Vastly underestimated species richness of Amazonian salamanders (Plethodontidae: Bolitoglossa) and implications about plethodontid diversification.,Molecular Phylogenetics and Evolution

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Vastly underestimated species richness of Amazonian salamanders (Plethodontidae: Bolitoglossa) and implications about plethodontid diversification.
Molecular Phylogenetics and Evolution ( IF 3.6 ) Pub Date : 2020-04-17 , DOI: 10.1016/j.ympev.2020.106841
Andrés F Jaramillo ₁ , Ignacio De La Riva ₂ , Juan M Guayasamin ₃ , Juan C Chaparro ₄ , Giussepe Gagliardi-Urrutia ₅ , Roberto C Gutiérrez ₆ , Isabela Brcko ₇ , Carles Vilà ₈ , Santiago Castroviejo-Fisher ₉

Affiliation

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.
Laboratorio de Biología Evolutiva, Instituto BIOSFERA-USFQ, Colegio de Ciencias Biológicas y Ambientales COCIBA, Universidad San Francisco de Quito (USFQ), Ecuador; University of North Carolina at Chapel Hill, Department of Biology, USA.
Museo de Biodiversidad del Perú (MUBI), Peru; Museo de Historia Natural de la Universidad Nacional de San Antonio Abad del Cusco, Peru.
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; Peruvian Center for Biodiversity and Conservation (PCB&C), Peru; Dirección de Investigación en Diversidad Biológica Terrestre Amazónica, Instituto de Investigaciones de la Amazonía Peruana (IIAP), Peru.
Museo de Historia Natural de la Universidad Nacional de San Agustín de Arequipa (MUSA), Peru.
Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Brazil.
Estación Biológica de Doñana (EBD-CSIC), Spain.
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; Department of Herpetology, American Museum of Natural History, USA.

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.

中文翻译：

大大低估了亚马逊sal的物种丰富度（Plethodontidae：Bolitoglossa）及其对正齿动物多样性的影响。

我们提供的数据表明，亚马逊地区of的数量被大大低估了。我们使用了366个样本中多达5个基因（3个线粒体和2个核）的DNA序列，其中189个对应于该地区9个公认物种中的8个的89个非亚马孙标称物种和177个亚马孙标本，包括类型或拓扑类型。通过包括除132种当前认可的物种中的一种和73％以外的所有Amazon Bolitoglossa已知物种的代表，我们的数据集代表了迄今为止研究的Bolitoglossa物种，标本和地理区域的最广泛样本。我们使用简约与树对齐和最大似然（ML）与相似性对齐（插入缺失作为二进制字符）进行了系统发育分析。我们的最佳拓扑用于按照最大程度地划分当前物种分类，单性，分支长度的差距，遗传距离和地理分布的一致性的标准来划定我们分配给标称物种和候选新物种的谱系。我们将物种定界协议的结果与自动条形码差距发现（ABGD）和多速率泊松树过程（mPTP）的结果进行了对比。最后，我们通过对树木定日期并使用扩散-变异分析（DIVA）来推断南美sal的历史生物地理。我们的研究结果揭示了一个进化支，包括几乎所有的亚马逊sal，其拓扑仅与目前公认的9种不兼容。按照我们的物种划分标准，我们在亚马孙地区确定了44种推定物种。ABGD和mPTP都推断出比目前公认的物种更多的物种，但它们的数量（23-49）和限制有所不同。我们的生物地理分析表明，从中美洲通过乔科（Chocó）和安第斯山脉（Andes）对亚马孙低地进行了垫脚石定殖，随后又有几处从亚马孙（Amazonia）散布回安第斯山脉。这些生物地理事件在时间上与中美洲和南美洲之间的早期陆桥（约10-15 MYA）以及中新世和上新世晚期亚马逊河地区的主要景观变化相一致，例如Pebas系统的排水，亚马逊河的建立。河流和安第斯山脉北部的主要造山运动。我们的生物地理分析表明，从中美洲通过乔科（Chocó）和安第斯山脉（Andes）对亚马孙低地进行了垫脚石定殖，随后又有几处从亚马孙（Amazonia）散布回安第斯山脉。这些生物地理事件在时间上与中美洲和南美洲之间的早期陆桥（约10-15 MYA）以及中新世和上新世晚期亚马逊河地区的主要景观变化相一致，例如Pebas系统的排水，亚马逊河的建立。河流和安第斯山脉北部的主要造山运动。我们的生物地理分析表明，从中美洲通过乔科（Chocó）和安第斯山脉（Andes）对亚马孙低地进行了垫脚石定殖，随后又有几处从亚马孙（Amazonia）散布回安第斯山脉。这些生物地理事件在时间上与中美洲和南美洲之间的早期陆桥（约10-15 MYA）以及中新世和上新世晚期亚马逊河地区的主要景观变化（例如Pebas系统的排水，亚马逊河的建立）相一致。河流和安第斯山脉北部的主要造山运动。

更新日期：2020-04-17

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