Mitochondrial DNA sequence variation and phylogeography of the scarlet kingsnake (Lampropeltis elapsoides)

References

• Akaike H. 1974. A new look at the statistical identification model. IEEE Trans Autom Control. 19:716–723.
   Web of Science ®Google Scholar
• Arévalo E, Davis SK, Sites JWJr. 1994. Mitochondrial DNA sequence divergence and phylogenetic relationships among eight chromosome races of the Sceloporus grammicus complex (Phrynosomatide) in central Mexico. System Biol. 43:387–418.
   Web of Science ®Google Scholar
• Armstrong MP, Frymire D, Zimmerer EJ. 2001. Analysis of sympatric populations of Lampropeltis triangulum sypsila and Lampropeltis triangulum elapsoides, in western Kentucky and adjacent Tennessee with relation to the taxonomic status of the scarlet kingsnake. J Herpetol. 35:688–693.
   Google Scholar
• Avise JC. 1996. Toward a regional conservation genetics perspective: Phylogeography of faunas in the southeastern United States. In: Avise JC, Hamrick JL. editors. Conservation genetics: Case histories from nature. New York: Chapman & Hall431–470.
   Google Scholar
• Avise JC. 2000. Phylogeography: The history and formation of species. Cambridge, MA: Harvard University Press.
   Google Scholar
• Bowen BW, Avise JC. 1990. Genetic structure of Atlantic and Gulf of Mexico populations of sea bass, menhaden and sturgeon: Influence of zoogeographic factors and life-history patterns. Mar Biol. 107:371–381.
   Web of Science ®Google Scholar
• Burbrink FT, Lawson R. 2007. How and when did Old World ratsnakes disperse into the New World?. Mol Phylogenet Evol. 43:173–189.
   PubMed Web of Science ®Google Scholar
• Cracraft JL, Helm-Bychowski K. 1991. Parsimony and phylogenetic inference using DNA sequences: Some methodological strategies. In: Miyamoto MM, Cracraft JL. editors. Phylogenetic analysis of DNA sequences. Oxford: Oxford University Press184–220.
   Google Scholar
• Crespi EJ, Rissler LJ, Browne RA. 2003. Testing Pleistocene refugia theory: Phylogeographical analysis of Desmognathus wrighti, a high-elevation salamander in the southern Appalachians. Mol Ecol. 12:969–984.
   PubMed Web of Science ®Google Scholar
• Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM, Gascuel O. 2008. Phylogeny.fr: Robust phylogenetic analysis for the non-specialist. Nucl Acids Res. 36:W465–W469.
   PubMed Web of Science ®Google Scholar
• Excoffier L, Lischer HEL. 2010. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resources. 10:564–567.
   PubMed Web of Science ®Google Scholar
• Excoffier L, Smouse PE, Quattro JM. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics. 131:479–491.
   PubMed Web of Science ®Google Scholar
• Fontanella FM, Feldman CR, Siddall ME, Burbrink FT. 2007. Phylogeography of Diadophis punctatus: Extensive lineage diversity and repeated patterns of historical demography in a trans-continental snake. Mol Phylogenet Evol. 46:1049–1070.
   Google Scholar
• Friedman M, DeSalle R. 2008. Mitochondrial DNA extraction and sequencing of formalin-fixed archival snake tissue. Mitochondrial DNA. 19:433–437.
   Google Scholar
• Fu YX. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking, and background selection. Genetics. 147:915–925.
   PubMed Web of Science ®Google Scholar
• Goloboff PA, Farris JS, Nixon KC. 2008. TNT, a free program for phylogenetic analysis. Cladistics. 24:1–13.
   Web of Science ®Google Scholar
• Hasegawa M, Kishino H, Yano T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 22:160–174.
   PubMed Web of Science ®Google Scholar
• Hillis DM, Bull JJ. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology. 42:182–192.
   Web of Science ®Google Scholar
• Hudson RR. 2002. Generating samples under a Wright–Fisher neutral model. Bioinformatics. 18:337–338.
   PubMed Web of Science ®Google Scholar
• Joly S, Stevens MI, Van Vuuren BJ. 2007. Haplotype networks can be misleading in the presence of missing data. Syst Biol. 56:857–862.
   PubMed Web of Science ®Google Scholar
• Keane TM, Naughton TJ, McInerney JO. 2007. MultiPhyl: A high-throughput phylogenomics webserver using distributed computing. Nucl Acids Res. 35:W33–W37.
   Google Scholar
• Macartney JM, Gregory PT, Larsen KW. 1988. A tabular survey of data on movements and home ranges of snakes. Journal of Herpetology. 22:61–73.
   Google Scholar
• Maddison WP, Maddison DR. 2005. MacClade 4: Analysis of phylogeny and character evolution. Version 4.08. Sunderland, MA: Sinauer Associates.
   Google Scholar
• Nixon KC. 2002. WinClada. Version 1.00.08. Ithaca, NY: Author Available at: http://www.cladistics.com/aboutWinc.htm[onle].
   Google Scholar
• Oliphant TE. 2006. Guide to NumPyTrelgol Publishing available at: http://numpy.scipy.org.
   Google Scholar
• Pyron RA, Burbrink FT. 2009. Neogene diversification and taxonomic stability in the snake tribe Lampropeltini (Serpentes: Colubridae). Molecular Phylogenetics and Evolution. 52:524–529.
   Google Scholar
• Rambaut A. 2009. FigTree. Version 1.3. available at: http://beast.bio.ed.ac.uk/FigTree.
   Google Scholar
• Rambaut A, Grassly NC. 1997. Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci. 13:235–238.
   PubMedGoogle Scholar
• Rodriguez-Robles JA, De Jesus-Escobar JM. 1999. Molecular systematics of New World lampropeltinine snakes (Colubridae): Implications for biogeography and evolution of food habits. Biol J Linn Soc. 68:355–385.
   Google Scholar
• Ronquist F, Huelsenbeck JP. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 19:1572–1574.
   PubMed Web of Science ®Google Scholar
• Russo CAM, Takezaki N, Nei M. 1996. Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol Biol Evol. 13:525–536.
   PubMed Web of Science ®Google Scholar
• Shedlock AM, Haygood MG, Pietsch TW, Bentzen P. 1997. Enhanced DNA extraction and PCR amplification of mitochondrial genes from formalin-fixed museum specimens. BioTechniques. 22:394–400.
   PubMed Web of Science ®Google Scholar
• Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123:597–601.
   PubMed Web of Science ®Google Scholar
• Wiens JJ. 1998. Does adding characters with missing data increase or decrease phylogenetic accuracy. Syst Biol. 47:625–640.
   PubMed Web of Science ®Google Scholar
• Wiens JJ. 2003. Missing data, incomplete taxa and phylogenetic accuracy. Syst Biol. 52:528–538.
   PubMed Web of Science ®Google Scholar
• Williams KL. 1988. Systematics and natural history of the American milk snake, Lampropeltis triangulum. Milwaukee: Milwaukee Public Museum.
   Google Scholar
• Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J Mol Evol. 39:306–314.
   PubMed Web of Science ®Google Scholar
• Zhang DX, Hewitt GM. 2003. Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Molecular Ecology. 12:563–584.
   PubMed Web of Science ®Google Scholar