globalchange  > 过去全球变化的重建
DOI: 10.1371/journal.pone.0089543
论文题名:
Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees
作者: Daniel L. Rabosky
刊名: PLOS ONE
ISSN: 1932-6203
出版年: 2014
发表日期: 2014-2-26
卷: 9, 期:2
语种: 英语
英文关键词: Speciation ; Phylogenetic analysis ; Phylogenetics ; Species diversity ; Species extinction ; Simulation and modeling ; Paleogenetics ; Evolutionary processes
英文摘要: A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify heterogeneous mixtures of dynamic processes within single phylogenies. I developed a method that can identify arbitrary numbers of time-varying diversification processes on phylogenies without specifying their locations in advance. The method uses reversible-jump Markov Chain Monte Carlo to move between model subspaces that vary in the number of distinct diversification regimes. The model assumes that changes in evolutionary regimes occur across the branches of phylogenetic trees under a compound Poisson process and explicitly accounts for rate variation through time and among lineages. Using simulated datasets, I demonstrate that the method can be used to quantify complex mixtures of time-dependent, diversity-dependent, and constant-rate diversification processes. I compared the performance of the method to the MEDUSA model of rate variation among lineages. As an empirical example, I analyzed the history of speciation and extinction during the radiation of modern whales. The method described here will greatly facilitate the exploration of macroevolutionary dynamics across large phylogenetic trees, which may have been shaped by heterogeneous mixtures of distinct evolutionary processes.
URL: http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0089543&type=printable
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资源类型: 期刊论文
标识符: http://119.78.100.158/handle/2HF3EXSE/18898
Appears in Collections:过去全球变化的重建
影响、适应和脆弱性
科学计划与规划
气候变化与战略
全球变化的国际研究计划
气候减缓与适应
气候变化事实与影响

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作者单位: Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan, United States of America

Recommended Citation:
Daniel L. Rabosky. Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees[J]. PLOS ONE,2014-01-01,9(2)
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