Phylogeography of Middle American gophersnakes: Mixed responses to biogeographical barriers across the Mexican Transition Zone

Journal of Biogeography

Volumn 38, Issue 8, 2011, Pages 1570-1584

  Bryson Jr , Robert W ^a   García Vázquez, Uri Omar ^b   Riddle, Brett R ^a  

^a UNIVERSITY OF NEVADA   (United States)

^b UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

Author keywords

Central America; Colubridae; Divergence dating; Historical biogeography; Introgression; Mexico; Mitochondrial DNA; North America; Pituophis; Vicariance

Indexed keywords

ARID REGION; ASSESSMENT METHOD; CLIMATE CHANGE; DIVERGENCE; ESTIMATION METHOD; GENE EXPRESSION; GENETIC DIFFERENTIATION; HETEROGENEITY; INTROGRESSION; MARINE ENVIRONMENT; MITOCHONDRIAL DNA; NEOGENE; PALEOENVIRONMENT; PHYLOGEOGRAPHY; PHYSIOLOGICAL RESPONSE; PLEISTOCENE; POPULATION DISTRIBUTION; SNAKE; TAXONOMY; TOPOLOGY; TRANSITION ZONE; UPLIFT; VICARIANCE;

GUATEMALA [CENTRAL AMERICA]; GUATEMALA [GUATEMALA (DPR)]; GUATEMALA [GUATEMALA (NTN)]; ISTHMUS OF TEHUANTEPEC; MEXICO [NORTH AMERICA];

COLUBRIDAE; PITUOPHIS;

EID: 79960206294     PISSN: 03050270     EISSN: 13652699     Source Type: Journal    
DOI: 10.1111/j.1365-2699.2011.02508.x     Document Type: Article

References (81)

1. Anducho-Reyes, M.A., Cognato, A.I., Hayes, J.L. & Zuniga, G. (2008) Phylogeography of the bark beetle Dendroctonus mexicanus Hopkins (Coleoptera: Curculionidae: Scolytinae). Molecular Phylogenetics and Evolution, 49, 930-940.
2. Arellano, E., González-Cozátl, F.X. & Rogers, D.S. (2005) Molecular systematics of Middle American harvest mice Reithrodontomys (Muridae), estimated from mitochondrial cytochrome b gene sequences. Molecular Phylogenetics and Evolution, 37, 529-540.
3. Arévalo, E., Davis, S.K. & Sites, J. (1994) Mitochondrial DNA sequence divergence and phylogenetic relationships among eight chromosome races of the Sceloporus grammicus complex (Phrynosomatidae) in Central Mexico. Systematic Biology, 43, 387-418.
4. Avise, J.C. (1998) The history and purview of phylogeography: a personal reflection. Molecular Ecology, 7, 371-379.
5. Ball, G.E. (1968) Barriers and southward dispersal of the holarctic boreomontane element of the family Carabidae in the mountains of Mexico. Annales de la Escuela Nacional de Ciencia de Mexico, 17, 91-112.
6. Barber, P.H. (1999) Phylogeography of Hyla arenicolor (Cope) based on mitochondrial sequence data. Molecular Ecology, 8, 547-562.
7. Barrier, E., Velasquillo, L., Chavez, M. & Gaulon, R. (1998) Neotectonic evolution of the Isthmus of Tehuantepec (southeastern Mexico). Tectonophysics, 287, 7-96.
8. Becerra, J.X. (2005) Timing the origin and expansion of the Mexican tropical dry forests. Proceedings of the National Academy of Sciences USA, 102, 10919-10923.
9. Becerra, J.X. & Venable, D.L. (1999) Macroevolution of insect-plant associations: the relevance of host biogeography to host affiliation. Proceedings of the National Academy of Sciences USA, 96, 12626-12631.
10. Bryson, R.W., Pastorini, J., Burbrink, F.T. & Forstner, M.R.J. (2007) A phylogeny of the Lampropeltis mexicana complex (Serpentes: Colubridae) based on mitochondrial DNA sequences suggests evidence for species-level polyphyly within Lampropeltis. Molecular Phylogenetics and Evolution, 43, 674-684.
11. Bryson, R.W., Nieto-Montes, A. & Reyes-Velasco, J. (2008) Phylogenetic position of Porthidium hespere (Viperidae: Crotalinae) and phylogeography of arid-adapted hognosed pitvipers based on mitochondrial DNA. Copeia, 2008, 170-176.
12. Bryson, R.W., Nieto-Montes, A., Jaeger, J.R. & Riddle, B.R. (2010) Elucidation of cryptic diversity in a widespread Nearctic treefrog reveals episodes of mitochondrial gene capture as frogs diversified across a dynamic landscape. Evolution, 64, 2315-2330.
13. Bryson, R.W., Murphy, R.W., Lathrop, A. & Lazcano, D. (2011) Evolutionary drivers of phylogeographical diversity in the highlands of Mexico: a case study of the Crotalus triseriatus species group of montane rattlesnakes. Journal of Biogeography, 38, 697-710.
14. Burbrink, F.T. & Lawson, R. (2007) How and when did the Old World rat snakes cross into the New World? Molecular Phylogenetics and Evolution, 43, 173-189.
15. Cadena, C.D., Klicka, J. & Ricklefs, R.E. (2007) Evolutionary differentiation in the Neotropical montane region: molecular phylogenetics and phylogeography of Buarremon brush-finches (Aves, Emberizidae). Molecular Phylogenetics and Evolution, 44, 993-1016.
16. Campbell, J.A. (1999) Distribution patterns of amphibians in Middle America. Patterns of distribution of amphibians: a global perspective (ed. by W.E. Duellman), pp. 111-210. Johns Hopkins University Press, Baltimore, MD.
17. Castoe, T.A., Chippindale, P.T., Campbell, J.A., Ammerman, L.K. & Parkinson, C.L. (2003) Molecular systematics of the Middle American jumping pitvipers (genus Atropoides) and phylogeography of the Atropoides nummifer complex. Herpetologica, 59, 420-431.
18. Castoe, T.A., Daza, J.M., Smith, E.N., Sasa, M.M., Kuch, U., Campbell, J.A., Chippindale, P.T. & Parkinson, C.L. (2009) Comparative phylogeography of pitvipers suggests a consensus of ancient Middle American highland biogeography. Journal of Biogeography, 36, 88-103.
19. Daza, J.M., Smith, E.N., Paez, V.P. & Parkinson, C.L. (2009) Complex evolution in the Neotropics: the origin and diversification of the widespread genus Leptodeira (Serpentes: Colubridae). Molecular Phylogenetics and Evolution, 53, 653-667.
20. Daza, J.M., Castoe, T.A. & Parkinson, C.L. (2010) Using regional comparative phylogeographic data from snake lineages to infer historical processes in Middle America. Ecography, 33, 343-354.
21. Douglas, M.E., Douglas, M.R., Schuett, G. & Porras, L. (2006) Evolution of rattlesnakes (Viperidae: Crotalus) in warm deserts of western North America shaped by Neogene vicariance and Quaternary climate change. Molecular Ecology, 15, 3353-3374.
22. Drummond, A.J. & Rambaut, A. (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
23. Duellman, W.E. (1960) A taxonomic study of the Middle American snake, Pituophis deppei. University of Kansas Publications, Museum of Natural History, 10, 601-610.
24. Duellman, W.E. (1966) The Central American herpetofauna: an ecological perspective. Copeia, 1966, 700-719.
25. Dunn, E.R. (1931) The herpetological fauna of the Americas. Copeia, 1931, 106-119.
26. Edwards, C.W. & Bradley, R.D. (2002) Molecular systematics and historical phylobiogeography of the Neotoma mexicana species group. Journal of Mammalogy, 83, 20-30.
27. Edwards, S. & Bensch, S. (2009) Looking forwards or looking backwards in avian phylogeography? A comment on Zink and Barrowclough. Molecular Ecology, 18, 2930-2933.
28. Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17, 368-376.
29. Felsenstein, J. (2004) Inferring phylogenies. Sinauer Associates, Sunderland, MA.
30. Ferrusquía-Villafranca, I. (1993) Geology of Mexico: a synopsis. Biological diversity of Mexico: origins and distribution (ed. by T.P. Ramamoorthy, R.A. Bye, A. Lot and J. Fa), pp. 3-107. Oxford University Press, New York.
31. Guiher, T.J. & Burbrink, F.T. (2008) Demographic and phylogeographic histories of two venomous North American snakes of the genus Agkistrodon. Molecular Phylogenetics and Evolution, 48, 543-553.
32. Hafner, D.J. & Riddle, B.R. (2005) Mammalian phylogeography and evolutionary history of northern Mexico's deserts. Biodiversity, ecosystems, and conservation in northern Mexico (ed. by J.-L. Cartron, G. Ceballos and R.S. Felger), pp. 225-245. Oxford University Press, New York.
33. Halffter, G. (1987) Biogeography of the montane entomofauna of Mexico and Central America. Annual Review of Entomology, 32, 95-114.
34. Hillis, D.M. & Bull, J.J. (1993) An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology, 42, 182-192.
35. Ho, S.Y.W. (2005) Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Molecular Biological Evolution, 22, 1561-1568.
36. Ho, S.Y.W. & Phillips, M.J. (2009) Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Systematic Biology, 58, 367-380.
37. Holman, J.A. (2000) Fossil snakes of North America: origin, evolution, distribution, paleoecology. Indiana University Press, Indianapolis, IN.
38. Huelsenbeck, J.P. & Crandall, K.A. (1997) Phylogeny estimation and hypothesis testing using maximum likelihood. Annual Review of Ecology and Systematics, 28, 437-466.
39. Hulsey, C.D., García de León, F.J., Johnson, Y.S., Hendrickson, D.A. & Near, T.J. (2004) Temporal diversification of Mesoamerican cichlid fishes across a major biogeographic boundary. Molecular Phylogenetics and Evolution, 31, 754-764.
40. Jaeger, J.R., Riddle, B.R. & Bradford, D.F. (2005) Cryptic Neogene vicariance and Quaternary dispersal of the red-spotted toad (Bufo punctatus): insights on the evolution of North American warm desert biotas. Molecular Ecology, 14, 3033-3048.
41. Kelly, C.M.R., Barker, N.P., Villet, M.H. & Broadley, D.G. (2009) Phylogeny, biogeography and classification of the snake superfamily Elapoidea: a rapid radiation in the late Eocene. Cladistics, 25, 38-63.
42. Lemmon, A.R., Brown, J.M., Stanger-Hall, K. & Lemmon, E.M. (2009) The effect of missing data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Systematic Biology, 58, 130-145.
43. Lemos-Espinal, J.A., Smith, H.M. & Chiszar, D. (2004) A second record of Pituophis deppei (Deppe's Gopher Snake) in Chihuahua. Bulletin of the Maryland Herpetological Society, 40, 81-83.
44. León-Paniagua, L., Navarro-Sigüenza, A.G., Hernández-Baños, B.E. & Morales, J.C. (2007) Diversification of the arboreal mice of the genus Habromys (Rodentia: Cricetidae: Neotominae) in the Mesoamerican highlands. Molecular Phylogenetics and Evolution, 42, 653-664.
45. Maddison, D.R. & Maddison, W.P. (2003) MacClade: analysis of phylogeny and character evolution, v. 4.08. Sinauer, Sunderland, MA.
46. Manea, V.C. & Manea, M. (2006) The origin of modern Chiapan volcanic arc in Southern Mexico inferred from thermal models. GSA Special Paper 412: Natural Hazards in Central America, 27-38.
47. Marshall, C.J. & Liebherr, J.K. (2000) Cladistic biogeography of the Mexican transition zone. Journal of Biogeography, 27, 203-216.
48. McCormack, J.E., Peterson, A.T., Bonaccorso, E. & Smith, T.B. (2008) Speciation in the highlands of Mexico: genetic and phenotypic divergence in the Mexican jay (Aphelocoma ultramarina). Molecular Ecology, 17, 2505-2521.
49. McDonald, J.A. (1993) Phytogeography and history of the alpine-subalpine flora of northeastern Mexico. Biological diversity in Mexico: origins and distribution (ed. by T.P. Ramamoorthy, R. Bye, A. Lot and J. Fa), pp. 681-703. Oxford University Press, New York.
50. Mittermeier, R.A., Gil, P.R., Hoffman, M., Pilgrim, J., Brooks, T., Mittermeier, C.G., Lamoreux, J. & da Fonseca, G.A.B. (2005) Hotspots revisited: Earth's biologically richest and most endangered terrestrial ecoregions. Conservation International, Washington, DC.
51. Moritz, C., Patton, J.L., Schneider, C.J. & Smith, T.B. (2000) Diversification of rainforest faunas: an integrated molecular approach. Annual Review of Ecology and Systematics, 31, 533-563.
52. Morrone, J.J. (2010) Fundamental biogeographic patterns across the Mexican Transition Zone: an evolutionary approach. Ecography, 33, 355-361.
53. Mulcahy, D.G. & Mendelson, J.R., III (2000) Phylogeography and speciation of the morphologically variable, widespread species Bufo valliceps, based on molecular evidence from mtDNA. Molecular Phylogenetics and Evolution, 17, 173-189.
54. Mulcahy, D.G., Morrill, B.H. & Mendelson, J.R. (2006) Historical biogeography of lowland species of toads (Bufo) across the Trans-Mexican Neovolcanic Belt and the Isthmus of Tehuantepec. Journal of Biogeography, 33, 1889-1904.
55. Navarro-Sigüenza, A.G., Peterson, A.T., Nyari, A., García-Deras, G. & García-Moreno, J. (2008) Phylogeography of the Buarremon brush-finch complex (Aves, Emberizidae) in Mesoamerica. Molecular Phylogenetics and Evolution, 47, 21-35.
56. Neiswenter, S.A. & Riddle, B.R. (2010) Diversification of the Perognathus flavus species group in emerging arid grasslands of western North America. Journal of Mammalogy, 91, 348-362.
57. Nylander, J.A.A. (2004) MRMODELTEST v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University, Uppsala.
58. Nylander, J.A.A., Wilgenbusch, J.C., Warren, D.L. & Swofford, D.L. (2008) AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference. Bioinformatics, 24, 581-583.
59. Peterson, A.T. & Nyári, Á.S. (2007) Ecological niche conservatism and Pleistocene refugia in the Thrush-like Mourner, Schiffornis sp., in the Neotropics. Evolution, 62, 173-183.
60. Posada, D. & Crandall, K.A. (1998) Modeltest: testing the models of DNA substitution. Bioinformatics, 14, 817-818.
61. Pyron, R.A. & Burbrink, F.T. (2009a) Neogene diversification and taxonomic stability in the snake tribe Lampropeltini (Serpentes: Colubridae). Molecular Phylogenetics and Evolution, 52, 524-529.
62. Pyron, R.A. & Burbrink, F.T. (2009b) Systematics of the Common Kingsnake (Lampropeltis getula; Serpentes: Colubridae) and the burden of heritage in taxonomy. Zootaxa, 2241, 22-32.
63. Pyron, R.A. & Burbrink, F.T. (2009c) Lineage diversification in a widespread species: roles for niche divergence and conservatism in the Common Kingsnake, Lampropeltis getula. Molecular Ecology, 18, 3443-3457.
64. Rambaut, A. & Drummond, A.J. (2007) Tracer v1.4. Available at: .
65. Reichling, S.B. (1995) The taxonomic status of the Louisiana pine snake (Pituophis melanoleucus ruthveni) and its relevance to the evolutionary species concept. Journal of Herpetology, 29, 186-198.
66. Riddle, B.R. & Hafner, D.J. (2006) A step-wise approach to integrating phylogeographic and phylogenetic biogeographic perspectives on the history of a core North American warm deserts biota. Journal of Arid Environments, 66, 435-461.
67. Rodríguez-Robles, J.A. & De Jesús-Escobar, J.M. (2000) Molecular systematics of New World gopher, bull, and pinesnakes (Pituophis: Colubridae), a transcontinental species complex. Molecular Phylogenetics and Evolution, 14, 35-50.
68. Ronquist, F. & Huelsenbeck, J.P. (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574.
69. Rosas-Elguera, J., Alva-Valdivia, L., Goguitchaichvili, A., Urrutia-Fucugauchi, J., Ortega-Rivera, M., Prieto, J. & Lee, J. (2003) Counterclockwise rotation of the Michoacan Block: implications for the tectonics of western Mexico. International Geology Review, 45, 814-826.
70. Rull, V. (2006) Quaternary speciation in the Neotropics. Molecular Ecology, 15, 4257-4259.
71. Rull, V. (2008) Speciation timing and neotropical biodiversity: the Tertiary-Quaternary debate in the light of molecular phylogenetic evidence. Molecular Ecology, 17, 2722-2729.
72. Rzedowski, J. (1996) Análisis preliminar de la flora vascular de los bosques mesofilos de montaña de México. Acta Botanica Mexicana, 35, 25-44.
73. Shimodaira, H. & Hasegawa, M. (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution, 16, 1114-1116.
74. Smith, H.M., Chiszar, D. & Lemos-Espinal, J.A. (2005) Geographic distribution. Pituophis deppei deppei. Herpetological Review, 36, 183.
75. Stamatakis, A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22, 2688-2690.
76. Sullivan, J., Arellano, E. & Rogers, D.S. (2000) Comparative phylogeography of Mesoamerican highland rodents: concerted versus independent response to past climatic fluctuations. The American Naturalist, 155, 755-768.
77. Sweet, S.S. & Parker, W.S. (1990) Pituophis melanoleucus (Daudin). Pine, bull, and gopher snakes. Catalogue of American Amphibians and Reptiles, 474, 1-8.
78. Swofford, D.L. (2002) PAUP*: phylogenetic analysis using parsimony (*and other methods), version 4.0b10. Sinauer, Sunderland, MA.
79. Van Devender, T.R. (1990) Late Quaternary vegetation and climate of the Chihuahuan Desert, United States and Mexico. Packrat middens: the last 40, 000years of biotic change (ed. by J.L. Betancourt, T.R. Van Devender and P.S. Martin), pp. 104-133. University of Arizona Press, Tucson, AZ.
80. Wüster, W., Graca Salomão, M.da., Quijada-Mascareñas, J.A., Thorpe, R.S. & Butantan British Bothrops Systematics Project (2002) Origin and evolution of the South American pitviper fauna: evidence from mitochondrial DNA sequence data. Biology of the vipers (ed. by G.W. Schuett, M. Höggren, M.E. Douglas and H.W. Greene), pp. 111-128. Eagle Mountain Publishing, Salt Lake City, UT.
81. Zink, R.M. (2002) Methods in comparative phylogeography, and their application to studying evolution in the North American aridlands. Integrative and Comparative Biology, 42, 953-959.