Birth–death models and coalescent point processes: The shape and probability of reconstructed phylogenies

Amaury Lambert and Tanja Stadler

Theoretical Population Biology, 2013, vol. 90, issue C, 113-128

Abstract: Forward-in-time models of diversification (i.e., speciation and extinction) produce phylogenetic trees that grow “vertically†as time goes by. Pruning the extinct lineages out of such trees leads to natural models for reconstructed trees (i.e., phylogenies of extant species). Alternatively, reconstructed trees can be modelled by coalescent point processes (CPPs), where trees grow “horizontally†by the sequential addition of vertical edges. Each new edge starts at some random speciation time and ends at the present time; speciation times are drawn from the same distribution independently. CPPs lead to extremely fast computation of tree likelihoods and simulation of reconstructed trees. Their topology always follows the uniform distribution on ranked tree shapes (URT).

Keywords: Random tree; Macroevolution; Incomplete sampling; Likelihood; Inference (search for similar items in EconPapers)
Date: 2013
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Citations: View citations in EconPapers (6)

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Persistent link: https://EconPapers.repec.org/RePEc:eee:thpobi:v:90:y:2013:i:c:p:113-128

DOI: 10.1016/j.tpb.2013.10.002

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