The history and purview of phylogeography: A personal reflection

Molecular Ecology

Volumn 7, Issue 4, 1998, Pages 371-379

  Avise, John C ^a  

^a University of Georgia ^*  (United States)

Author keywords

Allelic pathways; Coalescent theory; Gene trees; Genealogical concordance; Intraspecific phylogeny; Mitochondrial DNA

Indexed keywords

EID: 0031979043     PISSN: 09621083     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-294x.1998.00391.x     Document Type: Article

References (81)

1. Aquadro CF, Weaver AL, Schaeffer SW, Anderson WW (1991) Molecular evolution of inversions in Drosophila pseudoobscura: the amylase gene region. Proceedings of the National Academy of Sciences USA, 88, 305-309.
2. Avise JC (1989a) Gene trees and organismal histories: a phylogenetic approach to population biology. Evolution, 43, 1192-1208.
3. Avise JC (1989b) Nature's family archives. Natural History, 3, 24-27.
4. Avise JC (1991) Ten unorthodox perspectives on evolution prompted by comparative population genetic findings on mitochondrial DNA. Annual Review of Genetics, 25, 45-69.
5. Avise JC (1992) Molecular population structure and the biogeographic history of a regional fauna: a case history with lessons for conservation biology. Oikos, 63, 62-76.
6. Avise JC (1994) Molecular Markers, Natural History and Evolution. Chapman & Hall, New York.
7. Avise JC (1995) Mitochondrial DNA polymorphism and a connection between genetics and demography of relevance to conservation. Conservation Biology, 9, 686-690.
8. Avise JC (1996a) Space and time as axes in intraspecific phylogeography. In: Past and Future Rapid Environmental Changes: The Spatial and Evolutionary Responses of Terrestrial Biota (eds Huntley B, Cramer W, Morgan AV, Prentice HC, Allen JRM), pp. 381-388. Springer-Verlag, New York.
9. Avise JC (1996b) Toward a regional conservation genetics perspective: phylogeography of faunas in the southeastern United States. In: Conservation Genetics: Case Histories from Nature (eds Avise JC, Hamrick JL), pp. 431-470. Chapman & Hall, New York.
10. Avise JC, Ball RM Jr (1990) Principles of genealogical concordance in species concepts and biological taxonomy. Oxford Surveys in Evolutionary Biology, 7, 45-67.
11. Avise JC, Hamrick JL (1996) Conservation Genetics: Case Histories from Nature. Chapman & Hall, New York.
12. Avise JC, Wollenberg K (1997) Phylogenetics and the origin of species. Proceedings of the National Academy of Sciences USA, 94, 7748-7755.
13. Avise JC, Lansman RA, Shade RO (1979a) 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.
14. Avise JC, Giblin-Davidson C, Laerm J, Patton JC, Lansman RA (1979b) Mitochondrial DNA clones and matriarchal phylogeny within and among geographic populations of the pocket gopher, Geomys pinetis. Proceedings of the National Academy of Sciences USA, 76, 6694-6698.
15. Avise JC, Neigel JE, Arnold J (1984) Demographic influences on mitochondrial DNA lineage survivorship in animal populations. Journal of Molecular Evolution, 20, 99-105.
16. Avise JC, Arnold J, Ball RM Jr, Bermingham E, Lamb T, Neigel JE, Reeb CA, Saunders NC (1987a) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics, 18, 489-522.
17. Avise JC, Reeb CA, Saunders NC (1987b) Geographic population structure and species differences in mitochondrial DNA of mouthbrooding marine catfishes (Ariidae) and demersal spawning toadfishes (Batrachoididae). Evolution, 41, 991-1002.
18. Avise JC, Ball RM, Arnold J (1988) Current versus historical population sizes in vertebrate species with high gene flow: a comparison based on mitochondrial DNA lineages and inbreeding theory for neutral mutations. Molecular Biology and Evolution, 5, 331-344.
19. Avise JC, Quattro JM, Vrijenhoek RC (1992) Molecular clones within organismal clones: mitochondrial DNA phylogenies and the evolutionary histories of unisexual vertebrates. Evolutionary Biology, 26, 225-246.
20. Bermingham E, Avise JC (1986) Molecular zoogeography of freshwater fishes in the southeastern United States. Genetics, 113, 939-965.
21. Bernardi G, Sordino P, Powers DA (1993) Concordant mitochondrial and nuclear DNA phylogenies for populations of the teleost fish Fundulus heteroclitus. Proceedings of the National Academy of Sciences, USA, 90, 9271-9274.
22. Bowen BW, Avise JC (1990) Genetic structure of Atlantic and Gulf of Mexico populations of sea bass, menhaden, and sturgeon: the influence of zoogeographic factors and life-history patterns. Marine Biology, 107, 371-381.
23. Britten RJ, Davidson EH (1969) Gene regulation for higher cells: a theory. Science, 165, 349-357.
24. Britten RJ, Davidson EH (1971) Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty. Quarterly Review of Biology, 46, 111-138.
25. Brown WM (1980) Polymorphism in mitochondrial DNA of humans as revealed by restriction endonuclease analysis. Proceedings of the National Academy of Sciences, USA, 77, 3605-3609.
26. Brown WM, Vinograd J (1974) Restriction endonuclease cleavage maps of animal mitochondrial DNAs. Proceedings of the National Academy of Sciences, USA, 71, 4617-4621.
27. Brown WM, Wright JW (1975) Mitochondrial DNA and the origin of parthenogenesis in whiptail lizards (Cnemidophorus). Herpetological Review, 6, 70-71.
28. Brown WM, Wright JW (1979) Mitochondrial DNA analyses and the origin and relative age of parthenogenetic lizards (genus Cnemidophorus). Science, 203, 1247-1249.
29. Brown WM, George Jr M, Wilson AC (1979) Rapid evolution of animal mitochondrial DNA. Proceedings of the National Academy of Sciences, USA, 76, 1967-1971.
30. Brown WM, Prager EM, Wang A, Wilson AC (1982) Mitochondrial DNA sequences of primates: tempo and mode of evolution. Journal of Molecular Evolution, 18, 225-239.
31. Burton RS, Lee B-N (1994) Nuclear and mitochondrial gene genealogies and allozyme polymorphism across a major phylogeographic break in the copepod Tigriopus californicus. Proceedings of the National Academy of Sciences, USA, 91, 5197-5201.
32. Cann RL, Stoneking M, Wilson AC (1987) Mitochondrial DNA and human evolution. Nature, 325, 31-36.
33. Cavalli-Sforza LL, Menozzi P, Piazza A (1994) The History and Geography of Human Genes. Princeton University Press, Princeton, New Jersey.
34. Chapman RW, Stephens JC, Lansman RA, Avise JC (1982) Models of mitochondrial DNA transmission genetics and evolution in higher eukaryotes. Genetical Research, 40, 41-57.
35. Cracraft J (1988) Deep-history biogeography: retrieving the historical pattern of evolving continental biotas. Systematic Zoology, 37, 221-236.
36. Dawid IB, Blackler AW (1972) Maternal and cytoplasmic inheritance of mtDNA in Xenopus. Developmental Biology, 29, 152-161.
37. Densmore LD III, Moritz CC, Wright JW, Brown WM (1989) Mitochondrial DNA analyses and the origin and relative age of parthenogenetic lizards (genus Cnemidophorus). IV. Nine sexlineatus-group unisexuals. Evolution, 43, 969-983.
38. Donnelly P, Tavaré S (1986) The ages of alleles and a coalescent. Advances in Applied Probability, 18, 1-19.
39. Echelle AA, Dowling TE, Moritz CC, Brown WM (1989) Mitochondrial-DNA diversity and the origin of the Menidia clarkhubbsi complex of unisexual fishes (Atherinidae). Evolution, 43, 984-993.
40. Eller E, Harpending HC (1996) Simulations show that neither population expansion nor population stationarity in a West African population can be rejected. Molecular Biology and Evolution, 13, 1155-1157.
41. Ferris SD, Wilson AC, Brown WM (1981) Evolutionary tree for apes and humans based on cleavage maps of mitochondrial DNA. Proceedings of the National Academy of Sciences, USA, 78, 2432-2436.
42. Hey J (1994) Bridging phylogenetics and population genetics with gene tree models. In: Molecular Ecology and Evolution: Approaches and Applications (eds Schierwater B, Streit B, Wagner GP, DeSalle R), pp. 435-449. Birkhäuser Verlag, Basel, Switzerland.
43. Hillis DM, Moritz C, Mable BK (eds) (1996) Molecular Systematics, 2nd edn. Sinauer, Sunderland, MA.
44. Hudson RR (1983) Testing the constant-rate neutral allele model with protein sequence data. Evolution, 37, 203-217.
45. Hudson RR (1990) Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology, 7, 1-44.
46. Hutchinson III CA, Newbold JE, Potter SS, Edgell MH (1974) Maternal inheritance of mammalian mitochondrial DNA. Nature, 251, 536-538.
47. Kingman JFC (1982) The coalescent. Stochastic Processes and their Applications, 13, 235-248.
48. Lamb T, Jones TR, Avise JC (1992) Phylogeographic histories of representative herpetofauna of the southwestern US mitochondrial DNA variation in the desert iguana (Dipsosaurus dorsalis) and the chuckwalla (Sauromalus obesus). Journal of Evolutionary Biology, 5, 465-480.
49. Lessa EP (1993) Analysis of DNA sequence variation at population level by polymerase chain reaction and denaturing gradient gel electrophoresis. Methods in Enzymology, 224, 419-428.
50. Lotka AJ (1931) Population analysis - the extinction of families-I. Journal of the Washington Academy of Sciences, 21, 377-380.
51. Maddison W (1995) Phylogenetic histories within and among species. In: Experimental and Molecular Approaches to Plant Biosystematics (eds Hoch PC, Stephenson AG), pp. 273-287. Missouri Botanical Garden, St. Louis.
52. Moritz CC (1991) The origin and evolution of parthenogenesis in Heteronotia binoei (Gekkonidae): evidence for recent and localized origins of widespread clones. Genetics, 129, 211-219.
53. Moritz CC (1994a) Applications of mitochondrial DNA analysis in conservation: a critical review. Molecular Ecology, 3, 401-411.
54. Moritz CC (1994b) Defining 'evolutionarily significant units' for conservation. Trends in Ecology and Evolution, 9, 373-375.
55. Nee S, Holmes EC, Harvey PH (1995) Inferring population history from molecular phylogenies. Philosophical Transactions of the Royal Society of London, B349, 25-31.
56. Nei M, Roychoudhury AK (1993) Evolutionary relationships of human populations on a global scale. Molecular Biology and Evolution, 10, 927-943.
57. Neigel JE, Avise JC (1986) Phylogenetic relationships of mitochondrial DNA under various demographic models of speciation. In: Evolutionary Processes and Theory (eds Nevo E, Karlin S), pp. 515-534. Academic Press, New York.
58. Neigel JE, Ball RM Jr, Avise JC (1991) Estimation of single generation migration distances from geographic variation in animal mitochondrial DNA. Evolution, 45, 423-432.
59. Orti G, Hare MP, Avise JC (1997) Detection and isolation of nuclear haplotypes by PCR-SSCP. Molecular Ecology, 6, 575-580.
60. Palumbi SR, Baker CS (1994) Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales. Molecular Biology and Evolution, 11, 426-435.
61. Patton JL, da Silva MNF, Lara MC, Mustrangi MA (1997) Diversity, differentiation, and the historical biogeography of non-volant small mammals of the neotropical forests. In: Tropical Forest Remnants: Ecology, Management, and Conservation of Fragmented Communities (eds Laurance WF, Bierregaard RO Jr), pp. 455-465. University of Chicago Press, Chicago, Illinois.
62. Riddle BR (1996) The molecular phylogeographic bridge between deep and shallow history in continental biotas. Trends in Ecology and Evolution, 11, 207-211.
63. Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution, 9, 552-569.
64. Ryder OA (1986) Species conservation and the dilemma of sub-species. Trends in Ecology and Evolution, 1, 9-10.
65. Schaffer H (1970) The fate of neutral mutants as a branching process. In: Mathematical Topics in Population Genetics (ed. Kojima K), pp. 317-336. Springer-Verlag, New York.
66. da Silva MNF, Patton JL (1993) Amazonian phylogeography: mtDNA sequence variation in arboreal echimyid rodents (Caviomorpha). Molecular Phylogenetics and Evolution, 2, 243-255.
67. Slatkin M (1989) Detecting small amounts of gene flow from phylogenies of alleles. Genetics, 121, 609-612.
68. Slatkin M, Maddison WP (1989) A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics, 123, 603-613.
69. Slatkin M, Hudson RR (1991) Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics, 129, 555-562.
70. Smith TB, Wayne RK (eds) (1996) Molecular Genetic Approaches in Conservation. Oxford University of Press, New York.
71. Tajima F (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics, 105, 437-460.
72. Takahata N (1995) A genetic perspective on the origin and history of humans. Annual Review of Ecology and Systematics, 26, 343-372.
73. Templeton AR, Georgiadis NJ (1996) A landscape approach to conservation genetics: conserving evolutionary processes in the African bovidae. In: Conservation Genetics: Case Histories from Nature (eds Avise JC, Hamrick JL), pp. 398-430. Chapman & Hall, New York.
74. Templeton AR, Routman E, Phillips CA (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.
75. Turner TF, Trexler JC, Kuhn DN, Robison HW (1996) Life-history variation and comparative phylogeography of darters (Pisces: Percidae) from the North American central highlands, Evolution, 50, 2023-2036.
76. Upholt WB (1977) Estimation of DNA sequence divergence from comparison of restriction endonuclease digests. Nucleic Acids Research, 4, 1257-1265.
77. Upholt WB, Dawid IB (1977) Mapping of mitochondrial DNA of individual sheep and goats: rapid evolution in the D loop region. Cell, 11, 571-583.
78. Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theoretical Population Biology, 10, 256-276.
79. Watterson GA (1984) Lines of descent and the coalescent. Theoretical Population Biology, 26, 77-92.
80. Wenink PW, Baker AJ, Tilanus MGJ (1994) Mitochondrial controlregion sequences in two shorebird species, the turnstone and dunlin, and their utility in population genetic studies. Molecular Biology and Evolution, 11, 22-31.
81. Zink RM (1996) Comparative phylogeography in North American birds. Evolution, 50, 308-317.