Journal
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
Volume 279, Issue 1732, Pages 1300-1309Publisher
ROYAL SOC
DOI: 10.1098/rspb.2011.1439
Keywords
birth-death model; diversification; missing species
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Funding
- Netherlands Scientific Organization (NWO-ALW)
- European Science Foundation (ESF)
- Van Gogh Programme
- NERC [NE/E015956/1]
- NERC [NE/E018165/1, NE/E015956/1] Funding Source: UKRI
- Natural Environment Research Council [NE/E018165/1, NE/E015956/1] Funding Source: researchfish
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The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there are often limits to diversity. Here, we present a general approach to evaluate the likelihood of a phylogeny under a model that accommodates diversity-dependence and extinction. We find, by likelihood maximization, that extinction is estimated most precisely if the rate of increase in the number of lineages in the phylogeny saturates towards the present or first decreases and then increases. We demonstrate the utility and limits of our approach by applying it to the phylogenies for two cases where a fossil record exists (Cetacea and Cenozoic macroperforate planktonic foraminifera) and to three radiations lacking fossil evidence (Dendroica, Plethodon and Heliconius). We propose that the diversity-dependence model with extinction be used as the standard model for macro-evolutionary dynamics because of its biological realism and flexibility.
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