The reconstructed tree in the lineage-based model of protracted speciation

DOI10.1007/S00285-014-0767-XMaRDI QIDQ154193zbMATH OpenOpenAlexWikidataFDO

Authors Amaury Lambert, Hélène Morlon, Rampal S. Etienne, Amaury Lambert, Hélène Morlon, Rampal S. Etienne

Publication date 11 March 2014

Published in Journal of Mathematical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1301.5512

zbMATH Keywords

birth-death processcoalescent point processmultitype branching processphylogenyprotracted speciationreconstructed treescale functionsplitting treeLévy process

Mathematics Subject Classification ID

Processes with independent increments; Lévy processes (60G51) Point processes (e.g., Poisson, Cox, Hawkes processes) (60G55) Problems related to evolution (92D15) Applications of branching processes (60J85) Population dynamics (general) (92D25) Ecology (92D40) Branching processes (Galton-Watson, birth-and-death, etc.) (60J80)

Abstract: A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree produced by a given model of diversification. Etienne & Rosindell (2012) proposed a lineage-based model of diversification, called protracted speciation, where species remain incipient during a random duration before turning good species, and showed that this can explain the slowdown in lineage accumulation observed in real phylogenies. However, they were unable to provide a general likelihood formula. Here, we present a likelihood formula for protracted speciation models, where rates at which species turn good or become extinct can depend both on their age and on time. Our only restrictive assumption is that speciation rate does not depend on species status. Our likelihood formula utilizes a new technique, based on the contour of the phylogenetic tree and first developed in Lambert (2010). We consider the reconstructed trees spanned by all extant species, by all good extant species, or by all representative species, which are either good extant species or incipient species representative of some good extinct species. Specifically, we prove that each of these trees is a coalescent point process, that is, a planar, ultrametric tree where the coalescence times between two consecutive tips are independent, identically distributed random variables. We characterize the common distribution of these coalescence times in some, biologically meaningful, special cases for which the likelihood reduces to an elegant analytical formula or becomes numerically tractable.

Recommendations

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Cited in

(14)

• Lineages-through-time plots of neutral models for speciation
• Introducing a general class of species diversification models for phylogenetic trees
• Random ultrametric trees and applications
• Additional analytical support for a new method to compute the likelihood of diversification models
• A diffusion-based approach for simulating forward-in-time state-dependent speciation and extinction dynamics
• PBD
• The standard lateral gene transfer model is statistically consistent for pectinate four-taxon trees
• Dated Ancestral Trees from Binary Trait Data and Their Application to the Diversification of Languages
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• Birth-death models and coalescent point processes: the shape and probability of reconstructed phylogenies
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• Species-Driven Persistent Phylogeny
• The shape of phylogenies under phase-type distributed times to speciation and extinction
• The species problem from the modeler's point of view

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