Data from: Retroposed elements and their flanking regions resolve the evolutionary history of xenarthran mammals (armadillos, anteaters, and sloths)

Armadillos, anteaters, and sloths (Order Xenarthra) comprise 1 of the 4 major clades of placental mammals. Isolated in South America from the other continental landmasses, xenarthrans diverged over a period of about 65 Myr, leaving more than 200 extinct genera and only 31 living species. The presence of both ancestral and highly derived anatomical features has made morphoanatomical analyses of the xenarthran evolutionary history difficult, and previous molecular analyses failed to resolve the relationships within armadillo subfamilies. We investigated the presence/absence patterns of retroposons from ∼7,400 genomic loci, identifying 35 phylogenetically informative elements and an additional 39 informative rare genomic changes (RGCs). DAS-short interspersed elements (SINEs), previously described only in the Dasypus novemcinctus genome, were found in all living armadillo genera, including the previously unsampled Chlamyphorus, but were noticeably absent in sloths. The presence/absence patterns of the phylogenetically informative retroposed elements and other RGCs were then compared with data from the DNA sequences of the more than 12-kb flanking regions of these retroposons. Together, these data provide the first fully resolved genus tree of xenarthrans. Interestingly, multiple evidence supports the grouping of Chaetophractus and Zaedyus as a sister group to Euphractus within Euphractinae, an association that was not previously demonstrated. Also, flanking sequence analyses favor a close phylogenetic relationship between Cabassous and Tolypeutes within Tolypeutinae. Finally, the phylogenetic position of the subfamily Chlamyphorinae is resolved by the noncoding sequence data set as the sister group of Tolypeutinae. The data provide a stable phylogenetic framework for further evolutionary investigations of xenarthrans and important information for defining conservation priorities to save the diversity of one of the most curious groups of mammals.

犰狳、食蚁兽与树懒（异关节总目（Xenarthra））隶属于胎盘类哺乳动物四大核心演化支之一。该类群曾长期孤立于南美大陆，与其他大陆板块隔绝，历经约6500万年的演化分化，现存物种仅31种，却遗留了超过200个已灭绝的属级类群。由于兼具祖先类群与高度特化的解剖学特征，异关节类演化历史的形态解剖学分析始终存在较大难点，且既往分子研究未能明确犰狳亚科内部的系统发育关系。本研究针对约7400个基因组位点的逆转录转座子（retroposons）存在/缺失模式开展分析，共鉴定出35个系统发育信息元件，以及额外39个具有系统发育价值的稀有基因组变异（RGCs）。此前仅在九带犰狳（Dasypus novemcinctus）基因组中被报道的DAS型短散在重复序列（SINEs），本次研究在所有现存犰狳属类群（包括此前未被采样的铠犰狳属（Chlamyphorus））中均检测到该序列，但树懒类群中完全缺失该序列。随后，我们将上述系统发育信息逆转录转座子与其他稀有基因组变异的存在/缺失模式，与这些逆转录转座子侧翼超过12kb的DNA序列数据进行了比对分析。综合上述数据，本研究首次构建了完全解析的异关节类属级系统发育树。值得注意的是，多项证据支持带犰狳属（Chaetophractus）与Zaedyus共同作为真犰狳亚科（Euphractinae）内真犰狳属（Euphractus）的姊妹群，这一类群关联此前从未被证实。此外，侧翼序列分析支持圆耳犰狳属（Cabassous）与三带犰狳属（Tolypeutes）在三带犰狳亚科（Tolypeutinae）内存在紧密的系统发育关系。最后，基于非编码序列数据集，铠犰狳亚科（Chlamyphorinae）的系统发育位置被确定为三带犰狳亚科的姊妹群。本研究所得数据为异关节类的后续演化研究提供了稳定的系统发育框架，同时也为界定保护优先级、拯救这一最具奇特性的哺乳动物类群的多样性提供了重要依据。