A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea.
A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea.
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冠鲸类基因组、形态学和古生物学数据的超级矩阵分析
DOI：
10.1186/1471-2148-11-112
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发表时间：
2011-04-25
影响因子：
3.4
通讯作者：
Gatesy J
中科院分区：
文献类型：
--
作者：
Geisler JH;McGowen MR;Yang G;Gatesy J
背景鲸目动物（海豚、鼠海豚和鲸鱼）是水生物种的一个分支，其中包括体型最大、潜水最深、脑容量最大的哺乳动物。了解群体多样化的时间模式以及鲸目动物解剖结构和行为的进化需要一个可靠且解决良好的系统发育假设。尽管过去 20 年积累了大量的分子数据，但鲸目动物的 DNA 序列尚未与丰富的鲸目动物化石记录直接整合，以协调分子和形态特征之间的差异。结果我们将新的核 DNA 序列（包括功能性灭绝的长江海豚的 6 个基因片段（约 2800 个碱基对））与扩展的形态矩阵和已发表的基因组数据结合起来。对这些数据的不同分析解决了代表所有现存鲸类科和 11 个已灭绝科的 74 个类群的关系。使用简约方法分析生成的超级矩阵（61,155 个字符）及其子分区。对分子分区进行贝叶斯和最大似然 (ML) 搜索，并使用从这些搜索获得的分子支架来约束形态分区的简约搜索。基于对超级矩阵的分析和基于模型的分子分区分析，我们发现了对 15 个现存进化枝的压倒性支持。当包括灭绝的类群时，我们恢复了与化石记录显着相关的树木。根据我们所有的系统发育分析，这些树被用来重建鲸目动物多样化的时间和“河豚”共有的特征进化，这是一组非单系物种。结论超矩阵的简约分析和受限于机器学习/贝叶斯分子树的形态分析产生了广泛一致的系统发育假设。在这两项分析的树木中，我们研究中包括的所有渐新世类群都落在冠须鲸类和冠齿鲸类之外，表明这两个分支在渐新世晚期或更晚的时间辐射，这与最近的一些分子钟研究相反。我们的树木还表明，河豚共有的许多特征状态是在其海洋祖先中进化而来的，这与这些特征是对河流栖息地的趋同适应的假设相矛盾。
BackgroundCetacea (dolphins, porpoises, and whales) is a clade of aquatic species that includes the most massive, deepest diving, and largest brained mammals. Understanding the temporal pattern of diversification in the group as well as the evolution of cetacean anatomy and behavior requires a robust and well-resolved phylogenetic hypothesis. Although a large body of molecular data has accumulated over the past 20 years, DNA sequences of cetaceans have not been directly integrated with the rich, cetacean fossil record to reconcile discrepancies among molecular and morphological characters.ResultsWe combined new nuclear DNA sequences, including segments of six genes (~2800 basepairs) from the functionally extinct Yangtze River dolphin, with an expanded morphological matrix and published genomic data. Diverse analyses of these data resolved the relationships of 74 taxa that represent all extant families and 11 extinct families of Cetacea. The resulting supermatrix (61,155 characters) and its sub-partitions were analyzed using parsimony methods. Bayesian and maximum likelihood (ML) searches were conducted on the molecular partition, and a molecular scaffold obtained from these searches was used to constrain a parsimony search of the morphological partition. Based on analysis of the supermatrix and model-based analyses of the molecular partition, we found overwhelming support for 15 extant clades. When extinct taxa are included, we recovered trees that are significantly correlated with the fossil record. These trees were used to reconstruct the timing of cetacean diversification and the evolution of characters shared by "river dolphins," a non-monophyletic set of species according to all of our phylogenetic analyses.ConclusionsThe parsimony analysis of the supermatrix and the analysis of morphology constrained to fit the ML/Bayesian molecular tree yielded broadly congruent phylogenetic hypotheses. In trees from both analyses, all Oligocene taxa included in our study fell outside crown Mysticeti and crown Odontoceti, suggesting that these two clades radiated in the late Oligocene or later, contra some recent molecular clock studies. Our trees also imply that many character states shared by river dolphins evolved in their oceanic ancestors, contradicting the hypothesis that these characters are convergent adaptations to fluvial habitats.
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DOI：
10.1111/j.1096-0031.1994.tb00179.x
发表时间：
1994-09-01
期刊：
CLADISTICS-THE INTERNATIONAL JOURNAL OF THE WILLI HENNIG SOCIETY
影响因子：
--
作者：
BREMER, K
通讯作者：
BREMER, K
影响因子：
2.6
作者：
Bisconti, M
通讯作者：
Bisconti, M
影响因子：
3.5
作者：
Arnason, U;Gullberg, A;Janke, A
通讯作者：
Janke, A
影响因子：
4.9
作者：
Browning, JV;Miller, KG;Hernández, JC
通讯作者：
Hernández, JC
DOI：
10.1073/pnas.97.21.11343
发表时间：
2000-10-10
影响因子：
11.1
作者：
Cassens, I;Vicario, S;Milinkovitch, MC
通讯作者：
Milinkovitch, MC