The role of tropical dry forest as a long-term barrier to dispersal: A comparative phylogeographical analysis of dry forest tolerant and intolerant frogs

Molecular Ecology

Volumn 16, Issue 22, 2007, Pages 4789-4807

  Crawford, Andrew J ^a,c   Bermingham, Eldredge ^a   Carolina, Polanía S ^b  

^a SMITHSONIAN TROPICAL RESEARCH INSTITUTE   (Panama)

^b UNIVERSIDAD NACIONAL DE COLOMBIA   (Colombia)

^c APACHE POINT OBSERVATORY   (United States)

Author keywords

Central America; Dispersal; Phylogeography; SOWH test; Tropical dry forest; Tropical wet forest

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CENTRAL AMERICA; CHEMISTRY; CLASSIFICATION; COMPARATIVE STUDY; EVOLUTION; FROGS AND TOADS; GENETICS; GEOGRAPHY; PHYLOGENY; PHYSIOLOGY; POPULATION MIGRATION; TREE; TROPIC CLIMATE;

ANIMAL MIGRATION; ANIMALS; ANURA; CENTRAL AMERICA; DNA, MITOCHONDRIAL; EVOLUTION; GEOGRAPHY; MODELS, BIOLOGICAL; PHYLOGENY; TREES; TROPICAL CLIMATE;

ANURA;

EID: 36348957296     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2007.03524.x     Document Type: Article

References (103)

1. Arbogast BS, Edwards SV, Wakeley J, Beerli P, Slowinski JB (2002) Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annual Review of Ecology and Systematics, 33, 707 740.
2. Avise JC (2000) Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge, Massachusetts.
3. Ballard JWO, Whitlock MC (2004) The incomplete natural history of mitochondria. Molecular Ecology, 13, 729 744.
4. Bermingham E, Avise J (1986) Molecular zoogeography of freshwater fishes in the southeastern United States. Genetics, 113, 939 965.
5. Bermingham E, Martin AP (1998) Comparative mtDNA phylogeography of Neotropical freshwater fishes: testing shared history to infer the evolutionary landscape of lower Central America. Molecular Ecology, 7, 499 517.
6. Brumfield RT, Braun MJ (2001) Phylogenetic relationships in bearded manakins (Pipridae: Manacus) indicate that male plumage colour is a misleading taxonomic marker. The Condor, 103, 248 258.
7. Buckley TR (2002) Model misspecification and probabilistic tests of topology: evidence from empirical data sets. Systematic Biology, 51, 509 523.
8. Campbell P, Schneider CJ, Adnan AM, Zubaid A, Kunz TH (2006) Comparative population structure of Cynopterus fruit bats in peninsular Malaysia and southern Thailand. Molecular Ecology, 15, 29 47.
9. Castoe TA, Doan TM, Parkinson CL (2004) Data partitions and complex models in Bayesian analaysis: the phylogeny of gymnphthalmid lizards. Systematic Biology, 53, 1 22.
10. Coates AG, Aubry M-P, Berggren WA, Collins LS, Kunk M (2003) Early Neogene history of the Central American arc from Bocas del Toro, western Panama. GSA Bulletin, 115, 271 287.
11. Coen E (1983) Climate. In: Costa Rican Natural History (ed. Janzen DH pp. 35 46. University of Chicago Press, Chicago, Illinois.
12. Crawford AJ (2003a) Huge populations and old species of Costa Rican and Panamanian dirt frogs inferred from mitochondrial and nuclear gene sequences. Molecular Ecology, 12, 2525 2540.
13. Crawford AJ (2003b) Relative rates of nucleotide substitution in frogs. Journal of Molecular Evolution, 57, 636 641.
14. Crawford AJ, Smith EN (2005) Cenozoic biogeography and evolution in direct-developing frogs of Central America (Leptodactylidae: Eleutherodactylus) as inferred from a phylogenetic analysis of nuclear and mitochondrial genes. Molecular Phylogenetics and Evolution, 35, 536 555.
15. Cunningham CW (1997) Can the incongruence test predict when data should be combined? Molecular Biology and Evolution, 14, 733 740.
16. Dick CW, Abdul-Salim K, Bermingham E (2003) Molecular systematic analysis reveals cryptic tertiary diversification of a widespread tropical rain forest tree. American Naturalist, 162, 691 703.
17. Farris JS, Källersjö M, Kluge AG, Bult C (1995) Testing significance of incongruence. Cladistics, 10, 315 319.
18. Felsenstein J (1981) Evolutionary trees from DNA sequences - a maximum-likelihood approach. Journal of Molecular Evolution, 17, 368 376.
19. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783 791.
20. Felsenstein J (2004) Inferring Phylogenies. Sinauer & Associates Inc., Sunderland, Massachusetts.
21. Goebel AM, Donnelly JM, Atz ME (1999) PCR primers and amplification methods for 12S ribosomal DNA, the control region, cytochrome oxidase I, and cytochrome b in bufonids and other frogs, and an overview of PCR primers which have amplified DNA in amphibians successfully. Molecular Phylogenetics and Evolution, 11, 163 199.
22. Goldman N, Anderson JP, Rodrigo AG (2000) Likelihood-based tests of topologies in phylogenetics. Systematic Biology, 49, 652 670.
23. González MA, Eberhard JR, Lovette IJ, Olson SL, Bermingham E (2003) Mitochondrial DNA phylogeography of the Bay Wren (Troglodytidae: Thryothorus nigricapillus) complex. The Condor, 105, 228 238.
24. Graham A, Dilcher D (1995) The Cenozoic record of tropical dry forest in northern Latin America and the southern United States. In: Seasonally Dry Tropical Forests (eds Bullock SH, Mooney HA, Medina E pp. 124 145. Cambridge University Press, Cambridge, England, UK.
25. Graham CH, Ron SR, Santos JC, Schneider CJ, Moritz C (2004) Integrating phylogenetics and environmental niche models to explore speciation mechanisms in dendrobatid frogs. Evolution, 58, 1781 1793.
26. Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 22, 160 174.
27. Hasegawa M, Kishino H, Yano T (1987) Man's place in Hominoidea as inferred from molecular clocks of DNA. Journal of Molecular Evolution, 26, 132 147.
28. Hickerson MJ, Cunningham CW (2005) Contrasting Quaternary histories in an ecologically divergent sister pair of low-dispersing intertidal fish (Xiphister) revealed by multilocus DNA data. Evolution, 59, 344 360.
29. Holdridge LR (1967) Life Zone Ecology. Tropical Science Center, San José, Costa Rica.
30. Huelsenbeck JP, Rannala B (2004) Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Systematic Biology, 53, 904 913.
31. Huelsenbeck JP, Hillis DM, Jones R (1996) Parametric bootstrapping in molecular phylogenetics: applications and performance. In: Molecular Zoology: Advances, Strategies, and Protocols (eds Ferraris JD, Palumbi SR pp. 19 45. John Wiley and Sons, Inc, New York.
32. Ibáñez R, Solís FA, Jaramillo CA, Rand AS (2001) An overview of the herpetology of Panama. In: Mesoamerican Herpetology: Systematics, Zoogeography, and Conservation (eds Johnson JD, Webb RG, Flores-Villela O pp. 159 170. Centenial Museum, Special Publ. No. 1, University of Texas at El Paso, El Paso, Texas.
33. IUCN, Conservation International, and NatureServe (2004) Global Amphibian Assessment. Available from URL: http://www.globalamphibians.org [ accessed on 16 May 2005].
34. Kerdelhué C, Magnoux E, Lieutier F, Roques A, Rousselet J (2006) Comparative population genetic study of two oligophagous insects associated with the same hosts. Heredity, 97, 38 45.
35. Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111 120.
36. Kishino H, Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. Journal of Molecular Evolution, 29, 170 179.
37. Köhler G (2001) Anfibios y Reptiles de Nicaragua. Herpeton Verlag, Offenbach, Germany.
38. Köhler G (2003) Reptiles of Central America. Herpeton Verlag, Offenbach, Germany.
39. Kumar S, Tamura K, Nei M (2004) mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics, 5, 150 163.
40. Lips KR, Brem F, Brenes R et al 2006) Emerging infectious disease and the loss of biodiversity in a Neotropical amphibian community. Proceedings of the National Academy of Sciences, USA, 103, 3165 3170.
41. Lockhart PJ, Steel MA, Hendy MD, Penny D (1994) Recovering evolutionary trees under a more realistic model of sequence evolution. Molecular Biology and Evolution, 11, 605 612.
42. Lomolino MV, Sax DF, Brown JH (2004) Foundations of Biogeography Classic Papers with Commentaries. University of Chicago Press, Chicago, Illinois.
43. Lynch JD, Myers CW (1983) Frogs of the fitzingeri group of Eleutherodactylus in eastern Panama and Chocoan South America (Leptodactylidae). Bulletin of the American Museum of Natural History, 175, 484 568.
44. Lynch JD, Suárez-Mayorga ÁM (2004) Anfibios en el Chocó biogeográfico. In: Colombia Diversidad Biótica IV, El Chocó biogeográfico/Costa Pacífica (ed. Rangel-Ch JO pp. 633 667. Universidad Nacional de Colombia, Bogotá, Colombia.
45. Macey JR, Schulte JA II, Larson A et al 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.
46. Macey JR, Strasburg JL, Brisson JA, Vredenburg VT, Jennings M, Larson A (2001) Molecular phylogenetics of western North American frogs of the Rana boylii species group. Molecular Phylogenetics and Evolution, 19, 131 143.
47. Maxson LR, Myers CW (1985) Alburnin evolution in tropical poison frogs (Dendrobatidae): a preliminary report. Biotropica, 17, 50 56.
48. McCranie JR, Wilson LD (2002) The amphibians of Honduras. Contributions to Herpetology, 19, 1 625.
49. McDiarmid RW, Savage JM (2005) The herpetofauna of the Rincón area, Península de Osa, Costa Rica, a Central American lowland evergreen forest site. In: Ecology and Evolution in the Tropics: A Herpetological Perspective (eds Donnelly MA, Crother BI, Guyer C, Wake MH, White ME pp. 366 427. University of Chicago Press, Chicago, Illinois.
50. Minin V, Abdo Z, Joyce P, Sullivan J (2003) Performance-based selection of likelihood models for phylogeny estimation. Systematic Biology, 52, 674 683.
51. Miyamoto MM (1986) Phylogenetic relationships and systematics of the Eleutherodactylus fitzingeri group (Anura, Leptodactylidae). Copeia, 1986, 503 511.
52. Noonan BP, Gaucher P (2005) Phylogeography and demography of Guianan harlequin toads (Atelopus): diversification within a refuge. Molecular Ecology, 14, 3017 3031.
53. Nylander JAA, Ronquist F, Huelsenbeck JP, Nieves-Aldrey JL (2004) Bayesian phylogenetic analysis of combined data. Systematic Biology, 53, 47 67.
54. Pauly GB, Hillis DM, Cannatella DC (2004) The history of a Nearctic colonization: molecular phylogenetics and biogeography of the Nearctic toads (Bufo). Evolution, 58, 2517 2535.
55. Perdices A, Bermingham E, Montill A, Doadriob I (2002) Evolutionary history of the genus Rhamdia (Teleostei: Pimelodidae) in Central America. Molecular Phylogenetics and Evolution, 25, 172 189.
56. Piperno DR, Pearsall DM (1998) The Origins of Agriculture in the Lowland Neotropics. Academic Press, San Diego, California.
57. Pisani GR (1973) A Guide to Preservation Techniques for Amphibians and Reptiles. Herpetological Circular 1. Society for the Study of Amphibians and Reptiles, St. Louis, Missouri.
58. Pounds JA, Crump ML (1994) Amphibian declines and climate disturbance: the case of the golden toad and the harlequin frog. Conservation Biology, 8, 72 78.
59. Pounds JA, Fogden MPL, Savage JM, Gorman GC (1997) Tests of null models for amphibian declines on a tropical mountain. Conservation Biology, 11, 1307 1322.
60. Prager EM, Wilson AC (1988) Ancient origin of lactalbumin from lysozyme: analysis of DNA and amino acid sequences. Journal of Molecular Evolution, 27, 326 335.
61. Puschendorf R, Chaves G, Crawford AJ, Brooks DR (2005) Eleutherodactylus ranoides (NCN), dry forest population, refuge from decline? Herpetological Review, 36, 53.
62. Rambaut A, Grassly NC (1997) seq-general: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Computational and Applied Biosciences, 13, 235 238.
63. Rannala B, Yang Z (1996) Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. Journal of Molecular Evolution, 43, 304 311.
64. Reeves RG, Bermingham E (2006) Colonization, population expansion, and lineage turnover: phylogeography of Mesoamerican characiform fish. Biological Journal of the Linnean Society, 88, 235 255.
65. Remington CL (1968) Suture-zones of hybrid interaction between recently joined biotas. Evolutionary Biology, 2, 321 428.
66. Ricklefs RE, Schluter D (1993) Species diversity, regional and historical influences. In: Species Diversity in Ecological Communities (eds Ricklefs RE, Schluter D pp. 350 363. University Chicago Press, Chicago, Illinois.
67. Ridgely RS, Allnutt TF, Brooks T et al 2003) Digital Distribution Maps of the Birds of the Western Hemisphere, Version 1.0. NatureServe, Arlington, Virginia. Available from URL: http://www.natureserve.org/getData/birdMaps.jsp.
68. Roberts TE (2006) History, ocean channels, and distance determine phylogeographic patterns in three widespread Philippine fruit bats (Pteropodidae). Molecular Ecology, 15, 2183 2199.
69. Roberts JL, Brown JL, von May R, Arizabald W, Schulte R, Summers K (2006) Genetic divergence and speciation in lowland and montane peruvian [sic.] poison frogs. Molecular Phylogenetics and Evolution, 41, 149 164.
70. Ron SR, Santos JC, Cannatella DC (2006) Phylogeny of the túngara frog genus Engystomops (= Physalaemus pustulosus species group; Anura: Leptodactylidae). Molecular Phylogenetics and Evolution, 39, 392 403.
71. Ronquist F, Huelsenbeck JP (2003) mrbayes3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572 1574.
72. Ruíz-Carranza PM, Ardila-Robayo MC, Lynch JD (1996) Lista actualizada de la fauna de Amphibia de Colombia. Revista de la Academia Colombiana de Ciencias Exactas, Fisicas y Naturales, 20, 365 415.
73. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406 425.
74. Sanderson MJ (1997) A nonparametric approach to estimating divergence times in the absence of rate constancy. Molecular Biology and Evolution, 14, 1218 1231.
75. Savage JM (1982) The enigma of the Central American herpetofauna: dispersal or vicariance? Annals of the Missouri Botanical Garden, 69, 464 547.
76. Savage JM (2002) The Amphibians and Reptiles of Costa Rica: A Herpetofauna between Two Continents, between Two Seas. University of Chicago Press, Chicago, Illinois.
77. Savage JM, Bradford DH, Lips KR, Jaslow AP (2004) A new species of rainfrog (genus Eleutherodactylus) from the Serranía de Tabasará, west-central Panama and reanalysis of the fitzingeri species group. Herpetologica, 60, 519 529.
78. Schäuble CS, Moritz C (2001) Comparative phylogeography of two open forest frogs from eastern Australia. Biological Journal of the Linnean Society, 74, 157 170.
79. Schneider CJ, Cunningham M, Moritz C (1998) Comparative phylogeography and the history of endemic vertebrates in the Wet Tropics rainforests of Australia. Molecular Ecology, 7, 487 498.
80. Seutin G, White BN, Boag PT (1991) Preservation of avian blood and tissue samples for DNA analyses. Canadian Journal of Zoology, 69, 82 90.
81. Shi X, Gu H, Susko E, Field C (2005) The comparison of the confidence regions in phylogeny. Molecular Biology and Evolution, 22, 2285 2296.
82. Shimodaira H (2002) An approximately unbiased test of phylogenetic tree selection. Systematic Biology, 51, 492 508.
83. Shimodaira H, Hasegawa M (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution, 16, 1114 1116.
84. Simpson GG (1940) Mammals and land bridges. Journal of the Washington Academy of Sciences, 30, 137 163.
85. Stuart SN, Chanson JS, Cox NA et al 2004) Status and trends of amphibian declines and extinctions worldwide. Science, 306, 1783 1786.
86. Stuart BL, Inger RF, Voris HK (2006) High level of cryptic species diversity revealed by sympatric lineages of Southeast Asian forest frogs. Biology Letters, 2, 470 474.
87. Sullivan J (1996) Combining data with different distributions of among-site rate variation. Systematic Biology, 45, 375 380.
88. Swofford DL (1998) paup*. Phylogenetic Analysis Using Parsimony *and Other Methods, Version 4b10. Sinauer & Associates, Sunderland, Massachusetts.
89. Swofford DL, Olsen GJ, Waddell PJ, Hillis DM (1996) Phylogenetic inference. In: Molecular Systematics (eds Hillis DM, Moritz C, Mable BK pp. 407 514. Sinauer & Associates, Sunderland, Massachusetts.
90. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10, 512 526.
91. Tavaré S (1986) Some probabilistic and statistical problems on the analysis of DNA sequences. Lectures in Mathematics and the Life Sciences, 17, 57 86.
92. Templeton AR (1983) Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution, 37, 221 244.
93. Thorne JL, Kishino H (2002) Divergence time and evolutionary rate estimation with multilocus data. Systematic Biology, 51, 689 702.
94. Thorne JL, Kishino H, Painter IS (1998) Estimating the rate of evolution of the rate of molecular evolution. Molecular Biology and Evolution, 15, 1647 1657.
95. Tosi JA (1969) Ecological Map of Costa Rica. Tropical Science Center, San José, Costa Rica.
96. Vanzolini PE, Heyer WR (1985) The American herpetofauna and the interchange. In: The Great American Biotic Interchange (eds Stehli FG, Webb SD pp. 475 487. Plenum Press, New York.
97. Webb SD (1985) Late Cenozoic mammal dispersals between the Americas. In: The Great American Biotic Interchange (eds Stehli FG, Webb SD pp. 357 386. Plenum Press, New York.
98. Weigt LA, Crawford AJ, Rand AS, Ryan MJ (2005) Biogeography of the túngara frog, Physalaemus pustulosus: a molecular perspective. Molecular Ecology, 14, 3857 3876.
99. Wüster W, Ferguson JE, Quijada-Mascareñas JA, Pook CE, Da Graça Salomão M, Thorpe RS (2005) Tracing an invasion: landbridges, refugia, and the phylogeography of the Neotropical rattlesnake (Serpentes: Viperidae: Crotalus durissus). Molecular Ecology, 14, 1095 1108.
100. Yang Z (1994) Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of Molecular Evolution, 39, 306 324.
101. Yang Z, Rannala B (1997) Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Molecular Biology and Evolution, 14, 717 724.
102. Zeh JA, Zeh DW, Bonilla MM (2003a) Phylogeography of the harlequin beetle-riding pseudoscorpion and the rise of the Isthmus of Panamá. Molecular Ecology, 12, 2759 2769.
103. Zeh DA, Zeh JA, Bonilla MM (2003b) Phylogeography of the giant harlequin beetle (Acrocinus longimanus). Journal of Biogeography, 30, 747 753.