Approximate Bayesian Computation of diversification rates from molecular phylogenies: introducing a new efficient summary statistic, the nLTT. Issue 5 (11th March 2015)

• Record Type: Journal Article
• Authors: Janzen, Thijs; Höhna, Sebastian; Etienne, Rampal S.; Paradis, Emmanuel
• Is Part Of: Methods in ecology and evolution. Volume 6:Issue 5(2015:May)
• Page Start: 566
• Page End: 575
• Publication Date: 2015-03-11
• Subjects: Ecology -- Periodicals; Evolution -- Periodicals; 577
• DOI: 10.1111/2041-210X.12350
• Languages: English
• ISSNs: 2041-210X

Abstract

<abstract abstract-type="main" id="mee312350-abs-0001"> <title>Summary</title> <p> <list id="mee312350-list-0001" list-type="order"> <list-item> <p>Molecular phylogenies form a potential source of information on rates of diversification, and the mechanisms that underlie diversification patterns. Diversification models have become increasingly complex over the past decade, and we have reached a point where the computation of the analytical likelihood of the model given a phylogeny is either unavailable or intractable. For such models, a likelihood‐free approach such as Approximate Bayesian Computation (ABC) offers a solution. ABC is a Bayesian framework that uses one or more summary statistics instead of the likelihood function. Crucial to the performance of an ABC algorithm is the choice of summary statistics.</p> </list-item> <list-item> <p>Here, we analyse the applicability of three traditional and often‐used summary statistics (Gamma statistic, Phylogenetic Diversity and tree size) within an ABC framework and propose a new summary statistic: the normalized Lineages‐Through‐Time (nLTT) statistic.</p> </list-item> <list-item> <p>We find that the traditional summary statistics perform poorly and should not be used as a substitute of the likelihood. By contrast, we find that the nLTT statistic performs on par with the likelihood.</p> </list-item> <list-item> <p>We suggest to include the nLTT statistic in future ABC applications within phylogenetics. We argue that the use of ABC in diversification rate analysis is a promising new approach, but that care should be taken which summary statistics are chosen.</p> </list-item> </list> </p> </abstract>