HOME   ::  Journal List   ::   Article
Ryder, R. J. and Nicholls, G. K. (2011) 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, 60(1):71--92.

Full-text
   URL: http://onlinelibrary.wiley.com/doi/10.11...876.2010.00743.x/pdf

Related links
   Authoritative: http://dx.doi.org/10.1111/j.1467-9876.2010.00743.x   (Publisher's PDF... likely be available here.)
  Web search: Google Web Search   ::   Google Scholar
  Within this site: Cited by (1)   

Abstract

Nicholls and Gray have described a phylogenetic model for trait data. They used their model to estimate branching times on Indo-European language trees from lexical data. Alekseyenko and co-workers extended the model and gave applications in genetics. We extend the inference to handle data missing at random. When trait data are gathered, traits are thinned in a way that depends on both the trait and the missing data content. Nicholls and Gray treated missing records as absent traits. Hittite has 12% missing trait records. Its age is poorly predicted in their cross-validation. Our prediction is consistent with the historical record. Nicholls and Gray dropped seven languages with too much missing data. We fit all 24 languages in the lexical data of Ringe and co-workers. To model spatiotemporal rate heterogeneity we add a catastrophe process to the model. When a language passes through a catastrophe, many traits change at the same time. We fit the full model in a Bayesian setting, via Markov chain Monte Carlo sampling. We validate our fit by using Bayes factors to test known age constraints. We reject three of 30 historically attested constraints. Our main result is a unimodal posterior distribution for the age of Proto-Indo-European centred at 8400 years before Present with 95% highest posterior density interval equal to 7100¿9800 years before Present.

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

BibTex
@article{Ryder2011datingOfProto,
  author={Robin J. Ryder and Geoff K. Nicholls},
  title={Missing data in a stochastic Dollo model for binary trait data, and its application to the dating of Proto-Indo-European},
  journal={Journal of the Royal Statistical Society. Series C: Applied Statistics},
  year={2011},
  volume={60},
  number={1},
  pages={71-92},
  doi={10.1111/j.1467-9876.2010.00743.x},
  url={http://groups.lis.illinois.edu/amag/langev/paper/Ryder2011datingOfProto.html},
  keywords={Bayesian inference; Dating methods; Markov chain Monte Carlo methods; Missing data; Phylogenetics; Proto-Indo-European; Rate heterogeneity}
}

 HOME   ::  Journal List   ::   Article Comments to: junwang4 you-know-at gmail.com Last update: 1/11/13