Genomic and morphological data from the native lizard Teira dugesii, Madeira island (32.7607° N, 16.9595° W), Portugal, July 2019.

This dataset corresponds to Genotyping-by-sequencing (GBS) data, dorsal luminance data and data on head dimensions of the wall lizard Teira dugesii from starkly contrasting shingle beach and inland habitats on the Portuguese island of Madeira. The study used a matched pairs sampling design to examine morphological and genomic divergence between four beach and adjacent (<1 km) inland areas. Beach populations were found to be significantly darker than corresponding inland populations. Geometric morphometric analyses revealed divergence in head morphology: beach lizards have generally wider snouts. GBS analyses allowed rejection of the hypothesis that beach populations form a distinct lineage. Bayesian analyses provide strong support for models that incorporate gene flow, relative to those that do not, replicated at all pairs of matched sites. Madeiran lizards show morphological divergence between habitats in the face of gene flow, revealing how divergence may originate within small islands. A preprint describing the work is deposited here, while a full report on the work will be published in the journal Communications Biology in 2023.