Phylogeographic Breaks With and Without Contemporary Barriers to Migration in the Lizard Acanthodactylus erythrurus

Identifying phylogeographic breaks and deciphering the relative contributions of environmental extrinsic (e.g., geological barriers, ecological gradients) and organismal intrinsic (e.g., limited dispersal, reproductive incompatibilities) factors to their persistence remain challenging, especially in the absence of genomic data. Here, we address this issue using parapatric lineages of the lizard Acanthodactylus erythrurus in south-western Morocco. A previous study based on nine nuclear loci identified two phylogeographic units (coastal vs. inland) whose separation did not align with landscape features preventing migration. The coastal lineage was inferred to evolve under isolation by distance (IBD, the regular increase of genetic differentiation with geographic distance), despite the presence of large rivers across its range. This suggests either that phylogeographic breaks do not align with landscape features, or that the restricted marker set prevented an accurate inference of phylogeographic breaks. We tested these hypotheses using RADseq data and recovered three lineages, each separated by phylogeographic breaks and narrow contact zones with restricted admixture. Coastal populations that had been previously identified to evolve under IBD actually included two lineages separated by a major, permanent river, reducing migration. The inland phylogeographic break, correctly identified by the previous study, is located in a continuously distributed habitat. Neither of the breaks aligned with steep changes in bioclimatic variables, suggesting a negligible contribution of local adaptation. We conclude that intrinsic reproductive barriers, as evidenced by narrow clines in allele frequencies at multiple loci spread over the genome, play a major role in maintaining these phylogeographic breaks. Our results also highlight the difficulty of identifying phylogeographic breaks from pre-genomic molecular data.