title: Coalescent simulation in continuous space: algorithms for large neighbourhood size.
abstract: Many species have an essentially continuous distribution in space, in which there are no natural divisions between randomly mating subpopulations. Yet, the standard approach to modelling these populations is to impose an arbitrary grid of demes, adjusting deme sizes and migration rates in an attempt to capture the important features of the population. Such indirect methods are required because of the failure of the classical models of isolation by distance, which have been shown to have major technical flaws. A recently introduced model of extinction and recolonisation in two dimensions solves these technical problems, and provides a rigorous technical foundation for the study of populations evolving in a spatial continuum. The coalescent process for this model is simply stated, but direct simulation is very inefficient for large neighbourhood sizes. We present efficient and exact algorithms to simulate this coalescent process for arbitrary sample sizes and numbers of loci, and analyse these algorithms in detail.
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK. Electronic address: jerome.kelleher@ed.ac.uk.
authors.forename: J
authors.initials: J
authors.lastname: Kelleher
authors.affiliation: Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK. Electronic address: etheridg@stats.ox.ac.uk.
authors.forename: A M
authors.initials: AM
authors.lastname: Etheridge
authors.affiliation: Institute of Science and Technology, Am Campus I, A-3400 Klosterneuburg, Austria. Electronic address: n.barton@ist.ac.at.
authors.forename: N H
authors.initials: NH
authors.lastname: Barton
mesh_terms: D000465:Algorithms; D012111:Residence Characteristics
keywords: Coalescent simulation; Isolation by distance