The coup de grâce for the nested clade phylogeographic analysis?

Nested clade phylogeographic analysis (NCPA) has become a popular method for reconstructing the history of populations across species ranges. Ever since its invention in 1995, criticisms have been formulated, but the method, which has been regularly updated, continues to attract investigators. Molecular Ecology has published a large fraction of the literature on the topic — both pro and con. A recent study by Panchal and Beaumont (2007) finally allows a precise evaluation of the method by developing software that automates the somewhat complicated NCPA procedure. Using simulations of random‐mating populations, Panchal and Beaumont find a high frequency of false‐positives with their automated NCPA procedure (over 75%). These findings, which echo and amplify earlier warnings, appear serious enough to suggest to researchers to await further evaluation of the method. Although no other all‐encompassing method such as the NCAP currently exists to evaluate phylogeographic data sets, researchers have many alternative methods to test ever more refined hypotheses.

[1]  J. Wakeley.  The Evolution of Population Biology: Inferences about the structure and history of populations: coalescents and intraspecific phylogeography , 2004 .

[2]  J. L. Bouzat,et al.  Effects of recent population bottlenecks on reconstructing the demographic history of prairie‐chickens , 2007, Molecular ecology.

[3]  Mahesh Panchal,et al.  The automation of Nested Clade Phylogeographic Analysis , 2007, Bioinform..

[4]  P. Smouse.  To tree or not to tree , 1998 .

[5]  L Lacey Knowles,et al.  Statistical phylogeography. , 2002, Molecular ecology.

[6]  N. Ferrand,et al.  Nested clade analysis and the genetic evidence for population expansion in the phylogeography of the golden-striped salamander, Chioglossa lusitanica (Amphibia: Urodela) , 2002, Heredity.

[7]  W. Jordan,et al.  Using nested clade analysis to assess the history of colonization and the persistence of populations of an Iberian Lizard , 2002, Molecular ecology.

[8]  Templeton,et al.  Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history , 1998, Molecular ecology.

[9]  Alan R Templeton,et al.  Statistical phylogeography: methods of evaluating and minimizing inference errors , 2004, Molecular ecology.

[10]  Mahesh Panchal,et al.  THE AUTOMATION AND EVALUATION OF NESTED CLADE PHYLOGEOGRAPHIC ANALYSIS , 2007, Evolution; international journal of organic evolution.

[11]  E. Routman,et al.  Population genetic structure of the toad Bufo woodhousii: an empirical assessment of the effects of haplotype extinction on nested cladistic analysis , 2003, Molecular ecology.

[12]  K. Crandall,et al.  GeoDis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes , 2000, Molecular ecology.

[13]  Jody Hey,et al.  The study of structured populations — new hope for a difficult and divided science , 2003, Nature Reviews Genetics.

[14]  A. Templeton.  Using phylogeographic analyses of gene trees to test species status and processes , 2001, Molecular ecology.

[15]  R. Petit,et al.  Optimal randomization strategies when testing the existence of a phylogeographic structure. , 2002, Genetics.

[16]  A. Templeton,et al.  Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum. , 1995, Genetics.

[17]  A. Templeton.  “Optimal” Randomization Strategies When Testing the Existence of a Phylogeographic Structure: A Reply to Petit and Grivet , 2002 .

[18]  autoinfer1.0: a computer program to infer biogeographical events automatically , 2006 .

[19]  N. Ferrand,et al.  Current perspectives in phylogeography and the significance of South European refugia in the creation and maintenance of European biodiversity , 2007 .

[20]  Ych-chu Wang.  Molecular ecology , 1992, Journal of Northeast Forestry University.

[21]  L. Knowles,et al.  The burgeoning field of statistical phylogeography , 2003, Journal of evolutionary biology.