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.]

中文翻译：

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超保守元素提高新热带 Sigmodontine 啮齿动物（Cricetidae：Sigmodontinae）快速辐射内困难节点的分辨率

Sigmodontine 啮齿动物（Cricetidae，Sigmodontinae）是新大陆哺乳动物的第二大鼠科亚科和物种最丰富的群体，包括超过 410 种现存物种，大约 100 种。87属。尽管最近在阐明 sigmodontine 系统发育关系方面取得了进展，但 12 个主要属（即部落）之间的系统发育关系仍然很难解决，特别是在那些形成大分支 Oryzomyalia 的那些之间。这种模式被解释为该群体进入南美洲时快速辐射的结果。在这里，我们尝试使用目标捕获和超保守元素 (UCE) 的高通量测序来解决 Sigmodontinae 内的系统发育关系。我们对 56 个人的 UCE 进行了丰富和测序，并从四个已经可用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导致了在不同方法中一致的高度分辨的系统发育。基于物种树的合并方法、级联矩阵和贝叶斯分析恢复了在困难节点分辨率下一致的相似拓扑。我们恢复了对 Oryzomyalia 内部部落间关系的良好支持；例如，Oryzomyini 部落作为其余 oryzomyalid 部落的姐妹分类群出现。发散时间的估计与先前研究的结果一致。我们推断出中中新世末期的sigmodontine啮齿动物的冠龄，而稻瘟病菌的主要谱系似乎在晚中新世期间在很短的时间内发生了辐射。因此，具有广泛分类学采样的基因组规模数据集的收集首次为 Sigmodontinae 主要谱系之间的关系提供了解决方案。我们预计这里介绍的系统发育将成为该组未来系统和进化研究的支柱。鼠尾草属；稻瘟病菌; 系统基因组学；多分法；啮齿目动物；西格莫多利亚；种树；UCE。] 鼠尾草属；稻瘟病菌; 系统基因组学；多分法；啮齿目动物；西格莫多利亚；种树；UCE。] 鼠尾草属；稻瘟病菌; 系统基因组学；多分法；啮齿目动物；西格莫多利亚；种树；UCE。]