Missing data in a stochastic Dollo model for binary trait data, and its application to the dating of Proto-Indo-European

Journal of the Royal Statistical Society. Series C: Applied Statistics

Volumn 60, Issue 1, 2011, Pages 71-92

  Ryder, Robin J ^a   Nicholls, Geoff K ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Bayesian inference; Dating methods; Markov chain Monte Carlo methods; Missing data; Phylogenetics; Proto Indo European; Rate heterogeneity

Indexed keywords

EID: 79952583222     PISSN: 00359254     EISSN: 14679876     Source Type: Journal    
DOI: 10.1111/j.1467-9876.2010.00743.x     Document Type: Article

References (17)

1. Alekseyenko, A., Lee, C. and Suchard, M. (2008) Wagner and Dollo: a stochastic duet by composing two parsimonious solos. System. Biol., 57, 772-784.
2. Dyen, I., Kruskal, J. and Black, P. (1997) FILE IE-DATA1. (Raw data available from ; binary data available from .)
3. Felsenstein, J. (1981) Inferring Phylogenies. Sunderland: Sinauer Associates.
4. Garrett, A. (2006) Convergence in the formation of Indo-European subgroups: phylogeny and chronology. In Phylogenetic Methods and the Prehistory of Languages (eds P. Forster and C. Renfrew ). Cambridge: McDonald Institute for Archaeological Research.
5. Geyer, C. (1992) Practical Markov Chain Monte Carlo. Statist. Sci., 7, 473-483.
6. Gray, R. and Atkinson, Q. (2003) Language-tree divergence times support the Anatolian theory of Indo-European origin. Nature, 426, 435-439.
7. Lewis, P. (2001) A likelihood approach to estimating phylogeny from discrete morphological character data. System. Biol., 50, 913-925.
8. Mallory, J. (1989) In Search of the Indo-Europeans: Language Archaeology and Myth. Thames and Hudson.
9. McMahon, A. and McMahon, R. (2005) Language Classification by Numbers. Oxford: Oxford University Press.
10. Nicholls, G. K. and Gray, R. D. (2008) Dated ancestral trees from binary trait data and their application to the diversification of languages. J. R. Statist. Soc. B, 70, 545-566.
11. Raftery, A. (1996) Hypothesis testing and model selection. In Markov Chain Monte Carlo in Practice (eds W. R. Gilks, S. Richardson and D. J. Spiegelhalter ). London: Chapman and Hall.
12. Renfrew, C. (1987) Archaeology and language: the puzzle of Indo-European origins. Curr. Anthrop., 29, 437-441.
13. Ringe, D., Warnow, T. and Taylor, A. (2002) Indo-European and computational cladistics. Trans. Philol. Soc., 100, 59-129.
14. Ronquist, F., Huelsenbeck, J. and van der Mark, P. (2005) MrBayes 3.1 manual. School of Computational Science, Florida State University, Tallahassee.
15. Ryder, R. J. and Nicholls, G. K. (2010) Supplement to Missing data in a stochastic Dollo model for binary traits, and its application to the dating of Proto-Indo-European. (Available from .)
16. Warnow, T., Evans, S., Ringe, D. and Nakhleh, L. (2006) A Stochastic model of language evolution that incorporates homoplasy and borrowing. In Phylogenetic Methods and the Prehistory of Languages (eds P. Forster and C. Renfrew ). Cambridge: McDonald Institute for Archaeological Research.
17. Yule, G. (1925) A mathematical theory of evolution based on the conclusions of Dr. JC Willis, FRS. Phil. Trans. R. Soc. Lond. B, 213, 21-87.