Statistical phylogeography: Methods of evaluating and minimizing inference errors

Molecular Ecology

Volumn 13, Issue 4, 2004, Pages 789-809

  Templeton, Alan R ^a  

^a WASHINGTON UNIVERSITY   (United States)

Author keywords

Cross validation; Haplotype trees; Hypothesis testing; Nested clade analysis; Phylogeography; Statistical inference

Indexed keywords

DNA;

COMPUTER SIMULATION; GENETICS; GEOGRAPHY; HAPLOTYPE; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; POPULATION DYNAMICS; REVIEW; STATISTICAL ANALYSIS; STATISTICAL MODEL;

COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; DNA; EVOLUTION, MOLECULAR; GEOGRAPHY; HAPLOTYPES; LIKELIHOOD FUNCTIONS; PHYLOGENY; POPULATION DYNAMICS; RESEARCH DESIGN;

EID: 1642339467     PISSN: 09621083     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-294X.2003.02041.x     Document Type: Review

References (24)

1. 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.
2. Byrne M, MacDonald B, Coates D (2002) Phylogeographical patterns in chloroplast DNA variation within the Acacia acuminata (Leguminosae: Mimosoideae) complex in Western Australia. Journal of Evolutionary Biology, 15, 576-587.
3. Castelloe J, Templeton AR (1994) Root probabilities for intraspecific gene trees under neutral coalescent theory. Molecular Phylogenetics and Evolution, 3, 102-113.
4. Fullerton SM, Clark AG, Weiss KM et al. (2000) Apolipoprotein E variation at the sequence haplotype level: implications for the origin and maintenance of a major human polymorphism. American Journal of Human Genetics, 67, 881-900.
5. Good PI (1999) Resampling Methods: a Practical Guide to Data Analysis. Birkhäuser, Boston.
6. 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.
7. Irwin DE (2002) Phylogeographic breaks without geographic barriers to gene flow. Evolution, 56, 2383-2394.
8. Knowles LL (2001) Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshopprers. Molecular Ecology, 10, 691-701.
9. Knowles LL, Maddison WP (2002) Statistical phylogeography. Molecular Ecology, 11, 2623-2635.
10. Masta SE, Laurent NM, Routman EJ (2003) Population genetic structure of the toad Bufo woodhousii: an empirical assessment of the effects of haplotype extinction on nested cladistic analysis. Molecular Ecology, 12, 1541-1554.
11. Paulo OS, Jordan WC, Bruford MW, Nichols RA (2002) Using nested clade analysis to assess the history of colonization and the persistence of populations of an Iberian Lizard. Molecular Ecology, 11, 809-820.
12. Pfenninger M, Posada D (2002) Phylogeographic history of the land snail Candidula unifasciata (Helicellinae, Stylommatophora): fragmentation, corridor migration, and secondary contact. Evolution, 56, 1776-1788.
13. Stringer C (2002) Modern human origins: progress and prospects. Philosophical Transactions of the Royal Society of London B, 357, 563-579.
14. Templeton AR (1983) Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution, 37, 221-244.
15. Templeton AR (1998a) Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Molecular Ecology, 7, 381-397.
16. Templeton AR (1998b) Human races: a genetic and evolutionary perspective. American Anthropologist, 100, 632-650.
17. Templeton AR (2001) Using phylogeographic analyses of gene trees to test species status and processes. Molecular Ecology, 10, 779-791.
18. Templeton AR (2002) Out of Africa again and again. Nature, 416, 45-51.
19. Templeton AR (2003a) A maximum likelihood framework for cross validation of phylogeographic hypotheses. In: Evolutionary Theory and Processes: Modern Horizons (ed. Wasser SP). Kluwer Academic Publishers, the Netherlands, in press.
20. Templeton AR (2003b) Using haplotype trees for phylogeographic and species Inference in fish populations. Environmental Biology of Fishes, in press.
21. Templeton AR, Boerwinkle E, Sing CF (1987) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and an analysis of Alcohol Dehydrogenase activity in Drosophila. Genetics, 117, 343-351.
22. Templeton AR, Crandall KA, Sing CF (1992) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics, 132, 619-633.
23. 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.
24. Turner TF, Trexler JC, Harris JL, Haynes JL (2000) Nested cladistic analysis indicates population fragmentation shapes genetic diversity in a freshwater mussel. Genetics, 154, 777-785.