Inclusion of nuclear intron sequence data helps to identify the Asian sister group of New World pitvipers

Molecular Phylogenetics and Evolution

Volumn 54, Issue 1, 2010, Pages 172-178

  Malhotra, Anita ^a   Creer, Simon ^a   Pook, Catharine E ^a   Thorpe, Roger S ^a  

^a BANGOR UNIVERSITY   (United Kingdom)

Author keywords

Bayesian inference; Crotalinae; Mitochondrial DNA; Mixture model; Molecular phylogenetics; Nuclear intron; Parsimony ratchet; Reversible jump MCMC

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BAYES THEOREM; CELL NUCLEUS; CLASSIFICATION; DNA SEQUENCE; GENETICS; INTRON; MOLECULAR EVOLUTION; PHYLOGENY; SEQUENCE ALIGNMENT; SNAKE;

ANIMALS; BAYES THEOREM; CELL NUCLEUS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; INTRONS; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; VIPERIDAE;

CROTALINAE; GLOYDIUS; OVOPHIS OKINAVENSIS; TRIMERESURUS GRACILIS;

EID: 70649115444     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2009.09.007     Document Type: Article

References (33)

1. Borchsenius, F., 2009. FastGap 1.1. Department of Biological Sciences, University of Aarhus, Denmark. Available from: .
2. Brattstrom B.H. Evolution of pit vipers. Trans. San Diego Soc. Nat. Hist. 13 (1964) 185-268
3. Brown J.M., and Lemmon A.R. The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics. Syst. Biol. 56 (2007) 643-655
4. Castoe T.A., and Parkinson C.L. Bayesian mixed models and the phylogeny of pitvipers (Viperidae: Serpentes). Mol. Phylogenet. Evol. 39 (2006) 91-110
5. Creer S., Malhotra A., and Thorpe R.S. Assessing the phylogenetic utility of four mitochondrial genes and a nuclear intron in the Asian pit viper genus Trimeresurus: Separate, simultaneous, and conditional data combination analyses. Mol. Biol. Evol. 20 (2003) 1240-1251
6. Creer S., Malhotra A., Thorpe R.S., and Pook C.E. Targeting optimal introns for phylogenetic analyses in non-model taxa: experimental results in Asian pitvipers. Cladistics 21 (2005) 390-395
7. Creer S., Pook C.E., Malhotra A., and Thorpe R.S. Optimal intron analyses in the Trimeresurus radiation of Asian pitvipers. Syst. Biol. 55 (2006) 57-72
8. Dawson K.A., Malhotra A., Thorpe R.S., Guo P., Mrinalini, and Ziegler T. Mitochondrial DNA analysis reveals a new member of the Asian pitviper genus Viridovipera (Serpentes: Viperidae: Crotalinae). Mol. Phylogen. Evol. 49 (2008) 356-361
9. Friesen V.L., Congdon B.C., Kidd M.G., and Birt T.P. Polymerase chain reaction (PCR) primers for the amplification of five nuclear introns in vertebrates. Mol. Ecol. 8 (1999) 2141-2152
10. Gloyd, H.K., Conant, R., 1990. Snakes of the Agkistrodon Complex: A Monographic Review. Society for the Study of Reptiles and Amphibians. Contributions to Herpetology 6, Saint Louis, MO, USA.
11. Guo P., Malhotra A., Li P.P., Pook C.E., and Creer S. New evidence on the phylogenetic position of the poorly known Asian pitviper Protobothrops kaulbacki (Serpentes: Viperidae: Crotalinae) with a redescription of the species and a revision of the genus Protobothrops. Herpetological J. 17 (2007) 237-246
12. Guo, P., Malhotra, A., Creer, S., Pook, C.E., 2009. An evaluation of the systematic value of skull morphology in the Trimeresurus radiation (Serpentes: Viperidae: Crotalinae) of Asian pitvipers. J. Zool. Syst. Evol. Res. doi:10.1111/j.1439-0469.2009.00525.
13. Hoge A.R., and Romano-hoge S.A.R.W.L. Poisonous snakes of the world. Part 1: check list of the pitvipers, Viperoidea, Viperidae, Crotalinae. Mem. Inst. Butantan (1981) 179-309
14. Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
15. Kass R.E., and Raftery A.E. Bayes Factors. J. Am. Stat. Assoc. 90 (1995) 773-795
16. Kraus F., Mink D.G., and Brown W.M. Crotaline intergeneric relationships based on mitochondrial DNA sequence data. Copeia 1996 (1996) 763-773
17. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., and Higgins D.G. ClustalW and ClustalX version 2. Bioinformatics 23 (2007) 2947-2948
18. Lartillot N., and Philippe H. Computing Bayes factors using thermodynamic integration. Syst. Biol. 55 (2006) 195-207
19. Malhotra A., and Thorpe R.S. A phylogeny of the Trimeresurus group of pit-vipers: New evidence from a mitochondrial gene tree. Mol. Phylogenet. Evol. 16 (2000) 199-211
20. Malhotra A., and Thorpe R.S. A phylogeny of four mitochondrial gene regions suggests a revised taxonomy for Asian pitvipers (Trimeresurus and Ovophis). Mol. Phylogenet. Evol. 32 (2004) 83-100
21. Müller K. The efficiency of different search strategies in estimating parsimony jack-knife, bootstrap, and Bremer support. BMC Evol. Biol. 5 (2005) 58
22. Nylander, J.A.A., 2004. MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University.
23. Nylander J.A.A., Ronquist F., Huelsenbeck J.P., and Nieves-Aldrey J.L. Bayesian phylogenetic analysis of combined data. Syst. Biol. 53 (2004) 47-67
24. Ota H. Geographic patterns of endemism and speciation in amphibians and reptiles of the Ryukyu Archipelago, Japan, with special reference to their paleogeographical implications. Res. Popul. Ecol. 40 (1998) 189-204
25. Parkinson C.L. Molecular systematics and biogeographical history of pitvipers as determined by mitochondrial ribosomal DNA sequences. Copeia 576 (1999) 586
26. Parkinson C.L., Campbell J.A., and Chippindale P.T. Multigene phylogenetic analyses of pitvipers; with comments on the biogeographical history of the group. In: Schuett G.W., Höggren M., Douglas M.E., and Greene H.W. (Eds). Biology of the Vipers (2002), Eagle Mountain Publishing, Salt Lake City, UT 93-110
27. Parkinson C.L., Moody S.M., and Ahlquist J.E. Phylogenetic relationships of the "Agkistrodon Complex" based on mitochondrial DNA sequence data. In: Thorpe R.S., Wüster W., and Malhotra A. (Eds). Venomous Snakes: Ecology, Evolution and Snakebite (1997), The Zoological Society of London, Clarendon Press, Oxford, UK 63-78
28. Pagel M., and Meade A. A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Syst. Biol. 53 (2004) 571-581
29. Rambaut, A., Drummond, A.J., 2007. Tracer v1.4. Available from: .
30. Suchard M.A., Weiss R.E., and Sinsheimer J.S. Bayesian selection of continuous-time Markov chain evolutionary models. Mol. Biol. Evol. 18 (2001) 1001-1013
31. Swofford D.L. PAUP*: phylogenetic analysis using parsimony (* and other methods), version 4.0b10 (2002), Sinauer, Sunderland, MA
32. Toda M., Nishida M., Tu M.-C., Hikida T., and Ota H. Genetic variation, phylogeny and biogeography of the pit vipers of the genus Trimeresurus sensu lato (Reptilia: Viperidae) in the subtropical East Asian islands. In: Ota H. (Ed). Tropical Island Herpetofauna: Origin, Current Diversity, and Conservation (1999), Elsevier, Amsterdam, the Netherlands 249-270
33. Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M., Barton, G.J., 2009. Jalview version 2 - a multiple sequence alignment editor and analysis workbench. Bioinformatics. doi:10.1093/bioinformatics/btp033.