title: Ancestral population genomics using coalescence hidden Markov models and heuristic optimisation algorithms.
abstract: With full genome data from several closely related species now readily available, we have the ultimate data for demographic inference. Exploiting these full genomes, however, requires models that can explicitly model recombination along alignments of full chromosomal length. Over the last decade a class of models, based on the sequential Markov coalescence model combined with hidden Markov models, has been developed and used to make inference in simple demographic scenarios. To move forward to more complex demographic modelling we need better and more automated ways of specifying these models and efficient optimisation algorithms for inferring the parameters in complex and often high-dimensional models. In this paper we present a framework for building such coalescence hidden Markov models for pairwise alignments and present results for using heuristic optimisation algorithms for parameter estimation. We show that we can build more complex demographic models than our previous frameworks and that we obtain more accurate parameter estimates using heuristic optimisation algorithms than when using our previous gradient based approaches. Our new framework provides a flexible way of constructing coalescence hidden Markov models almost automatically. While estimating parameters in more complex models is still challenging we show that using heuristic optimisation algorithms we still get a fairly good accuracy.
authors.affiliation: Bioinformatics Research Centre, Aarhus University, C.F. Møllers Allé 8, 8000 Aarhus, Denmark. Electronic address: ycheng@birc.au.dk.
authors.forename: Jade Yu
authors.initials: JY
authors.lastname: Cheng
authors.affiliation: Bioinformatics Research Centre, Aarhus University, C.F. Møllers Allé 8, 8000 Aarhus, Denmark. Electronic address: mailund@birc.au.dk.
authors.forename: Thomas
authors.initials: T
authors.lastname: Mailund
mesh_terms: D000465:Algorithms; D005828:Genetics, Population / Q000379:methods*; D023281:Genomics / Q000379:methods*; D008390:Markov Chains
keywords: Coalescent hidden Markov models; Demographic inference; Genetic algorithm; Numerical optimisation; Particle swarm optimisation; Sequential Markov coalescence