Supporting data: The fasta file and partition file generated by aligning the mined RAD loci from the Falco biarmicus whole genome to the variable RAD loci in our RADseq analysis of Falco cherrug.

To explicitly root our phylogenetic tree, we mined our RAD loci’s homologous genomic bits from the publicly available reference genome of Falco peregrinus (assembly: GCA_001887755) and Falco biarmicus (assembly: GCA_023638135). These are explicit outgroup samples for the phylogenetic analyses of relationships between populations of Falco cherrug and Falco rusticolus. F. peregrinus is a distant outgroup, whereas F. biarmicus is a close outgroup from the Hierofalcon group. The RAD loci sequences with observed heterozygosity of < 0.05 and zero missingness (i.e. present in all individuals) were recovered with Stacks, and then checked for polymorphic sites. Loci containing at least one polymorphic site (n = 422) were subject to consensus sequence generation using the EMBOSS tool consambig. Loci sequences were matched against the reference genome of Falco biarmicus using blastn v. 2.5.0 with an expected e-value of 1e-25. The genomic region with the highest score was retained and aligned with RAD loci sequences using MUSCLE v. 3.8. Alignments of loci were concatenated with AMAS.py. The resulting fasta and partition files were used in this dataset's downstream analyses, where we used F. peregrinus as the outgroup sample.