Molecular Phylogenetics and Evolution xxx (2006) xxx–xxx www.elsevier.com/locate/ympev 1055-7903/$ - see front matter  2006 Elsevier Inc. All rights reserved. doi:10.1016/j.ympev.2006.08.022 ARTICLE IN PRESS Please cite this article in press as: Haney, R.A. et al., The Pleistocene history of the sheepshead minnow (Cyprinodon variegatus): Non- equilibrium evolutionary dynamics. . . , Mol. Phylogenet. Evol. (2006), doi:10.1016/j.ympev.2006.08.022 The Pleistocene history of the sheepshead minnow (Cyprinodon variegatus): Non-equilibrium evolutionary dynamics within a diversifying species complex Robert A. Haney a,¤ , Brian R. Silliman b , Adam J. Fry c , Craig A. Layman d , David M. Rand a a Department of Ecology and Evolutionary Biology, Box G-W, Brown University, Providence, RI 02912, USA b Department of Zoology, University of Florida, Gainesville, FL 32611, USA c Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA d Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA Received 7 May 2006; revised 24 August 2006; accepted 31 August 2006 Abstract The sheepshead minnow, Cyprinodon variegatus, is a widespread Wsh species that typically inhabits coastal tidal marsh and mangrove swamp environments, ranging from Cape Cod, Massaschusetts to northern Mexico and into the Caribbean. This wide range crosses sev- eral biogeographic boundaries which are coincident with genetic structuring within numerous species originating in the Pleistocene. In addition, the more northerly reaches of this species range have been further subject to the evolutionary consequences of Pleistocene glaci- ation due to local extinction and recolonization of formerly glaciated sites. C. variegatus thus provides an excellent vertebrate model sys- tem within which to test the extent of genetic diVerentiation among populations in a dominant coastal ecosystem and examine patterns of historical demography in populations distributed along a latitudinal gradient. Using mitochondrial control region and ND2 sequence data, we discovered monophyletic clades within C. variegatus with divergence times within the Pleistocene, and very low gene Xow between most sites. IntraspeciWc genetic breaks appear to correspond broadly to biogeographic or oceanic boundaries. Pleistocene climate change appears to have had dramatic impacts on the size and distribution of populations within and near the glacial margins, but has also aVected populations far from formerly glaciated regions.  2006 Elsevier Inc. All rights reserved. Keywords: Gene Xow; Demography; Mitochondrial control region; Cyprinodon; Phylogeography 1. Introduction The coastal regions of the eastern United States span a range of climate zones, and the representation of taxa within coastal communities subsequently varies strongly from the northern Atlantic to the Gulf of Mexico. Traditionally, this region has been subdivided into three to four biogeographic zones based on the distribution of marine taxa (Briggs, 1974, 1995), although more recent analysis of estuarine invertebrate community composition suggests the presence of a greater number of biogeographic provinces for these taxa (Engle and Sum- mers, 1999). The discipline of phylogeography originated in this region with the discovery that the boundaries among biogeographic regions were coincident with dis- ruptions of gene Xow among populations within numer- ous species, suggesting a connection between microevolution and macroecological process (Avise et al., 1987a, 2000). Further, the depth of phylogenetic breaks in some taxa indicated that historical factors, in particular Pleistocene glacial cycles, may have initiated diVerentiation among populations that is maintained to the present by current patterns and ecological gradients (Reeb and Avise, 1990). * Corresponding author. Fax: +1 401 863 2166. E-mail address: Robert_Haney@brown.edu (R.A. Haney).