Phylogenomic analyses and improved resolution of Cetartiodactyla.
Phylogenomic analyses and improved resolution of Cetartiodactyla.
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DOI：
10.1016/j.ympev.2011.02.009
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发表时间：
2011-11
影响因子：
4.1
通讯作者：
Xuming Zhou;Shixia Xu;Yunxia Yang;K. Zhou;Guang Yang
中科院分区：
文献类型：
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作者：
Xuming Zhou;Shixia Xu;Yunxia Yang;K. Zhou;Guang Yang
鲸偶蹄目动物的古老性、多样性以及在生态学和进化中的重要性激发了许多试图解决它们的系统发育关系的尝试。然而，基于有限的核基因或线粒体DNA序列样本的先前分析产生的结果要么彼此不一致，要么支持度较弱，要么对分析条件高度敏感。在这里，我们提出了强有力的支持结果的基础上超过1.4Mb的对齐的DNA序列矩阵从110个单拷贝的核蛋白编码基因的21个鲸蹄类物种，这代表了主要的鲸蹄类谱系，和三种奇蹄目和食肉目作为外类群。系统发育分析这一新开发的基因组序列数据，使用基于密码子的模型和最近开发的模型的自相关率解决了系统发育关系的主要鲸蹄类谱系和这些谱系具有高度的信心。鲸类作为河马科的姐妹类群与偶蹄目动物共巢，而蹄足目被证实是鲸类的唯一基础分支。在鲸类中，齿鲸类相对于须鲸类的单系地位、抹香鲸总科在齿鲸类中的基础地位、江豚类的非单系性以及海豚科与单齿鲸科+海豚科的姐妹关系得到了有力的支持。特别是，Tursiops（短吻海豚）和Stenella（斑点海豚）的群体被确认为非自然群体。此外，一个非常狭窄的时间框架的3000万年（百万年）被发现的快速多样化的海豚科在中新世晚期，这使得它很难解决系统发育关系内的海豚科，特别是对以前的研究与有限的数据集。本研究提供了一个统计学支持的系统发育框架鲸偶蹄目，这是朝着结束一些经常激烈的，长达一个世纪的辩论，他们的进化迈出了重要的一步。
The remarkable antiquity, diversity, and significance in the ecology and evolution of Cetartiodactyla have inspired numerous attempts to resolve their phylogenetic relationships. However, previous analyses based on limited samples of nuclear genes or mitochondrial DNA sequences have generated results that were either inconsistent with one another, weakly supported, or highly sensitive to analytical conditions. Here, we present strongly supported results based upon over 1.4Mb of an aligned DNA sequence matrix from 110 single-copy nuclear protein-coding genes of 21 Cetartiodactyla species, which represent major Cetartiodactyla lineages, and three species of Perissodactyla and Carnivora as outgroups. Phylogenetic analysis of this newly developed genomic sequence data using a codon-based model and recently developed models of the rate autocorrelation resolved the phylogenetic relationships of the major cetartiodactylan lineages and of those lineages with a high degree of confidence. Cetacea was found to nest within Artiodactyla as the sister group of Hippopotamidae, and Tylopoda was corroborated as the sole base clade of Cetartiodactyla. Within Cetacea, the monophyletic status of Odontoceti relative to Mysticeti, the basal position of Physeteroidea in Odontoceti, the non-monophyly of the river dolphins, and the sister relationship between Delphinidae and Monodontidae+Phocoenidae were strongly supported. In particular, the groups of Tursiops (bottlenose dolphins) and Stenella (spotted dolphins) were validated as unnatural groups. Additionally, a very narrow time frame of ∼3My (million years) was found for the rapid diversification of delphinids in the late Miocene, which made it difficult to resolve the phylogenetic relationships within the Delphinidae, especially for previous studies with limited data sets. The present study provides a statistically well-supported phylogenetic framework of Cetartiodactyla, which represents an important step toward ending some of the often-heated, century-long debate on their evolution.