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Genetica

, Volume 135, Issue 3, pp 439–455 | Cite as

Multilocus phylogeography and phylogenetics using sequence-based markers

  • Patrícia H. Brito
  • Scott V. Edwards
Article

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.

Keywords

Multilocus analysis Indel Intron Genomic phylogeography SNP Species tree 

Notes

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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Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  1. 1.Department of Organismic and Evolutionary BiologyHarvard UniversityCambridge USA
  2. 2.Instituto Gulbenkian de CiênciaOeirasPortugal

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