Cryptic diversity and biogeographical patterns within the black salamander (Aneides flavipunctatus) complex

Journal of Biogeography

Volumn 42, Issue 2, 2015, Pages 280-291

  Reilly, Sean B ^a   Wake, David B ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Amphibians; California; Mendocino Triple Junction; Mitochondrial DNA; Nuclear loci; Phylogeography; San Andreas Fault

Indexed keywords

AMPHIBIAN; BIOGEOGRAPHICAL REGION; CRYPSIS; GENE FLOW; PACIFIC PLATE; PHYLOGENETICS; PHYLOGENY; PHYLOGEOGRAPHY; SAN ANDREAS FAULT; SPECIES DIVERSITY;

CALIFORNIA; OREGON; UNITED STATES;

AMPHIBIA; ANEIDES FLAVIPUNCTATUS;

EID: 84920921599     PISSN: 03050270     EISSN: 13652699     Source Type: Journal    
DOI: 10.1111/jbi.12413     Document Type: Article

References (55)

1. Atwater, T. (1989) Plate tectonic history of the northeast Pacific and western North America. The geology of North America, Vol. N, The eastern Pacific Ocean and Hawaii (ed. by E.L. Winterer, D.M. Hussong and R.W. Decker ), pp. 21-72. Geological Society of America, Boulder, CO.
2. Brown, R.P. & Yang, Z. (2011) Rate variation and estimation of divergence times using strict and relaxed clocks. BMC Evolutionary Biology, 11, 271.
3. Calsbeek, R., Thompson, J.N. & Richardson, J.E. (2003) Patterns of molecular evolution and diversification in a biodiversity hotspot: the California Floristic Province. Molecular Ecology, 12, 1021-1029.
4. Collins, J.T. & Taggart, T.W. (2002) Standard common and current scientific names for North American amphibians, turtles, reptiles & crocodilians. Center for North American Herpetology, Lawrence, KS.
5. Cope, E.D. (1883) Notes on the geographical distribution of Batrachia and Reptilia in western North America. Proceedings of the Academy of Natural Sciences of Philadelphia, 35, 10-35.
6. Currat, M., Ruedi, M., Petit, R.J. & Excoffier, L. (2008) The hidden side of invasions: massive introgression by local genes. Evolution, 62, 1908-1920.
7. Darriba, D., Taboada, G.L., Doallo, R. & Posada, D. (2012) jModelTest2: more models, new heuristics and parallel computing. Nature Methods, 9, 722.
8. Drummond, A.J. & Rambaut, A. (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
9. Dupré, W.R., Morrison, R.B., Clifton, H.E., Lajoie, K.R., Ponti, D.J., Powell, C.L., II, Mathieson, S.A., Sarna-Wojcicki, A.M., Leithold, E.L., Lettis, W.R., McDowell, P.F., Rockwell, T.K., Unruh, J.R. & Yeats, R.S. (1991) Quaternary geology of the Pacific margin. The geology of North America, Vol. K-2, Quaternary nonglacial geology: conterminous U.S. (ed. by R.B. Morrison ), pp. 141-214. Geological Society of America, Boulder, CO.
10. Edgar, R.C. (2004) Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792-1797.
11. Furlong, K.P. & Schwartz, S.Y. (2004) Influence of the Mendocino triple junction on the tectonics of coastal California. Annual Review of Earth and Planetary Sciences, 32, 403-433.
12. García-París, M., Alcobendas, M., Buckley, D. & Wake, D.B. (2003) Dispersal of viviparity across contact zones in Iberian populations of fire salamanders (Salamandra) inferred from discordance of genetic and morphological traits. Evolution, 57, 129-143.
13. Guedj, B. & Guillot, G. (2011) Estimating the location and shape of hybrid zones. Molecular Ecology Resources, 11, 1119-1123.
14. Guillot, G., Estoup, A., Mortier, F. & Cosson, J.F. (2005) A spatial statistical model for landscape genetics. Genetics, 170, 1261-1280.
15. Guillot, G., Santos, F. & Estoup, A. (2008) Analysing georeferenced population genetics data with Geneland: a new algorithm to deal with null alleles and a friendly graphical user interface. Bioinformatics, 24, 1406-1407.
16. Harden, D.R. (2004) California geology, 2nd edn. Prentice Hall, Upper Saddle River, NJ.
17. Harper, G.D. (1984) Middle to Late Jurassic tectonic evolution of the Klamath Mountains, California-Oregon. Tectonics, 3, 759-772.
18. Hedin, M., Starrett, J. & Hayashi, C. (2013) Crossing the uncrossable: novel trans-valley biogeographic patterns revealed in the genetic history of low-dispersal mygalomorph spiders (Antrodiaetidae, Antrodiaetus) from California. Molecular Ecology, 22, 508-526.
19. Heled, J. & Drummond, A.J. (2010) Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution, 27, 570-580.
20. Herd, D.G. (1978) Intercontinental plate boundary east of Cape Mendocino, California. Geology, 6, 721-725.
21. Hey, J. (2005) On the number of New World founders: a population genetic portrait of the peopling of the Americas. PLoS Biology, 3, 965-975.
22. Hey, J. (2010) Isolation with migration models for more than two populations. Molecular Biology and Evolution, 27, 905-920.
23. Irwin, D.E. (2012) Local adaptation along smooth ecological gradients causes phylogeographic breaks and phenotypic clustering. The American Naturalist, 180, 35-49.
24. Jockusch, E.L., Martínez-Solano, I., Hansen, R.W. & Wake, D.B. (2012) Morphological and molecular diversification of slender salamanders (Caudata: Plethodontidae: Batrachoseps) in the southern Sierra Nevada of California with descriptions of two new species. Zootaxa, 3190, 1-30.
25. Kelsey, H.M. & Carver, G.A. (1988) Late Neogene and Quaternary tectonics associated with northward growth of the San Andreas transform fault, northern California. Journal of Geophysical Research, 93, 4797-4819.
26. Kuchta, S.R., Parks, D.S., Mueller, R.L. & Wake, D.B. (2009) Closing the ring: historical biogeography of the salamander ring species Ensatina eschscholtzii. Journal of Biogeography, 36, 982-995.
27. Lapointe, F.J. & Rissler, L.J. (2005) Congruence, consensus, and the comparative phylogeography of codistributed species in California. The American Naturalist, 166, 290-299.
28. Larson, A. (1980) Paedomorphosis in relation to rates of morphological and molecular evolution in the salamander Aneides flavipunctatus. Evolution, 34, 1-17.
29. Liebgold, E.B., Brodie, E.D., III & Cabe, P.R. (2010) Female philopatry and male-biased dispersal in a direct-developing salamander, Plethodon cinereus. Molecular Ecology, 20, 249-257.
30. Lock, J., Kelsey, H., Furlong, K. & Woolace, A. (2006) Late Neogene and Quaternary landscape evolution of the northern California Coast Ranges: evidence for Mendocino triple junction tectonics. Geographical Society of America Bulletin, 118, 1232-1246.
31. Lowe, C.H. (1950) Speciation and ecology in salamanders of the genus Aneides. PhD Thesis, University of California, Los Angeles, CA.
32. Lynch, J.F. (1981) Patterns of ontogenetic and geographic variation in the black salamander, Aneides flavipunctatus. Smithsonian Contributions to Zoology, 324, 1-53.
33. McKenzie, D.P. & Morgan, W.J. (1969) The evolution of triple junctions. Nature, 224, 125-133.
34. Myers, G.S. & Maslin, T.P. (1948) The California plethodont salamander, Aneides flavipunctatus (Strauch): with description of a new subspecies and notes of other western Aneides. Biological Society of Washington, 61, 127-128.
35. Myers, N., Mittermeier, R.A., Mittermeier, C.G., da Fonseca, G.A.B. & Kent, J. (2000) Biodiversity hotspots for conservation priorities. Nature, 403, 853-858.
36. Papenfuss, T.J. & Parham, J.F. (2013) Four new species of California legless lizards (Aniella). Breviora, 536, 1-17.
37. Rambaut, A. & Drummond, A.J. (2009) Tracer v1.5.0. Available at: http://beast.bio.ed.ac.uk/ (accessed on 23 May 2013).
38. Reilly, S.B., Marks, S.B. & Jennings, W.B. (2012) Defining evolutionary boundaries across parapatric ecomorphs of Black Salamanders (Aneides flavipunctatus) with conservation implications. Molecular Ecology, 21, 5745-5761.
39. Reilly, S.B., Mulks, M.F., Reilly, J.M., Jennings, W.B. & Wake, D.B. (2013) Genetic diversity of Black Salamanders (Aneides flavipunctatus) across watersheds in the Klamath Mountains. Diversity, 5, 657-679.
40. Reilly, S.B., Portik, D.M., Koo, M.S. & Wake, D.B. (2014) Discovery of a new, disjunct population of a narrowly distributed salamander (Taricha rivularis) in California presents conservation challenges. Journal of Herpetology, 48, 371-379.
41. Rheindt, F.E. & Edwards, S.V. (2011) Genetic introgression: an integral but neglected component of speciation in birds. The Auk, 128, 620-632.
42. Rissler, L.J. & Apodaca, J.J. (2007) Adding more ecology into species delimitation: ecological niche models and phylogeography help define cryptic species in the Black Salamander (Aneides flavipunctatus). Systematic Biology, 56, 924-942.
43. Rissler, L.J., Hijmans, R.J., Graham, C.H., Moritz, C. & Wake, D.B. (2006) Phylogeographic lineages and species comparisons in conservation analyses: a case study of California herpetofauna. The American Naturalist, 167, 655-666.
44. Rohwer, S., Bermingham, E. & Wood, C. (2001) Plumage and mitochondrial DNA haplotype variation across a moving hybrid zone. Evolution, 55, 405-422.
45. Rozas, J., Sánchez-DelBarrio, J.C., Messeguer, X. & Rozas, R. (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496-2497.
46. Sarna-Wojcicki, A.M., Meyer, C.E., Bowman, H.R., Hall, N.T., Russell, P.C., Woodward, M.J. & Slate, J.L. (1985) Correlation of the Rockland ash bed, a 400, 000-year-old stratigraphic marker in northern California and western Nevada and implications for middle Pleistocene paleogeography of central California. Quaternary Research, 23, 236-257.
47. Starrett, J. & Hedin, M. (2007) Multilocus geneologies reveal multiple cryptic species and biogeographical complexity in the California turret spider Antrodiaetus riversi (Mygalomorphae, Antrodiaetidae). Molecular Ecology, 16, 583-604.
48. Staub, N.L., Brown, C.W. & Wake, D.B. (1995) Patterns of growth and movements in a population of Ensatina eschscholtzii platensis (Caudata: Plethodontidae) in the Sierra Nevada, California. Journal of Herpetology, 29, 593-599.
49. Stebbins, R.C. (2003) Western reptiles and amphibians, 3rd edn. Peterson Field Guide Series, New York, NY.
50. Stephens, M. & Scheet, N.J. (2005) Accounting for decay of linkage disequilibrium in haplotype inference and missing-data inputation. American Journal of Human Genetics, 76, 449-462.
51. Stephens, M., Smith, N.J. & Donnelly, P. (2001) A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics, 68, 978-989.
52. Sutton, D.A. & Nadler, C.F. (1974) Systematic revision of three townsend chipmunks (Eutamias townsendii). The Southwestern Naturalist, 19, 199-212.
53. Tan, A.M. & Wake, D.B. (1995) MtDNA phylogeography of the California newt, Taricha torosa (Caudata, Salamandridae). Molecular Phylogenetics and Evolution, 4, 383-394.
54. Woerner, A.E., Cox, M.P. & Hammer, M.F. (2007) Recombination-filtered genomic datasets by information maximization. Bioinformatics, 23, 1851-1853.
55. Zwickl, D.J. (2006) Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. PhD Thesis, The University of Texas, Austin, TX.