Extreme population subdivision throughout a continuous range: Phylogeography of Batrachoseps attenuatus (Caudata: Plethodontidae) in western North America

Molecular Ecology

Volumn 16, Issue 20, 2007, Pages 4335-4355

  Martínez Solano, Iñigo ^a,b   Jockusch, Elizabeth L ^b   Wake, David B ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

Batrachoseps attenuatus; mtDNA; Phylogeography; RAG 1; Sacramento San Joaquin Delta; San Andreas Fault

Indexed keywords

MITOCHONDRIAL DNA; RNA 16S;

AMPHIBIA; ANIMAL; ARTICLE; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; MOLECULAR GENETICS; NORTH AMERICA; NUCLEOTIDE SEQUENCE; PHYLOGENY; TIME;

ANIMALS; DNA, MITOCHONDRIAL; GEOGRAPHY; MOLECULAR SEQUENCE DATA; NORTH AMERICA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; TIME FACTORS; URODELA; VARIATION (GENETICS);

BATRACHOSEPS ATTENUATUS; CAUDATA; PLETHODONTIDAE; SALAMANDROIDEA;

EID: 34848912488     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2007.03527.x     Document Type: Article

References (62)

1. Atwater BF (1979) Ancient processes at the site of southern San Francisco Bay: movement of the crust and changes in sea level. In : San Francisco Bay: The Urbanized Estuary (ed. Conomos TJ pp. 31 45. Pacific Division, American Association for the Advancement of Science, San Francisco, California.
2. Avise JC (1974) Systematic value of electrophoretic data. Systematic Zoology, 23, 465 481.
3. Avise JC (2000) Phylogeography. Harvard University Press, Cambridge, Massachusetts.
4. Bermingham E, Moritz C (1998) Comparative phylogeography: concepts and applications. Molecular Ecology, 7, 367 369.
5. Blake MC (1984) Franciscan Geology of Northern California. US Geological Survey, Menlo Park, California.
6. Brunsfeld SJ, Sullivan J, Soltis DE, Soltis PS (2001) Comparative phylogeography of north-western North America: a synthesis. In : Integrating Ecology and Evolution in a Spatial Context (eds Silvertown J, Antonovics J pp. 319 338. Blackwell Science, Oxford, UK.
7. Burnham K (2005) Point Lobos to Point Reyes; evidence of approximately 180 km offset on the San Gregorio and northern San Andreas Faults. In : Cenozoic Deformation in the Central Coast Ranges, California (eds Stevens C, Cooper J pp. 1 28. Society for Sedimentary Geology, USA.
8. Cabe PR, Page RB, Hanlon TJ et al 2007) Fine-scale population differentiation and gene flow in a terrestrial salamander (Plethodon cinereus) living in a continuous habitat. Heredity, 98, 53 60.
9. Calsbeek R, Thompson JN, Richardson JE (2003) Patterns of molecular evolution and diversification in a biodiversity hotspot: the California floristic province. Molecular Ecology, 12, 1021 1029.
10. Carstens BC, Degenhardt JD, Stevenson AL, Sullivan J (2005) Accounting for coalescent stochasticity in testing phylogeographical hypotheses: modelling Pleistocene population structure in the Idaho giant salamander Dicamptodon aterrimus. Molecular Ecology, 14, 255 265.
11. Clark JM (1985) Fossil plethodontid salamanders from the Late Miocene of California. Journal of Herpetology, 19, 41 47.
12. Drummond AJ, Rambaut A (2005) beast Version 1.3. URL: http//evolve.zoo.ox.ac.uk/beast.
13. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed phylogenetics and dating with confidence. Public Library of Science, Biology, 4, 699 710.
14. Dupré WR (1990) Quaternary geology of the Monterey Bay region, California. In : Geology and Tectonics of the Central California Coastal Region, San Francisco to Monterey (eds Garrison RE, Greene HG, Hicks KR, Weber GE, Wright TL pp. 185 191. US Geological Survey, Menlo Park, California.
15. Feldman CR, Spicer GS (2006) Comparative phylogeography of woodland reptiles in California: repeated patterns of cladogenesis and population expansion. Molecular Ecology, 15, 2201 2222.
16. Fu YX (1997) Statistical tests of neutrality against population growth, hitchhiking and background selection. Genetics, 147, 915 925.
17. Galloway AJ (1977) Geology of the Point Reyes Peninsula, Marin County, California. California Division of Mines and Geology Bulletin, 202, 1 72.
18. Hare MP (2001) Prospects for nuclear gene phylogeography. Trends in Ecology & Evolution, 16, 700 706.
19. Hendrickson JR (1954) Ecology and systematics of salamanders of the genus Batrachoseps. University of California Publications in Zoology, 54, 1 46.
20. Hewitt GM (1999) Postglacial recolonization of European biota. Biological Journal of the Linnean Society, 68, 87 112.
21. Jockusch EL (1997) Geographic variation and phenotypic plasticity of number of trunk vertebrae in slender salamanders, Batrachoseps (Caudata: Plethodontidae). Evolution, 51, 1964 1980.
22. Jockusch EL, Wake DB (2002) Falling apart and merging: diversification of slender salamanders (Plethodontidae: Batrachoseps) in the American West. Biological Journal of the Linnean Society, 76, 361 391.
23. Kass RE, Raftery AE (1995) Bayes factors. Journal of the American Statistical Association, 430, 773 795.
24. Kuchta SR, Tan AM (2005) Isolation by distance and post-glacial range expansion in the rough-skinned newt, Taricha granulosa. Molecular Ecology, 14, 225 244.
25. Kumar S, Tamura K, Nei M (2004) mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics, 5, 150 163.
26. Lapointe FJ, Rissler LJ (2005) Congruence, consensus, and the comparative phylogeography of codistributed species in California. American Naturalist, 166, 290 299.
27. Larson A, Wake DB, Yanev KP (1984) Measuring gene flow among populations having high levels of genetic fragmentation. Genetics, 106, 293 308.
28. Mahoney MJ (2004) Molecular systematics and phylogeography of the Plethodon elongatus species group: combining phylogenetic and population genetic methods to investigate species history. Molecular Ecology, 13, 149 166.
29. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Research, 27, 209 220.
30. Matocq MD (2002) Phylogeographical structure and regional history of the dusky-footed woodrat, Neotoma fuscipes. Molecular Ecology, 11, 229 242.
31. Mead LS, Tilley SG, Katz LA (2001) Genetic structure of the blue ridge dusky salamander (Desmognathus orestes): inferences from allozymes, mitochondrial DNA, and behavior. Evolution, 55, 2287 2302.
32. Moritz C, Richardson KS, Ferrier S et al 2001) Biogeographic concordance and efficiency of taxon indicators for establishing conservation priority in a tropical rainforest biota. Proceedings of the Royal Society of London. Series B, Biological Sciences, 268, 1875 1881.
33. Moritz C, Schneider CJ, Wake DB (1992) Evolutionary relationships within the Ensatina eschscholtzii complex confirm the ring species interpretation. Systematic Biology, 41, 273 291.
34. Mueller RL (2006) Evolutionary rates, divergence dates, and the performance of mitochondrial genes in Bayesian phylogenetic analysis. Systematic Biology, 55, 289 300.
35. Nei M (1972) Genetic distance between populations. American Naturalist, 106, 283 292.
36. Palumbi SR (1996) Nucleic acids II: the polymerase chain reaction. In : Molecular Systematics (eds Hillis DM, Moritz C, Mable BK pp. 205 247. Sinauer Associates, Sunderland, Massachusetts.
37. Posada D, Crandall KA (1998) modeltest: testing the model of DNA substitution. Bioinformatics, 14, 817 818.
38. Posada D, Crandall KA, Templeton AR (2000) geodis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Molecular Ecology, 9, 487 488.
39. Rambaut A, Drummond A (2004) tracer Version 1.1. MCMC Trace Analysis Tool. University of Oxford. URL: http//evolve.zoo.ox.ac.uk/software.html.
40. Ramírez MG, Chi B (2004) Cryptic speciation, genetic diversity and gene flow in the California turret spider Atypoides riversi (Araneae: Antrodiaetidae). Biological Journal of the Linnean Society, 82, 27 37.
41. Ramos-Onsins SE, Rozas J (2002) Statistical properties of new neutrality tests against population growth. Molecular Biology and Evolution, 19, 2092 2100.
42. Richmond JQ, Reeder TW (2002) Evidence for parallel ecological speciation in scincid lizards of the Eumeces skiltonianus species group (Squamata: Scincidae). Evolution, 56, 1498 1513.
43. Riddle BR, Hafner DJ, Alexander LF, Jaeger JR (2002) Cryptic vicariance in the historical assembly of a Baja California peninsular desert biota. Proceedings of the National Academy of Sciences, USA, 97, 14438 14443.
44. Rissler LJ, Hijmans RJ, Graham CH, Moritz C, Wake DB (2006) Phylogeographic lineages and species comparisons in conservation analyses: a case study of California herpetofauna. American Naturalist, 167, 655 666.
45. Ronquist F, Huelsenbeck JP (2003) mrbayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572 1574.
46. Rozas J, Sánchez-Del Barrio JC, Messeguer X, Rozas R (2003) dnasp, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496 2497.
47. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
48. San Mauro D, Gower DJ, Oommen OV, Wilkinson M, Zardoya R (2004) Phylogeny of caecilian amphibians (Gymnophiona) based on complete mitochondrial genomes and nuclear RAG1. Molecular Phylogenetics and Evolution, 33, 413 427.
49. 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.
50. Schneider S, Roessli D, Excoffier L (2000) arlequin: A Software for Population Genetics Data Analysis, Version 2.000. Genetics and Biometry Laboratory, Department of Anthropology, University of Geneva.
51. Sims JD (1993) Chronology of displacement on the San Andreas Fault in Central California: evidence from reversed positions of exotic rock bodies near Parkfield, California. In : The San Andreas Fault System; Displacement, Palinspastic Reconstruction, and Geologic Evolution (eds Powell RE, Weldon RJ II, Matti JC pp. 231 256. Geological Society of America, Boulder, Colorado.
52. Slatkin M, Hudson RR (1991) Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics, 129, 555 562.
53. Smouse PE, Long JC, Sokal RR (1986) Multiple regression and correlation extensions of the Mantel test of matrix correspondence. Systematic Zoology, 35, 627 632.
54. Starrett J, Hedin M (2007) Multilocus genealogies reveal multiple cryptic species and biogeographical complexity in the California turret spider Antrodiaetus riversi (Mygalomorphae, Antrodiaetidae). Molecular Ecology, 16, 583 604.
55. Stebbins RC (2003) Western Reptiles and Amphibians, 3rd edn. Houghton Mifflin, New York.
56. Swenson NG, Howard DJ (2005) Clustering of contact zones, hybrid zones, and phylogeographic breaks in North America. American Naturalist, 166, 581 591.
57. Swofford DL (2002) paup* Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4. Sinauer Associates, Sunderland, Massachusetts.
58. Wake DB (1997) Incipient species formation in salamanders of the Ensatina complex. Proceedings of the National Academy of Sciences, USA, 94, 7761 7767.
59. Wake DB (2006) Problems with species: patterns and processes of species formation in salamanders. Annals of the Missouri Botanical Garden, 93, 8 23.
60. Yanev KP (1978) Evolutionary studies of the plethodontid salamander genus Batrachoseps. PhD Dissertation. University of California, Berkeley, California.
61. Yanev KP (1980) Biogeography and distribution of three parapatric salamander species in coastal and borderland California. In : The California Islands: Proceedings of a Multidisciplinary Symposium (ed. Power DM pp. 531 550. Santa Barbara Museum of Natural History, Santa Barbara, California.
62. Zhang DX, Hewitt GM (2003) Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Molecular Ecology, 12, 563 584.