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The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events
Stockholm University, Faculty of Science, Department of Mathematics. University of California, USA.
Number of Authors: 1
2015 (English)In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 380, 321-331 p.Article in journal (Refereed) Published
Abstract [en]

The homogeneous reconstructed evolutionary process is a birth-death process without observed extinct lineages. Each species evolves independently with the same diversification rate-speciation rate, lambda(t), and extinction rate, mu(t)-that may change over time. The process is commonly applied to model species diversification where the data are reconstructed phylogenies, e.g. trees estimated from present-day molecular data, and used to infer diversification rates. In the present paper I develop the general probability density of a reconstructed tree under any homogeneous, time-dependent birth-death process. I demonstrate how to adapt this probability density when conditioning on the survival of one or two initial lineages, or on the process realizing n species, and also how to transform between the probability density of a reconstructed tree and the probability density of the speciation times. I demonstrate the use of the general time-dependent probability density functions by deriving the probability density of a reconstructed tree under a birth-death-shift model with explicit mass-extinction events. I extend these functions to several special cases, including the pure-birth process, the pure-death process, the birth-death process, and the critical-branching process. Thus, I specify equations for the most commonly used birth-death models in a unified framework (e.g. same condition and same data) using a common notation.

Place, publisher, year, edition, pages
2015. Vol. 380, 321-331 p.
Keyword [en]
Birth-death process, Diversification, Incomplete taxon sampling, Probability density function, Likelihood
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:su:diva-120885DOI: 10.1016/j.jtbi.2015.06.005ISI: 000359505200032OAI: oai:DiVA.org:su-120885DiVA: diva2:945050
Available from: 2016-06-30 Created: 2015-09-18 Last updated: 2016-06-30Bibliographically approved

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