Phylogenetic relationships and divergence dates of softshell turtles (Testudines: Trionychidae) inferred from complete mitochondrial genomes
Phylogenetic relationships and divergence dates of softshell turtles (Testudines: Trionychidae) inferred from complete mitochondrial genomes
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从完整线粒体基因组推断的鳖（龟类：鳖科）的系统发育关系和分化日期
DOI：
10.1111/jeb.13070
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发表时间：
2017-05-01
影响因子：
2.1
通讯作者：
Nie, L.
中科院分区：
文献类型：
--
作者：
Li, H.;Liu, J.;Nie, L.
鳖是世界上分布最广的爬行动物之一，除南极洲外，各大洲都有发现。这个组的成员之间的系统发育关系以前已经研究过;然而，关于它的分类，它的地理位置和分歧时间的分歧仍然知之甚少。在这里，我们提出了一个全面的有丝分裂基因组学研究的软壳龟。我们测序了10个软壳龟的完整线粒体基因组，除了GenBank序列的Dogania subplana，Lissemys punctata，Trionyx triunguis，其中包括所有现存的属内鳖科除了Cyclanorbis和Cycloderma。这些数据与其他海龟的有丝分裂基因组进行系统发育分析。分别使用BEAST和RASP软件计算发散时间校准和祖先重建。系统发育分析表明，鳖科是刺龟科的姐妹类群，支持鳖亚科和环鼻亚科的单系性，这与形态学数据和分子生物学分析相一致。我们的系统发育分析已经建立了一个姐妹分类群之间的关系，亚洲Rafetus和亚洲Palea+Pelodiscus+Dogania+Nilssonia+Amyda，而以前的研究分组亚洲Rafetus与美国的Apalone。分歧时间估计和区域祖先重建结果表明，现存鳖科起源于亚洲约1.08亿年前（MA），辐射主要发生在晚白垩世-早始新世和渐新世两个暖期。通过结合估计的分歧时间和重建的祖先地区的软壳龟，我们确定的软壳龟的扩散出亚洲可能采取了三条路线。此外，扩散的时间似乎与印度-亚洲碰撞和白令海峡开放的时间一致，这为我们估计的发散时间的准确性提供了证据。总的来说，这组的有丝分裂基因组被用来探索的起源和传播路线的鳖，并提供了新的见解，这组的进化。
The softshell turtles (Trionychidae) are one of the most widely distributed reptile groups in the world, and fossils have been found on all continents except Antarctica. The phylogenetic relationships among members of this group have been previously studied; however, disagreements regarding its taxonomy, its phylogeography and divergence times are still poorly understood as well. Here, we present a comprehensive mitogenomic study of softshell turtles. We sequenced the complete mitochondrial genomes of 10 softshell turtles, in addition to the GenBank sequence of Dogania subplana, Lissemys punctata, Trionyx triunguis, which cover all extant genera within Trionychidae except for Cyclanorbis and Cycloderma. These data were combined with other mitogenomes of turtles for phylogenetic analyses. Divergence time calibration and ancestral reconstruction were calculated using BEAST and RASP software, respectively. Our phylogenetic analyses indicate that Trionychidae is the sister taxon of Carettochelyidae, and support the monophyly of Trionychinae and Cyclanorbinae, which is consistent with morphological data and molecular analysis. Our phylogenetic analyses have established a sister taxon relationship between the Asian Rafetus and the Asian Palea+Pelodiscus+Dogania+Nilssonia+Amyda, whereas a previous study grouped the Asian Rafetus with the American Apalone. The results of divergence time estimates and area ancestral reconstruction show that extant Trionychidae originated in Asia at around 108million years ago (MA), and radiations mainly occurred during two warm periods, namely Late Cretaceous-Early Eocene and Oligocene. By combining the estimated divergence time and the reconstructed ancestral area of softshell turtles, we determined that the dispersal of softshell turtles out of Asia may have taken three routes. Furthermore, the times of dispersal seem to be in agreement with the time of the India-Asia collision and opening of the Bering Strait, which provide evidence for the accuracy of our estimation of divergence time. Overall, the mitogenomes of this group were used to explore the origin and dispersal route of Trionychidae and have provided new insights on the evolution of this group.