Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction

被引:404
作者
Beaulieu, Jeremy M. [1 ,2 ]
O'Meara, Brian C. [2 ]
机构
[1] Univ Tennessee, Natl Inst Biol & Math Synth, Knoxville, TN 37996 USA
[2] Univ Tennessee, Dept Ecol & Evolutionary Biol, Knoxville, TN 37996 USA
基金
美国国家科学基金会;
关键词
Comparative methods; diversification; extinction; hidden states; speciation; MOLECULAR PHYLOGENIES; EVOLUTIONARY RADIATIONS; SPECIES DIVERSIFICATION; CAMPANULID ANGIOSPERMS; PLANT DIVERSIFICATION; STABILIZING SELECTION; PENALIZED LIKELIHOOD; CLADE DIPSACALES; RATES; CHARACTERS;
D O I
10.1093/sysbio/syw022
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
The distribution of diversity can vary considerably from clade to clade. Attempts to understand these patterns often employ state-dependent speciation and extinction models to determine whether the evolution of a particular novel trait has increased speciation rates and/or decreased extinction rates. It is still unclear, however, whether these models are uncovering important drivers of diversification, or whether they are simply pointing to more complex patterns involving many unmeasured and co-distributed factors. Here we describe an extension to the popular state-dependent speciation and extinction models that specifically accounts for the presence of unmeasured factors that could impact diversification rates estimated for the states of any observed trait, addressing at least one major criticism of BiSSE (Binary State Speciation and Extinction) methods. Specifically, our model, which we refer to as HiSSE (Hidden State Speciation and Extinction), assumes that related to each observed state in the model are "hidden" states that exhibit potentially distinct diversification dynamics and transition rates than the observed states in isolation. We also demonstrate how our model can be used as character-independent diversification models that allow for a complex diversification process that is independent of the evolution of a character. Under rigorous simulation tests and when applied to empirical data, we find that HiSSE performs reasonably well, and can at least detect net diversification rate differences between observed and hidden states and detect when diversification rate differences do not correlate with the observed states. We discuss the remaining issues with state-dependent speciation and extinction models in general, and the important ways in which HiSSE provides a more nuanced understanding of trait-dependent diversification.
引用
收藏
页码:583 / 601
页数:19
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