Analysis of diversification: combining phylogenetic and taxonomic data

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Abstract
The estimation of diversification rates using phylogenetic data has attracted a lot of attention in the past decade. In this context, the analysis of incomplete phylogenies (e.g. phylogenies resolved at the family level but unresolved at the species level) has remained difficult. I present here a likelihood–based method to combine partly resolved phylogenies with taxonomic (species–richness) data to estimate speciation and extinction rates. This method is based on fitting a birth–and–death model to both phylogenetic and taxonomic data. Some examples of the method are presented with data on birds and on mammals. The method is compared with existing approaches that deal with incomplete phylogenies. Some applications and generalizations of the approach introduced in this paper are further discussed.

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