Hybridization increases genetic variation, hence hybrid species may have greater evolutionary potential once their admixed genomes have stabilized and incompatibilities have been purged. Yet, little is known about how such hybrid lineages evolve at the genomic level following their formation, in particular their adaptive potential. Here we investigate how the Italian sparrow (Passer italiae), a homoploid hybrid species, has evolved and locally adapted to its variable environment. Using restriction site-associated DNA sequencing (RAD-seq) on several populations across the Italian peninsula, we evaluate how genomic constraints and novel genetic variation have influenced population divergence and adaptation. We show that population divergence within this hybrid species has evolved in response to climatic variation, suggesting ongoing local adaptation. As found previously in other non-hybrid species, climatic differences appear to increase population differentiation. We also report strong population divergence in a gene known to affect beak morphology. Most of the strongly divergent loci among Italian sparrow populations do not seem to be differentiated between its parent species, the house and Spanish sparrows. Unlike in the hybrid, population divergence within each of the parental taxa has occurred mostly at loci with high allele frequency difference between the parental species, suggesting that novel combinations of parental alleles in the hybrid have not necessarily enhanced its evolutionary potential. Rather, our study suggests that constraints linked to incompatibilities may have restricted the evolution of this admixed genome, both during and after hybrid species formation.

Genomic DNA was purified from blood samples. Double digestion of the genomic DNA for ddRAD sequencing was performed using EcoR I and MseI restriction enzymes. Molecular identifier tags were added with PCR amplification. Library pools were size selected for fragments between 500-600bp. The size selected library pools were then sequenced using an Illumina Nextseq500 machine and the 1x75bp sequencing format. A series of genomic tools were used to filter raw reads and call variants, vcftools, plink, bcftools, GATK, among others.

Here we provide the VCF files and final data files generated from statistical analysis. As well as the scripts used to analyse the data. Scripts for processing the raw reads to obtain final VCF are included as well as the scripts used for the statistical analysis and final figures found in the study. All files used in the R scripts are also provided.

The README.txt file explain the different categories of files and those used by the scripts.