A Composite Likelihood Method for Estimating Phylogenetic Tree from Dependent Loci

• Activity Number: 521
• Type: Topic Contributed
• Date/Time: Wednesday, August 7, 2013 : 10:30 AM to 12:20 PM
• Sponsor: Biometrics Section
• Author(s): Arindam RoyChoudhury*+
• Companies: Department of Biostatistics, Columbia University
• Keywords: phylogeny ; population tree ; coalescent ; composite likelihood ; dependent data

Abstract

We present a composite likelihood method for estimating phylogenetic trees from dependent loci based on a structured coalescent model. The allele counts in the same set of individual at nearby genetic loci are usually associated with each other due to shared coalescent events and linkage disequilibrium. However, the phylogenetic parameters could be estimated from the marginal distributions of these loci. As the allele counts in the loci are associated, it is often difficult to derive their joint likelihood. To simplify the derivation we treat the loci as if they have independent allele counts, computing a composite likelihood. We establish that the inferences based on the composite likelihood are consistent. Our method is exact and does not use MCMC algorithms. We also modify our methods to account for unsampled loci.