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、食蚁兽与树懒同属于贫齿目（Xenarthra），是胎盘类哺乳动物四大主要演化支之一。由于长期与其他大陆板块隔绝于南美洲，贫齿类动物经历了约6500万年的演化分化，现存物种仅31种，却留下了超过200个已灭绝的属。贫齿类兼具祖先型与高度特化的解剖学特征，这使得其演化历史的形态解剖学分析难度极大；而既往的分子分析也未能厘清犰狳亚科内部的系统发育关系。本研究对约7400个基因组位点上的逆转录转座子（retroposon）存在/缺失模式进行了分析，共鉴定出35个具有系统发育信息价值的元件，以及另外39个具有信息价值的稀有基因组变异（RGCs）。此前仅在九带犰狳（Dasypus novemcinctus）基因组中报道过的DAS短散在重复序列（SINEs），在所有现存犰狳属物种中均被检测到——包括此前未被采样的倭犰狳属（Chlamyphorus），但树懒类中完全缺失这类序列。随后，研究人员将这些具有系统发育信息价值的逆转录转座元件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区域的DNA序列数据进行了比对分析。综合以上数据，本研究首次构建了完全解析的贫齿类动物属级系统发育树。值得注意的是，多项证据支持将披毛犰狳属（Chaetophractus）与密毛犰狳属（Zaedyus）聚为一支，作为真犰狳亚科（Euphractinae）内真犰狳属（Euphractus）的姊妹群，这一关联此前从未被证实。此外，侧翼序列分析显示，三带犰狳亚科（Tolypeutinae）内的裸尾犰狳属（Cabassous）与三带犰狳属（Tolypeutes）具有紧密的系统发育关系。最后，本研究通过非编码序列数据集明确了倭犰狳亚科（Chlamyphorinae）的系统发育位置，其为三带犰狳亚科的姊妹群。本研究的数据为贫齿类动物的后续演化研究提供了稳定的系统发育框架，同时也为确定保护优先级、拯救这一最奇特哺乳动物类群之一的物种多样性提供了重要参考依据。