原创力文档a supermatrix analysis of genomic, morphological, and paleontological data from crown cetaceasupermatrix分析基因组、形态和古生物皇冠鲸类的数据.pdfVIP
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a supermatrix analysis of genomic, morphological, and paleontological data from crown cetaceasupermatrix分析基因组、形态和古生物皇冠鲸类的数据
Geisler et al. BMC Evolutionary Biology 2011, 11:112
/1471-2148/11/112
RESEARCH ARTICLE Open Access
A supermatrix analysis of genomic,
morphological, and paleontological data from
crown Cetacea
Jonathan H Geisler 1*, Michael R McGowen2,3, Guang Yang4 and John Gatesy2
Abstract
Background: Cetacea (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.
Results: We 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 reconstru
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