Statistical phylogeography

Molecular Ecology

Volumn 11, Issue 12, 2002, Pages 2623-2635

  Knowles, L Lacey ^a   Maddison, Wayne P ^a  

^a UNIVERSITY OF ARIZONA   (United States)

Author keywords

Biogeography; Coalescence; Genealogy; Phylogeography; Population genetics; Speciation

Indexed keywords

ANIMALS; EVOLUTION, MOLECULAR; GEOGRAPHY; GRASSHOPPERS; MODELS, GENETIC; MODELS, STATISTICAL; PHYLOGENY; SONGBIRDS;

EID: 0036900040     PISSN: 09621083     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-294X.2002.01637.x     Document Type: Article

References (68)

1. Arbogast B, Edwards SV, Wakeley J, Beerli P, Slowinski JB (2002) Estimating divergence times from molecular data on phylogenetic and population genetic time scales. Annual Review of Ecology and Systematics, in press.
2. Avise JC (1989) Gene trees and organismal histories: A phylogenetic approach to population biology. Evolution, 43, 1192-1208.
3. Avise JC (1994) Molecular Markers, Natural History, and Evolution. Chapman & Hall, London.
4. Avise JC, Ball RM (1990) Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology, 7, 43-67.
5. Bahlo M, Griffiths RC (2000) Inference from gene trees in a subdivided population. Theoretical Population Biology, 57, 79-95.
6. Barton NH, Wilson I (1995) Genealogies and geography. Philosophical Transactions of the Royal Society of London B, 349, 49-59.
7. Beerli P, Felsenstein J (1999) Maximum likelihood estimation of a migration rates and effective population numbers in two populations using a coalescent approach. Genetics, 152, 763-773.
8. Beerli P, Felsenstein J (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proceedings of the National Academy of Sciences of the USA, 98, 4563-4568.
9. Beerli P, Hotz H, Uzzell T (1996) Geologically dated sea barriers calibrate a protein clock for Aegean water frogs. Evolution, 50, 1676-1687.
10. Bertorelle G, Rannala B (1998) Using rare mutations to estimate population divergence times: A maximum likelihood approach. Proceedings of the National Academy of Sciences of the USA, 95, 15452-15457.
11. Clement M, Posada D, Crandall K (2000) TCS: A computer program to estimate gene genealogies. Molecular Ecology, 9, 167-1660.
12. Cruzan MB, Templeton AR (2000) Paleoecology and coalescence: Phylogeographic analysis of hypotheses from the fossil record. Trends in Ecology and Evolution, 15, 491-496.
13. Donnely P, Tavaré S (1995) Coalescents and genealogical structure under neutrality. Annu. Rev. Genet., 29, 401-421.
14. Edwards SV (1993) Mitochondrial gene genealogy and gene flow among island and mainland populations of a sedentary songbird, the Grey-crowned Babbler, Pomatostomus temporalis. Evolution, 47, 118-1137.
15. Edwards SV, Beerli P (2000) Perspective: Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution, 54, 1839-1854.
16. Emerson BC, Paradis E, Thébaud C (2001) Revealing the demographic histories of species using DNA sequences. TREE, 16, 707-716.
17. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics, 131, 479-491.
18. Griffiths RC (1998) GENETREE. Available from http:// http://www.maths.monash.edu.au/~mbahlo/mpg/gtree.html.
19. Hare MP (2001) Prospects for nuclear gene phylogeography. TREE, 16, 700-706.
20. Harrison R (1991) Molecular changes at speciation. Annual Review of Ecology and Systematics, 22, 281-308.
21. Hudson R (1990) Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology, 7, 1-44.
22. Huelsenbeck JP, Crandall KA (1997) Phylogeny estimation and hypothesis testing using maximum likelihood. Annual Review of Ecology and Systematics, 28, 437-466.
23. Hugall A, Mortiz C, Moussalli A, Stanisic J (2002) Reconciling paleodistribution models and comparative phylogeography in the wet tropics rainforest land snail Gnarosophia bellendenkerensis. Proceedings of the National Academy of Sciences of the USA, in Press.
24. Kidd DM, Ritchie MG (2000) Inferring the patterns and causes of geographic variation in Ephippiger ephippiger (Orthoptera, Tettigoniidae) using geographical information systems (GIS). Biological Journal of the Linnean Society, 71, 269-295.
25. Kingman JFC (1982) The coalescent. Stochastic Process. Appl., 13, 235-248.
26. Kishino H, Thorne JL, Bruno WJ (2001) Paeformance of a divergence time estimation method under a probabilistic model of rate evolution. Molecular Biology and Evolution, 18, 352-361.
27. Klicka J, Zink RM (1997) The improtance of recent ice ages in speclarion: A failed paradigm. Science, 277, 1666-1669.
28. Kliman RM, Andolfatto P, Coyne JA et al. (2000) The population genetics of the origin and divergence of the Drosophila simulans complex species. Genetics, 156, 1913-1931.
29. Knowles LL (2000) Tests of Pleistocene speciation in montane grasshoppers from the sky islands of western North America (genus Melanoplus). Evolution, 54, 1337-1348.
30. Knowles LL (2001a) Genealogical portraits of speciation in montane grasshoppers (genus Melanoplus) from the sky islands of the Rocky Mountains. Proceedings of the Royal Society of London Series B, 268, 1-6.
31. Knowles LL (2001b) Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshoppers. Molecular Ecology, 10, 691-701.
32. Knowles LL (2003) The burgeoning field of statistical phylogeography. Journal of Evolutionary Biology, in press.
33. Knowles LL, Futuyma DJ, Eanes WF, Rannala B (1999) Insights into speciation mode from historical demography in the phytophagous beetle Ophraella. Evolution, 53, 1846-1856.
34. Kuhner M, Yamato J, Felsenstein J (1998) Maximum likelihood estimation of population growth rates based on the coalescent. Genetics, 149, 429-434.
35. Maddison W (1997) Gene trees in species trees. Systematic Biology, 46, 523-536.
36. Maddison WP, Maddison DR (2000) MESQUITE: A Modular Programming System for Evolutionary Analysis. Prototype v.0.9d17. http://mesquiteproject.org.
37. Maddison W, McMahon M (2000) Divergence and reticulation among montane populations of a jumping spider (Habronattus pugillis Griswold). Systematic Biology, 49, 400-421.
38. Masta SE, Maddison WP (2002) Sexual selection driving diversification in jumping spiders. Proceedings of the National Academy of Sciences of the USA, 99, 4442-4447.
39. Mengel RM (1964) The probable history of species formation in some northern wood warblers (Parulidae). Living Bird, 3, 9-43.
40. Milot E, Gibbs HL, Hobson KA (2000) Phylogeography and genetic structure of northern populations of the yellow warbler (Dendroica petechia). Molecular Ecology, 9, 677-681.
41. Nee S, Holmes EC, Rambaut A, Harvey PH (1995) Inferring population history from molecular phylogenies. Philosophical Transactions of the Royal Society of London Series B, 349, 25-31.
42. Nielsen R, Slatkin M (2000) Likelihood analysis of ongoing gene flow and historical association. Evolution, 54, 44-50.
43. 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.
44. Riddle BR (1996) The molecular phylogeographic bridge between deep and shallow history in continental biotas. Trends in Ecology and Evolution, 11, 187-228.
45. Rosenberg NA (2002) The probability of topological concordance of gene trees and species trees. Theoretical Population Biology, 61, 225-247.
46. Sanderson MJ (1997) A nonparametric approach to estimating divergence times in the absence of rate constancy. Molecular Biology and Evolution, 14, 1218-1231.
47. Schneider CJ, Cunningham M, Moritz C (1998) Comparitive phylogeography and the history of endemic vertebrates in the wet tropic rainforests of Australia. Molecular Ecology, 7, 487-498.
48. da Silva MNF, Patton JL (1998) Molecular phylogeography and the evolution and conservation of Amazonian mammals. Molecular Ecology, 7, 475-486.
49. Slatkin M (1987) The average number of sites separating DNA sequences drawn from a subdivided population. Theoretical Population Biology, 32, 42-49.
50. Slatkin M, Bertorelle G (2001) The use of intraallelic variability for testing neutrality and estimating population growth rate. Genetics, 155, 865-874.
51. Slatkin M, Hudson RR (1991) Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics, 129, 555-562.
52. Slatkin M, Maddison WP (1989) A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics, 123, 603-613.
53. Stone G (2000) Phylogeography, hybridization and speciation. Trends in Ecology and Evolution, 15, 354-355.
54. Takahata N (1989) Gene genealogy in 3 related populations - Consistency probability between gene and population trees. Genetics, 122, 957-966.
55. Takahata N (1991) Genealogy of neutral genes and spreading of selected mutations in a geographically structured population. Genetics, 129, 585-595.
56. Takahata N (1993) Allelic genealogy and human evolution. Molecular Biology and Evolution, 10, 2-22.
57. Takahata N, Satta Y (1997) Evolution of the primate lineage leading to modern humans: Phylogenetic and demographic inferences from DNA sequences. Proceedings of the National Academy of Sciences of the USA, 94, 4811-4815.
58. Takahata N, Satta Y, Klein J (1995) Divergence time and population size in the lineage leading to modern humans. Theoretical Population Biology, 48, 198-221.
59. Tang H, Siegmund DO, Peidong S, Oefner PJ, Feldman MW (2002) Estimation of coalescence times from nucleotide sequence data using a tree-based partition. Genetics, 161, 447-459.
60. Templeton AR (1998a) Nested clade analyses of phylogeographic data: Testing hypotheses about gene flow and population history. Molecular Ecology, 7, 381-397.
61. Templeton AR (1998b) The role of molecular genetics in speciation studies. In: Molecular Approaches to Ecology (eds DeSalle R, Schierwater B), pp. 131-156. Birkhäuser-Verlag, Basel.
62. Templeton AR (2002a) Out of Africa again and again. Nature, 416, 45-51.
63. Templeton AR (2002b) 'Optimal' randomization strategies when testing the existence of a phylogeographic structure: A reply to Petit and Grivet. Genetics, 161, 473-475.
64. Templeton AR, Routman E, Phillips CA (1995) Separating population structure from population history: A cladistic analysis of the geographic distribution of mitochondrial DNA haplotypes in the Tiger Salamander, Ambystoma Tigrinum. Genetics, 140, 767-782.
65. Wakeley J (2000) The effects of subdivison on the genetic divergence of populations and species. Evolution, 54, 1092-1101.
66. Wakeley J (2001) The coalescent in an island model of population subdivision with variation among demes. Theoretical Population Biology, 59, 133-144.
67. Wakeley J (2002) Inferences about the structure and history of populations: Coalescents and intraspecific phylogeography. In: The Evolution of Population Biology - Modern Synthesis (eds Singh R, Uyenoyama M, Jain S), Cambridge University Press, Cambridge, in press.
68. Wakeley J, Hey J (1998) Testing speciation models with DNA sequence data. In: Molecular Approaches to Ecology (eds DeSalle R, Schierwater B), pp. 157-175. Birkhäuser-Verlag, Basel.