Phylogeography and species boundaries of the western North American Nightsnake (Hypsiglena torquata): Revisiting the subspecies concept

Molecular Phylogenetics and Evolution

Volumn 46, Issue 3, 2008, Pages 1095-1115

  Mulcahy, Daniel G ^a  

^a UTAH STATE UNIVERSITY   (United States)

Author keywords

Baja California; Biogeography; Deserts; Eridiphas; Pseudoleptodeira; tanzeri

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; GENETICS; GEOGRAPHY; MOLECULAR GENETICS; NORTH AMERICA; NUCLEOTIDE SEQUENCE; PHYLOGENY; SNAKE; SPECIES DIFFERENCE; SPECIES DIFFERENTIATION;

ANIMALS; COLUBRIDAE; DNA, MITOCHONDRIAL; GENETIC SPECIATION; GEOGRAPHY; MOLECULAR SEQUENCE DATA; NORTH AMERICA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

ERIDIPHAS; HYPSIGLENA TORQUATA; PSEUDOLEPTODEIRA;

EID: 40849114523     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2007.12.012     Document Type: Article

References (119)

1. Arévalo E., Davis S.K., and Sites Jr. J.W. Mitochondrial DNA sequence divergence and phylogenetic relationships among eight chromosome races of the Sceloporus grammicus complex (Phrynosomatidae) in central Mexico. Syst. Biol. 43 (1994) 387-418
2. Ashton K.G. Body size variation among mainland populations of the Western Rattlesnake (Crotalus viridis). Evolution 55 (2001) 2523-2533
3. Ashton K.G., and de Queiroz A. Molecular systematics of the Western Rattlesnake, Crotalus viridis (Viperidae), with comments of the utility of the D-Loop in phylogenetic studies of snakes. Mol. Phylogenet. Evol. 21 (2001) 176-189
4. Blaney R.M. Systematics of the common kingsnake, Lampropeltis getulus (Linnaeus). Tulane Stud. Zool. Bot. 19 (1977) 47-103
5. Bogert C.M., and Oliver J.A. Preliminary analysis of the herpetofauna of Sonora. Bull. Amer. Mus. Nat. Hist. 83 (1945) 297-426
6. Boulenger, G.A., 1894. Catalogue of the Snakes in the British Museum (Natural History), vol. 2, London, pp. 1-382.
7. Brandley M.C., Schmitz A., and Reeder T.W. Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Syst. Biol. 54 (2005) 373-390
8. Burbrink F.T., Lawson R., and Slowinski J.B. Mitochondrial DNA phylogeography of the polytypic North American rat snake (Elaphe obsoleta), A critique of the subspecies concept. Evolution 54 (2000) 2107-2118
9. Cardosos A., and Vogler A.P. DNA taxonomy, phylogeny and Pleistocene diversification of the Cicindela hybrida species group (Coleoptera: Cicindelidae). Mol. Ecol. 14 (2005) 3531-3546
10. Carreño A.L., and Helenes J. Geology and ages of the islands. In: Case T.J., Cody M.L., and Ezcurra E.A. (Eds). New Island Biogeography of the Sea of Cortés (2002), Oxford University Press, New York, NY 14-40
11. Clement M., Posada D., and Crandall K.A. TCS: a computer program to estimate gene-genealogies. Mol. Ecol. 9 (2000) 1657-1660
12. Collins J.T. Viewpoint: A new taxonomic arrangement for some North American amphibians and reptiles. Herp. Rev. 22 (1991) 42-43
13. Conant R., and Collins J.T. A field guide to the reptiles and amphibians of eastern and central North America (1991), Houghton Mifflin Co., Boston, MA
14. Cope E.D. Catalogue of the Colubridae in the Museum of the Academy of Natural Sciences of Philadelphia, with notes and descriptions of new species. Proc. Acad. Nat. Sci. Phil. 2 (1860) 241-266
15. Coyne J.A., and Orr H.A. Speciation (2004), Sinauer Associates, Sunderland, MA
16. Crandall K.A., and Fitzpatrick Jr. J.F. Crayfish molecular systematics: using a combination of procedures to estimate phylogeny. Syst. Biol. 45 (1996) 1-26
17. Darwin C. On the origin of species by means of natural selection, or preservation of favored races in the struggle for life (1859), Murray, London, UK
18. Davis J.I., and Nixon K.C. Populations, genetic variation, and the delimitation of phylogenetic species. Syst. Biol. 41 (1992) 421-435
19. de Queiroz K. The general lineage concept of species, species criteria, and the process of speciation. In: Howard D.J., and Berlocher S.H. (Eds). Endless Forms: Species and Speciation (1998), Oxford Univ. Press, Oxford, MA 57-75
20. de Queiroz K. A unified species concept and its consequences for the future of taxonomy. Proc. Calif. Acad. Sci. 56 (2005) 196-215
21. de Queiroz K. Species concepts and species delimitation. Syst. Biol. 56 (2007) 879-886
22. Dixon J.R. A taxonomic re-evaluation of the night snake, Hypsiglena ochrorhyncha and relatives. Southwstrn. Nat. 10 (1965) 125-131
23. Dixon J.R., and Lieb C.S. A new night snake from Mexico (Serpentes: Colubridae). Contr. Sci. Nat. Hist. Mus. Los Angeles Co. 222 (1972) 1-7
24. Dixon J.R., and Dean R.H. Status of the southern populations of the night snake (Hypsiglena: Colubridae) exclusive of California and Baja California. Southwstrn. Nat. 31 (1986) 307-318
25. Dobzhansky Th. Genetics and the Origin of Species. First ed. (1937), Columbia Univ. Press, New York, NY
26. Douglas M.E., Douglas M.R., Schuett G.W., and Porras L.W. Phylogeography of the Western Rattlesnake (Crotalus viridis) complex, with emphasis on the Colorado Plateau. In: Schuett G.W., Hoggren M., Douglas M.E., and Greene H.W. (Eds). Biology of the Vipers (2002), Eagle Mountain Publishing, Utah 11-50
27. Dowling H.G., and Jenner J.V. Taxonomy of American xenodontine snakes. II. The status and relationships of Pseudoleptodeira. Herpetologica 43 (1987) 190-200
28. Duellman W.E. A monographic study of the colubrid snake genus Leptodeira. Bull. Amer. Mus. Nat. Hist. 114 (1958) 1-152
29. Dugès, A., 1865. Memoirs in the Section of Science Academy Scientific Letters Montpellier, vol. 6, pp. 32-33.
30. Dunn E.R. Notes on North American Leptodeira. Proc. Nat. Acad. Sci. 22 (1936) 689-698
31. Farris J.S. Phylogenetics under Dollo's law. Syst. Zool. 26 (1977) 77-88
32. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17 (1981) 368-376
33. Frost D.R., and Hillis D.M. Species concepts and practice: herpetological applications. --Herpetol 46 (1990) 87-104
34. Frost D.R., Kluge A.G., and Hillis D.M. Species in contemporary herpetology: comments on phylogenetic inference and taxonomy. Herp. Rev. 23 (1992) 46-54
35. Fu J., and Murphy R.W. Discriminating and locating character covariation: an application of permutation tail probability analyses. Syst. Biol. 48 (1999) 380-395
36. Funk D.J., and Omland K.E. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu. Rev. Ecol. Evol. Syst. 34 (2003) 397-423
37. Gehlbach, F.R., 1965. Herpetology of the Zuni mountains region, northwestern New Mexico. In: Proc. U.S. Nat. Mus., Washington, DC, Smithsonian Institute 116, pp. 243-332.
38. Grismer L.L. Geographic origins for the reptiles on islands in the Gulf of California, Mexico. Herp. Nat. Hist. 2 (1994) 17-40
39. Grismer L.L. An evolutionary classification of reptiles on islands in the Gulf of California. Herpetologica 55 (1999) 446-469
40. Grismer L.L. Amphibians and Reptiles of Baja California (2002), Univ. of California Press, Berkeley, CA
41. Günther A. Description of Leptodeira torquata, a new snake from Central America. Ann. of Nat. Hist. 5 (1860) 169-171
42. Günther A. Reptilia and Batrachia: Biologia Centrali-Americana (1894), Taylor and Francis, London, UK
43. Hardy L.M., and McDiarmid R.W. The amphibians and reptiles of Sinaloa, Mexico. Univ. of Kan. Pub. Mus. Nat. Hist. 18 (1969) 39-252
44. Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
45. Jaeger J.R., Riddle B.R., and Bradford D.F. 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. 14 (2005) 3033-3048
46. Jockusch E.L., and Wake D.B. Falling apart and merging: diversification of slender salamanders (Plethodontidae, Batrachoseps) in the American West. Biol. J. Linn. Soc. 76 (2002) 361-391
47. Klauber L.M. The subspecies of the Spotted Night Snake. Copeia 1938 (1938) 192-193
48. Klauber L.M. Four papers on the application of statistical methods to herpetological problems (III. The correlation between scalation and life zones in San Diego County snakes). Bull. Zool. Soc. San Diego 17 (1941) 1-95
49. Kraus F., and Brown W.S. Phylogenetic relationships of colubroid snakes based on mitochondrial DNA sequences. Zool. J. Linn. Soc. 122 (1998) 455-487
50. Kumazawa Y., Hideoshi O., Nishida M., and Ozawa T. The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions. Genetics 150 (1998) 313-329
51. Leaché A.D., and Reeder T.W. Molecular systematics of the eastern fence lizard (Sceloporus undulatus): a comparison of parsimony, likelihood, and Bayesian approaches. Syst. Biol. 51 (2002) 44-68
52. Leaché A.D., and Mulcahy D.G. Phylogeny, divergence times, and species limits of spiny lizards (Sceloporus magister species group) in western North America deserts and Baja California. Mol. Ecol. 16 (2007) 5216-5233
53. Lemos-Espinal J.A., Smith H.M., Chiszar D., and Woolrich-Piña G. 2003 Snakes from Chihuahua and adjacent states of Mexico. Bull. Chicago Herp. Soc. 39 (2004) 206-213
54. Leviton A.E., and Tanner W.W. The generic allocation of Hypsiglena slevini Tanner (Serpentes: Colubridae). Occ. Pap. Calif. Acad. Sci. 27 (1960) 1-7
55. Leviton A.E., Gibbs R.H., Heal E., and Dawson C.E. Standards in herpetology and ichthyology: part I. Standard symbolic codes for institutional resource collections in herpetology and ichthyology. Copeia 1985 (1985) 802-832
56. Lindell J., Ngo A., and Murphy R.W. Deep genealogies and the mid-peninsular seaway of Baja California. J. Biogeog. 33 (2006) 1327-1331
57. Liner, E.A., 1994. Scientific and common names for the amphibians and reptiles of Mexico in English and Spanish. Society for the Study of Amphibians and Reptiles Herp. Circ. Pub. No. 23.
58. Lowe C.H. The eastern limit of the Sonoran Desert in the United States with additions to the known herpetofauna of New Mexico. Ecology 36 (1955) 343-345
59. Macey J.R., and Verma A. Homology in phylogenetic analysis, alignment of transfer RNA genes and the phylogenetic position of snakes. Mol. Phylogenet. Evol. 4 (1997) 272-279
60. MacMahon J.A., and Wagner F.H. The Mojave, Sonoran and Chihuahuan Deserts of North America. In: Evenari M., Noy-Meir I., and Goodall D.W. (Eds). Hot Deserts and Arid Shrublands (1985), Elsevier Science Publishers BV, Amsterdam 105-202
61. Maddison, D.R., Maddison, W.P., 2005. MacClade 4.08, Analysis of phylogeny and character evolution. Sinauer Associates, Sunderland, Massachusetts.
62. Manier M.K. Geographic variation in the long-nosed snake, Rhinocheilus lecontei (Colubridae): beyond the subspecies debate. Biol. J. Linn. Soc. 83 (2004) 65-85
63. Mateos M. Comparative phylogeography of livebearing fishes in the genera Poeciliopsis and Poecilia (Poeciliidae: Cyprinodontiformes) in central Mexico. J. Biogeo. 32 (2005) 775-780
64. Matocq M.D. Phylogeographical structure and region history of the dusky-footed woodrat, Neotoma fuscipes. Mol. Ecol. 11 (2002) 229-242
65. Mayr E. Systematics and the origin of species (1942), Columbia University Press, New York, NY
66. Mocquard F. Contributions a la faune herpetologuique de la Basse-California. Nouv. Arch. Mus. d'Hist. Nat. 1 (1899) 297-344
67. Morafka D.J. Is there a Chihuahuan Desert? A Quantitative Evaluation Through a Herpetofaunal Perspective. In: Wauer R.H., and Riskind D.H. (Eds). Transactions of the Symposium on the Biological Resources of the Chihuahuan Desert Region United States and Mexico (1977), U.S. Department of the Interior, Alpine, TX 437-454
68. Morando M., Avila L.J., and Sites Jr. J.W. Sampling strategies for delimiting species: genes, individuals, and populations in the Liolaemus elongatus-kriegi complex (Squamata: Liolaemidae) in Andean-Patagonian South America. Syst. Biol. 52 (2003) 159-185
69. Moritz C., and Faith D.P. Comparative phylogeography and the identification of genetically divergent areas for conservation. Mol. Ecol. 7 (1998) 419-429
70. Moritz C., Schneider C.J., and Wake D.B. Evolutionary relationships within the Ensatina eschscholtzii complex confirm the ring species interpretation. Syst. Biol. 41 (1992) 273-291
71. Mulcahy, D.G., 2006. Historical biogeography of North American nightsnakes and their relationships among the Dipsadines: Evidence for vicariance associated with Miocene formations of northwestern Mexico. Ph.D. thesis, Utah State University.
72. Mulcahy D.G. Molecular systematics of neotropical cat-eyed snakes: a test of the monophyly of Leptodeirini (Colubridae: Dipsadinae) with implications for character evolution and biogeography. Biol. J. Linn. Soc. 92 3 (2007) 483-500
73. Mulcahy D.G., Spaulding A., Mendelson III J.R., and Brodie Jr. E.D. Phylogeography of the Flat-tailed Horned lizard (Phrynosoma mcallii) and systematics of the P. mcallii-platyrhinos mtDNA complex. Mol. Ecol. 15 (2006) 1807-1826
74. Murphy R., and Ottley J.R. Distribution of amphibians and reptiles on islands in the Gulf of California. Ann. Carnegie Mus. 53 (1984) 207-230
75. Murphy R.W., and Aguirre-Léon G. Nonavian reptiles: origins and evolution. In: Case T.J., Cody M.L., and Ezcurra E.A. (Eds). New Island Biogeography of the Sea of Cortés (2002), Oxford Univ. Press, New York, NY 181-220
76. Nylander, J.A., 2004. MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University.
77. Omland K.E., Baker J.M., and Peters J.L. Genetic signatures of intermediate divergence: population history of Old and New World Holarctic ravens (Corvus corax). Mol. Ecol. 15 (2006) 795-808
78. Palumbi S.R. Nucleic acids II: the polymerase chain reaction. In: Hillis D.M., Moritz C., and Mable B.K. (Eds). Molecular Systematics (1996), Sinauer Associates, Sunderland, MA 205-250
79. Pook C.E., Wüster W., and Thorpe R.S. Historical biogeography of the Western Rattlesnake (Serpentes: Viperidae: Crotalus viridis), inferred from mitochondrial DNA sequence information. Mol. Phylogenet. Evol. 15 (2000) 269-282
80. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
81. Radtkey R.R., Fallon S.M., and Case T.J. Character displacement in some Cnemidophorus lizards revisited: a phylogenetic analysis. Proc. Nat. Acad. Sci. 94 (1997) 3734-9740
82. Rambaut A., and Drummond A.J. TRACER (2004), Univ. of Oxford, Oxford, UK
83. Richmond J.Q., and Reeder T.W. Evidence for parallel ecological speciation in scincid lizards of the Eumeces skiltonianus species group (Squamata: Scincidae). Evolution 56 (2002) 1498-1513
84. Riddle B.R., and Hafner D.J. A step-wise approach to integrating phylogeographic and phylogenetic biogeographic perspectives on the history of a core North American warm deserts biota. J. Arid Environ. 66 (2006) 435-461
85. Riddle B.R., Hafner D.J., Alexander L.F., and Jaeger J.R. Cryptic vicariance in the historical assembly of a Baja California Peninsula desert biota. Proc. Nat. Acad. Sci. 97 (2000) 13734-14438
86. Riddle B.R., Hafner D.J., and Alexander L.F. Phylogeography and systematics of the Peromyscus eremicus species group and the historical biogeography of North American warm regional deserts. Mol. Phylogenet. Evol. 17 (2000) 145-160
87. Rodríguez-Robles J.A., and De Jesus-Escobar J.M. Molecular systematics of New World lampropeltine snakes (Colubridae): implications for biogeography and evolution of food habits. Biol. J. Linn. Soc. 68 (1999) 355-385
88. Rodríguez-Robles J.A., Denardo D.F., and Staub R.E. Phylogeography of the California mountain kingsnake, Lampropeltis zonata (Colubridae). Mol. Ecol. 8 (1999) 1923-1934
89. Rodríguez-Robles J.A., and De Jesus-Escobar J.M. Molecular systematics of New World Gopher, Bull, and Pinesnakes (Pituophis: Colubridae), a transcontinental species complex. Mol. Phylogenet. Evol. 14 (2000) 35-50
90. Schulte II J.A., Macey J.R., and Papenfuss T.J. A genetic perspective on the geographic association of taxa in the Sceloporus magister complex. Mol. Phylogenet. Evol. 39 (2006) 873-880
91. Sinclair E.A., Bezy R.L., Bolles K., Camarillo J.L., Crandall R.K.A., and Sites Jr. J.W. Testing species boundaries in an ancient species complex with deep phylogeographic history: genus Xantusia (Squamata: Xantusiidae). Am. Nat. 164 (2004) 396-414
92. Sites Jr. J.W., and Crandall K.A. Testing species boundaries in biodiversity studies. Conserv. Biol. 11 (1997) 1289-1297
93. Sites Jr. J.W., and Marshall J.C. Operational criteria for delimiting species. Ann. Rev. Ecol. Evol. Syst. 35 (2004) 199-227
94. Stebbins R.C. A field guide to western reptiles and amphibians. 3rd ed. (2003), Houghton Mifflin Company, Boston, MA
95. Swofford, D.L. 2000. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods) Version 4.0b10. Sinauer Associates, Sunderland, MA.
96. Tan A.M., and Wake D.B. MtDNA phylogeography of the California newt, Taricha torosa (Caudata, Salamandridae). Mol. Phylogenet. Evol. 4 (1995) 383-394
97. Tanner W.W. Two new species of Hypsiglena from western North America. Great Basin Nat. 4 (1943) 53-54
98. Tanner W.W. A taxonomic study of the genus Hypsiglena. Great Basin Nat. 5 (1944) 25-92
99. Tanner W.W. Additional note on the genus Hypsiglena with a description of a new subspecies. Herpetologica 10 (1954) 54-56
100. Tanner W.W. The night snakes of Baja California. Tran. San Diego Soc. Nat. Hist. 14 (1966) 189-196
101. Tanner W.W. A new Hypsiglena from Tiburon Island, Sonora, Mexico. Great Basin Nat. 41 (1981) 139-142
102. Tanner W.W. Snakes of western Chihuahua. Great Basin Nat. 45 (1985) 615-676
103. Tanner W.W., and Banta B.H. Description of a new Hypsiglena from San Martin Island, Mexico, with a Resume of the Reptile Fauna of the island. Herpetologica 18 (1962) 21-25
104. Taylor E.H. On Mexican snakes of the genera Trimorphodon and Hypsiglena. Univ. Kan. Sci. Bull. 25 (1938) 357-383
105. Templeton A.R. Using phylogeographic analyses of gene trees to test species status and processes. Mol. Ecol. 10 (2001) 779-791
106. Templeton A.R. Statistical phylogeography: methods of evaluating and minimizing inference errors. Mol. Ecol. 13 (2004) 789-809
107. Templeton A.R., Crandall K.A., and Sing C.F. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132 (1992) 619-633
108. Templeton A.R., Routman R.E., and Phillips C.A. 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 (1995) 767-782
109. Upton D.E., and Murphy R.W. Phylogeny of the side-blotched lizards (Phrynosomatidae: Uta) based on mtDNA sequences: support for a midpeninsular seaway in Baja California. Mol. Phylogenet. Evol. 8 (1997) 104-113
110. Van Devender T.R., and Spaulding W.G. Development of vegetation and climate in the southwestern United States. In: Wells S.G., and Haragan D.R. (Eds). Origin and Evolution of Deserts (1983), University of New Mexico Press, New Mexico 131-156
111. Van Devender T.R., Thompson R.S., and Betancourt J.L. Vegetation history of the deserts of southwestern North America; The nature and timing of the Late Wisconsin-Holocene transition. In: Ruddiman W.F., and Wright Jr. H.E. (Eds). The Geology of North America Vol. K-3 (1987), Geological Society of America, Boulder 323-352
112. Wake D.B. Incipient species formation in salamanders of the Ensatina complex. Proc. Nat. Acad. Sci. 94 (1997) 3734-7761
113. Wake D.B. Problems with species: patterns and processes of species formation in salamanders. Ann. Miss. Bot. Garden 93 (2006) 8-23
114. Wiens J.J., and Penkrot T.A. Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloporus). Syst. Biol. 51 (2002) 69-91
115. Wiens J.J., Reeder T.W., Montes A.N., and de Oca. Molecular phylogenetics and evolution of sexual dichromatism among populations of the Yarrow's Spiny Lizard (Sceloporus jarrovii). Evolution 53 (1999) 1884-1897
116. Wilson E.O., and Brown Jr. W.L. The subspecies concept and its taxonomic application. Syst. Zool. 2 (1953) 97-111
117. Zamudio K.R., and Greene H.W. Phylogeography of the bushmaster (Lachesis muta: Viperidae): implications for neotropical biogeography, systematics, and conservation. Biol. J. Linn. Soc. 62 (1997) 421-442
118. Zamudio K.R., Jones K.B., and Ward R.H. Molecular systematics of the short-horned lizards: biogeography and taxonomy of a widespread species complex. Syst. Biol. 46 (1997) 284-305
119. Zweifel R.G. Results of the Puritan-American Museum of Natural History expedition to western Mexico 2. Notes on reptiles and amphibians from the pacific coastal islands of Baja California. Amer. Mus. Nov. 1895 (1958) 1-17