Using haplotype trees for phylogeographic and species inference in fish populations

Environmental Biology of Fishes

Volumn 69, Issue 1-4, 2004, Pages 7-20

  Templeton, Alan R ^a  

^a WASHINGTON UNIVERSITY   (United States)

Author keywords

Diversity; History; Hybridization

Indexed keywords

BIODIVERSITY; EVOLUTION; GENETIC VARIATION; HYBRIDIZATION;

LEUCISCUS; LEUCISCUS CEPHALUS; PHYLO; SALMO; SALMO TRUTTA; SALMONIDAE;

EID: 3543021006     PISSN: 03781909     EISSN: None     Source Type: Journal    
DOI: 10.1023/B:EBFI.0000022870.76912.0c     Document Type: Conference Paper

References (30)

1. Antunes, A., A.R. Templeton, R. Guyomard & P. Alexandrino. 2002. The role of nuclear genes in intraspecific evolutionary inference: Genealogy of the transferrin gene in the brown trout. Mol. Biol. Evol. 19: 1272-1287.
2. Behnke, R.J. 1972. The systematics of salmonid fishes of recently glaciated lakes. J. Fish. Res. Board Can. 29: 639-671.
3. Bernatchez, L. 2001. The evolutionary history of brown trout (Salmo trutta L.) inferred from phylogeographic, nested clade, and mismatch analyses of mitochondrial DNA variation. Evolution 55: 351-379.
4. Bernatchez, L., R. Guyomard & R. Bonhomme. 1992. DNA sequence variation of the mitochondrial control region among geographically and morphologically remote European brown trout Salmo trutta populations. Mol. Ecol. 1: 161-173.
5. Bouza, C., J. Arias, J. Castro, L. Sánchez & P. Martínez. 1999. Genetic structure of brown trout, Salmo trutta L., at the southern limit of the distribution range of the anadromous form. Mol. Ecol. 8: 1991-2002.
6. Castelloe, J. & A.R. Templeton. 1994. Root probabilities for intraspecific gene trees under neutral coalescent theory. Mol. Phylogen. Evol. 3: 102-113.
7. Clark, A.G. 1990. Inference of haplotypes from PCR-amplified samples of diploid populations. Mol. Biol. Evol. 7: 111-122.
8. Crandall, K.A. & A.R. Templeton. 1999. Statistical approaches to detecting recombination. pp. 153-176. In: K.A. Crandall (ed.) The Evolution of HIV, The Johns Hopkins University Press, Baltimore.
9. Durand, J.D., A.R. Templeton, B. Guinand, A. Imsiridou & Y. Bouvet. 1999. Nested clade and phylogeographic analyses of the chub, Leuciscus cephalus (Teleostei, Cyprinidae) in Greece: Implications for Balkan Peninsula biogeography. Mol. Phylogen. Evol. 13: 566-580.
10. García-Marín, J.L., F.M. Utter & C. Pla. 1996. Origins and relationships of native populations of Salmo trutta (brown trout) in Spain. Heredity 77: 313-323.
11. Hull, D.L. 1997. The ideal species concept - and why we can't get it. pp. 357-380. In: M.F. Claridge, H.A. Dawah & M.R. Wilson (ed.) Species: The Units of Biodiversity, Chapman & Hall, London.
12. O'Brien, S.J. & E. Mayr. 1991. Bureaucratic mischief: Recognizing endangered species and subspecies. Science 251: 1187-1188.
13. Povz, M. 1995. Status of freshwater fishes in the Adriatic catchment of Slovenia. Biol. Conserv. 72: 171-177.
14. Rieseberg, L.H. 1997. Hybrid origins of plant species. Ann. Rev. Ecol. Syst. 28: 359-389.
15. Sommani, E. 1960. II Salmo marmoratus Cuv. sua origine e distribuzione nell'Italia settentrionale. Bolletino di Pesca, Piscicoltura e Idrobiologia 15: 40-47.
16. Swofford, D. 2002. PAUP*: Phylogenetic Analysis Using Parsimony (and other methods). Version 4. Sinauer, Sunderland, MA.
17. Templeton, A.R. 1989. The meaning of species and speciation: A genetic perspective, pp. 3-27. In: D. Otte & J.A. Endler (ed.) Speciation and its Consequences, Sinauer, Sunderland, Massachusetts.
18. Templeton, A.R. 1998a. Nested clade analyses of phylogeographic data: Testing hypotheses about gene flow and population history. Mol. Ecol. 7: 381-397.
19. Templeton, A.R. 1998b. Species and speciation: Geography, population structure, ecology, and gene trees. pp. 32-43. In: D.J. Howard & S.H. Berlocher (ed.) Endless Forms: Species and Speciation, Oxford University Press, Oxford.
20. Templeton, A.R. 1999. Using gene trees to infer species from testable null hypothesis: Cohesion species in the Spalax ehrenbergi complex. pp. 171-192. In: S.P. Wasser (ed.) Evolutionary Theory and Processes: Modern Perspectives, Papers in Honour of Eviatar Nevo, Kluwer Academic Publishers, Dordrecht.
21. Templeton, A.R. 2001. Using phylogeographic analyses of gene trees to test species status and processes. Mol. Ecol. 10: 779-791.
22. Templeton, A.R. 2002. Out of Africa again and again. Nature 416: 45-51.
23. Templeton, A.R. & C.F. Sing. 1993. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination. Genetics 134: 659-669.
24. Templeton, A.R., E. Boerwinkle & C.F. Sing. 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.
25. Templeton, A.R., K.A. Crandall & C.F. Sing. 1992. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping & DNA sequence data. III. Cladogram estimation. Genetics 132: 619-633.
26. Templeton, A.R., E. Routman & C. Phillips. 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.
27. Templeton, A.R., A.G. Clark, K.M. Weiss, D.A. Nickerson, J. Stengård, E. Boerwinkle & C.F. Sing. 2000a. Recombinational and mutational hotspots within the human Lipoprotein Lipase gene. Amer. J. Hum. Gen. 66: 69-83.
28. Templeton, A.R., S.D. Maskas & M.B. Cruzan. 2000b. Gene trees: A powerful tool for exploring the evolutionary biology of species and speciation. Plant Species Biol. 15: 211-222.
29. Templeton, A.R., K.M. Weiss, D.A. Nickerson, E. Boerwinkle & C.F. Sing. 2000c. Cladistic structure within the human Lipoprotein lipase gene and its implications for phenotypic association studies. Genetics 156: 1259-1275.
30. Wright, S. 1943. Isolation by distance. Genetics 28: 114-138.