Pos-Graduação em Ecologia e Evolução da Biodiversidade, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Laboratorio de Sistemática de Vertebrados, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil.
Museo Nacional de Ciencias Naturales (MNCN-CSIC), Spain.
Mol Phylogenet Evol. 2020 Aug;149:106841. doi: 10.1016/j.ympev.2020.106841. Epub 2020 Apr 17.
We present data showing that the number of salamander species in Amazonia is vastly underestimated. We used DNA sequences of up to five genes (3 mitochondrial and 2 nuclear) of 366 specimens, 189 corresponding to 89 non-Amazonian nominal species and 177 Amazonian specimens, including types or topotypes, of eight of the nine recognized species in the region. By including representatives of all known species of Amazonian Bolitoglossa, except for one, and 73% of the currently 132 recognized species of the genus, our dataset represents the broadest sample of Bolitoglossa species, specimens, and geographic localities studied to date. We performed phylogenetic analyses using parsimony with tree-alignment and maximum likelihood (ML) with similarity alignment, with indels as binary characters. Our optimal topologies were used to delimit lineages that we assigned to nominal species and candidate new species following criteria that maximize the consilience of the current species taxonomy, monophyly, gaps in branch lengths, genetic distances, and geographic distribution. We contrasted the results of our species-delimitation protocol with those of Automated Barcode Gap Discovery (ABGD) and multi-rate Poisson Tree Processes (mPTP). Finally, we inferred the historical biogeography of South American salamanders by dating the trees and using dispersal-vicariance analysis (DIVA). Our results revealed a clade including almost all Amazonian salamanders, with a topology incompatible with just the currently recognized nine species. Following our species-delimitation criteria, we identified 44 putative species in Amazonia. Both ABGD and mPTP inferred more species than currently recognized, but their numbers (23-49) and limits vary. Our biogeographic analysis suggested a stepping-stone colonization of the Amazonian lowlands from Central America through the Chocó and the Andes, with several late dispersals from Amazonia back into the Andes. These biogeographic events are temporally concordant with an early land bridge between Central and South America (~10-15 MYA) and major landscape changes in Amazonia during the late Miocene and Pliocene, such as the drainage of the Pebas system, the establishment of the Amazon River, and the major orogeny of the northern Andes.
我们提供的数据表明，亚马逊地区的蝾螈物种数量被严重低估。我们使用了 366 个样本的多达 5 个基因（3 个线粒体和 2 个核基因）的 DNA 序列，其中 189 个对应于 89 个非亚马逊地区的命名物种和 177 个亚马逊地区的样本，包括该地区 9 个公认物种中的 8 个的模式种或原型种。通过包括除一个之外的所有已知亚马逊地区玻利托格洛萨物种的代表，以及目前 132 个该属物种中的 73%，我们的数据集代表了迄今为止研究过的玻利托格洛萨物种、标本和地理区域最广泛的样本。我们使用简约法进行了系统发育分析，包括树对齐和最大似然法（ML），具有相似性对齐，插入缺失作为二进制字符。我们的最优拓扑用于界定我们根据当前物种分类学、单系性、分支长度、遗传距离和地理分布的一致性、最大原则分配给命名物种和候选新物种的谱系。我们将我们的物种界定协议的结果与自动条形码间隙发现（ABGD）和多率泊松树过程（mPTP）的结果进行了对比。最后，我们通过对树木进行测时并使用扩散-分歧分析（DIVA）来推断南美的有尾两栖类动物的历史生物地理学。我们的结果揭示了一个包括几乎所有亚马逊蝾螈的分支，其拓扑结构与目前公认的九个物种不兼容。根据我们的物种界定标准，我们在亚马逊地区确定了 44 个假定物种。ABGD 和 mPTP 都推断出了比目前公认的更多的物种，但它们的数量（23-49）和范围不同。我们的生物地理学分析表明，从中美洲经恰科和安第斯山脉到亚马逊低地的是一个逐步的殖民过程，随后有几次从亚马逊返回安第斯山脉的晚期扩散。这些生物地理学事件与中美洲和南美洲之间早期陆桥（约 10-15 百万年前）以及上新世和更新世期间亚马逊地区的主要景观变化（如佩巴斯系统的排水、亚马逊河的建立以及北安第斯山脉的主要造山运动）时间上是一致的。
