Data for Morales et al. Perpendicular axes of incipient speciation in a widespread passerine with mitonuclear discordance

Contents:<br>SampleInfo:Table 1. Samples screened for nuclear DNA (nDNA) and mitochondrial ND2 variation (N=69). Sample = sample identifier; mtDNA = mitolineage (mito:A or mito:B); Population = population grouping used for Hardy Weinberg Equilibrium and DAPC analyses (See Fig. 2B); ND2 accession = mitochondrial ND2 sequence NCBI accession number. IMa samples used for the three:population IMa2 model assigned to one of each three genetic clusters: N= northern, SC= southern:coastal or SI= southern:inland. The last seven columns contain STRUCTURE posterior probability assignment score (Q) for K =2 and K = 3, and the cluster to which each sample was assigned based on its posterior probability being ≥ 0.8 (K2: N= northern, S= southern and Adx = admixed; K3: N= northern, SC= southern:coastal, SI= southern:inland and Adx = admixed).Table 2. Table S2 Samples screened for mitochondrial genome (mitogenome) variation (N=32). Sample = sample identifier; mtDNA = mitolineage; Mitogenome accession = NCBI accession number<br>Hybrid_capture_probes.fasta: capture probe design in fasta format<br>Alignments:RawData: raw files of alignments produced after phasingIMa_alignments: alignments cleaned from ambiguities and trimmed to a single linked non:recombinant unit with IMgc. 400 of this alignments were selected at random for the IMa analysis <br>BLAST_OUTPUT.txt<br>SNP data:SNP_STRUCTURE_MAF0.05_MissingData_10.str: SNPs in STRUCTURE format before outlier filtering NEUTRAL_SNPs_MAF0.05_MissingData_10.str: SNP file after outlier filtering used for the DAPCA analysisRANDOM_NEUTRAL_SNP_MAF0.05_MissingData_10.str: SNP file after outlier filtering containing only one SNP per capture probe used for the STRUCTURE analysis<br>B