Coherent and incoherent inference in phylogeography and human evolution

Proceedings of the National Academy of Sciences of the United States of America

Volumn 107, Issue 14, 2010, Pages 6376-6381

  Templeton, Alan R ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Approximate Bayesian computation; Coalescence; Logic; Nested clade analysis; Statistics

Indexed keywords

ARTICLE; BAYES THEOREM; CLADISTICS; EVOLUTION; HYPOTHESIS; LOGIC; PHYLOGEOGRAPHY; PRIORITY JOURNAL; PROBABILITY; SIMULATION; STATISTICAL ANALYSIS; STATISTICAL MODEL; VALIDITY;

EVOLUTION; HUMANS; PHYLOGENY; PROBABILITY;

EID: 77950899209     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0910647107     Document Type: Article

References (31)

1. Gabriel KR (1969) Simultaneous test procedures-some theory of multiple comparisons. Ann Math Stat 40:224-250.
2. Lavine M, Schervish MJ (1999) Bayes factors: What they are and what they are not. Am Stat 53:119-122.
3. Avise JC, Lansman RA, Shade RO (1979) The use of restriction endonucleases to measure mitochondrial DNA sequence relatedness in natural populations. I. Population structure and evolution in the genus Peromyscus. Genetics 92:279-295.
4. Avise JC, et al. (1987) Intraspecific phylogeography: The mitochondrial DNA bridge between population genetics and systematics. Annu Rev Ecol Syst 18:489-522.
5. 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.
6. Templeton AR (2002) Out of Africa again and again. Nature 416:45-51.
7. Templeton AR (2004) A maximum likelihood framework for cross validation of phylogeographic hypotheses. Evolutionary Theory and Processes: Modern Horizons, ed Wasser SP (Kluwer Academic, Dordrecht, The Netherlands), pp 209-230.
8. Templeton AR (2004) Statistical phylogeography: Methods of evaluating andminimizing inference errors. Mol Ecol 13:789-809.
9. Knowles LL (2004) The burgeoning field of statistical phylogeography. J Evol Biol 17: 1-10.
10. Nielsen R, Beaumont MA (2009) Statistical inferences in phylogeography. Mol Ecol 18: 1034-1047.
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. (Pubitemid 351377241)
12. Beaumont MA, Panchal M (2008) On the validity of nested clade phylogeographical analysis. Mol Ecol 17:2563-2565. (Pubitemid 351724947)
13. Fagundes NJR, et al. (2007) Statistical evaluation of alternative models of human evolution. Proc Natl Acad Sci USA 104:17614-17619. (Pubitemid 350210884)
14. Beaumont MA, Zhang WY, Balding DJ (2002) Approximate Bayesian computation in population genetics. Genetics 162:2025-2035.
15. Templeton AR (2009) Statistical hypothesis testing in intraspecific phylogeography: Nested clade phylogeographical analysis vs. approximate Bayesian computation. Mol Ecol 18:319-331.
16. Fisher RA (1922) On the mathematical foundations of theoretical statistics. Philos Trans R Soc LondonA 22:309-368.
17. Akaike H (1973) Information theory and an extension of the maximum likelihood principle. Second International Symposium on Information Theory, eds Petrov BN, Csaki F (Akademiai Kiado, Budapest), pp 267-281.
18. Schwarz G (1978) Estimating the dimension of a model. Ann Stat 6:461-464.
19. Templeton AR (2006) Population Genetics and Microevolutionary Theory (John Wiley & Sons, Hoboken, NJ), p 705.
20. Lavine M (1991) Sensitivity in Bayesian statistics-the prior and the likelihood. J Am Stat Assoc 86:396-399.
21. Heled J, Drummond AJ (2008) Bayesian inference of population size history from multiple loci. BMC Evol Biol, 8 (1):289. Available at: http://www.biomedcentral.com/ 1471-2148/8/289.
22. Pyron RA, Burbrink FT (2009) Lineage diversification in a widespread species: Roles for niche divergence and conservatism in the Common Kingsnake, Lampropeltis getula. Mol Ecol 18:3443-3457.
23. Shepard DB, Burbrink FT (2009) Phylogeographic and demographic effects of Pleistocene climatic fluctuations in a montane salamander, Plethodon fourchensis. Mol Ecol 18:2243-2262.
24. Sinharay S, Stern HS (2002) On the sensitivity of Bayes factors to the prior distributions. Am Stat 56:196-201.
25. Cheverud JM (2001) A simple correction for multiple comparisons in interval mapping genome scans. Heredity 87:52-58.
26. Fisher RA (1921) On the "probable error" of a coefficient of correlation deduced from a small sample. Metron 1:3-32.
27. Templeton AR (2005) Haplotype trees and modern human origins. Yearb Phys Anthropol 48:33-59. (Pubitemid 43200502)
28. Templeton AR (2007) Population biology and population genetics of Pleistocene Hominins. Handbook of Palaeoanthropology, eds Henke W, Tattersall I (Springer-Verlag, Berlin), Vol 3, pp 1825-1859.
29. Templeton AR (2007) Perspective: Genetics and recent human evolution. Evolution 61:1507-1519.
30. Templeton AR (2009) Testing the null hypothesis of reproductive isolation between two geographical regions in a specific time period with multi-locus nested clade analysis. The Evolution of Eibi Nevo in Honor of His 80th Birthday, eds Korol A, Wasser SP (Institute of Evolution, University of Haifa, Haifa, Israel), pp 81-84.
31. Templeton AR (2009) Why does a method that fails continue to be used: The answer. Evolution 63:807-812.