A new method for handling missing species in diversification analysis applicable to randomly or nonrandomly sampled phylogenies

Systematic Biology
Natalie CusimanoSusanne S Renner

Abstract

Chronograms from molecular dating are increasingly being used to infer rates of diversification and their change over time. A major limitation in such analyses is incomplete species sampling that moreover is usually nonrandom. While the widely used γ statistic with the Monte Carlo constant-rates test or the birth-death likelihood analysis with the δ AICrc test statistic are appropriate for comparing the fit of different diversification models in phylogenies with random species sampling, no objective automated method has been developed for fitting diversification models to nonrandomly sampled phylogenies. Here, we introduce a novel approach, CorSiM, which involves simulating missing splits under a constant rate birth-death model and allows the user to specify whether species sampling in the phylogeny being analyzed is random or nonrandom. The completed trees can be used in subsequent model-fitting analyses. This is fundamentally different from previous diversification rate estimation methods, which were based on null distributions derived from the incomplete trees. CorSiM is automated in an R package and can easily be applied to large data sets. We illustrate the approach in two Araceae clades, one with a random species sampling...Continue Reading

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Citations

May 3, 2012·Proceedings of the National Academy of Sciences of the United States of America·Kangshan MaoSusanne S Renner
Feb 11, 2014·Systematic Biology·Daniele SilvestroNicolas Salamin
Jul 30, 2014·Proceedings of the National Academy of Sciences of the United States of America·Robert E Ricklefs, Knud A Jønsson
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