
--
作者：
Tsai, Whitney L.E.;Mota-Vargas, Claudio;Rojas-Soto, Octavio;Bhowmik, Ravi;Liang, Emily Y.;Maley, James M.;Zarza, Eugenia;McCormack, John E.
自然历史收藏品作为基因组资源越来越受到重视。他们的标本反映了数百年来收藏家和策展人的共同努力。对于许多稀有或濒危物种，标本是唯一现成的DNA来源。我们利用从历史收集的标本来研究木鹧鸪属Dendrortyx的进化历史。这三种树蛙分布在墨西哥中部和中美洲的高地，南至哥斯达黎加。其中一个物种濒临灭绝，一般来说，Dendrortyx是秘密的，在组织收集中代表性很差。我们从历史博物馆标本中提取DNA，并对超保守元件（UCEs）和线粒体DNA（mtDNA）进行测序，以评估它们的同源性和分歧时间。由数百到数千个核标记构建的系统发育得到了很好的解决，并且在很大程度上与mtDNA的同源性一致。分歧时间揭示了一个异常古老的鸟类分歧在上新世特万特佩克地峡约360万年前。结合其他最近的研究，我们的研究结果挑战的一般模式，高原鸟类分歧在中美洲是相对年轻的更新世冰川周期的影响相比，爬行动物和植物的老分歧，这被认为是重叠更多的山脉形成的时期。我们还发现了单系遗传谱系的证据，在山脉内的前。大尾类的分类地位有待进一步研究。我们的研究证明了博物馆基因组学的力量，可以深入了解缺乏现代样本的群体的进化历史。
Natural history collections are increasingly valued as genomic resources. Their specimens reflect the combined efforts of collectors and curators over hundreds of years. For many rare or endangered species, specimens are the only readily available source of DNA. We leveraged specimens from a historical collection to study the evolutionary history of wood-partridges in the genusDendrortyx. The threeDendrortyxspecies are found in the highlands of central Mexico and Central America south to Costa Rica. One of these species is endangered, and in general,Dendrortyxare secretive and poorly represented in tissue collections. We extracted DNA from historical museum specimens and sequenced ultraconserved elements (UCEs) and mitochondrial DNA (mtDNA) to assess their phylogeny and divergence times. Phylogenies built from hundreds to thousands of nuclear markers were well resolved and largely congruent with an mtDNA phylogeny. The divergence times revealed an unusually old avian divergence across the Isthmus of Tehuantepec in the Pliocene around 3.6 million years ago. Combined with other recent studies, our results challenge the general pattern that highland bird divergences in Mesoamerica are relatively young and influenced by the Pleistocene glacial cycles compared to the older divergences of reptiles and plants, which are thought to overlap more with periods of mountain formation. We also found evidence for monophyletic genetic lineages in mountain ranges within the widespreadD. macroura, which should be investigated further with integrative taxonomic methods. Our study demonstrates the power of museum genomics to provide insight into the evolutionary histories of groups where modern samples are lacking.