Phylogeography of declining relict and lowland leopard frogs in the desert Southwest of North America

Journal of Zoology

Volumn 280, Issue 4, 2010, Pages 343-354

  Olah Hemmings V ^a   Jaeger, J R ^a   Sredl, M J ^b   Schlaepfer, M A ^c   Jennings, R D ^d   Drost, C A ^e   Bradford, D F ^f   Riddle, B R ^a  

^a UNIVERSITY OF NEVADA   (United States)

^b ARIZONA GAME AND FISH DEPARTMENT   (United States)

^c STATE UNIVERSITY OF NEW YORK   (United States)

^d WESTERN NEW MEXICO UNIVERSITY   (United States)

^e U S GEOLOGICAL SURVEY   (United States)

^f U S ENVIRONMENTAL PROTECTION AGENCY   (United States)

Author keywords

Lithobates; Mitochondrial DNA; Mojave Desert; Population structure; Rana onca; Rana yavapaiensis; Sonoran Desert

Indexed keywords

ANCESTRY; DEMOGRAPHY; EVOLUTIONARY THEORY; FROG; LAST GLACIAL MAXIMUM; MITOCHONDRIAL DNA; PHYLOGEOGRAPHY; POPULATION DECLINE; POPULATION STRUCTURE; RANGE EXPANSION; SAMPLING;

MOJAVE DESERT; SONORAN DESERT; UNITED STATES;

ANURA; FELIDAE; LITHOBATES; PANTHERA PARDUS; RANA ONCA; RANA YAVAPAIENSIS;

EID: 77952537591     PISSN: 09528369     EISSN: 14697998     Source Type: Journal    
DOI: 10.1111/j.1469-7998.2009.00667.x     Document Type: Article

References (67)

1. Arbogast BS, Edwards SV, Wakeley J, Beerli P, Slowinski JB. Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Ann. Rev. Ecol. Syst. 2002, 33:707-740.
2. Austin JD, Zamudio KR. Incongruence in the pattern and timing of intra-specific diversification in bronze frogs and bullfrogs (Ranidae). Mol. Phylogenet. Evol. 2008, 48:1041-1053.
3. Avise JC. Phylogeography: the history and formation of species 2000, Cambridge, Harvard University Press
4. Babik W, Branicki W, Sandera M, Litvinchuk S, Borkin LJ, Irwin JT, Rafinski J. Mitochondrial phylogeography of the moor frog, Rana arvalis. Mol. Ecol. 2004, 13:1469-1480.
5. Ballard JWO, Whitlock MC. The incomplete natural history of mitochondria. Mol. Ecol. 2004, 13:729-744.
6. Bandelt HJ, Forster P, Röhl A. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 1999, 16:37-48.
7. Betancourt JL, Van Devender TR, Martin PS. Packrat Middens: the last 40,000 years of biotic change 1990, Tucson, University of Arizona Press
8. Blaustein AR, Belden LK, Olson DH, Green DM, Root TL, Kiesecker JM. Amphibian breeding and climate change. Conserv. Biol. 2001, 15:1804-1809.
9. Bradford DF, Jaeger JR, Jennings RD. Population status and distribution of a decimated amphibian, the relict leopard frog (Rana onca). Southwest. Nat. 2004, 49:218-228.
10. Carstens BC, Richards CL. Integrating coalescent and ecological niche modeling in comparative phylogeography. Evolution 2007, 61:1439-1454.
11. Clarkson RW, Rorabaugh JC. Status of leopard frogs (Rana pipiens complex: Ranidae) in Arizona and Southeastern California. Southwest. Nat. 1989, 34:531-538.
12. Collins WD, Bitz CM, Blackmon ML, Bonan GB, Bretherton CS, Carton JA, Chang P, Doney SC, Hack JJ, Henderson TB, Kiehl JT, Large WG, McKenna DS, Santer BD, Smith RD. The community climate system model version 3 (CCSM3). J. Climate 2006, 19:2122-2143.
13. Crawford AJ. Huge populations and old species of Costa Rican and Panamanian dirt frogs inferred from mitochondrial and nuclear gene sequences. Mol. Ecol. 2003, 12:2525-2540.
14. Douglas ME, Douglas MR, Schuett GW, Porras LW. Evolution of rattlesnakes (Viperidae; Crotalus) in the warm deserts of western North America shaped by Neogene vicariance and Quaternary climate change. Mol. Ecol. 2006, 15:3353-3374.
15. Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214. art.no.
16. Edwards SV, Beerli P. Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 2000, 54:1839-1854.
17. Excoffier L, Laval G, Schneider S. Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol. Bioinform. Online 2005, 1:47-50.
18. Excoffier L, Schneider S. Why hunter-gatherer populations do not show signs of Pleistocene demographic expansions. Proc. Natl. Acad. Sci. USA 1999, 96:10597-10602.
19. Farris JS, Kallersjo M, Kluge AG, Bult C. Testing significance of incongruence. Cladistics 1995, 10:315-319.
20. Fehlberg SD, Ranker TA. Evolutionary history and phylogeography of Encelia farinosa (Asteraceae) from the Sonoran, Mojave, and Peninsular deserts. Mol. Phylogenet. Evol. 2009, 50:326-335.
21. Frost JS, Bagnara JT. A new species of leopard frog (Rana pipiens complex) from Northwestern Mexico. Copeia 1976, 1976:332-338.
22. Fu YX. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 1997, 147:915-925.
23. Gelczis L, Drost C. A surprise in surprise Canyon: a new amphibian species for Grand Canyon National Park. Nature Notes 2004, 1-3.
24. Grant WS, Bowen BW. Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. J. Hered. 1998, 89:415-426.
25. Hafner DJ, Riddle BR. Mammalian phylogeography and evolutionary history of northern Mexico's deserts. Biodiversity, ecosystems, and conservation in northern Mexico 2005, 225-245. Cartron J-L, Ceballos GFelger RS. In, (Eds), New York, Oxford University Press
26. Hasumi H, Emori S. 2004, K-1 Technical Report 1, Center for Climate System Research, University of Tokyo, Tokyo
27. Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A. Very high resolution interpolated climate surfaces for global land areas. Int. J. Climatol. 2005, 25:1965-1978.
28. Hillis DM, Wilcox TP. Phylogeny of the New World true frogs (Rana). Mol. Phylogenet. Evol. 2005, 34:299-314.
29. Huelsenbeck JP, Crandall KA. Phylogeny estimation and hypothesis testing using maximum likelihood. Ann. Rev. Ecol. Syst. 1997, 28:437-466.
30. Jaeger JR, Riddle BR, Bradford DF. Cryptic Neogene vicariance and Quaternary dispersal of the red-spotted toad (Bufo punctatus): insights on the evolution of North American warm desert biotas. Mol. Ecol. 2005, 14:3033-3048.
31. Jaeger JR, Riddle BR, Jennings RD, Bradford DF. Rediscovering Rana onca: evidence for phylogenetically distinct leopard frogs from the border region of Nevada, Utah, and Arizona. Copeia 2001, 2001:339-354.
32. Jennings MR, Hayes MP. Decline of native ranid frogs in the desert southwest. Herpetology of the North American Deserts, proceedings of a symposium. Special Publication No. 5 1994, 183-211. Brown PR, Wright JW. In, (Eds), Van Nuys, Southwestern Herpetologists Society
33. Jennings RD. 1995, Unpublished report submitted to New Mexico Department of Game and Fish, Endangered Species Program, Santa Fe
34. Lee JE, Yang DE, Kim YR, Lee H, Lee HI, Yung SY, Lee HY. Genetic relationships of Rana amurensis based on mitochondrial cytochrome b gene sequences. Korean J. Biol. Sci. 1999, 3:303-309.
35. Macey JR, Schulte JA, Larson A, Fang Z, Wang Y, Tuniyev BS, Papenfuss TJ. Phylogenetic relationships of toads in the Bufo bufo species group from the eastern escarpment of the Tibetan Plateau: a case of vicariance and dispersal. Mol. Phylogenet. Evol. 1998, 9:80-87.
36. Macey JR, Strasburg JL, Brisson JA, Vrendenburg VT, Jennings M, Larson A. Molecular phylogenetics of western North American frogs of the Rana boylii species group. Mol. Phylogenet. Evol. 2001, 19:131-143.
37. Miller MP. Alleles in space (AIS): computer software for the joint analysis of interindividual spatial and genetic information. J. Hered 2005, 96:722-724.
38. Nylander JAA. MrModeltest v2. Program distributed by the author 2004, Evolutionary Biology Centre, Uppsala University
39. Nylander JAA, Ronquist F, Huelsenbeck JP, Nieves Aldrey JL. Bayesian phylogenetic analysis of combined data. Syst. Biol. 2004, 53:47-67.
40. Pearson RG, Raxworthy C, Nakamura M, Peterson AT. Predicting species' distributions from small numbers of occurrence records: a test case using cryptic geckos in Madagascar. J. Biogeogr. 2007, 34:102-117.
41. Peterson AT. Predicting species' geographic distributions based on ecological niche modeling. Condor 2001, 103:599-605.
42. Pfeiler E, Markow TA. Phylogenetic relationships of leopard frogs (Rana pipiens complex) from an isolated coastal mountain range in southern Sonora, Mexico. Mol. Phylogenet. Evol. 2008, 49:343-348.
43. Phillips AM. 1977, PhD dissertation, University of Arizona at Tucson
44. Phillips SJ, Anderson RP, Schapire RE. Maximum entropy modeling of species geographic distributions. Ecol. Model. 2006, 190:231-259.
45. Platz JE, Frost JS. Rana yavapaiensis a new species of leopard frog (Rana pipiens complex). Copeia 1984, 1984:940-948.
46. Posada D, Buckley TR. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 2004, 53:793-808.
47. Quattro JM, Leberg PL, Douglas ME, Vrijenhoek RC. Molecular evidence for a unique evolutionary lineage of endangered Sonoran desert fish (Genus Poeciliopsis). Conserv. Biol. 1996, 10:128-135.
48. Raes N, Ter Steege H. A null-model for significance testing of presence only species distribution models. Ecography 2007, 30:727-736.
49. Rambaut A, Drummond AJ. 2007, http://beast.bio.ed.ac.uk/Tracer, Tracer v1.4. Available from, accessed on 20 January 2009
50. Ramos-Onsins SE, Rozas J. Statistical properties of new neutrality tests against population growth. Mol. Biol. Evol. 2002, 19:2092-2100.
51. Riddle BR, Hafner DJ, Alexander LF. Phylogeography and systematics of the Peromyscus eremicus species group and the historical biogeography of North American warm regional deserts. Mol. Phylogenet. Evol. 2000, 17:145-160.
52. Riddle BR, Honeycut RL, Lee PL. Mitochondrial DNA phylogeography in northern grasshopper mice (Onychomys leucogaster) - the influence of Quaternary climatic oscillations on population dispersion and divergence. Mol. Ecol. 1993, 2:183-193.
53. Rogers AR, Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 1992, 9:552-569.
54. Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
55. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 2003, 19:2496-2497.
56. Schneider S, Excoffier L. Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics 1999, 152:1079-1089.
57. Sredl MJ. Rana yavapaiensis Platz and Frost, 1984, Lowland leopard frog. Amphibian declines: the conservation status of United States species 2005, 596-599. Lannoo MJ. In, (Ed.), Berkeley, University of California Press
58. Sredl MJ, Collins PE, Howland JM. Mark-recapture studies of Arizona leopard frogs. Technical report, no. 121. Ranid frog conservation and management 1997, 1-20. Sredl MJ, In, (Ed.), Phoenix, Nongame and Endangered Wildlife Program, Arizona Game and Fish Department
59. Swofford DL. PAUP*, phylogenetic analysis using parsimony (*and other methods), version 4.0b10 2002, Sunderland, Sinauer Associates
60. Tamura K, Dudley J, Nei M, Kumar S. MEGA 4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
61. Thompson RS, Anderson KH. Biomes of western North America at 18,000, 6000 and 0 14C yr BP reconstructed from pollen and packrat midden data. J. Biogeogr. 2000, 27:555-584.
62. Vences M, Chiari Y, Raharivololoniaina L, Meyer A. High mitochondrial diversity within and among populations of Malagasy poison frogs. Mol. Phylogenet. Evol. 2004, 30:295-307.
63. Vitt LJ, Ohmart RD. Herpetofauna of the lower Colorado river: Davis Dam to the Mexican border. Proc. West. Found. Vertebr. Zool. 1978, 2:35-72.
64. Waltari E, Hijmans RJ, Peterson AT, Nyari AS, Perkins SL, Guralnick RP. Locating Pleistocene refugia: comparing phylogeographic and ecological niche model predictions. PLoS One 2007, 2:e563.
65. Wiens JJ, Graham CH. Niche conservatism: integrating evolution, ecology, and conservation biology. Ann. Rev. Ecol. Evol. Syst. 2005, 36:519-539.
66. Wilcox TP, Zwickl DJ, Heath TA, Hillis DM. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Mol. Phylogenet. Evol. 2002, 25:361-371.
67. Zink RM, Barrowclough GF. Mitochondrial DNA under siege in avian phylogeography. Mol. Ecol. 2008, 17:2107-2121.