Recently diverged taxa showing marked phenotypic and ecological diversity are optimal systems to understand the genetic processes underlying speciation. We used genome-wide markers to investigate the diversification of the Reunion grey white eye (Zosterops borbonicus) on the small volcanic island of Reunion (Mascarene archipelago), where this species complex exhibits four geographic forms that are parapatrically distributed across the island and differ strikingly in plumage colour. One form restricted to the highlands is separated by a steep ecological gradient from three distinct lowland forms which meet at narrow hybrid zones that are not associated with environmental variables. Analyses of genomic variation based on SNP data from genotyping-by-sequencing and pooled RADseq approaches, reveal that signatures of selection associated with elevation can be found at multiple regions across the genome, whereas most loci associated with the lowland forms are located on the Z sex chromosome. We identified TYRP1, a Z-linked colour gene, as a likely candidate locus underlying colour variation among lowland forms. Tests of demographic models revealed that highland and lowland forms diverged in the presence of gene flow, and divergence has progressed as gene flow was restricted by selection at loci across the genome. This system is promising to investigate how natural selection and reproductive isolation shape the genomic landscape of divergence at multiple stages of the speciation process.

The VCF files correspond to SNPs called with freebayes, then filtered with VCFTools, with Zosterops lateralis used as a reference. There is one VCF file for autosomes (including the scaffolds mapping to Zebra Finch's 4A that are actually fused to ZW chromosomes), and another one for Z-linked markers.

There are also files with allele counts for each of the 13 pools included in the RAD-seq experiment. The file data.auto contains allele counts for autosomal markers, while data.Z contains data for Z-linked markers. At last, the file Orientation_Z_lateralis_scaffolds_Zebra_finch.txt contains information about the LASTZ alignment of Z. lateralis scaffolds on the Zebra Finch genome. Median position of alignments on the Zebra Finch genome and orientation are provided to order Z. lateralis scaffolds along Zebra Finch chromosomes.

For the files listing allele counts, for each pool, the number of reference allele is under a column named reference_count_PoolName and the total number of reads covering the sequenced site is under a column named pool_depth_PoolName