Interordinal gene capture, the phylogenetic position of Steller's sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia.
Interordinal gene capture, the phylogenetic position of Steller's sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia.
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序间基因捕获、基于分子和形态学数据的虎头海牛的系统发育位置，以及海牛的宏观进化历史。
DOI：
10.1016/j.ympev.2015.05.022
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发表时间：
2015
影响因子：
4.1
通讯作者：
Springer MS
中科院分区：
文献类型：
--
作者：
Springer MS
最近灭绝(约1768年)的史特勒海牛(海牛)是北太平洋一种体型较大、无牙的西里安海牛。根据以前的形态和分子研究，这个分类单元与这个支系的其他成员的亲缘关系是不确定的，无论是存活的还是灭绝的。我们利用杂交捕获方法和第二代测序技术，从26个核基因中获得了30kb的外显子序列。Gigas和Dugong Dugon我们还获得了牙齿相关釉质蛋白(Enam)基因的完整编码序列。利用儒艮和海牛序列设计的杂交探针在检索序列方面都是高效的。Gigas(平均覆盖率=98.8%)，以及对ENAM区域(99.0%覆盖率)的更多分歧的探头，这些探头完全由鼻目动物(非洲象)和悬臂猿(Hyrax角)设计。新的序列与所有其他非泡沫目的代表的可用序列相结合。我们还通过添加新的分类群和九个新的颅后特征，扩展了以前发表的关于活的和化石的锡雷尼亚的形态矩阵。分子数据的最大似然和简约分析为h的关联提供了强有力的支持。GigasandD.将活的三叶虫(海牛)排除在外。对形态数据的简约分析也支持包含h。Dugongidae与D.鸭嘴龙和鸭嘴龙化石。基于具有硬约束和软约束的校准密度方法的时间树分析表明了这一点。GigasandD.杜贡人在渐新世分化，而西里昂王冠最后一次共享共同祖先是在始新世。ENAM基因的编码序列。Gigas不包含移码突变或终止密码子，但在内含子2的受体剪接位置存在易位突变(AG To CG)。这种在无牙海牛中的中断与之前的研究一致，该研究记录了各种无牙和无釉质脊椎动物的牙齿特异基因突变，包括鸟类、海龟、土豚、穿山甲、异种脊椎动物和须鲸。此外，分支点的dN/ds分析为ENAM的正选择提供了证据，在发生广泛牙齿减少的茎分枝上进行了正选择，随后在水毛分枝上进行了中性进化。最后，我们给出了一棵人工合成的进化树，展示了这一分支历史上的几个关键创新，包括与鲸目动物进化史中发生的特征状态变化相似的特征状态变化。
The recently extinct (ca. 1768) Steller’s sea cow (Hydrodamalis gigas) was a large, edentulous North Pacific sirenian. The phylogenetic affinities of this taxon to other members of this clade, living and extinct, are uncertain based on previous morphological and molecular studies. We employed hybridization capture methods and second generation sequencing technology to obtain >30 kb of exon sequences from 26 nuclear genes for bothH. gigasandDugong dugon. We also obtained complete coding sequences for the tooth-related enamelin (ENAM) gene. Hybridization probes designed using dugong and manatee sequences were both highly effective in retrieving sequences fromH. gigas(mean = 98.8% coverage), as were more divergent probes for regions ofENAM(99.0% coverage) that were designed exclusively from a proboscidean (African elephant) and a hyracoid (Cape hyrax). New sequences were combined with available sequences for representatives of all other afrotherian orders. We also expanded a previously published morphological matrix for living and fossil Sirenia by adding both new taxa and nine new postcranial characters. Maximum likelihood and parsimony analyses of the molecular data provide robust support for an association ofH. gigasandD. dugonto the exclusion of living trichechids (manatees). Parsimony analyses of the morphological data also support the inclusion ofH. gigasin Dugongidae withD. dugonand fossil dugongids. Timetree analyses based on calibration density approaches with hard- and soft-bounded constraints suggest thatH. gigasandD. dugondiverged in the Oligocene and that crown sirenians last shared a common ancestor in the Eocene. The coding sequence for theENAMgene inH. gigasdoes not contain frameshift mutations or stop codons, but there is a transversion mutation (AG toCG) in the acceptor splice site of intron 2. This disruption in the edentulous Steller’s sea cow is consistent with previous studies that have documented inactivating mutations in tooth-specific loci of a variety of edentulous and enamelless vertebrates including birds, turtles, aardvarks, pangolins, xenarthrans, and baleen whales. Further, branch-site dN/dS analyses provide evidence for positive selection inENAMon the stem dugongid branch where extensive tooth reduction occurred, followed by neutral evolution on theHydrodamalisbranch. Finally, we present a synthetic evolutionary tree for living and fossil sirenians showing several key innovations in the history of this clade including character state changes that parallel those that occurred in the evolutionary history of cetaceans.
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2000
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DOI：
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DOI：
--
发表时间：
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期刊：
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影响因子：
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通讯作者：
I. Greenwald