On the validity of nested clade phylogeographical analysis

Molecular Ecology

Volumn 17, Issue 11, 2008, Pages 2563-2565

  Beaumont, Mark A ^a   Panchal, Mahesh ^a  

^a UNIVERSITY OF READING   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; GEOGRAPHY; METHODOLOGY; NOTE; PHYLOGENY; POPULATION GENETICS; STATISTICAL ANALYSIS; STATISTICS;

COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; GENETICS, POPULATION; GEOGRAPHY; PHYLOGENY;

EID: 44249106348     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2008.03786.x     Document Type: Note

References (20)

1. Brisson JA, de Toni DC, Duncan I, Templeton AR (2005) Abdominal pigmentation variation in Drosophila polymorpha: geographic variation in the trait, and underlying phylogeography. Evolution, 59, 1046 1059.
2. Clement M, Posada D, Crandall KA (2000) tcs: a computer program to estimate gene genealogies. Molecular Ecology, 9, 1657 1659.
3. Excoffier L, Laval G, Schneider S (2005) arlequin (ver. 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics, Online 1, 47 50.
4. Fagundes NJR, Ray N, Beaumont M et al 2007) Statistical evaluation of alternative models of human evolution. Proceedings of the National Academy of Sciences, USA, 104, 17614 17619.
5. Knowles LL, Maddison WP (2002) Statistical phylogeography. Molecular Ecology, 11, 2623 2635.
6. Panchal M (2007) The automation of nested clade phylogeographic analysis. Bioinformatics, 23, 509 510.
7. Panchal M, Beaumont MA (2007) The automation and evaluation of nested clade phylogeographic analysis. Evolution, 61, 1466 1480.
8. Petit RJ (2008) The coup de grâce for the nested clade phylogeographic analysis? Molecular Ecology, 17, 516 518.
9. Petit RJ, Grivet D (2002) Optimal randomization strategies when testing the existence of a phylogeographic structure. Genetics, 161, 469 471.
10. Popper KR (1959) The Logic of Scientific Discovery. Hutchinson, London.
11. Posada D, Crandall KA, Templeton AR (2000) geodis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Molecular Ecology, 9, 487 488.
12. Posada D, Crandall KA, Templeton AR (2006) Nested clade analysis statistics. Molecular Ecology Notes, 6, 590 593.
13. Tarantola (2006) Popper, Bayes and the inverse problem. Nature Physics, 2, 492 494.
14. Templeton AR (2002b) Out of Africa again and again. Nature, 416, 45 51.
15. Templeton AR (2004b) Statistical phylogeography: methods of evaluating and minimizing inference errors. Molecular Ecology, 13, 789 809.
16. Templeton AR (2005) Haplotype trees and modern human origins. Yearbook of Physical Anthropology, 48, 33 59.
17. Templeton AR (2008) Nested clade analysis: an extensively validated method for strong phylogeographic inference. Molecular Ecology, 17, 1877 1880.
18. Templeton AR, Boerwinkle E, Sing CF (1987) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. 1. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila. Genetics, 117, 343 351.
19. Templeton AR, Routman E, Phillips C (1995) Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum. Genetics, 140, 767 782.
20. Wakeley J (2004) Recent trends in population genetics: more data! More math! Simple models? Journal of Heredity, 95, 397 405.