Molecular Ecology (2002) 11, 437–445 © 2002 Blackwell Science Ltd Blackwell Science Ltd The usefulness of amplified fragment length polymorphism markers for taxon discrimination across graduated fine evolutionary levels in Caribbean Anolis lizards R. OGDEN and R. S. THORPE School of Biological Sciences, University of Wales, Bangor LL57 2UW, UK Abstract Fine-level taxon discrimination is important in biodiversity assessment and ecogeographical research. Genomic markers are often required for studies on closely related taxa, however, most existing mitochondrial and nuclear markers require prior knowledge of the genome and are impractical for use in small conservation projects. This study describes the applica- tion of amplified fragment length polymorphism (AFLP) to discriminate at four progressively finer evolutionary levels of Caribbean Anolis lizards from the central Lesser Antilles. AFLP is shown to be a rapid and effective method for discriminating between species. Separation increases with primer pair number and choice of primer combination appears to be noncritical. Initial population-level results show markedly less discriminatory power. A screening technique for the identification of population informative markers combining princ- ipal component and principal coordinate analyses is presented and assessed. Subsequent results show selected conspecific AFLP data to be remarkably congruent with those of mitochondrial DNA, microsatellite and morphological markers. The use of AFLP as a low-cost nuclear marker in species-level taxon discrimination is supported, whereas population level application demands further consideration. Keywords: AFLP, Anolis, biodiversity assessment, genetic differentiation, population discrimination, species discrimination Received 26 July 2001; revision received 6 November 2001; accepted 6 November 2001 Introduction Genetic identification of discrete taxa is important in the detection and conservation of biodiversity. Highly speciose genera often present systematicists with difficulty in iden- tifying individual species, because of either strong morph- ological similarity between taxa or marked morphological differences within taxa, necessitating the use of molecular markers. Anolis lizards in the Caribbean are one such group, exhibiting rapid geographical and adaptive radiations throughout the region (Roughgarden 1995). The ability to distinguish between Anolis taxa is important at an inter- specific level in assessing genetic diversity particularly on satellite islands, and at a population level in the study of evolutionary processes on small islands. The four neigh- bouring islands of Dominica, Martinique, St. Lucia and Barbados in the central Lesser Antilles typify the pattern of Anolis phylogeography, each supporting an endemic species that displays distinct morphological and molecular intra- specific diversity. In addition, phylogenetic studies of the relationships between species show that a large range of interspecific diversification exists within this island group. As such, it provides an excellent model for an assessment of the emerging molecular technique, amplified fragment length polymorphism (AFLP; Vos et al. 1995), in a novel application to taxonomic discrimination in reptiles. Originally restricted to use in the separation of microbial and plant species, AFLP has recently been extended for use in vertebrates such as snakes (Giannasi et al. 2001), herring gulls (de Knijff et al. 2001), domestic cattle (Nijman et al. 1999), cichlid fish (Albertson et al. 1999) and catfish (Liu et al. 1998, 1999). The technique produces large numbers of reproducible markers for assessing diversity across the Correspondence: Rob Ogden. Fax: 44 1248 371644; E-mail: bsp631@bangor.ac.uk