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  In defence of model-based inference in phylogeography (reply)

Beaumont, M. A., Nielsen, R., Robert, C., Hey, J., Gaggiotti, O., Knowles, L., et al. (2010). In defence of model-based inference in phylogeography (reply). Molecular Ecology, 19(3), 436-446. doi:10.1111/j.1365-294X.2009.04515.x.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-000F-D4DA-7 Version Permalink: http://hdl.handle.net/21.11116/0000-0003-3A95-4
Genre: Journal Article

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BEAUMONT_et_al-2010-Molecular_Ecology.pdf (Publisher version), 157KB
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 Creators:
Beaumont, Mark A., Author
Nielsen, Rasmus, Author
Robert, Christian, Author
Hey, Jody, Author
Gaggiotti, Oscar, Author
Knowles, Lacey, Author
Estoup, Arnaud, Author
Panchal, Mahesh1, Author              
Corander, Jukka, Author
Hickerson, Mike, Author
Sisson, Scott A., Author
Fagundes, Nelson, Author
Chikhi, Lounès, Author
Beerli, Peter, Author
Vitalis, Renaud, Author
Cornuet, Jean-Marie, Author
Huelsenbeck, John, Author
Foll, Matthieu, Author
Yang, Ziheng, Author
Rousset, Francois, Author
Balding, David, AuthorExcoffier, Laurent, Author more..
Affiliations:
1Department Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445634              

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Free keywords: molecular evolution; phylogeography; population genetics-empirical; population genetics-theoretical
 Abstract: Recent papers have promoted the view that model-based methods in general, and those based on Approximate Bayesian Computation (ABC) in particular, are flawed in a number of ways, and are therefore inappropriate for the analysis of phylogeographic data. These papers further argue that Nested Clade Phylogeographic Analysis (NCPA) offers the best approach in statistical phylogeography. In order to remove the confusion and misconceptions introduced by these papers, we justify and explain the reasoning behind model-based inference. We argue that ABC is a statistically valid approach, alongside other computational statistical techniques that have been successfully used to infer parameters and compare models in population genetics. We also examine the NCPA method and highlight numerous deficiencies, either when used with single or multiple loci. We further show that the ages of clades are carelessly used to infer ages of demographic events, that these ages are estimated under a simple model of panmixia and population stationarity but are then used under different and unspecified models to test hypotheses, a usage the invalidates these testing procedures. We conclude by encouraging researchers to study and use model-based inference in population genetics.

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Language(s): eng - English
 Dates: 2010-02
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: -
 Identifiers: eDoc: 447233
DOI: 10.1111/j.1365-294X.2009.04515.x
Other: 2957/S 39302
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Title: Molecular Ecology
Source Genre: Journal
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Pages: - Volume / Issue: 19 (3) Sequence Number: - Start / End Page: 436 - 446 Identifier: ISSN: 0962-1083 (print)
ISSN: 1365-294X (online)