Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja s/n, Valdivia 5090000, Chile.
Microbial Genomics Laboratory, Institut Pasteur Montevideo, Mataojo 2020, Montevideo 11400, Uruguay.
Syst Biol. 2021 Oct 13;70(6):1090-1100. doi: 10.1093/sysbio/syab023.
Sigmodontine rodents (Cricetidae, Sigmodontinae) represent the second largest muroid subfamily and the most species-rich group of New World mammals, encompassing above 410 living species and ca. 87 genera. Even with advances on the clarification of sigmodontine phylogenetic relationships that have been made recently, the phylogenetic relationships among the 12 main groups of genera (i.e., tribes) remain poorly resolved, in particular among those forming the large clade Oryzomyalia. This pattern has been interpreted as consequence of a rapid radiation upon the group entrance into South America. Here, we attempted to resolve phylogenetic relationships within Sigmodontinae using target capture and high-throughput sequencing of ultraconserved elements (UCEs). We enriched and sequenced UCEs for 56 individuals and collected data from four already available genomes. Analyses of distinct data sets, based on the capture of 4634 loci, resulted in a highly resolved phylogeny consistent across different methods. Coalescent species-tree-based approaches, concatenated matrices, and Bayesian analyses recovered similar topologies that were congruent at the resolution of difficult nodes. We recovered good support for the intertribal relationships within Oryzomyalia; for instance, the tribe Oryzomyini appears as the sister taxa of the remaining oryzomyalid tribes. The estimates of divergence times agree with the results of previous studies. We inferred the crown age of the sigmodontine rodents at the end of the Middle Miocene, while the main lineages of Oryzomyalia appear to have radiated in a short interval during the Late Miocene. Thus, the collection of a genomic-scale data set with a wide taxonomic sampling provided resolution for the first time of the relationships among the main lineages of Sigmodontinae. We expect the phylogeny presented here will become the backbone for future systematic and evolutionary studies of the group.[Coalescent; Muroidea; Oryzomyalia; phylogenomics; polytomy; Rodentia; Sigmodontalia; species tree; UCEs.].
沙鼠型啮齿动物（仓鼠科，沙鼠亚科）是第二大的鼠科亚科，也是新世界哺乳动物中物种最丰富的群体，包括超过 410 种现存物种和约 87 个属。即使最近在澄清沙鼠型啮齿动物的系统发育关系方面取得了进展，但 12 个主要属群（即部落）之间的系统发育关系仍然没有得到很好的解决，特别是在形成大支系 Oryzomyalia 的那些属群之间。这种模式被解释为该群体进入南美洲后快速辐射的结果。在这里，我们试图利用目标捕获和高通量测序超保守元件（UCEs）来解决沙鼠亚科内的系统发育关系。我们对 56 个个体进行了 UCE 富集和测序，并从四个已有的基因组中收集了数据。基于 4634 个位点的捕获，对不同数据集的分析产生了一个高度分辨率的系统发育树，在不同的方法中都是一致的。基于合并的支序物种树方法、串联矩阵和贝叶斯分析得到了相似的拓扑结构，在困难节点的分辨率上是一致的。我们很好地支持了 Oryzomyalia 内的部落间关系；例如，Oryzomyini 部落似乎是其余 Oryzomyalid 部落的姊妹群。分化时间的估计与先前研究的结果一致。我们推断沙鼠型啮齿动物的冠群年龄在中中新世末期，而 Oryzomyalia 的主要谱系似乎在晚中新世的一个短时间内辐射。因此，通过广泛的分类采样收集基因组规模的数据为首次解决沙鼠亚科的主要谱系之间的关系提供了分辨率。我们预计，这里提出的系统发育将成为该群体未来系统学和进化研究的基础。[支序；鼠科；Oryzomyalia；系统基因组学；多系性；啮齿目；Sigmodontalia；物种树；UCEs。]
