Four species - L. melanops, L. shehuen, L. xanthoviridis, L. fitzingerii - and their hybrids Raw sequence reads

Hybridization is an evolutionary process that can generate diverse outcomes, such as reinforcing species boundaries, generating new species, or facilitating the introgression of locally-adapted alleles into new genomic backgrounds. Liolaemus is a highly diverse clade of South American lizards with ~260 species and five to ten new species described each year. Hybridization has been posed as a potential mechanism generating the exceptional diversity within this genus, yet no study has systematically studied hybrid zones between Liolaemus species. Here, we compared three hybrid zones between four species in the Liolaemus fitzingerii group of lizards in Central Argentina where two species, L. melanops and L. xanthoviridis, each hybridize with two other species (name the two other species). We sampled three transects that were each approximately 120km in length and sequenced both mitochondrial and genome-wide SNP data for 267 individuals. In our analyses of nuclear DNA, we also compared bi-allelic SNPs to phased alleles (50bp RAD loci). Population structure analyses confirmed that boundaries separating species are sharp, and all clines are $<$65km wide. Cline center estimates were consistent between SNPs and phased alleles, but cline width estimates were significantly different with the SNPs producing wider estimates. The mitochondrial clines are narrower and shifted 4-20km southward in comparison to the nuclear clines in all three hybrid zones, indicating that either each of the species has sex-biased dispersal (males northward or females southward), the population densities are unequal, or that the hybrid zones are moving north over time. These comparisons indicate that some patterns of hybridization are similar across hybrid zones (mtDNA clines all narrower and shifted to the south), whereas cline width is variable. Although hybridization is common in the L. fitzingerii group, it is geographically localized and hybrid zones tend to act as species boundaries, rather than promoters of speciation. This study provides insights into both biotic and abiotic mechanisms helping to maintain species boundaries within the speciose Liolaemus system.