The study of zones of secondary contact provides insight into the maintenance of reproductive isolation. Tension zone theory supplies powerful tools for assessing how dispersal and selection shape hybrid zones. We present a multimodal analysis of phenotypic clines in conjunction with clines at molecular markers in a hybrid zone between Larus glaucescens and Larus occidentalis. We developed a new method to analyze simultaneously clines of quantitative traits and molecular data. Low linkage disequilibrium and the lack of coincidence between clines at six microsatellites, a mitochondrial DNA region, and two phenotypic traits indicated introgression. However, the hypothesis of neutral diffusion was rejected based on evidence that all of the clines were concordant and narrower than expected for neutral clines, indicating some indirect selection. The analysis of phenotypic variance gave evidence of restricted phenotypic introgression and together with the bimodal distribution of phenotypes suggested that disruptive selection is acting across the hybrid zone, especially on the coloration of bare parts. Multimodal analysis of phenotypic clines also highlighted a shift between the peak of intermediates and the cline center, left behind by hybrid zone motion. High-resolution analysis of phenotypes distribution thus proved useful for detecting hybrid zone movement even without temporal data.

The genetic architecture of speciation, i.e., how intrinsic genomic incompatibilities promote reproductive isolation (RI) between diverging lineages, is one of the best-kept secrets of evolution. To directly assess whether incompatibilities arise in a limited set of large-effect speciation genes, or in a multitude of loci, we examined the geographic and genomic landscapes of introgression across the hybrid zones of 41 pairs of frog and toad lineages in the Western Palearctic region. As the divergence between lineages increases, phylogeographic transitions progressively become narrower, and larger parts of the genome resist introgression. This suggests that anuran speciation proceeds through a gradual accumulation of multiple barrier loci scattered across the genome, which ultimately deplete hybrid fitness by intrinsic postzygotic isolation, with behavioral isolation being achieved only at later stages. Moreover, these loci were disproportionately sex linked in one group (Hyla) but not in others (Rana and Bufotes), implying that large X-effects are not necessarily a rule of speciation with undifferentiated sex chromosomes. The highly polygenic nature of RI and the lack of hemizygous X/Z chromosomes could explain why the speciation clock ticks slower in amphibians compared to other vertebrates. The clock-like dynamics of speciation combined with the analytical focus on hybrid zones offer perspectives for more standardized practices of species delimitation. Significance Reproductive isolation is instrumental to the formation of new species (speciation), but it remains largely enigmatic how many incompatibilities are required to prevent hybridization and where they lie across the genome. By studying patterns of admixture in amphibian hybrid zones, we found that reproductive isolation is initiated by numerous small-effect incompatibilities scattered across the genome rather than concentrated in a few important genes. Unlike mammals and birds, in which Y/W degeneracy is a major cause of hybrid dysfunctions, the undifferentiated sex chromosomes of amphibians do not always host more genetic incompatibilities than other chromosomes. These combined results might explain why amphibian speciation is relatively slow, and its clock-like dynamics offer practical perspectives to categorize evolutionary lineages into species or subspecies.

Background: The evolutionary history of the biota of North Africa and Arabia is inextricably tied to the complex geological and climatic evolution that gave rise to the prevalent deserts of these areas. Reptiles constitute an exemplary group in the study of the arid environments with numerous well-adapted members, while recent studies using reptiles as models have unveiled interesting biogeographical and diversification patterns. In this study, we include 207 specimens belonging to all 12 recognized species of the genusStenodactylus. Molecular phylogenies inferred using two mitochondrial (12S rRNA and 16S rRNA) and two nuclear (c-mosandRAG-2) markers are employed to obtain a robust time-calibrated phylogeny, as the base to investigate the inter- and intraspecific relationships and to elucidate the biogeographical history ofStenodactylus, a genus with a large distribution range including the arid and hyper-arid areas of North Africa and Arabia.Results: The phylogenetic analyses of molecular data reveal the existence of three major clades within the genusStenodactylus, which is supported by previous studies based on morphology. Estimated divergence times between clades and sub-clades are shown to correlate with major geological events of the region, the most important of which is the opening of the Red Sea, while climatic instability in the Miocene is hypothesized to have triggered diversification. High genetic variability is observed in some species, suggesting the existence of some undescribed species. TheS. petrii-S. stenurusspecies complex is in need of a thorough taxonomic revision. New data is presented on the distribution of the sister speciesS. sthenodactylusandS. mauritanicus.Conclusions: The phylogenetic hypothesis for the genusStenodactyluspresented in this work permits the reconstruction of the biogeographical history of these common desert dwellers and confirms the importance of the opening of the Red Sea and the climatic oscillations of the Miocene as major factors in the diversification of the biota of North Africa and Arabia. Moreover, this study traces the evolution of this widely distributed and highly specialized group, investigates the patterns of its high intraspecific diversity and elucidates its systematics.