Nested clade analysis: An extensively validated method for strong phylogeographic inference

Molecular Ecology

Volumn 17, Issue 8, 2008, Pages 1877-1880

  Templeton, Alan R ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Computer simulation; Cross validation; False positives; Nested clade analysis; Phylogeography; Statistics

Indexed keywords

GEOGRAPHY; MOLECULAR EVOLUTION; NOTE; PHYLOGENY;

EVOLUTION, MOLECULAR; GEOGRAPHY; PHYLOGENY;

EID: 42049111199     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2008.03731.x     Document Type: Note

References (20)

1. Eswaran V, Harpending H, Rogers AR (2005) Genomics refutes an exclusively African origin of humans. Journal of Human Evolution, 49, 1 18.
2. Fagundes NJR, Ray N, Beaumont M et al 2007) Statistical evaluation of alternative models of human evolution. Proceedings of the National Academy of Sciences, 104, 17614 17619.
3. Hutchison DW, Templeton AR (1999) Correlation of pairwise genetic and geographic distance measures: Inferring the relative influences of gene flow and drift on the distribution of genetic variability. Evolution, 53, 1898 1914.
4. Knowles LL, Maddison WP (2002) Statistical phylogeography. Molecular Ecology, 11, 2623 2635.
5. Panchal M, Beaumont MA (2007) The automation and evaluation of nested clade phylogeographic analysis. Evolution, 61, 1466 1480.
6. Petit RJ (2008) The coup de grâce for the nested clade phylogeographic analysis? Molecular Ecology, 17, 516 518.
7. Petit RJ, Grivet D (2002) Optimal randomization strategies when testing the existence of a phylogeographic structure. Genetics, 161, 469 471.
8. Popper KR (1959) The Logic of Scientific Discovery. Hutchinson, London.
9. Posada D, Maxwell TJ, Templeton AR (2005) treescan: a bioinformatic application to search for genotype/phenotype associations using haplotype trees. Bioinformatics, 21, 2130 2132.
10. 2 tests for nested categorized data. Annals of Human Genetics, 54, 315 320.
11. Strasburg J, Kearney M, Moritz C, Templeton A (2007) Combining phylogeography with distribution modeling: multiple Pleistocene range expansions in a parthenogenetic gecko from the Australian arid zone. PLoS ONE, 2, e760.
12. Templeton AR (1998) Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Molecular Ecology, 7, 381 397.
13. Templeton AR (2002a) 'Optimal' randomization strategies when testing the existence of a phylogeographic structure: a reply to Petit and Grivet. Genetics, 161, 473 475.
14. Templeton AR (2002b) Out of Africa again and again. Nature, 416, 45 51.
15. Templeton AR (2004a) A maximum likelihood framework for cross validation of phylogeographic hypotheses. In : Evolutionary Theory and Processes: Modern Horizons (ed. Wasser SP pp. 209 230. Kluwer Academic Publishers, Dordrecht, The Netherlands.
16. Templeton AR (2004b) Statistical phylogeography: methods of evaluating and minimizing inference errors. Molecular Ecology, 13, 789 809.
17. Templeton AR (2005) Haplotype trees and modern human origins. Yearbook of Physical Anthropology, 48, 33 59.
18. Templeton AR (2007) Perspective: genetics and recent human evolution. Evolution, 61, 1507 1519.
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. Westfall PH, Young SS (1993) Resampling-Based Multiple Testing. John Wiley & Sons, New York.