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In defence of model‐based inference in phylogeography
Author(s) -
BEAUMONT MARK A.,
NIELSEN RASMUS,
ROBERT CHRISTIAN,
HEY JODY,
GAGGIOTTI OSCAR,
KNOWLES LACEY,
ESTOUP ARNAUD,
PANCHAL MAHESH,
CORANDER JUKKA,
HICKERSON MIKE,
SISSON SCOTT A.,
FAGUNDES NELSON,
CHIKHI LOUNÈS,
BEERLI PETER,
VITALIS RENAUD,
CORNUET JEANMARIE,
HUELSENBECK JOHN,
FOLL MATTHIEU,
YANG ZIHENG,
ROUSSET FRANCOIS,
BALDING DAVID,
EXCOFFIER LAURENT
Publication year - 2010
Publication title -
molecular ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.619
H-Index - 225
eISSN - 1365-294X
pISSN - 0962-1083
DOI - 10.1111/j.1365-294x.2009.04515.x
Subject(s) - approximate bayesian computation , phylogeography , biology , inference , panmixia , population , clade , population genetics , evolutionary biology , confusion , statistical hypothesis testing , statistical inference , bayesian probability , econometrics , data science , computer science , artificial intelligence , statistics , genetics , phylogenetics , demography , mathematics , genetic structure , genetic variation , psychology , sociology , psychoanalysis , gene
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.