FROM THE COVER Gene flow and the maintenance of species boundaries ERICA L. LARSON,* † THOMAS A. WHITE,* ‡ CHARLES L. ROSS § and RICHARD G. HARRISON* *Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA, †Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA, ‡CMPG Lab, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland, §School of Natural Science, Hampshire College, Amherst, MA 01002, USA Abstract Hybrid zones are regions where individuals from genetically differentiated popula- tions meet and mate, resulting in at least some offspring of mixed ancestry. Patterns of gene flow (introgression) in hybrid zones vary across the genome, allowing assessment of the role of individual genes or genome regions in reproductive isolation. Here, we document patterns of introgression between two recently diverged species of field crickets. We sampled at a very fine spatial scale and genotyped crickets for 110 highly differentiated single nucleotide polymorphisms (SNPs) identified through transcrip- tome scans. Using both genomic and geographic cline analysis, we document remark- ably abrupt transitions (<100 m) in allele frequencies for 50 loci, despite high levels of gene flow at other loci. These are among the steepest clines documented for any hybridizing taxa. Furthermore, the cricket hybrid zone provides one of the clearest examples of the semi-permeability of species boundaries. Comparisons between data from the fine-scale transect and data (for the same set of markers) from sampling a much larger area in a different region of the cricket hybrid zone reveal consistent pat- terns of introgression for individual loci. The consistency in patterns of introgression between these two distant and distinct regions of the hybrid zone suggests that strong selection is acting to maintain abrupt discontinuities within the hybrid zone and that genomic regions with restricted introgression likely include genes that contribute to nonecological prezygotic barriers. Keywords: genomic clines, Gryllus, habitat isolation, introgression, spatial scale, speciation Received 12 October 2013; revision received 14 November 2013; accepted 16 November 2013 Introduction Species are often viewed as cohesive entities, groups of populations connected by gene flow and reproductively isolated from other such groups (Mayr 1963). Alterna- tively, species can be defined as diagnosably distinct (Nixon & Wheeler 1990) or exclusive groups (Baum & Shaw 1995) of individuals. In fact, cohesion, diagnos- ability and exclusivity are properties of individual genes or genome regions and not of whole organisms (or lineages) (Barton & Hewitt 1985; Harrison 1990; Wu 2001; Nosil et al. 2009). Because of independent assort- ment and recombination, each genome region may have a unique evolutionary history, and boundaries between species will be semi-permeable, with permeability depending on the genome region. In the face of ongoing gene flow, some regions of the genome can become (or remain) strongly differentiated, if these regions contain genes that contribute to reproductive isolation or local adaptation. Hybrid zones provide a unique opportunity to identify the role of individual genes in reproductive iso- lation. Hybridization and introgression over many gen- erations result in the shuffling of divergent genomes. For a given gene, the strength of selection, the role in reproductive isolation, together with genetic linkage relationships, will determine the extent of introgression. Alleles that are advantageous in the genomic back- ground of either parental species will be easily exchanged via hybridization, whereas genomic regions that contribute to barriers between species will have low gene flow and characteristically steep clines (Barton & Hewitt 1985; Harrison 1990; Payseur 2010). Allele Correspondence: Erica L. Larson, Fax: (406) 243-4184; E-mail: erica.larson@mso.umt.edu © 2013 John Wiley & Sons Ltd Molecular Ecology (2014) 23, 1668–1678 doi: 10.1111/mec.12601