Population genetic structure of the toad Bufo woodhousii: An empirical assessment of the effects of haplotype extinction on nested cladistic analysis

Molecular Ecology

Volumn 12, Issue 6, 2003, Pages 1541-1554

  Masta, Susan E ^a,b   Laurent, Nicole M ^a   Routman, Eric J ^a  

^a SAN FRANCISCO STATE UNIVERSITY   (United States)

^b PORTLAND STATE UNIVERSITY   (United States)

Author keywords

Bufo woodhousii; Haplotype extinction; Lineage sorting; Mitochondrial DNA; Nested clade analysis; Phylogeography

Indexed keywords

ANIMALS; BASE SEQUENCE; BUFONIDAE; CLIMATE; DATA INTERPRETATION, STATISTICAL; DNA, MITOCHONDRIAL; GENETIC DRIFT; GENETICS, POPULATION; GEOGRAPHY; HAPLOTYPES; MOLECULAR SEQUENCE DATA; MOVEMENT; PHYLOGENY; SEQUENCE ANALYSIS, DNA; UNITED STATES; VARIATION (GENETICS);

AMPHIBIA; ANURA; BUFO; BUFO WOODHOUSII; REPTILIA;

EID: 0038460135     PISSN: 09621083     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-294X.2003.01829.x     Document Type: Article

References (78)

1. Alexandrino J, Arntzen JW, Ferrand N (2002) Nested clade analysis and the genetic evidence for population expansion in the phylogeography of the golden-striped salamander, Chioglossa lusitanica (Amphibia: Urodela). Heredity, 88, 66-74.
2. Arbogast AF (1996) Stratigraphic evidence for late-Holocene aeolian sand mobilization and soil formation in south-central Kansas, USA. Journal of Arid Environments, 34, 403-414.
3. 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.
4. Ball RM, Avise JC (1992) Mitochondrial DNA phylogeographic differentiation among avian populations and the evolutionary significance of subspecies. Auk, 109, 626-636.
5. Bernatchez L, Wilson CC (1998) Comparative phylogeography of Neararctic and Palearctic fishes. Molecular Ecology, 7, 431-452.
6. Blair WF (1953) Growth, dispersal and age at sexual maturity of the Mexican toad (Bufo valliceps Wiegmann). Copeia, 1953, 208-212.
7. Breden F (1987) The effect of post-metamorphic dispersal on the population genetic structure of Fowler's toad, Bufo woodhousei fowleri. Copeia, 2, 386-395.
8. Cann RL, Stoneking M, Wilson AC (1987) Mitochondrial DNA and human evolution. Nature, 325, 31-36.
9. Carbone I, Kohn LM (2001) A microbial population-species interface: nested cladistic and coalescent inference with multilocus data. Molecular Ecology, 10, 947-964.
10. Castelloe J, Templeton AR (1994) Root probabilities for intraspecifc gene trees under neutral coalescent theory. Molecular Phylogenetics and Evolution, 3, 102-113.
11. Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Molecular Ecology, 9, 1657-1660.
12. Conant R, Collins JT (1991) A Field Guide to Reptiles and Amphibians: Eastern and Central North America. Houghton Mifflin, Boston, MA.
13. Crandall KA (1996) Multiple interspecies transmissions of human and simian T-cell leukemia/lymphoma virus type I sequences. Molecular Biology and Evolution, 13, 115-131.
14. Crandall KA, Templeton AR (1993) Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics, 134, 959-969.
15. Creer S, Malhotra A, Thorpe RS, Chou W-H (2001) Multiple causation of phylogeographical pattern as revealed by nested clade analysis of the bamboo viper (Trimeresurus stejnegeri) within Taiwan. Molecular Ecology, 10, 1967-1981.
16. Cross FB (1970) Fishes as indicators of Pleistocene and recent environments in the central plains. In: Pleistocene and Recent Environments of the Central Great Plains (eds Dort W, Jones JK), pp. 241-257. University Press of Kansas, Lawrence.
17. Dreeszen VH (1970) The stratigraphic framework of Pleistocene glacial and periglacial deposits in the Central Plains. In: Pleistocene and Recent Environments of the Central Great Plains (eds Dort W, Jones JK), pp. 9-22. University Press of Kansas, Lawrence.
18. Durand JD, Templeton AR, Guinand B, Imsiridou A, Bouvet Y (1999) Nested clade and phylogeographic analyses of the chub, Leuiscus cephalus (Telostei, Cyprinidae), in Greece: implications for the Balkan Peninsula biogeography. Molecular Phylogenetics and Evolution, 13, 566-580.
19. Ellsworth DL, Honeycutt RL, Silvy NJ, Rittenhouse KD, Smith MH (1994) Mitochondrial-DNA and nuclear-gene differentiation in North American prairie grouse (genus Tympanuchus). Auk, 111, 661-671.
20. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17, 368-376.
21. Ford MJ, Aquadro CF (1996) Selection on X-linked genes during speciation in the Drosophila athabasca complex. Genetics, 144, 689-703.
22. Fu Y-X (1997) Statistical tests of neutrality of mutation against population growth, hitchhiking and background selection. Genetics, 147, 915-925.
23. Gerber AS, Loggins R, Kumar S, Dowling TE (2001) Does nonneutral evolution shape observed patterns of DNA variation in animal mitochondrial genomes? Annual Review of Genetics, 35, 539-566.
24. Hammer MF, Karafet T, Rasanayagam A et al. (1998) Out of Africa and back again: nested cladistic analysis of human Y chromosome variation. Molecular Biology and Evolution, 15, 427-441.
25. Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 21, 160-174.
26. Hewitt GM (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biology Journal of the Linnean Society, 58, 247-276.
27. Hewitt GM (1999) Post-glacial re-colonization of European biota. Biology Journal of the Linnean Society, 68, 87-112.
28. Hewitt G (2000) The genetic legacy of the Quaternary ice ages. Nature, 405, 907-913.
29. Hokit DG, Blaustein AR (1997) Effects of kinship on interactions between tadpoles of Rana cascadae. Ecology, 78, 1722-1735.
30. Holliday VT (1997) Origin and evolution of lunettes on the High Plains of Texas and New Mexico. Quaternary Research, 47, 54-69.
31. Holman JA (1995) Pleistocene Amphibians and Reptiles in North America. Oxford University Press, New York.
32. Hudson RR (1990) Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology, 7, 1-44.
33. Ibrahim K, Nicols RA, Hewitt GM (1996) Spatial patterns of genetic variation generated by different forms of dispersal during range expansion. Heredity, 77, 282-291.
34. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Mammalian Protein Metabolism (ed. Munro HN), pp. 21-132. Academic Press, New York.
35. Kapp RO (1970) Pollen analysis of pre-Wisconsin sediments from the Great Plains. In: Pleistocene and Recent Environments of the Central Great Plains (eds Dort W, Jones JK), pp. 144-155. University Press of Kansas, Lawrence.
36. Knowles LL, Maddison WP (2002) Statistical phylogeography. Molecular Ecology, 11, 2623-2653.
37. Kuhner MK, Yamato J, Felsenstein J (1998) Maximum likelihood estimation of population growth rates based on the coalescent. Genetics, 149, 429-434.
38. Macey JR, Schulte JA II, Larson A, Fang Z, Wang Y, Tuniyev BS, Papenfuss TJ (1998) Phylogenetic relationships of toads in the Bufo bufo species group from the eastern escarpment of the Tibetan plateau: a case of vicariance and dispersal. Molecular Phylogenetics and Evolution, 9, 80-87.
39. Maddison DR, Maddison WP (2000) MACCLADE 4. Sinauer Associates, Sunderland, MA.
40. Masta SE, Sullivan BK, Lamb T, Routman EJ (2002) Molecular systematics, hybridization, and phylogeography of the Bufo americanus complex in eastern North America. Molecular Phylogenetics and Evolution, 24, 302-314.
41. Matos JA, Schaal BA (2000) Chloroplast evolution in the Pinus montezumae complex: a coalescent approach to hybridization. Evolution, 54, 1218-1233.
42. McDonald JH, Kreitman M (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature, 351, 652-654.
43. Muhs DR, Stafford TW, Swinehart JB et al. (1997) Late Holocene eolian activity in the mineralogically mature Nebraska sand hills. Quaternary Research, 48, 162-176.
44. Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
45. Nei M, Maruyama T, Chakraborty R (1975) The bottleneck effect and genetic variability in populations. Evolution, 29, 1-10.
46. Neigel JE, Avise JC (1993) Application of a random walk model to geographic distributions of animal mitochondrial DNA variation. Genetics, 135, 1209-1220.
47. Neigel JE, Ball RM, Avise JC (1991) Estimation of single generation migration distances from geographic variation in animal mitochondrial DNA. Evolution, 45, 423-432.
48. Nichols RA, Hewitt GM (1994) The genetic consequences of long distance dispersal during colonization. Heredity, 72, 312-317.
49. Pielou EC (1991) After the Ice Age: the Return of Life to Glaciated North America. University of Chicago Press, Chicago.
50. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics, 14, 817-818.
51. 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.
52. Rautio SA, Bura EA, Berven KA, Gamboa GJ (1991) Kin recognition in wood frog tadpoles (Rana sylvatica) - factors affecting spatial proximity to siblings. Canadian Journal of Zoology, 69, 2569-2571.
53. Rogers AR (1995) Genetic evidence for a Pleistocene population explosion. Evolution, 49, 608-615.
54. Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution, 9, 552-569.
55. Routman E (1993) Population structure and genetic diversity of metamorphic and paedomorphic populations of the tiger salamander, Ambystoma tigrinum. Journal of Evolutionary Biology, 6, 329-357.
56. Rozas J, Rozas R (1999) DNASP, Version 3. an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics, 15, 174-175.
57. Saidapur SK, Girish S (2000) The ontogeny of kin recognition in tadpoles of the toad Bufo melanostictus (Anura; Bufonidae). Journal of Biosciences, 25, 267-273.
58. Schneider SD, Roessli D, Excoffier L (2000) ARLEQUIN, Version 2.0: A Software for Population Genetic Data Analysis. Genetics and Biometry Laboratory, University of Geneva, Geneva, Switzerland.
59. Seddon JM, Santucci F, Reeve NJ, Hewitt GM (2001) DNA footprints of European hedgehogs, Erinaceus europaeus and E. concolor: Pleistocene refugia, postglacial expansion and colonization routes. Molecular Ecology, 10, 2187-2198.
60. Shaffer HB, McKnight ML (1996) The polytypic species revisited: genetic differentiation and molecular phylogenetics of the tiger salamander Ambystoma tigrinum (Amphibia: Caudata) complex. Evolution, 50, 417-433.
61. Shannon FA, Lowe CHJ (1955) A new subspecies of Bufo woodhousei from the inland southwest. Herpetologica, 11, 185-190.
62. Sherry ST, Rogers AR, Harpending H, Soodyall H, Jenkins T, Stoneking M (1994) Mismatch distributions of mtDNA reveal recent human population expansion. Human Biology, 66, 761-775.
63. Simonsen KL, Churchill GA, Aquadro CF (1995) Properties of statistical tests of neutrality for DNA polymorphism data. Genetics, 141, 413-429.
64. Slatkin M, Hudson RR (1991) Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics, 129, 555-562.
65. Strimmer K, Pybus OG (2001) Exploring the demographic history of DNA sequences using the generalized skyline plot. Molecular Biology and Evolution, 18, 2298-2305.
66. Swofford DL (2000) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4. Sinauer Associates, Sunderland, MA.
67. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595.
68. Templeton AR (1998) Nested clade analysis of phylogeographic data: testing hypotheses about gene flow and population history. Molecular Ecology, 7, 381-397.
69. Templeton AR (2002) Out of Africa again and again. Nature, 416, 45-51.
70. 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.
71. 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.
72. Templeton AR, Sing CF (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.
73. Van Devender TR, Mead JI (1978) Early Holocene and late Pleistocene amphibians and reptiles in Sonoran Desert packrat middens. Copeia, 3, 464-475.
74. Wayne ML, Simonsen KL (1998) Statistical tests of neutrality in the age of weak selection. Trends in Ecology and Evolution, 13, 236-240.
75. Wilke T, Pfenninger M (2002) Separating historic events from recurrent processes in cryptic species: phylogeography of mud snails (Hydrobia spp.). Molecular Ecology, 11, 1439-1451.
76. Wright J, HE (1970) Vegetational history of the Central Plains. In: Pleistocene and Recent Environments of the Central Great Plains (eds Dort W, Jones JK), pp. 157-172. University Press of Kansas, Lawrence.
77. Zink RM (1996) Comparative phylogeography in North American birds. Evolution, 50, 308-317.
78. Zink RM, Dittmann DL (1993) Gene flow, refugia, and evolution of geographic variation in the song sparrow (Melospiza melodia). Evolution, 47, 717-729.