Methodological advances for the combined study of genetic, genealogical and geographical information in evolutionary and distributional analyses;Avances metodológicos para el estudio conjunto de la información genética, genealógica y geográfica en análisis evolutivos y de distribución

Revista Chilena de Historia Natural

Volumn 82, Issue 2, 2009, Pages 277-297

  Vázquez Domínguez, Ella ^a   Castañeda Rico, Susette ^a   Garrido Garduño, Tania ^a   Gutiérrez García, Tania A ^a  

^a INSTITUTO DE ECOLOGÍA   (Mexico)

Author keywords

Coalescence; DNA; Gene genealogies; Phylogeography; Summary statistics

Indexed keywords

EID: 70349264340     PISSN: 0716078X     EISSN: 07176317     Source Type: Journal    
DOI: None     Document Type: Article

References (95)

1. ALLENDORF F & G LUIKART (2007) Conservation and the genetics of populations. Blackwell Publishing, Oxford, United Kingdom. 642 pp.
2. AVISE JC, J ARNOLD, RM BALL, E BERMINGHAM, T LAMB, JE NIEGEL, CA REEB & NC SAUNDERS (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics 18: 489-522.
3. AVISE JC & D WALKER (1998) Pleistocene phylogeographic effects on avian populations and the speciation process. Proceedings of the Royal Society of London B 265: 457-463.
4. AVISE JC (2000) Phylogeography. The history and formation of species. Harvard University Press, Cambridge, United Kingdom. 447 pp.
5. BAHLO M & RC GRIFFITHS (2000) Inference from gene trees in a subdivided population. Theoretical Population Biology 57: 79-95.
6. BEDFORD T & DL HARTL (2008) Overdispersion of the molecular clock: temporal variation of genespecific substitution rate in Drosophila. Molecular Biology and Evolution 25: 1631-1638.
7. BEHLING H & M LICHTE (1997) Evidence of dry and cold climatic conditions at glacial times in tropical southeastern Brazil. Quaternary Research 48: 348-358.
8. BEHLING H & RRB NEGRELLE (2001) Tropical rain forest and climate dynamics of the Atlantic lowland, Southern Brazil, during the Late Quaternary. Quaternary Research 56: 383-389.
9. BLEEKER W, C WEBER-SPARENBERG & H HURKA (2002) Chloroplast DNA variation and biogeography in the genus Rorippa Scop. (Brassicaceae). Plant Biology 4: 104-111.
10. BROWN WM (1985) The mitochondrial genome of animals. En: MacIntyre RJ (ed) Molecular evolutionary genetics: 95-130. Plenum, New York, USA.
11. BROWN WM, M GEORGE & AC WILSON (1979) Rapid evolution of animal mitochondrial DNA. Proceedings of the National Academy of Sciences USA 76: 1967-1971.
12. BRUMFIELD RT, P BEERLI, DA NICKERSON & SV EDWARDS (2003) The utility of single nucleotide polymorphisms in inferences of population history. Trends in Ecology and Evolution 18: 249-256.
13. BURBRINK FT, F FONTANELLA, R PYRON, TQ GUIHER & C JIMÉNEZ (2008) Phylogeography across a continent: the evolutionary and demographic history of the North American racer (Serpentes: Colubridae: Coluber constrictor). Molecular Phylogenetics and Evolution 47: 274-288.
14. CARBONE I & LM KOHN (2001) A microbial population-species interface: nested cladistics and coalescent inference with multilocus data. Molecular Ecology 10: 947-964.
15. CARSTENS BC & CL RICHARDS (2008) Integrating coalescent and ecological niche modeling in comparative phylogeography. Evolution 61: 1439-1454.
16. CARVALHO GR (ed) (1998) Advances in molecular ecology. IOS Press, Amsterdam, Netherlands. 314 pp.
17. CASSENS I, K VAN WAEREBEEK, B BEST, EA CRESPO, J REYES & MC MILINKOVITCH (2003) The phylogeography of dusky dolphins (Lagenorhynchus obscurus): a critical examination of network methods and rooting procedures. Molecular Ecology 12: 1781-1792.
18. CLEMENT M, D POSADA & KA CRANDALL (2000) TCS: a computer program to estimate gene genealogies. Molecular Ecology 9: 1657-1660.
19. CRANDALL KA & AR TEMPLETON (1993) Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics 134: 959-969.
20. CRISP MD & LG COOK (2005) Do early branching lineages signify ancestral traits? Trends in Ecology & Evolution 20: 122-128.
21. CRUZAN MB & AR TEMPLETON (2000) Paleoecology and coalescence: phylogeographic analysis of hypotheses from the fossil record. Trends in Ecology & Evolution 15: 491-496.
22. DEVITT TJ (2006) Pylogeography of the Western Lyresnake (Trimophodom biscutatus): testing aridland biogeographical hypotheses across the Neartic-Neotropical transition. Molecular Ecology 15: 4387-4407.
23. DRUMMOND AJ, A RAMBAUT, B SHAPIRO & OG PYBUS (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Molecuar Biology and Evolution 22: 1185-1192.
24. EGUIARTE L, V SOUZA & X AGUIRRE (2007) La ecología molecular de plantas y animales. INE/Conabio, México. 592 pp.
25. EMERSON BC, E PARADIS & C THÉBAUD (2001) Revealing the demographic histories of species using DNA sequences. Trends in Ecology & Evolution 16: 707-716.
26. EXCOFFIER L, G LAVAL & S SCHNEIDER (2005) Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1: 47-50.
27. FREELAND JR (2005) Molecular ecology. John Wiley & Sons, Ltd., London, United Kingdom. 388 pp.
28. FRUTOS SD & RA VAN DEN BUSSCHE (2002) Genetic diversity and gene flow in nine-banded armadillos in Paraguay. Journal of Mammalogy 83: 815-823.
29. FU YX (1994) Estimating effective population size or mutation rate using the frequencies of mutations of various classes in a sample of DNA sequences. Genetics 138: 1375-1386.
30. FU YX & WH LI (1993) Statistical tests of neutrality of mutations. Genetics 133: 693-709.
31. GAGGIOTTI OE, O LANGE, K RASSMANN & C GLIDDONS (1999) A comparison of two indirect methods for estimating average levels of gene flow using microsatellite data. Molecular Ecology 8: 1513-1520.
32. GARCÍA-MORENO J, AG NAVARRO-SIGÜENZA, AT PETERSON & LA SÁNCHEZ-GONZÁLEZ (2004) Genetic variation coincides with geographic structure in the common bush-tanager (Chlorospingus ophthalmicus) complex from Mexico. Molecular Phylogenetics and Evolution 33: 186-196.
33. GODINHO R, B MENDONÇA, EG CRESPO & N FERRAND (2006) Genealogy of the nuclear bfibrinogen locus in a highly structured lizard species: comparison with mtDNA and evidence for intragenic recombination in the hybrid zone. Heredity 96: 454-463.
34. GRAZZIOTIN FG, M MONZEL, S ECHEVERRIGARAY & SL BONIATO (2006) Phylogeography of the Bothrops jararaca complex (Serpentes: Viperidae): past fragmentation and island colonization in the Brazilian Atlantic Forest. Molecular Ecology 15: 3969-3982.
35. HARE MP (2001) Prospects for nuclear gene phylogeography. Trends in Ecology & Evolution 16: 700-706.
36. HARRIS D, DS ROGERS & J SULLIVAN (2000) Phylogeography of Peromyscus furvus (Rodentia; Muridae) based on cytochrome b sequence data. Molecular Ecology 9: 2129-2135.
37. HASBÚN CR, A GÓMEZ, G KHÖLER & DH LUNA (2005) Mitochondrial DNA phylogeography of the Mesoamerican spiny-yailed lizards (Ctenosaura quinquecarinata complex): historical biogeography, species status and conservation. Molecular Ecology 14: 3095-3107.
38. HAWKINS JA (2006) Using phylogeny to investigate the origins of the Cape flora: the importance of taxonomic, gene and genome sampling strategies. Diversity and Distributions 12: 27-33.
39. HEY J & CA MACHADO (2003) The study of structured populations - new hope for a difficult and divided science. Genetics 4: 535-543.
40. HICKERSON MJ, G DOLMAN & C MORITZ (2006) Comparative phylogeographic summary statistics for testing simultaneous vicariance. Molecular Ecology 15: 209-223.
41. HOLMES EC, S NEE, A RAMBAUT, GP GARNETT & PH HARVEY (1995) Revealing the history of infectious disease epidemics through phylogenetic trees. Philosophical Transactions of the Royal Society of London B 349: 33-40.
42. HOLMES EC, OG PYBUS & PH HARVEY (1999) The molecular population genetics of HIV-1. En: Crandall KA (ed) The evolution of HIV: 177-207. Johns Hopkins University Press, Baltimore, USA.
43. HUDSON RR (1990) Gene genealogies and the coalescent process. En: Futuyma D & J Antonovics (eds) Oxford surveys in evolutionary biology: 1-44.
44. Oxford University Press, Oxford, United Kingdom. HUDSON RR (1998) Island models and the coalescent process. Molecular Ecology 7: 413-418.
45. HUDSON RR, M SLATKIN & WP MADDISON (1992) Estimation of levels of gene flow from DNA sequence data. Genetics 132: 583-589.
46. HUSMEIER D & F WRIGHT (2001) Probabilistic divergence measures for detecting interspecies recombination. Bioinformatics 17: S123-S131.
47. HUSON DH (1998) SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14: 68-73.
48. KELCHNER SA & MA THOMAS (2006). Model use in phylogenetics: nine key questions. Trends in Ecology & Evolution 22: 87-94.
49. KINGMAN JFC (1982) The coalescent. Stochastic Processes and their Applications 13: 235-248.
50. KNOWLES LL & WP MADDISON (2002) Statistical phylogeography. Molecular Ecology 11: 2623-2635.
51. KNOWLES LL (2003) The burgeoning field of statistical phylogeography. Journal of Evolutionary Biology 17: 1-10.
52. KOCH MA, C KIEFER, D EHRICH, J VOGEL, C BROCHMANN & K MUMMENHOFF (2006) Three times out of Asia Minor: the phylogeography of Arabis alpine L. (Brassicaceae). Molecular Ecology 15: 825-839.
53. LESSA EP, JA COOK & JL PATTON (2003) Genetic footprints of demographic expansion in North America, but not Amazonia, during the Late Quaternary. Proceedings of the National Academy of Sciences 100: 10331-10334.
54. LUIKART G & PR ENGLAND (1999) Statistical analysis of microsatellite DNA data. Trends in Ecology & Evolution 14: 253-256.
55. LUNT DH, LE WHIPPLE & BC HYMAN (1998) Mitochondrial DNA variable number tandem repeats (VNTRs): utility and problems in molecular ecology. Molecular Ecology 7: 1441-1455.
56. MARTIN AP & SR PALUMBI (1993) Body size, metabolic rate, generation time, and the molecular clock. Proceedings of the National Academy of Sciences USA 90: 4087-4091.
57. MEJÍA-MADRID H, E VÁZQUEZ-DOMÍNGUEZ & G PÉREZ-PONCE DE LEÓN (2007) Phylogeography and freshwater basins in Central Mexico: recent history as revealed by the fish parasite Rhabdochona lichtenfelsi (Nematoda). Journal of Biogeography 34: 787-801.
58. MUWANIKA VB, S NYAKAANA, HR SIEGISMUND & P ARCTANDER (2003) Pylogeography and population structure of the common warthog (Phacochoerus africanus) inferred from variation in mitochondrial DNA sequences and microsatellite loci. Heredity 91: 361-372.
59. MUMMENHOFF K, H BRÜGGEMANN & JL BOWMAN (2001) Chloroplast DNA phylogeny and biogeography of Lepidium (Brassicaceae). American Journal of Botany 88: 2051-2063.
60. NORDBORG M (2000) Coalescent theory. En: Balding DJ, MJ Bishop & C Cannings (eds) Handbook of statistical genetics: 1-37. John Wiley & Sons, London, United Kingdom.
61. PALMER JD (1990) Contrasting modes and tempos of genome evolution in plants and algae. Trends in Genetics 6: 115-120.
62. PANCHAL M (2007) The automation of nested clade phylogeographic analysis. Bioinformatics 23: 509-510.
63. PETERS JL, W GRETES & KE OMLAND (2005) Late Pleistocene divergence between eastern and western populations of wood ducks (Aix sponsa) inferred by the "isolation with migration" coalescent method. Molecular Ecology 14: 3407-3418.
64. PETIT RJ (2008) The coup de grâce for the nested clade phylogeographic analysis? Molecular Ecology 17: 516-518.
65. POSADA D (2006) ModelTestServer: a web-based tool for the statistical selection of models of nucleotide substitution online. Nucleic Acids Research 34: W700-W703.
66. POSADA D & KA CRANDALL (2001) Intraspecific gene genealogies: tress grafting into networks. Trends in Ecology & Evolution 16: 37-45.
67. POSADA D, KA CRANDALL & AR TEMPLETON (2000) GeoDis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Molecular Ecology 9: 487-488.
68. POSADA D, KA CRANDALL & AR TEMPLETON (2006) Nested clade analysis statistics. Molecular Ecology Notes 6: 590-593.
69. REEB V, P HAUGEN, D BHATTACHARYA & F LUTZONI (2007) Evolution of Pleopsidium (Lichenized Ascomycota) S943 group I introns and the phylogeography of an intron-encoded putative homing endonuclease. Journal of Molecular Evolution 64: 1432-11432
70. RICHARDSON BA, J BRUSFELD & B KLOPFENSTEIN (2002) DNA from bird-dispersed seed and winddisseminated pollen provides insights into postglacial colonization and population genetic structure of whitebark pine (Pinus albicaulis). Molecular Ecology 11: 215-227.
71. RIDDLE BR, DJ HAFNER, LF ALEXANDER & JR JAEGER (2000) Cryptic vicariance in the historical assembly of a Baja California peninsular desert biota. Proceedings of the National Academy of Sciences USA 97: 14438-14443.
72. ROGERS AR & H HARPENDING (1992) Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9: 552-569.
73. SMITH TB, K HOLDER, D GIRMAN, K O'KEEFE, B LARISON & T CHAN (2000) Comparative avian phylogeography of Cameroon and Equatorial Guinea mountains: implications for conservation. Molecular Ecology 9: 1505-1516.
74. SMIT HA, TJ ROBINSON & BJ VAN VUUREN (2007) Coalescence methods reveal the impact of vicariance on the spatial genetic structure of Elephantulus edwardii (Afrotheria, Macroscelidea). Molecular Ecology 16:2680-2692.
75. SOLTIS DE, PS SOLTIS & BJ MILLIGAN (1992) Intraspecific chloroplast DNA variation: systematic and phylogenetic implications. En: Soltis PS & JJ Doyle (eds) Molecular systematics of plants: 117-150. Chapman & Hall, New York, USA.
76. SPELLMAN G & J KLICKA (2007) Pylogeography of the White-breasted Nuthatch (Sitta carolinensis): diversification in North American pine and oak woodlands. Molecular Ecology 16: 1729-1740.
77. STRIMMER K & OG PYBUS (2001) Exploring the demographic history of DNA sequences using the generalized skyline plot. Molecular Biology and Evolution 18: 2298-2305.
78. TAJIMA F (1983) Evolutionary relationships of DNA sequences in finite populations. Genetics 105: 437-460.
79. TEMPLETON AR (1983) Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of man and the apes. Evolution 37: 221-244.
80. TEMPLETON AR (1998) Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Molecular Ecology 7: 381-397.
81. TEMPLETON AR (2002) Out of Africa again and again. Nature 416: 45-51.
82. TEMPLETON AR (2004) Statistical phylogeography: methods of evaluating and minimizing inference errors. Molecular Ecology 13: 789-809.
83. TEMPLETON AR (2008) Nested clade analysis: an extensively validated method for strong phylogeographic inference. Molecular Ecology 17: 1877-1880.
84. TEMPLETON AR & CF 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.
85. TEMPLETON AR, KA CRANDALL & CF SING (1992) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132: 619-633.
86. TEMPLETON AR, 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.
87. VÁZQUEZ-DOMÍNGUEZ E (2002) Phylogeography, historical patterns and conservation of natural areas. En: Nelson G, JC Day, LM Sportza, J Loucky & C Vásquez (eds) Protected areas and the regional planning imperative in North America: 369-378. University of Calgary Press, Calgary, Canada.
88. VÁZQUEZ-DOMÍNGUEZ E (2007a) ¿Cuál es el enfoque de la ecología molecular? Ejemplos con un ratón espinoso. En: Sánchez-Rojas G & AE Rojas- Martínez (eds) Tópicos en sistemática, biogeografía, ecología y conservación de mamíferos: 59-70.
89. Universidad Autónoma del Estado de Hidalgo, Serie Ciencia al día 1, México.
90. VÁZQUEZ-DOMÍNGUEZ E (2007b) Filogeografía y vertebrados. En: Eguiarte L, V Souza & X Aguirre (eds) La ecología molecular de plantas y animales: 441-466. INE/Conabio, México.
91. VÁZQUEZ-DOMÍNGUEZ E, A MEJÍA-MADRID & R VEGA (2009) Oryzomys couesi en el sureste de México: estimaciones genéticas y filogeográficas. En: Cervantes FA, J Vargas-Cuenca & Y Hortelano- Moncada (eds) 60 años de la Colección Nacional de Mamíferos del Instituto de Biología, UNAM. Aportaciones al conocimiento y conservación de los mamíferos mexicanos. Instituto de Biología, UNAM, México.
92. WAINSCOAT J (1987) Out of the garden of Eden. Science 234: 194-196.
93. WRIGHT S (1931) Evolution in Mendelian populations. Genetics 16: 97-159.
94. WRIGHT S (1943) Isolation by distance. Genetics 28: 114-138.
95. ZUCKERKANDL E & L PAULING (1965) Evolutionary divergence and convergence in proteins. En: Bryson V & HJ Voegel (eds) Evolving genes and proteins: 97-166. Academic Press, New York, USA.