Department of Natural History, Royal Ontario Museum, Toronto, ON M5S 2C6, Canada; Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
Department of Natural History, Royal Ontario Museum, Toronto, ON M5S 2C6, Canada; Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
Mol Phylogenet Evol. 2020 Feb;143:106690. doi: 10.1016/j.ympev.2019.106690. Epub 2019 Nov 21.
Mammals are one of the better known groups of animals, and in the Neotropics bats typically comprise about half of the mammalian species diversity. But, well resolved species-level phylogenies are still lacking for most taxa of bats. One broadly distributed genus is the mastiff bats, Molossus. Species within this genus are morphologically very similar, which results in a confusing and unstable taxonomy. In addition, low levels of genetic divergence among some clades make resolution of phylogenetic relationships difficult. Most authors recognize Molossus as being monophyletic, however, phylogenetic relationships within the genus remain poorly understood based on traditional Sanger sequencing of individual genes. We propose a more comprehensive framework based on large-scale genomic data derived from Next Generation Sequencing techniques to better understand evolutionary relationships within a group of closely related species with a rich taxonomic history. In this study, we utilized the NGS method of Genotype by Sequencing (GBS) to test the monophyly of the genus, understand evolutionary relationships within Molossus and investigate the genetic integrity of currently recognized species. Given that both de novo and reference genome pipelines are often used in the assembly of Single Nucleotide Polymorphism data from GBS, and that several tree inference methodologies have been proposed for SNP data, we test whether different alignments and phylogenetic approaches produce similar results. We also examined how the process of SNP identification and mapping can affect the consistency of the analyses. Our data provide the first high resolution phylogeny for the genus Molossus, bringing new insights into recognition of species boundaries and relationships among taxa. This study clarifies the taxonomy of Molossus and elevates the number of species in the genus from 11 to 14. We suggest the revalidation of the names M. nigricans, and M. fluminensis, which were synonymized under the name M. rufus; and M. bondae, previously synonymized under the name M. currentium. Different alignments and phylogenetic inferences produce consistent results, supporting use of SNP approach in addressing evolutionary questions on a macroevolutionary scale where the genetic distance among clades is low.
哺乳动物是广为人知的动物群体之一，在新热带地区，蝙蝠通常约占哺乳动物物种多样性的一半。但是，大多数蝙蝠类群仍然缺乏分辨率高的物种水平系统发育关系。一个广泛分布的属是鬃毛狗蝠属，Molossus。该属内的物种在形态上非常相似，导致分类学上的混乱和不稳定。此外，一些支系之间的遗传分化程度较低，使得系统发育关系的解决变得困难。大多数作者认为 Molossus 是单系的，然而，基于传统的个体基因 Sanger 测序，该属内的系统发育关系仍然知之甚少。我们提出了一个更全面的框架，基于从下一代测序技术获得的大规模基因组数据，以更好地了解具有丰富分类历史的一组密切相关物种的进化关系。在这项研究中，我们利用下一代测序技术的基因型测序 (GBS) 方法来测试该属的单系性，了解 Molossus 内的进化关系，并研究目前公认的物种的遗传完整性。鉴于从头和参考基因组管道通常用于从 GBS 中组装单核苷酸多态性数据，并且已经提出了几种用于 SNP 数据的树推断方法，我们测试了不同的对齐和系统发育方法是否会产生相似的结果。我们还研究了 SNP 识别和映射过程如何影响分析的一致性。我们的数据提供了 Molossus 属的第一个高分辨率系统发育，为物种边界和分类群之间的关系提供了新的见解。这项研究澄清了 Molossus 的分类学，并将该属的物种数量从 11 种增加到 14 种。我们建议重新验证 M. nigricans 和 M. fluminensis 的名称，它们曾被同义词化到 M. rufus 名下；以及 M. bondae，之前曾被同义词化到 M. currentium 名下。不同的对齐和系统发育推断产生一致的结果，支持在遗传距离较低的宏观进化尺度上使用 SNP 方法来解决进化问题。
