Mitochondrial variation in sharp-tailed snakes (Contia tenuis): Evidence of a cryptic species

Journal of Herpetology

Volumn 36, Issue 4, 2002, Pages 648-655

  Feldman, Chris R ^a,b   Spicer, Greg S ^a  

^a SAN FRANCISCO STATE UNIVERSITY   (United States)

^b UTAH STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMPHIBIA; CONTIA TENUIS; REPTILIA; SERPENTES; VERTEBRATA;

EID: 0036945929     PISSN: 00221511     EISSN: None     Source Type: Journal    
DOI: 10.1670/0022-1511(2002)036[0648:MVISTS]2.0.CO;2     Document Type: Article

References (67)

1. AREVALO, E., S. K. DAVIS, AND J. W. SITES. 1994. Mitochondrial DNA sequence divergence and phylogenetic relationships among eight chromosome races of the Sceloporus grammicus complex (Phrynostomatidae) in Central Mexico. Systematic Biology 43:387-418.
2. AVISE, J. C. 1989. Gene trees and organismal histories: a phylogenetic approach to population biology. Evolution 43:1192-1208.
3. _. 2000. Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge, MA.
4. AVISE, J. C., J. ARNOLD, R. M. BALL, E. BERMINGHAM, T. LAMB, J. E. NEIGEL, C. A. REEB, AND N. C. SAUNDERS. 1987. Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics 18:489-522.
5. BARROWCLOUGH, G., R. J. GUTIERREZ, AND J. G. GROTH. 1999. Phylogeography of the spotted owl (Strix occidentalis) populations based on mitochondrial DNA sequences: gene flow, genetic structure and a novel biogeographic pattern. Evolution 53:919-931.
6. BOUNDY, J. 1999. Systematics of the garter snake Thamnophis atratus at the southern end of its range Proceedings of the California Academy of Sciences 51:311-336.
7. BREMER, K. 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42:795-803.
8. _. 1994. Branch support and tree stability. Cladistics 10:295-304.
9. CADLE, J. E. 1984. Molecular systematics of Neotropical xenodontine snakes III. Overview of xenodontine phylogeny and the history of new world snakes. Copeia 1984:641-652.
10. COOK JR., S. F. 1960. On the occurrence and life history of Contia tenuis. Herpetologica 16:163-173.
11. CRACRAFT, J. 1983. Species concepts and speciation analysis. In R. Johnston (ed.), Current Ornithology, pp. 159-187. Plenum Press, New York.
12. DE QUEIROZ, K. 1998. The general lineage concept of species, species criteria, and the process of speciation: a conceptual unification and terminological recommendations. In D. J. Howard and S. H. Berlocher (eds.), Endless Forms: Species and Speciation, pp. 57-75. Oxford University Press, New York.
13. DUPRE, W. R. 1990. Quaternary geology of the Monterey Bay region, California. In R. E. Garrison (ed.), Geology and Tectonics of the Central California Coast Region, San Francisco to Monterey, pp. 185-191. Society of Economic Paleontology and Mineralogy, Bakersfield, CA.
14. DUPRE, W. R., R. B. MORRISON, H. E. CLIFTON, K. R. LAJOIE, D. J. PONTI, C. L. POWELL III, S. A. MATHIESON, A. M. SARNA-WOJCICKI, E. L. LEITHOLD, W. R. LETTIS, P. F. MCDOWELL, T. K. ROCKWELL, J. R. UNRUH, AND R. S. YEATS. 1991. Quaternary geology of the Pacific margin. In R. B. Morrison (ed), The Geology of North America. Quaternary Nonglacial Geology: Conterminous U.S. Vol. K-2, pp. 141-214. Geology Society of America, Boulder, CO.
15. FELDMAN, C. R. 2000. Comparative phylogeography of three Californian reptiles: Contia tenuis, Diadophis punctatus, Elgaria multicarinata. Unpubl. master's thesis. San Francisco State University, San Francisco, CA.
16. FELSENSTEIN, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17:368-376.
17. _. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
18. GOLDMAN, N. 1993. Statistical tests of models of DNA substitution. Journal of Molecular Evolution 63: 182-198.
19. GOOD, D. A. 1989. Hybridization and cryptic species in Dicamptodon (Caudata: Dicamptodontidae). Evolution 43:728-744.
20. HASEGAWA, M., H. KISHINO, AND T. YANO. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 21:160-174.
21. HENDY, M. D., AND D. PENNY. 1982. Branch and bound algorithms to determine minimal evolutionary trees. Mathematical Biosciences 59:277-290.
22. HIGHTON, R. 1989. Biochemical evolution in the slimy salamanders of the Plethodon glutinosus complex in the Eastern United States. I. Geographic protein variation. Illinois Biological Monographs 57:1-78.
23. HOWARD, A. D. 1979. Geologic History of Middle California. University of California Press, Berkeley.
24. HOYER, R. F. 2001. Discovery of a probable new species in the genus Contia. Northwestern Naturalist 82: 116-122.
25. JOCKUSCH, E. L., K. P. YANEV, AND D. B. WAKE. 2001. Molecular phylogenetic analysis of slender salamanders genus Batrachoseps (Amphibia: Plethodontidae), from central coastal California with descriptions of four new species. Herpetological Monographs 15:54-99.
26. KRAUS, F., AND W. M. BROWN. 1998. Phylogentic relationships of colubriod snakes based on mitochondrial DNA sequences. Zoological Journal of the Linnean Society London 122:455-487.
27. KUMAZAWA, Y., AND M. NISHIDA. 1993. Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. Journal of Molecular Evolution 37:380-398.
28. _. 1995. Variations in mitochondrial tRNA gene organization of reptiles as a phylogenetic marker. Molecular Biology and Evolution 12:759-772.
29. KUMAZAWA, Y., H. OTA, M. NISHIDA, AND T. OZAWA. 1996. Gene rearrangements in snake mitochondrial genomes: highly concerted evolution of control-region-like sequences duplicated and inserted into a tRNA gene cluster. Molecular Biology and Evolution 13:1242-1254.
30. _. 1998. The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions. Genetics 150:313-329.
31. LEONARD, W. P., AND K. OVASKA. 1998. CONTIA (Girard). Catalogue of American Amphibians and Reptiles 677.1-677.7.
32. MACEY, J. R., AND A. VERMA. 1997. Homology in phylogenetic analysis: alignment of transfer RNA genes and the phylogenetic position of snakes. Molecular Phylogenetics and Evolution 7:272-279.
33. MACEY, J. R., A. LARSON, N. B. ANANJEVA, Z. FANG, AND T. J. PAPENFUSS. 1997. Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Molecular Biology and Evolution 14:91-104.
34. MACEY, J. R., Y. WANG, N. B. ANANJEVA, A. LARSON, AND T. J. PAPENFUSS. 1999. Vicariant patterns of fragmentation among gekkonid lizards of the genus Teratoscincus produced by the Indian collision: a molecular phylogenetic perspective and an area cladogram for Central Asia. Molecular Phylogenetics and Evolution 12:250-272.
35. MACEY, J. R., J. L. STRASBURG, J. A. BRISSON, V. T. VREDENBURG, M. JENNINGS, AND A. LARSON. 2001. Molecular phylogenetics of western North American frogs of the Rana boylii species group. Molecular Phylogenetics and Evolution 19:131-143
36. MADDISON, W. P., M. J. DONOGHUE, AND D. R. MADDISON. 1984. Outgroup analysis using parsimony. Systematic Zoology 33:83-103.
37. MALDONADO, J. E., C. VILA, AND R. K. WAYNE. 2001. Tripartite genetic subdivisions in the ornate shrew (Sorex ornatus). Molecular Ecology 10:127-147.
38. MANIATIS, T., E. F. FRISTCH, AND J. SAMBROOK. 1982. Molecular Cloning; A Laboratory Manual. Cold Spring Harbor Publication, Cold Spring Harbor, NY.
39. MATOCQ, M. D. 2002. Phylogeographic structure and regional history of the dusky-footed woodrat (Neotema fuscipes). Molecular Ecology 11:229-242.
40. MATOCQ, M. D., M. N. F. DA SILVA, AND J. L. PATRON. 2000. Population genetic structure of two ecologically distinct spiny rats: separating history and current ecology. Evolution 54:1423-1432.
41. MORITZ, C., C. J. SCHNEIDER, AND D. B. WAKE. 1992. Evolutionary relationships within the Ensatina eschscholtzii complex confirm the ring species interpretation. Systematic Biology 41:273-291.
42. OAKESHOTT, G. B. 1978. California's Changing Landscapes: A Guide to the Geology of the State. 2nd Ed. McGraw-Hill Co., Inc., New York.
43. OMLAND, K. E., C. L. TARR, W. I. BOARMAN, J. M. MARZLUFF, AND R. C. FLEiSCHER. 2000. Cryptic genetic variation and paraphyly in ravens. Proceedings of the Royal Society of London B Biological Sciences 267:2475-2482.
44. PARKINSON, C. L., K. R. ZAMUDIO, AND H. W. GREENE. 2000. Phylogeography of the pit viper clade Agkistrodon: historical ecology, species status, and conservation of cantils. Molecular Ecology 9:411-420.
45. PATTON, J. L., AND M. F. SMITH. 1990. The evolutionary dynamics of the pocket gopher Thomomys bottae, with emphasis on California populations. University of California Publications in Zoology 123: 1-161.
46. POSADA, D., AND K. A. CRANDALL. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818.
47. RODRIGUEZ-ROBLES, J. A., AND J. M. DE JESUS-ESCOBAR. 1999. Molecular systematics of new world lampropeltinine snakes: implications for biogeography and evolution of food habits. Biological Journal of the Linnean Society 68:355-385.
48. _. 2000. Molecular systematics of new world gopher, bull, and pine snakes (Pituophis: Colubridae), a transcontinental species complex. Molecular Phylogenetics and Evolution 14:35-50.
49. RODRIGUEZ-ROBLES, J. A., D. F. DENARDO, AND R. E. STAUB. 1999. Phylogeography of the California mountain kingsnake, Lampropeltis zonata (Colubridae). Molecular Ecology 8:1923-1934.
50. RODRIGUEZ-ROBLES, J. A., G. R. STEWART, AND T. J. PAPENFUSS. 2001. Mitochondrial DNA-based phylogeography of North American rubber boas, Charina bottae. Molecular Phylogenetics and Evolution 18:227-237.
51. ROZAS, J., AND R. ROZAS. 1999. DnaSp version 3: integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174-175.
52. SANGER, F., S. NICKLEN, AND A. R. COULSON. 1977. DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences 74:5463-5467.
53. STEBBINS, R. C. 1985. A Field Guide to the Western Reptiles and Amphibians. Houghton Mifflin Co., Boston, MA.
54. SWOFFORD, D. L., G. J. OLSEN, P. J. WADDELL, AND D. M. HILLIS. 1996. Phylogenetic inference. In D. M. Hillis, C. Moritz, and B. K. Mable (eds.), Molecular Systematics. 2nd ed., pp. 407-543. Sinauer Associates, Inc., Sunderland, MA.
55. TAN, A. M., AND D. B. WAKE. 1995. MtDNA phylogeography of the California newt, Taricha torosa (Caudata, Salimandridae). Molecular Phylogenetics and Evolution 4:383-394.
56. TAJIMA, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
57. TEMPLETON, A. R., E. ROUTMAN, AND C. A. PHILLIPS. 1995. Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum. Genetics 140:767-782.
58. TILLEY, S. G., R. B. MERRITT, B. Wu, AND R. HIGHTON. 1978. Genetic differentiation in salamanders of the Desmognathus ochrophaeus complex (Plethodontidae). Evolution 32:93-115.
59. WAKE, D. B. 1997. Incipient species formation in salamanders of the Ensatina complex. Proceedings of the National Academy of Sciences 94:7761-7767.
60. WAKE, D. B., AND C. J. SCHNEIDER. 1998. Taxonomy of the plethodontid salamander genus Ensatina. Herpetologica 54:279-298.
61. WALKER, D., AND J. C. AVISE. 1998. Principles of phylogeography as illustrated by freshwater and terrestrial turtles in the southeastern United States. Annual Review of Ecology and Systematics 29:23-58.
62. WILGENBUSCH, J., AND K. DE QUEIROZ. 2000. Phylogenetic relationships among the phrynosomatid sand lizards inferred from mitochondrial DNA sequences generated by heterogeneous evolutionary processes. Systematic Biology 99:592-612.
63. YANEV, K. P. 1980. Biogeography and distribution of three parapatric salamander species in coastal and borderland California. In D. M. Power (ed.), The California Islands: Proceedings of a Multidisciplinary Symposium, pp. 531-550. Santa Barbara Museum of Natural History, Santa Barbara, CA.
64. YANG, Z. 1994a. Estimating patterns of nucleotide substitution. Journal of Molecular Evolution 39: 105-111.
65. _. 1994b. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of Molecular Evolution 39:306-314.
66. _. 1996. Maximum likelihood models for combined analyses of multiple sequence data. Journal of Molecular Evolution 42:587-596.
67. ZAMUDIO, K. R., AND H. W. GREENE. 1997. Phylogeography of the bushmaster (Lachesis muta: Viperidae): implications for Neotropical biogeography, systematics, and conservation. Biological Journal of the Linnean Society 62:421-442.