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DIM SUM: demography and individual migration simulated using a Markov chain

Authors

  • JEREMY M. BROWN,

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    • Present address: Jeremy M. Brown, Department of Integrative Biology, University of California, Berkeley, 3060 Valley Life Sciences Building, Berkeley, CA 94720-3140, USA.

  • KEVIN SAVIDGE,

    1. Section of Integrative Biology and Center for Computational Biology and Bioinformatics, University of Texas – Austin, 1 University Station C0930, Austin, TX 78712, USA
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  • EMILY JANE B. McTAVISH

    1. Section of Integrative Biology and Center for Computational Biology and Bioinformatics, University of Texas – Austin, 1 University Station C0930, Austin, TX 78712, USA
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Jeremy M. Brown, Fax: (510) 643-6264; E-mail: jeremymbrown@gmail.com

Abstract

An increasing number of studies seek to infer demographic history, often jointly with genetic relationships. Despite numerous analytical methods for such data, few simulations have investigated the methods’ power and robustness, especially when underlying assumptions have been violated. DIM SUM (Demography and Individual Migration Simulated Using a Markov chain) is a stand-alone Java program for the simulation of population demography and individual migration while recording ancestor-descendant relationships. It does not employ coalescent assumptions or discrete population boundaries. It is extremely flexible, allowing the user to specify border positions, reactions of organisms to borders, local and global carrying capacities, individual dispersal kernels, rates of reproduction and strategies for sampling individuals. Spatial variables may be specified using image files (e.g., as exported from gis software) and may vary through time. In combination with software for genetic marker simulation, DIM SUM will be useful for testing phylogeographic (e.g., nested clade phylogeographic analysis, coalescent-based tests and continuous-landscape frameworks) and landscape-genetic methods, specifically regarding violations of coalescent assumptions. It can also be used to explore the qualitative features of proposed demographic scenarios (e.g. regarding biological invasions) and as a pedagogical tool. DIM SUM (with user’s manual) can be downloaded from http://code.google.com/p/bio-dimsum.

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