Evolutionary history of the genus Sus inferred from cytochrome b sequences

Molecular Phylogenetics and Evolution

Volumn 45, Issue 2, 2007, Pages 757-762

  Mona, Stefano ^a   Randi, Ettore ^b   Tommaseo Ponzetta, Mila ^a  

^a UNIVERSITY OF BARI   (Italy)

^b Istituto Nazionale per la Fauna Selvatica   (Italy)

Author keywords

Bayesian model selection; Cytochrome b; Molecular dating; Sus

Indexed keywords

CYTOCHROME B;

ANIMAL; ARTICLE; CLASSIFICATION; DNA SEQUENCE; GENETICS; MOLECULAR EVOLUTION; PHYLOGENY; SOUTHEAST ASIA; SPECIES DIFFERENTIATION; SWINE; TIME;

ANIMALS; ASIA, SOUTHEASTERN; CYTOCHROMES B; EVOLUTION, MOLECULAR; GENETIC SPECIATION; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SWINE; TIME FACTORS;

SUS;

EID: 34948884524     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2007.05.025     Document Type: Article

References (37)

1. Alves E., Ovilo C., Rodriguez M.C., and Silio L. Mitochondrial DNA sequence variation and phylogenetic relationships among Iberian pigs and other domestic and wild pig populations. Anim. Genet. 34 (2003) 319-324
2. Bollback J.P. Bayesian model adequacy and choice in phylogenetics. Mol. Biol. Evol. 19 (2002) 1171-1180
3. Drummond A.J., Ho S.Y., Phillips M.J., and Rambaut A. Relaxed phylogenetics and dating with confidence. Plos. Biol. 4 5 (2006) e88
4. Gelman A., and Rubin D.B. Inference from iterative simulation using multiple sequences (with discussion). Stat. Sci. 7 (1992) 457-511
5. Gelman A., Meng X.-L., and Stern H. Posterior predictive assessment of model fitness via realized discrepancies. Stat. Sinica 6 (1996) 733-807
6. Gerloff U., Schlötterer C., Rassmann K., Rambold I., Hohmann G., Fruth B., and Tautz D. Amplification of hypervariable simple sequence repeats (microsatellites) from excremental DNA of wild living Bonobos (Pan paniscus). Mol. Ecol. 4 (1995) 515-518
7. Giuffra E., Kijas J.M., Amarger V., Carlborg O., Jeon J.T., and Andersson L. The origin of the domestic pig: independent domestication and subsequent introgression. Genetics 154 (2000) 1785-1791
8. Goldman N. Statistical tests of models of DNA substitution. J. Mol. Evol. 36 2 (1993) 182-198
9. Grillo G., Attimonelli M., Liuni S., and Pesole G. CLEANUP: a fast computer program for removing redundancies from nucleotide sequence databases. Comput. Appl. Biosci. 12 (1996) 1-8
10. Groves C.P. Ancestors for the Pigs: Taxonomy and Phylogeny of the Genus Sus (1981), Australian National University Press, Canberra
11. Groves C.P. Taxonomy of the wild pigs (Sus) of the Philippines. Zool. J. Linn. Soc. 120 (1997) 163-191
12. Groves, C.P., Grubb, P., 1993. The Eurasian suids, Sus and Babyrousa-taxonomy and description. in: Oliver, W.L.R. (Ed.), Pigs, Peccaries, and Hippos. Status Survey and Conservation Action Plan. International Union for the Conservation of Nature, Gland, pp. 107-111.
13. Groves C.P., Shaller G.B., Amato G., and Khounboline K. Rediscovery of the wild pig Sus bucculentus. Nature 386 (1997) 335
14. Hajibabaei M., Janzen D.H., Burns J.M., Hallwachs W., and Hebert P.D. DNA barcodes distinguish species of tropical Lepidoptera. Proc. Natl. Acad. Sci. U.S.A. 103 4 (2006) 968-971
15. Hebert P.D., Stoeckle M.Y., Zemlak T.S., and Francis C.M. Identification of birds through DNA barcodes. Plos. Biol. 2 10 (2004) e312
16. Hein J., Schierup M., and Wiuf C. Gene Genealogies, Variation and Evolution: A Primer in Coalescent Theory (2004), Oxford University Press, Oxford
17. Ho S.Y., and Jermiin L. Tracing the decay of the historical signal in biological sequence data. Syst. Biol. 53 4 (2004) 623-637
18. Johns G.C., and Avise J.C. A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene. Mol Biol. Evol. 15 11 (1998) 1481-1490
19. Kass R.E., and Raftery A.E. Bayes factors. J. Am. Stat. Assoc. 90 (1995) 773-795
20. Kim K.I., Lee J.H., Li K., Zhang Y.P., Lee S.S., Gongora J., and Moran C. Phylogenetic relationships of Asian and European pig breeds determined by mitochondrial DNA D-loop sequence polymorphism. Anim. Genet. 33 (2002) 19-25
21. Larson G., Dobney K., Albarella U., Fang M., Matisoo-Smith E., Robins J., Lowden S., Finlayson H., Brand T., Willerslev E., Rowley-Conwy P., Andersson L., and Cooper A. Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science 307 (2005) 1618-1621
22. Laud P.W., and Ibrahim J. Predictive model selection. J. Roy. Stat. Soc. B 57 (1995) 247-262
23. Lucchini V., Meijaard E., Diong C.H., Groves C.P., and Randi E. New phylogenetic perspectives among species of South-East Asian wild pigs (Sus sp.) based on mtDNA sequences and morphometric data. J. Zool., Lond. 266 (2005) 25-35
24. Nielsen R., and Matz M. Statistical approaches for DNA barcoding. Syst. Biol. 55 1 (2006) 162-169
25. Nylander, J.A., 2004. MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University.
26. Nylander J.A., Ronquist F., Huelsenbeck J.P., and Nieves-Aldrey J.L. Bayesian phylogenetic analysis of combined data. Syst. Biol. 53 1 (2004) 47-67
27. Rambaut A., and Drummond A.J. TRACER (2004), University of Oxford, Oxford
28. Randi E., Lucchini V., and Diong C.H. Evolutionary genetics of the Suiformes as reconstructed using mtDNA sequencing. J. Mamm. Evol. 3 (1996) 163-193
29. Robins J.H., Ross H.A., Allen M.S., and Matisoo-Smith E. Taxonomy: Sus bucculentus revisited. Nature 440 (2006) E7
30. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 12 (2003) 1572-1574
31. Schmidt H.A., Strimmer K., Vingron M., and von Haeseler A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18 3 (2002) 502-504
32. Steinke D., Vences M., Salzburger W., and Meyer A. TaxI: a software tool for DNA barcoding using distance methods. Philos. T. Roy. Soc. B 360 (2005) 1975-1980
33. Suchard M.A., Weiss R.E., and Sinsheimer J.S. Models for estimating Bayes factors with applications to phylogeny and tests of monophyly. Biometrics 61 3 (2005) 665-673
34. Tamura K., and Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10 (1993) 512-526
35. Welch J.J., Fontanillas E., and Bromham L. Molecular dates for the "Cambrian explosion": the influence of prior assumptions. Syst. Biol. 54 4 (2005) 672-678
36. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13 (1997) 555-556
37. Yang Z., and Rannala B. Branch-length prior influences Bayesian posterior probability of phylogeny. Syst. Biol. 54 3 (2005) 455-470