Molecular Ecology (2009) 18, 1678–1691 doi: 10.1111/j.1365-294X.2009.04142.x © 2009 Blackwell Publishing Ltd Blackwell Publishing Ltd Natural selection influences AFLP intraspecific genetic variability and introgression patterns in Atlantic eels P. A. GAGNAIRE,* V. ALBERT,† B. JÓNSSON‡ and L. BERNATCHEZ† *Institut des Sciences de l’Evolution (ISEM UMR 5554 CNRS-UMII), Université de Montpellier II, CC 065, Place E. Bataillon, 34095 Montpellier cedex 5, France, †Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada G1V 0A6, ‡Institute of Freshwater Fisheries, Northern Division, Sau∂árkrókur, Iceland, IS 550 Abstract Investigating patterns of genetic variation in hybridizing species provides an opportunity to understand the impact of natural selection on intraspecific genetic variability and inter- specific gene exchange. The Atlantic eels Anguilla rostrata and A. anguilla each occupy a large heterogeneous habitat upon which natural selection could differentially shape genetic variation. They also produce viable hybrids only found in Iceland. However, the possible footprint of natural selection on patterns of genetic variation within species and introgressive hybridization in Icelandic eels has never been assessed. We revisited amplified fragment length polymorphism data collected previously using population genomics and admixture analyses to test if (i) genetic variation could be influenced by non-neutral mechanisms at both the intra- and interspecific levels, and if (ii) selection could shape the spatio-temporal distribution of Icelandic hybrids. We first found candidate loci for directional selection within both species. Spatial distributions of allelic frequencies displayed by some of these loci were possibly related with the geographical patterns of life-history traits in A. rostrata, and could have been shaped by natural selection associated with an environmental gradient along European coasts in A. anguilla. Second, we identified outlier loci at the interspecific level. Non-neutral introgression was strongly suggested for some of these loci. We detected a locus at which typical A. rostrata allele hardly crossed the species genetic barrier, whereas three other loci showed accelerated patterns of introgression into A. anguilla in Iceland. Moreover, the level of introgression at these three loci increased from the glass eel to the yellow eel stage, supporting the hypothesis that differential survival of admixed genotypes partly explains the spatio-temporal pattern of hybrid abund- ance previously documented in Iceland. Keywords: AFLP, Anguilla, introgressive hybridization, natural selection, outlier loci, species genetic barrier Received 5 November 2008; revision received 5 January 2009; accepted 22 January 2009 Introduction Discerning the relative influence of neutral vs. selective processes acting in natural populations is a fundamental step towards the comprehension of species’ evolution. Populations living in heterogeneous habitats are likely to undergo diverse selective constraints that can differentially shape genetic variation among them, occasionally leading to reproductive isolation (Mayr 1947). Direct observation of the genetic effects of natural selection can be conveniently assessed when adaptive phenotypic traits and genes underlying these adaptations are known. In most nonmodel organisms, a priori knowledge concerning the genes governing adaptive traits is often not available, thus, it becomes necessary to use indirect methods to identify loci potentially under selection. Such ‘population genomics’ approaches are based on the principle of screening sufficient number of molecular markers randomly distributed across the whole genome in a large number of individuals, to detect loci whose level of differentiation between popula- tions exceeds that expected under neutral expectations. Correspondence: Louis Bernatchez, Fax: 1 418 656 7176; E-mail: louis.bernatchez@bio.ulaval.ca