Molecular Ecology (2004) 13, 2841–2850 doi: 10.1111/j.1365-294X.2004.02253.x © 2004 Blackwell Publishing Ltd Blackwell Publishing, Ltd. Landscape connectivity influences gene flow in a roe deer population inhabiting a fragmented landscape: an individual–based approach A. COULON,* J. F. COSSON,† J. M. ANGIBAULT,* B. CARGNELUTTI,* M. GALAN,* , † N. MORELLET, * , † E. PETIT,‡ S. AULAGNIER * and A. J. M. HEWISON * *Institut de Recherche sur les Grands Mammifères, Institut National de la Recherche Agronomique, B.P. 27, 31326 Castanet–Tolosan cedex, France; †Centre de Biologie et de Gestion des Populations, Institut National de la Recherche Agronomique, Montferrier-sur-Lez France; ‡ UMR 6652 Ethologie Evolution Ecologie, Université de Rennes 1, Paimpont, France Abstract Changes in agricultural practices and forest fragmentation can have a dramatic effect on landscape connectivity and the dispersal of animals, potentially reducing gene flow within populations. In this study, we assessed the influence of woodland connectivity on gene flow in a traditionally forest-dwelling species — the European roe deer — in a fragmented landscape. From a sample of 648 roe deer spatially referenced within a study area of 55 × 40 km, inter- individual genetic distances were calculated from genotypes at 12 polymorphic micro- satellite loci. We calculated two geographical distances between each pair of individuals: the Euclidean distance (straight line) and the ‘least cost distance’ (the trajectory that maximizes the use of wooded corridors). We tested the correlation between genetic pairwise distances and the two types of geographical pairwise distance using Mantel tests. The correlation was better using the least cost distance, which takes into account the distribution of wooded patches, especially for females (the correlation was stronger but not significant for males). These results suggest that in a fragmented woodland area roe deer dispersal is strongly linked to wooded structures and hence that gene flow within the roe deer population is influenced by the connectivity of the landscape. Keywords: Capreolus capreolus, connectivity, dispersal, gene flow, habitat fragmentation, isolation- by-distance Received 5 January 2004; revision received 7 May 2004; accepted 7 May 2004 Introduction During recent decades, changes in agricultural practices, rural decline and the extension of urban areas have greatly modified European landscapes: large forested areas have been divided into small remnants, small wooded areas have disappeared, the surface area of cultivated fields has increased and some habitats have been transformed into scrubland ( Burgess & Sharpe 1981). These modifications have led to a general fragmentation of wooded habitat, which can be defined as a decrease in the wooded surface area and the isolation of the remaining fragments (Stewart et al . 2000). A consequence of habitat fragmentation is a decrease in connectivity (Baudry & Burel 1998), which is ‘the degree to which the landscape facilitates or impedes movement among resource patches’ (Taylor et al . 1993). Indeed, hetero- geneity generated by fragmentation can create barriers to movement because unfavourable habitat does not provide cover against predators, or because distances between suit- able patches are greater than those that species are able to cross in one step (Arnold et al . 1993). Consequently, the movement abilities of animals, and particularly their fac- ulty to disperse, may be altered by landscape fragmenta- tion (e.g. Diffendorfer et al . 1995). This alteration can have dramatic consequences on populations, partly because of the reduction of gene flow between populations, which leads to greater inbreeding and loss of genetic diversity within fragments ( Frankham et al . 2002). The consequences Correspondence: A. Coulon. Fax: 05 61-28-55-00; E-mail: coulon@toulouse.inra.fr