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Multilocus phylogeography and phylogenetics using sequence-based markers

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An Erratum to this article was published on 04 March 2010

Abstract

We review recent trends in phylogeography and phylogenetics and argue that these two fields stand to be reunited by the common yardstick provided by sequence and SNP data and by new multilocus methods for phylogenetic analysis. Whereas the modern incarnation of both fields was spawned by PCR approaches applied to mitochondrial DNA in the late 1980s, the two fields diverged during the 1990s largely due to the adoption by phylogeographers of microsatellites, in contrast to the adoption of nuclear sequence data by phylogeneticists. Sequence-based markers possess a number of advantages over microsatellites, even on the recent time scales that are the purview of phylogeography. Using examples primarily from vertebrates, we trace the maturation of nuclear gene phylogeography and phylogenetics and suggest that the abundant instances of gene tree heterogeneity beckon a new generation of phylogenetic methods that focus on estimating species trees as distinct from gene trees. Whole genomes provide a powerful common yardstick on which both phylogeography and phylogenetics can assume their proper place as ends of a continuum.

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Acknowledgments

PHB was supported by a postdoctoral fellowship awarded by the Fundação para a Ciência e Tecnologia, Portugal. We thank our lab colleagues and Carlos Bustamante for helpful discussion. We are grateful for the criticisms of two anonymous reviewers and to Craig Moritz and Rauri Bowie for their perspective and for providing detailed comments on the manuscript.

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Authors and Affiliations

  1. Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA

    Patrícia H. Brito & Scott V. Edwards

  2. Instituto Gulbenkian de Ciência, Rua Quinta Grande, 6, Apartado 14, Oeiras, 2781-901, Portugal

    Patrícia H. Brito

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  1. Patrícia H. Brito
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  2. Scott V. Edwards
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Correspondence to Scott V. Edwards.

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Invited review for Genetica (ESF Workshop on Ecological Genomics, Tällberg, Sweden 11/07).

An erratum to this article can be found online at http://dx.doi.org/10.1007/s10709-010-9444-1.

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Brito, P.H., Edwards, S.V. Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica 135, 439–455 (2009). https://doi.org/10.1007/s10709-008-9293-3

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