Range-wide phylogeographic analysis of the spotted frog complex (Rana luteiventris and Rana pretiosa) in northwestern North America

Molecular Phylogenetics and Evolution

Volumn 49, Issue 1, 2008, Pages 198-210

  Funk, W Chris ^a,b   Pearl, Christopher A ^a   Draheim, Hope M ^a,c   Adams, Michael J ^a   Mullins, Thomas D ^a   Haig, Susan M ^a  

^a FOREST AND RANGELAND ECOSYSTEM SCIENCE CENTER   (United States)

^b Department of Ecosystem Science and Sustainability   (United States)

^c UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Conservation genetics; Mitochondrial DNA; Northwestern North America; Phylogeography; Population expansion; Rana; Spotted frog

Indexed keywords

CYTOCHROME B; MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; CLASSIFICATION; DNA SEQUENCE; ENVIRONMENTAL PROTECTION; FROG; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; MITOCHONDRIAL GENE; MITOCHONDRION; MOLECULAR EVOLUTION; NORTH AMERICA; PHYLOGENY; POPULATION GENETICS; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE; SPECIES DIFFERENTIATION; STATISTICAL MODEL;

ANIMALS; CONSERVATION OF NATURAL RESOURCES; CYTOCHROMES B; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENES, MITOCHONDRIAL; GENETIC SPECIATION; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; LIKELIHOOD FUNCTIONS; MITOCHONDRIA; NORTH AMERICA; PHYLOGENY; RANIDAE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

ANURA; RANA LUTEIVENTRIS; RANA PRETIOSA;

EID: 52049100111     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2008.05.037     Document Type: Article

References (73)

1. Akaike H. A new look at the statistical model identification. IEEE Trans. Automatic Control 19 (1974) 716-723
2. Allendorf F.W., and Luikart G. Conservation and the Genetics of Populations (2007), Blackwell Publishing, Oxford
3. Avise J.C. Phylogeography (2000), Harvard University Press, Cambrdige, MA
4. Berger L., Speare R., Daszak P., Green D.E., Cunningham A.A., Goggin C.L., Slocombe R., Ragan M.A., Hyatt A.D., McDonald K.R., Hines H.B., Lips K.R., Marantelli G., and Parkes H. Chytridiomycosis causes amphibian mortality associated with population declines in the rain forests of Australia and Central America. Proc. Natl. Acad. Sci. USA. 95 (1998) 9031-9036
5. Bickford D., Lohman D.J., Sodhi N.S., Ng P.K.L., Meier R., Winker K., Ingram K.K., and Das I. Cryptic species as a window on diversity and conservation. Trends Ecol. Evol. 22 (2007) 148-155
6. Bos D.H., and Sites Jr. J.W. Phylogeography and conservation genetics of the Colombia spotted frog (Rana luteiventris; Amphibia, Ranidae). Mol. Ecol. 10 (2001) 1499-1513
7. Brunsfeld S.J., Sullivan J., Soltis D.E., and Soltis P.S. Comparative phylogeography of northwestern North America: a synthesis. In: Silvertown J., and Antonovics J. (Eds). Integrating Ecology and Evolution in a Spatial Context (2001), Blackwell Publishing, Williston, VT 319-339
8. Bürger R., and Lynch M. Evolution and extinction in a changing environment: a quantitative-genetic analysis. Evolution 49 (1995) 151-163
9. Carstens B.C., Stevenson A.L., Degenhardt J.D., and Sullivan J. Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group. Syst. Biol. 53 (2004) 781-792
10. Carstens B.C., Brunsfeld S.J., Demboski J.R., Good J.M., and Sullivan J. Investigating the evolutionary history of the Pacific Northwest mesic forest ecosystem: hypothesis testing within a comparative phylogeographic framework. Evolution 59 (2005) 1639-1652
11. Conroy C.J., and Cook J.A. Phylogeography of a post-glacial colonizer: Microtus longicaudus (Rodentia: Muridae). Mol. Ecol. 9 (2000) 165-175
12. Corn P.S. What we know and don't know about amphibian declines in the west. In: Covington W.W., and DeBano L.F. (Eds). Sustainable Ecological Systems: Implementing an Ecological Approach to Land Management (1994), U.S.D.A. Forest Service, General Technical Report, RM-247, Fort Collins, CO 59-67
13. Corkran C.C., and Thoms C. Amphibians of Oregon, Washington, and British Columbia. (1996), Lone Pine Publishing, Vancouver, BC
14. Crow J.F., and Kimura M. An Introduction to Population Genetics Theory (1970), Burgess Publishing, Minneapolis, MN
15. Demboski J.R., and Cook J.A. Phylogeography of the dusky shrew, Sorex monticolus (Insectivora, Soricidae): insight into deep and shallow history in northwestern North America. Mol. Ecol. 10 (2001) 1227-1240
16. Drost C.A., and Fellers G.M. Collapse of a regional frog fauna in the Yosemite area of the California Sierra Nevada, USA. Conserv. Biol. 10 (1996) 414-425
17. Endler J.A. Geographic Variation, Speciation, and Clines (1977), Princeton University Press, Princeton, New Jersey
18. Excoffier L., Smouse P.E., and Quattro J.M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131 (1992) 479-491
19. Excoffier L., Laval G., and Schneider S. Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol. Bioinform. Online 1 (2005) 47-50
20. Fu Y.-X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147 (1997) 915-925
21. Funk W.C., Blouin M.S., Corn P.S., Maxell B.A., Pilliod D.S., Amish S., and Allendorf F.W. Population structure of Columbia spotted frogs (Rana luteiventris) is strongly affected by the landscape. Mol. Ecol. 14 (2005) 483-496
22. Funk W.C., Greene A.E., Corn P.S., and Allendorf F.W. High dispersal in a frog species suggests that it is vulnerable to habitat fragmentation. Biol. Lett. 1 (2005) 13-16
23. Funk W.C., Forsman E.D., Mullins T.D., and Haig S.M. and dispersal among spotted owl (Strix occidentalis) subspecies. Evol. Appl. 1 (2008) 161-171
24. Graham A. Late Cretaceous and Cenozoic History of North American Vegetation (1999), Oxford University Press, New York
25. Green D.M., Sharbel T.F., Kearsley J., and Kaiser H. Postglacial range fluctuation, genetic subdivision and speciation in the western North American spotted frog complex, Rana pretiosa. Evolution 50 (1996) 374-390
26. Green D.M., Kaiser H., Sharbel T.F., Kearsley J., and McAllister K.R. Cryptic species of spotted frogs, Rana pretiosa complex, in western North America. Copeia 1997 (1997) 1-8
27. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41 (1999) 95-98
28. Harpending R.C. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum. Biol. 66 (1994) 591-600
29. Hayes M.P., and Jennings M.R. Decline of ranid frog species in western North America: are bullfrogs (Rana catesbeiana) responsible?. J. Herpetol. 20 (1986) 490-509
30. Hayes, M.P., Engler, J. D., Haycock, R.D., Knopp, D.H., Leonard, W.P., McAllister, K.R., Todd, L.L., 1997. Status of the Oregon spottedfrog (Rana pretiosa) across its geographic range. Oregon Chapter of the Wildlife Society, Corvallis, OR.
31. Hillis D.M., and Wilcox T.P. Phylogeny of the new world true frogs (Rana). Mol. Phylogenet. Evol. 34 (2005) 299-314
32. Irwin D.E. Phylogeographic breaks without geographic barriers to gene flow. Evolution 56 (2002) 2383-2394
33. IUCN, Conservation International, and NatureServe. 2006. Global Amphibian Assessment. Available from: . Downloaded on 16 March 2008.
34. Janzen F.J., Krenz J.G., Haselkorn T.S., Brodie Jr. E.D., and Brodie III E.D. Molecular phylogeography of common garter snakes (Thamnophis sirtalis) in western North America: implications for regional historical forces. Mol. Ecol. 11 (2002) 1739-1751
35. Matocq M.D. Phylogeographical structure and regional history of the dusky-footed woodrat, Neotoma fuscipes. Mol. Ecol. 11 (2002) 229-242
36. McAllister K.R., Leonard W.P., and Storm R.M. Spotted frog (Rana pretiosa) surveys in the Puget Trough of Washington, 1989-1991. Northwest. Nat. 74 (1993) 10-15
37. Miller M.P., Haig S.M., and Wagner R.S. Conflicting patterns of genetic structure produced by nuclear and mitochondrial markers in the Oregon slender salamander (Batrachoseps wrighti): implications for conservation efforts and species management. Conserv. Genet. 6 (2005) 275-287
38. Miller M.P., Bellinger M.R., Forsman E.D., and Haig S.M. Effects of historical climate change, habitat connectivity, and vicariance on genetic structure and diversity across the range of the red tree vole (Phenacomys longicaudis) in the Pacific northwestern United States. Mol. Ecol. 15 (2006) 145-159
39. Miller M.P., Haig S.M., and Wagner R.S. Phylogeography and spatial genetic structure of the southern torrent salamander: implications for conservation and management. J. Hered. 97 (2006) 561-570
40. Monsen K.J., and Blouin M.S. Genetic structure in a montane ranid frog: restricted gene flow and nuclear-mitochondrial discordance. Mol. Ecol. 12 (2003) 3275-3286
41. Moritz C. Defining "Evolutionarily Significant Units" for conservation. Trends Ecol. Evol. 9 (1994) 373-375
42. Nielson M., Lohman K., and Sullivan J. Phylogeography of the tailed frog (Ascaphus truei): implications for the biogeography of the Pacific Northwest. Evolution 55 (2001) 147-160
43. Nielson M., Lohman K., Daugherty C.H., Allendorf F.W., Knudsen K.L., and Sullivan J. Allozyme and mitochondrial DNA variation in the tailed frog (Anura:Ascaphus): the influence of geography and gene flow. Herpetologica 62 (2006) 235-258
44. Pearl C.A., and Hayes M.P. Rana pretiosa, Oregon spotted frog. In: Lannoo M.J. (Ed). Amphibian Declines: The Conservation Status of United States Species (2005), University California Press, Berkeley, CA 577-580
45. Pilliod D.S., Peterson C.R., and Ritson P.I. Seasonal migration of Columbia spotted frogs (Rana luteiventris) among complementary resources in a high mountain basin. Can. J. Zool. 80 (2002) 1849-1862
46. Piry S., Luikart G., and Cornuet J.-M. Bottleneck: a computer program for detecting recent reductions in the effective population size using allele frequency data. J. Hered. 90 (1999) 502-503
47. Pounds J.A., Bustamante M.R., Coloma L.A., Consuegra J.A., Fogden M.P.L., Foster P.N., La Marca E., Masters K.L., Merino-Viteri A., Puschendorf R., Ron S.R., Sanchez-Azofeifa G.A., Still C.J., and Young B.E. Widespread amphibian extinctions from epidemic disease driven by global warming. Nature 439 (2006) 161-167
48. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
49. Reaser, J.K., 1997. Amphibian declines: conservation science and adaptive management. Doctoral dissertation. Stanford University, Palo Alto, CA.
50. Reaser J.K., and Pilliod D.S. Rana luteiventris Columbia spotted frog. In: Lannoo M.J. (Ed). Amphibian Declines: The Conservation Status of United States Species (2005), University California Press, Berkeley, CA 559-563
51. Recuero E., Martínez-Solano I., Parra-Olea G., and García-París M. Phylogeography of Pseudacris regilla (Anura: Hylidae) in western North America, with a proposal for a new taxonomic rearrangement. Mol. Phylogenet. Evol. 39 (2006) 293-304
52. Remington C.L. Suture-zones of hybrid interaction between recently joined biotas. In: Dobzhansky T., Hecht M.K., and Steere W.C. (Eds). Evolutionary Biology (1968), Plenum, New York 321-428
53. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
54. Shaffer H.B., Fellers G.M., Voss S.R., Oliver J.C., and Pauly G.B. Species boundaries, phylogeography and conservation genetics of the red-legged frog (Rana aurora / draytonii) complex. Mol. Ecol. 13 (2004) 2667-2677
55. Soltis D.E., Gitzendanner M.A., Strenge D.D., and Soltis P.S. Chloroplast DNA intraspecific phylogeography of plants from the Pacific Northwest of North America. Plant Syst. Evol. 206 (1997) 353-373
56. Spellman G.M., Riddle B., and Klicka J. Phylogeography of the mountain chickadee (Poecile gambeli): diversification, introgression, and expansion in response to Quaternary climate change. Mol. Ecol. 16 (2007) 1055-1068
57. Spinks P.Q., and Shaffer H.B. Range-wide molecular analysis of the western pond turtle (Emys marmorata): cryptic variation, isolation by distance, and their conservation implications. Mol. Ecol. 14 (2005) 2047-2064
58. Spruell P., Hemmingsen A.R., Howell P.J., Kanda N., and Allendorf F.W. Conservation genetics of bull trout: geographic distribution of variation at microsatellite loci. Conserv. Genet. 4 (2003) 17-29
59. Steele C.A., Carstens B.C., Storfer A., and Sullivan J. Testing hypotheses of speciation timing in Dicamptodon copei and Dicamptodon aterrimus (Caudata: Dicamptodontidae). Mol. Phylogenet. Evol. 36 (2005) 90-100
60. Steele C.A., and Storfer A. Coalescent-based hypothesis testing supports multiple Pleistocene refugia in the Pacific Northwest for the Pacific giant salamander (Dicamptodon tenebrosus). Mol. Ecol. 15 (2006) 2477-2487
61. Stuart S.N., Chanson J.S., Cox N.A., Young B.E., Rodrigues A.S.L., Fischman D.L., and Waller R.W. Status and trends of amphibian declines and extinctions worldwide. Science 306 (2004) 1783-1786
62. Sullivan J., Abdo Z., Joyce P., and Swofford D.L. Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation. Mol. Biol. Evol. 22 (2005) 1386-1392
63. Swenson N.G., and Howard D.J. Clustering of contact zones, hybrid zones, and phylogeographic breaks in North America. Am. Nat. 166 (2005) 581-591
64. *: Phylogenetic Analysis Using Parsimony (* and Other Methods). Sinauer, Sunderland, Massachusetts.
65. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123 (1989) 585-595
66. USFWS (US Fish and Wildlife Service), 1993. Endangered and threatened wildlife and plants; finding on petition to list the spotted frog. Fed. Regist. 58, 27260-27263.
67. USFWS (US Fish and Wildlife Service), 1996. Endangered and threatened wildlife and plants; determination of threatened status of the California red-legged frog. Fed. Regist. 61, 25813-25833.
68. USFWS (US Fish and Wildlife Service), 1997. Endangered and threatened species; review of plant and animal taxa; proposed rule. Fed. Regist. 62, 49398-49411.
69. USFWS (US Fish and Wildlife Service), 1999. Endangered and threatened wildlife and plants: proposed endangered status for the southern California distinct vertebrate population segment of the mountain yellow-legged frog. Fed. Regist. 64, 71714-71722.
70. USFWS (US Fish and Wildlife Service), 2004. Species assessment and listing priority assignment form, Rana luteiventris, Columbia spotted frog (Great Basin DPS).
71. Werner J.K., Maxell B.A., Hendricks P., and Flath D.L. Amphibians and Reptiles of Montana (2004), Mountain Press Publishing Company, Missoula, MT
72. Whiteley A.R., Spruell P., and Allendorf F.W. Can common species provide valuable information for conservation?. Mol. Ecol. 15 (2006) 2767-2786
73. Zamudio K.R., Jones K.B., and Ward R.H. Molecular systematics of short-horned lizards: biogeography and taxonomy of a widespread species complex. Syst. Biol. 46 (1997) 284-305