Artificial neural networks can learn to estimate extinction rates from molecular phylogenies

Folmer Bokma*

*Corresponding author for this work

    Research output: Contribution to journalArticleAcademicpeer-review

    7 Citations (Scopus)


    Molecular phylogenies typically consist of only extant species, yet they allow inference of past rates of extinction, because. recently originated species are less likely to be extinct than ancient species. Despite the simple structure of the assumed underlying speciation-extinction process, parametric functions to estimate extinction rates from phylogenies turned out to be complex and often difficult to derive. Moreover, these parametric functions are specific to a particular process (e.g. complete species level phylogeny with constant birth and death rates) and a particular type of data (e.g. times between bifurcations). Here, it is shown that artificial neural networks can substitute for parametric estimation functions once they have been sufficiently trained on simulated data. This technique can in principle be used for different processes and data types, and because it circumvents the time-consuming and difficult task of deriving parametric estimation functions, it may greatly extend the possibilities to make macro-evolutionary inferences from molecular phylogenies. This novel approach is explained, applied to estimate speciation and extinction rates from a molecular phylogeny of the reef fish genus Naso (Acanturidae), and its performance is compared to that of maximum likelihood estimation. (c) 2006 Elsevier Ltd. All rights reserved.

    Original languageEnglish
    Pages (from-to)449-454
    Number of pages6
    JournalJournal of Theoretical Biology
    Issue number3
    Publication statusPublished - 7-Dec-2006


    • artificial intelligence
    • macroevolution
    • modelling
    • parameter estimation
    • speciation

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