Molecular Ecology (2008) 17, 2122–2133 doi: 10.1111/j.1365-294X.2008.03673.x Journal compilation © 2008 Blackwell Publishing Ltd No claim to original US government works Blackwell Publishing Ltd Habitat fragmentation and genetic diversity of an endangered, migratory songbird, the golden-cheeked warbler (Dendroica chrysoparia) DENISE L. LINDSAY,*† KELLY R. BARR,† RICHARD F. LANCE,* SCOTT A. TWEDDALE,‡ TIMOTHY J. HAYDEN‡ and PAUL L. LEBERG† *U.S. Army Engineer Research and Development Center — Environmental Laboratory, Vicksburg, MS 39180, USA, †Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504, USA, ‡U.S. Army Engineer Research and Development Center—Construction Engineering Research Laboratory, Champaign, IL 61826, USA Abstract Landscape genetic approaches offer the promise of increasing our understanding of the influence of habitat features on genetic structure. We assessed the genetic diversity of the endangered golden-cheeked warbler (Dendroica chrysoparia) across their breeding range in central Texas and evaluated the role of habitat loss and fragmentation in shaping the population structure of the species. We determined genotypes across nine microsatellite loci of 109 individuals from seven sites representing the major breeding concentrations of the species. No evidence of a recent population bottleneck was found. Differences in allele frequencies were highly significant among sites. The sampled sites do not appear to represent isolated lineages requiring protection as separate management units, although the amount of current gene flow is insufficient to prevent genetic differentiation. Measures of genetic differentiation were negatively associated with habitat connectivity and the percentage of forest cover between sites, and positively associated with geographic distance and the percentage of agricultural land between sites. The northernmost site was the most genetically differentiated and was isolated from other sites by agricultural lands. Fragmentation of breeding habitat may represent barriers to dispersal of birds which would pose no barrier to movement during other activities such as migration. Keywords: connectivity, genetic distance, habitat specialist, microsatellite, passerine, population structure Received 11 August 2007; revision received 16 November 2007; accepted 4 December 2007 Introduction Fragmentation may decrease connectivity and increase distance between remnant habitat patches. In the case of threatened and endangered avian species, the risk of extinction due to the effects of fragmentation is greater because they usually exist at low densities (Saunders et al. 1991; Johnson 2001). Smaller, more isolated patches of habitat are characterized by a decreased likelihood of males attracting females and less successful dispersal of offspring (Rappole et al. 2003). Decreased dispersal can lead to a more restricted distribution and further reduce abundance (Villard et al. 1999). Moreover, as distance between patches of habitat increases, recolonization of vacated patches becomes more difficult and the ability of breeders to move among populations decreases (Wiens 1994). The fragmentation of habitat and consequent reduction in population size and gene flow could result in increased loss of genetic diversity within populations and increased genetic differentiation among populations (Frankham 1995). Few investigations of avian populations have reported an association between anthropogenic habitat fragmentation and reduced gene flow leading to increased differentiation. Most studies that have found an association between fragmented populations, and genetic differentiation have involved relatively sedentary gallinaceous birds or Correspondence: Denise L. Lindsay, Fax: +1-601-634-4017; E-mail: denise.l.lindsay@usace.army.mil