In defence of model-based inference in phylogeography

Research output: Contribution to journal › Review › Research › peer-review

Standard

In defence of model-based inference in phylogeography. / 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, Jean Marie; Huelsenbeck, John; Foll, Matthieu; Yang, Ziheng; Rousset, Francois; Balding, David; Excoffier, Laurent.

In: Molecular Ecology, Vol. 19, No. 3, 2010, p. 436-446.

Research output: Contribution to journal › Review › Research › peer-review

Harvard

Beaumont, MA, Nielsen, R, Robert, C, Hey, J, Gaggiotti, O, Knowles, L, Estoup, A, Panchal, M, Corander, J, Hickerson, M, Sisson, SA, Fagundes, N, Chikhi, L, Beerli, P, Vitalis, R, Cornuet, JM, Huelsenbeck, J, Foll, M, Yang, Z, Rousset, F, Balding, D & Excoffier, L 2010, 'In defence of model-based inference in phylogeography', Molecular Ecology, vol. 19, no. 3, pp. 436-446. https://doi.org/10.1111/j.1365-294X.2009.04515.x

APA

Beaumont, M. A., Nielsen, R., Robert, C., Hey, J., Gaggiotti, O., Knowles, L., Estoup, A., Panchal, M., Corander, J., Hickerson, M., Sisson, S. A., Fagundes, N., Chikhi, L., Beerli, P., Vitalis, R., Cornuet, J. M., Huelsenbeck, J., Foll, M., Yang, Z., ... Excoffier, L. (2010). In defence of model-based inference in phylogeography. Molecular Ecology, 19(3), 436-446. https://doi.org/10.1111/j.1365-294X.2009.04515.x

Vancouver

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

Author

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, Jean Marie ; Huelsenbeck, John ; Foll, Matthieu ; Yang, Ziheng ; Rousset, Francois ; Balding, David ; Excoffier, Laurent. / In defence of model-based inference in phylogeography. In: Molecular Ecology. 2010 ; Vol. 19, No. 3. pp. 436-446.

Bibtex

@article{d6030cd597c54bdebecd96f9d800226d,
title = "In defence of model-based inference in phylogeography",
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.",
keywords = "Molecular evolution, Phylogeography, Population genetics-empirical, Population genetics-theoretical",
author = "Beaumont, {Mark A.} and Rasmus Nielsen and Christian Robert and Jody Hey and Oscar Gaggiotti and Lacey Knowles and Arnaud Estoup and Mahesh Panchal and Jukka Corander and Mike Hickerson and Sisson, {Scott A.} and Nelson Fagundes and Loun{\`e}s Chikhi and Peter Beerli and Renaud Vitalis and Cornuet, {Jean Marie} and John Huelsenbeck and Matthieu Foll and Ziheng Yang and Francois Rousset and David Balding and Laurent Excoffier",
year = "2010",
doi = "10.1111/j.1365-294X.2009.04515.x",
language = "English",
volume = "19",
pages = "436--446",
journal = "Molecular Ecology",
issn = "0962-1083",
publisher = "Wiley-Blackwell",
number = "3",

}

RIS

TY - JOUR

T1 - In defence of model-based inference in phylogeography

AU - Beaumont, Mark A.

AU - Nielsen, Rasmus

AU - Robert, Christian

AU - Hey, Jody

AU - Gaggiotti, Oscar

AU - Knowles, Lacey

AU - Estoup, Arnaud

AU - Panchal, Mahesh

AU - Corander, Jukka

AU - Hickerson, Mike

AU - Sisson, Scott A.

AU - Fagundes, Nelson

AU - Chikhi, Lounès

AU - Beerli, Peter

AU - Vitalis, Renaud

AU - Cornuet, Jean Marie

AU - Huelsenbeck, John

AU - Foll, Matthieu

AU - Yang, Ziheng

AU - Rousset, Francois

AU - Balding, David

AU - Excoffier, Laurent

PY - 2010

Y1 - 2010

N2 - 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.

AB - 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.

KW - Molecular evolution

KW - Phylogeography

KW - Population genetics-empirical

KW - Population genetics-theoretical

U2 - 10.1111/j.1365-294X.2009.04515.x

DO - 10.1111/j.1365-294X.2009.04515.x

M3 - Review

AN - SCOPUS:74549201612

VL - 19

SP - 436

EP - 446

JO - Molecular Ecology

JF - Molecular Ecology

SN - 0962-1083

IS - 3

ER -

ID: 222644280