ESTIMATING THE DURATION OF SPECIATION FROM PHYLOGENIES |
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Authors: | Rampal S. Etienne Hélène Morlon Amaury Lambert |
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Affiliation: | 1. Community and Conservation Ecology Group, Centre for Ecological and Evolutionary Studies, University of Groningen, , The Netherlands;2. Center for Applied Mathematics, Ecole Polytechnique, , 91128 Palaiseau Cedex, France;3. Institut de Biologie de l’ENS, CNRS UMR 8197, , 75005 Paris, France;4. Collège de France, Center for Interdisciplinary Research in Biology, CNRS UMR 7241, , Paris, France;5. UPMC Univ Paris 06, Laboratoire de Probabilités et Modèles Aléatoires, CNRS UMR 7599, , Paris, France |
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Abstract: | Speciation is not instantaneous but takes time. The protracted birth–death diversification model incorporates this fact and predicts the often observed slowdown of lineage accumulation toward the present. The mathematical complexity of the protracted speciation model has barred estimation of its parameters until recently a method to compute the likelihood of phylogenetic branching times under this model was outlined (Lambert et al. 2014 ). Here, we implement this method and study using simulated phylogenies of extant species how well we can estimate the model parameters (rate of initiation of speciation, rate of extinction of incipient and good species, and rate of completion of speciation) as well as the duration of speciation, which is a combination of the aforementioned parameters. We illustrate our approach by applying it to a primate phylogeny. The simulations show that phylogenies often do not contain enough information to provide unbiased estimates of the speciation‐initiation rate and the extinction rate, but the duration of speciation can be estimated without much bias. The estimate of the duration of speciation for the primate clade is consistent with literature estimates. We conclude that phylogenies combined with the protracted speciation model provide a promising way to estimate the duration of speciation. |
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Keywords: | Birth– death model extinction macroevolution phylogeny protracted speciation speciation |
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