Molecular Ecology (2008) 17, 1313–1327 doi: 10.1111/j.1365-294X.2007.03640.x © 2008 The Authors Journal compilation © 2008 Blackwell Publishing Ltd Blackwell Publishing Ltd Ancient hybridization and mitochondrial capture between two species of chipmunks JEFFREY M. GOOD,* SARAH HIRD,† NOAH REID,† JOHN R. DEMBOSKI,‡ SCOTT J. STEPPAN,§ TINA R. MARTIN-NIMS§ and JACK SULLIVAN† *Department of Ecology and Evolutionary Biology, University of Arizona, Biosciences West, Tucson, AZ 85721, USA, †Department of Biological Sciences, Box 443051, University of Idaho, Moscow, ID 83844-3051, USA, ‡Department of Zoology, Denver Museum of Nature & Science, 2001 Colorado Boulevard, Denver, CO 80205-5798, USA, §Department of Biological Sciences, Florida State University, Tallahassee, FL 32306-1100, USA Abstract Models that posit speciation in the face of gene flow are replacing classical views that hybridization is rare between animal species. We use a multilocus approach to examine the history of hybridization and gene flow between two species of chipmunks (Tamias ruficaudus and T. amoenus). Previous studies have shown that these species occupy different ecological niches and have distinct genital bone morphologies, yet appear to be incompletely isolated reproductively in multiple areas of sympatry. We compared data from four sequenced nuclear loci and from seven microsatellite loci to published cytochrome b sequences. Interspecific gene flow was primarily restricted to introgression of the T. ruficaudus mitochondrial genome into a sympatric subspecies of T. amoenus, T. a. canicaudus, with the four sequenced nuclear loci showing little to no interspecific allele sharing. Microsatellite data were consistent with high levels of differentiation between the species and also showed no current gene flow between broadly sympatric populations of T. a. canicaudus and T. ruficaudus. Coalescent analyses date the mtDNA introgression event from the mid-Pleistocene to late Pliocene. Overall, these data indicate that introgression has had a minimal impact on the nuclear genomes of T. amoenus and T. ruficaudus despite multiple independent hybridization events. Our findings challenge long-standing assumptions on patterns of reproductive isolation in chipmunks and suggest that there may be other examples of hybridization among the 23 species of Tamias that occur in western North America. Keywords: gene flow, hybridization, multilocus, reproductive isolation, speciation, Tamias Received 14 July 2007; revision accepted 17 November 2007 Introduction Several recent studies have shown that closely related animal species often share a history of introgressive hybridization (Machado et al. 2002; Grant et al. 2005; Melo-Ferreira et al. 2005; Turner et al. 2005; Berthier et al. 2006; Putnam et al. 2007). These data challenge the notion that recurrent gene flow between distinct animal species is rare (Dobzhansky 1951; Mayr 1963) and suggest that hybridization may be a frequent, potentially important, transient phase before the completion of reproductive isolation in animals. However, because introgressive hybridization is often cryptic, the frequency and genetic impact of hybridization during animal speciation remains an important and unresolved issue in evolutionary biology. Gene flow between animal species often appears hetero- geneous across the genome, leading to the concept of semipermeable species limits (Harrison 1990; Wu 2001). Under this model, genomic regions involved in reproductive isolation are expected to show little or no introgression, whereas regions that are unlinked to hybrid incompatibilities ought to be exchanged more easily between hybridizing species (Rieseberg et al. 1999). Thus, genetic data sampled from across the genome can provide important information on both the genetic architecture of reproductive isolation Correspondence: Jack Sullivan, Fax: + 01 208 885 7905; E-mail: jacks@uidaho. edu