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Retrospective coalescent methods and the reconstruction of metapopulation histories in the sea

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Abstract

Phylogeographic analyses are a key interface between ecological and evolutionary ways of knowing because such analyses integrate the cumulative effects of demographic (ecological) processes over geological (evolutionary) time scales. Newly developed coalescent methods allow evolutionary ecologists to overcome some limitations associated with inferring population history from classic methods such as Wright’s F ST. Here we briefly contrast classic and coalescent methods for looking backward in time through a population genetic lens, focusing on the key advantages of the isolation-with-migration (IM) class of coalescent methods for distinguishing ancient connectedness from actual recurrent contemporary gene flow as causes of genetic similarity or differentiation among populations. Making this critical distinction can lead to the discovery of otherwise obscured histories underlying conventional patterns of spatial variation. We illustrate the importance of these insights using analyses of Pacific fishes, snails, and sea stars in which population sizes and divergence times are more important than rates of contemporary gene flow as determinants of population genetic differentiation. We then extend the IM method to genetic data from two model metapopulation species (California abalone, Australian damselfish). The analyses show the potential use of non-equilibrium IM methods for differentiating among metapopulation models that make different predictions about population parameters and have different implications for the design of marine protected areas and other conservation goals. At face value, the results largely rule out classic metapopulation dynamics (dominated by extinction and colonization rather than connectivity via ongoing recurrent gene flow) but, at the same time, do not strongly support a modern marine metapopulation dynamic (ecologically significant connectivity between demes). However, the results also highlight the need for much more data (i.e., loci) sampled on different spatial scales in order to determine whether metapopulation dynamics might exist on smaller scales than are typically sampled by most phylogeographers and landscape geneticists.

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Acknowledgments

We thank John Pandolfi and Nancy Budd for an invitation to participate in the publication of this volume. The authors’ research, some of which was presented here, has been primarily supported by grants from the National Science Foundation (NSF OCE-0550526 and OCE-0961996) and from the Natural Sciences and Engineering Research Council (NSERC 2004-203052). Thanks to J. Hey and Amy Lawton-Rauh for extensive discussion and insights into the IMa model. Ron Burton, Jake Kritzer, Haris Lessios, Peter Sale, and two anonymous reviewers read the manuscript and provided numerous useful criticisms and suggestions.

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  1. Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA

    Peter B. Marko

  2. Department of Biological Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada

    Michael W. Hart

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Marko, P.B., Hart, M.W. Retrospective coalescent methods and the reconstruction of metapopulation histories in the sea. Evol Ecol 26, 291–315 (2012). https://doi.org/10.1007/s10682-011-9467-9

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