Importance of genetic drift during Pleistocene divergence as revealed by analyses of genomic variation

Molecular Ecology

Volumn 14, Issue 13, 2005, Pages 4023-4032

  Knowles, L Lacey ^a   Richards, Corinne L ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

AFLPs; Coalescence; Genomic; Historical demography; Sky islands; Speciation; Statistical phylogeography

Indexed keywords

MELANOPLUS OREGONENSIS;

PRIMER DNA;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CLIMATE; COMPARATIVE STUDY; GENETIC DRIFT; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; GRASSHOPPER; NUCLEIC ACID AMPLIFICATION; PHYLOGENY; POPULATION GENETICS; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SPECIES DIFFERENCE; UNITED STATES;

ANIMALS; BAYES THEOREM; CLIMATE; DNA PRIMERS; GENETIC DRIFT; GENETICS, POPULATION; GEOGRAPHY; GRASSHOPPERS; IDAHO; MODELS, GENETIC; MONTANA; NUCLEIC ACID AMPLIFICATION TECHNIQUES; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; SPECIES SPECIFICITY; VARIATION (GENETICS); WYOMING;

EID: 33645033975     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2005.02711.x     Document Type: Article

References (66)

1. Avise JC (1994) Molecular Markers, Natural History, and Evolution. Chapman & Hall, London.
2. Avise JC, Walker D (1998) Pleistocene phylogeographic effects on avian populations and the speciation process. Proceedings of the Royal Society of London. Series B, Biological Sciences, 265, 457-463.
3. Ayoub NA, Riechert SE (2004) Molecular evidence for Pleistocene glacial cycles driving diversification of a North American desert spider, Agelenopsis aperta. Molecular Ecology, 13, 3453-3465.
4. Beaumont MA, Nichols RA (1996) Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society of London. Series B, Biological Sciences, 263, 1619-1626.
5. Bermingham E, Rohwer S, Freeman S, Woods C (1992) Vicariance biogeography in the Pleistocene and speciation in North American wood warblers: a test of Mengel's model. Proceedings of the National Academy of Sciences, USA, 89, 6624-6628.
6. Bush MB (1994) Amazonian speciation: a necessarily complex model. Journal of Biogeography, 21, 5-17.
7. Carisio L, Cervella P, De Palestrini CI, Pero M, Rolando A (2004) Biogeographical patterns of genetic differentiation in dung beetles of the genus Trypocopris (Coleoptera, Geotrupidae) inferred from mtDNA and AFLP analyses. Journal of Biogeography, 31, 1149-1162.
8. Comes HP, Kadereit JW (2003) Spatial and temporal patterns in the evolution of the flora of the European Alpine system. Taxon, 52, 451-462.
9. Coyne JA, Orr HA (2004) Speciation. Sinauer Associates, Sunderland, Massachusetts.
10. Cracraft J, Prum RO (1988) Patterns and processes of diversification: speciation and historical congruence in some Neotropical birds. Evolution, 42, 603-620.
11. Eberhard WG (1996) Female Control: Sexual Selection by Cryptic Female Choice. Princeton University Press, Princeton, New Jersey.
12. Edwards SV, Beerli P (2000) Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeography studies. Evolution, 54, 1839-1854.
13. Elias SA (1996) The Ice-Age History of National Parks in the Rocky Mountains. Smithsonian Institution Press, Washington and London.
14. 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.
15. Galbreath KE, Cook JA (2004) Genetic consequences of Pleistocene glaciations for the tundra vole (Microtus oeconomus) in Beringia. Molecular Ecology, 13, 135-148.
16. Gavrilets S (1997) Evolution and speciation on holey adaptive landscapes. Trends in Ecology & Evolution, 12, 307-312.
17. Gavrilets S (2003) Models of speciation: what have we learned in 40 years? Evolution, 57, 2197-2215.
18. Green DM, Sharbel TF, Kearsley J, Kaiser H (1996) Postglacial range fluctuation, genetic subdivision and speciation in the western North American spotted frog complex, Rana pretiosa. Evolution, 50, 374-390.
19. Haffer J (1969) Speciation in Amazonian forest birds. Science, 165, 131-137.
20. Haffer J (1997) Alternative models of vertebrate speciation in Amazonia: an overview. Biodiversity and Conservation, 6, 451-476.
21. Hawthorne DJ (2001) AFLP-based genetic linkage map of the Colorado potato beetle Leptinotarsa decemlineata: sex chromosomes and a pyrethroid-resistance candidate gene. Genetics, 158, 695-700.
22. Hewitt GM (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnean Society, 58, 247-276.
23. Hewitt GM (1999) Post-glacial re-colonization of European biota. Biological Journal of the Linnean Society, 68, 87-112.
24. Hey J, Machado CA (2003) The study of structured populations - new hope for a difficult and divided science. Nature Reviews Genetics, 4, 535-543.
25. Hollin JT, Schilling DH (1981) Late Wisconsin-Weichselian mountain glaciers and small ice caps. In: The Last Great Ice Sheets (eds Denton GH, Hughes TJ), pp. 179-198. John Wiley & Sons, New York.
26. Holsinger KE (1999) Analysis of genetic diversity in geographically structured populations: a Bayesian perspective. Hereditas, 130, 245-255.
27. Holsinger KE, Wallace LE (2004) Bayesian approaches for the analysis of population genetic structure: an example from Platanthera leucophaea (Orchidaceae). Molecular Ecology, 13, 887-894.
28. Holsinger KE, Lewis PO, Dey DK (2002) A Bayesian approach to inferring population structure from dominant markers. Molecular Ecology, 11, 1157-1164.
29. Hudson RR, Boos DD, Kaplan NL (1992) A statistical test for detecting geographic subdivision. Molecular Biology and Evolution, 9, 138-151.
30. Huntley B, Webb T III (1989) Migration: species' response to climatic variations caused by changes in the Earth's orbit. Journal of Biogeography, 16, 5-19.
31. Hutchinson DW, Templeton AR (2000) 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, 1889-1914.
32. Joseph L, Moritz C, Hugall A (1995) Molecular support for vicariance as a source of diversity in rainforest. Proceedings of the Royal Society of London. Series B, Biological Sciences, 260, 177-182.
33. Klicka J, Zink RM (1997) The importance of recent ice ages in speciation: a failed paradigm. Science, 277, 1666-1669.
34. Knowles LL (2000) Tests of Pleistocene speciation in montane grasshoppers from the sky islands of western North America (genus Melanoplus). Evolution, 54, 1337-1348.
35. 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, Biological Sciences, 268, 319-324.
36. Knowles LL (2001b) Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshoppers. Molecular Ecology, 10, 691-701.
37. Knowles LL (2004) The burgeoning field of statistical phylogeography. Journal of Evolutionary Biology, 17, 1-10.
38. Knowles LL, Maddison WP (2002) Statistical phylogeography. Molecular Ecology, 11, 2623-2635.
39. Knowles LL, Otte D (2000) Phylogenetic analysis of montane grasshoppers from western North America (genus Melanoplus, Acrididae: Melanoplinae). Annals of the Entomological Society of America, 93, 421-431.
40. Knowles LL, Coelho A, McNellis J, Greene KP, Futuyma DJ (1999) Tests of inbreeding effects on host shift potential in the phytophagous beetle Ophraella communa. Evolution, 53, 561-567.
41. Knowles LL, Chappell TM, Marquez EJ (2005) Concordance of hybrid clines reveals sexual selection's role in genitalic divergence and speciation. Evolution, in review.
42. Kocher TD, Lee WJ, Sobolewska H, Penman D, McAndrew B (1998) A genetic linkage map of a cichlid fish, the Tilapia (Oreochromis niloticus). Genetics, 148, 1225-1232.
43. Latta RG, Linhart YB, Mitton JB (2001) Cytonuclear disequilibrium and genetic drift in a natural population of ponderosa pine. Genetics, 158, 843-850.
44. Maddison W (1997) Gene trees in species trees. Systematic Biology, 46, 523-536.
45. Mayewski PA, Denton GH, Hughes TJ (1981) Late Wisconsin ice sheets in North America. In: The Last Great Ice Sheets (eds Denton GH, Hughes TJ), pp. 67-89. John Wiley & Sons, New York.
46. Mengel RM (1964) The probable history of species formation in some northern wood warblers. Living Bird, 3, 9-43.
47. Mueller UG, Wolfenbarger L (1999) AFLP genotyping and fingerprinting. Trends in Ecology & Evolution, 14, 389-394.
48. Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
49. Orr HA, Betancourt AJ (2001) Haldane's sieve and adaptation from the standing genetic variation. Genetics, 157, 875-884.
50. Parsons YM, Shaw KL (2002) Mapping unexplored genomes: a genetic linkage map of the Hawaiian cricket Laupala. Genetics, 162, 1275-1282.
51. Pielou EC (1991) After the Ice Age: The Return of Life to Glaciated North America. University of Chicago Press, Chicago.
52. Pritchard JK, Stephens M, Donnelly P (2000) Inferences of population structure using multilocus genotype data. Genetics, 155, 945-959.
53. Riddle BR (1996) The molecular phylogeographic bridge between deep and shallow history in continental biotas. Trends in Ecology & Evolution, 11, 187-228.
54. Roy K, Valentine JW, Jablonski D, Kidwell JM (1996) Scales of Climatic variability and time averaging in Pleistocene biotas: implications for ecology and evolution. Trends in Ecology & Evolution, 11, 458-463.
55. Schönswetter P, Tribsch A, Niklfeld H (2004) Amplified fragment length polymorphism (AFLP) suggests old and recent immigration in the alps by the arctic-alpine annual Comastoma tenellum (Gentianaceae). Journal of Biogeography, 31, 1673-1681.
56. Singh G (1988) History of aridland vegetation and climate: a global perspective. Biological Review, 63, 159-195.
57. Takahata N (1989) Gene genealogy in three related populations: consistency probability between gene and population trees. Genetics, 122, 957-966.
58. Vekemans X, Beauwens T, Lemaire M, Roldán-Ruiz I (2002) Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Molecular Ecology, 11, 139-151.
59. Vos P, Hagers R, Bleeker M et al. (1995) AFLP: new technique for DNA fingerprinting. Nucleic Acids Research, 23, 4407-4414.
60. Wang Z, Baker AJ, Hill GE, Edwards SV (2003) Reconciling actual and inferred population histories in the house finch (carpodacus mexicanus) by AFLP analysis. Evolution, 57, 2852-2864.
61. Webb T III, Bartlein PJ (1992) Global changes during the last 3 million years, climatic controls and biotic responses. Annual Review of Ecology and Systematics, 23, 141-173.
62. Weir JT, Schluter D (2004) Ice sheets promote speciation in boreal birds. Proceedings of the Royal Society of London. Series B, Biological Sciences, 271, 1881-1887.
63. Whitlock MC, Fowler K (1996) The distribution among populations in phenotypic variance with inbreeding. Evolution, 50, 1919-1926.
64. Wolfe JA (1987) An overview of the origins of the modern vegetation and flora of the northern Rocky Mountains. Annals of the Missouri Botanical Garden, 74, 785-803.
65. Yeh WB, Chang YL, Lin CH, Wu FS, Yang JT (2004) Genetic differentiation of Loxoblemmus appendicularis complex (Orthoptera: Gryllidae): speciation through vicariant and glaciation events. Annals of the Entomological Society of America, 97, 613-623.
66. Zink RM, Dittmann DL (1993) Gene flow, refugia, and evolution of geographic variation in the song sparrow (Melospiza melodia). Evolution, 47, 717-729.