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How reliably can we infer diversity-dependent diversification from phylogenies ? [Methods in Ecology and Evolution]

Keywords : Birth–death model, conditioning, diversity dependence, extinction, parametric bootstrap, simulations

par Frédéric Magné - publié le

1.Slowdowns in lineage accumulation in phylogenies suggest that speciation rates decline as diversity increases. Likelihood methods have been developed to detect such diversity dependence. However, a thorough test of whether such approaches correctly infer diversity dependence is lacking.
2.Here, we simulate phylogenetic branching under linear negative diversity-dependent and diversity-independent models and estimate from the simulated phylogenies the maximum-likelihood parameters for three different conditionings – on survival of the birth–death process given the crown age, on tree size (N) and on tree size given the crown age. We report the accuracy of recovering the simulation parameters and the reliability of the model selection based on the χ2 likelihood ratio test.(...)

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