Data from: New DNA data from a Transthyretin nuclear intron suggest an Oligocene to Miocene diversification of living South America opossums (Marsupialia: Didelphidae).

Phylogenetic relationships of 19 species of didelphid marsupials were studied using two nuclear markers, the non-coding transthyretin intron 1 (TTR) and the coding interphotoreceptor retinoid binding protein exon 1 (IRBP), and two mitochondrial genes, the protein-coding cytochrome b (cyt-b) and the structural 12S ribosomal DNA (12S rDNA). Evolutionary dynamics of these four markers were compared to each other, revealing the appropriate properties presented by TTR intron 1 together with its well supported and resolved phylogenetic signal. Nuclear markers supported the monophyly of medium and large-sized opossums Metachirus+(Chironectes, Lutreolina, Didelphis, Philander), and the paraphyly of mouse-sized opossums, with the genera Gracilinanus, Thylamys, and Marmosops as a sister group to medium and large-sized didelphids. Conflicting branching patterns between mitochondrial and nuclear data involved the phylogenetic position of Marmosa-Micoureus-Monodelphis relative to other mouse-sized opossums. Nuclear phylogenetic inferences among genera were confirmed by the presence of synapomorphic indels observed in TTR intron 1. A Bayesian relaxed molecular clock dating of didelphid evolution using nuclear markers estimated their origin in the Middle Eocene (39.8 million years ago), with subsequent diversification during the Oligocene (Deseadan) and Miocene.本研究针对19种负鼠科（Didelphidae）有袋类的系统发育关系展开分析，所用分子标记包括两类核基因序列：非编码的转甲状腺素蛋白内含子1（transthyretin intron 1，TTR）、编码型光感受器间类视黄醇结合蛋白外显子1（interphotoreceptor retinoid binding protein exon 1，IRBP），以及两类线粒体基因：编码蛋白质的细胞色素b（cytochrome b，cyt-b）与结构型12S核糖体DNA（12S rDNA）。研究对四类分子标记的进化动态开展两两比对，结果表明TTR内含子1具备优异的分子标记特性，其提供的系统发育信号支持度高且解析度清晰。核基因标记支持中、大型负鼠构成单系群：Metachirus + (Chironectes、Lutreolina、Didelphis、Philander)；而小型鼠形负鼠则为并系群，其中Gracilinanus、Thylamys与Marmosops三个属构成的支系，为中、大型负鼠科类群的姊妹群。线粒体与核基因数据在分支拓扑结构上存在冲突，具体表现为Marmosa-Micoureus-Monodelphis支系相较于其他小型鼠形负鼠的系统发育位置存在争议。TTR内含子1中存在的共源插入缺失（synapomorphic indels），验证了属级水平的核基因系统发育推断结果。本研究基于核基因标记，采用贝叶斯宽松分子钟法对负鼠科的演化时间进行估算，结果显示其起源于始新世中期（距今约3980万年），随后在渐新世（德萨丹期）与中新世发生物种辐射分化。