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数据集内容： 样本信息：表1 用于筛查细胞核DNA（nuclear DNA, nDNA）与线粒体ND2基因变异的样本集（N=69）。各字段说明如下：Sample为样本标识符；mtDNA为线粒体谱系（记为mito:A或mito:B）；Population为用于哈迪-温伯格平衡与判别主成分分析（Discriminant Analysis of Principal Components, DAPC）的种群分组（详见图2B）；ND2 accession为线粒体ND2基因序列的美国国家生物技术信息中心（NCBI）登录号。用于三群体IMa2模型分析的样本被分配至三个遗传簇之一：N代表北部种群，SC代表南部沿海种群，SI代表南部内陆种群。最后七列为K=2与K=3时的STRUCTURE群体结构分析后验概率赋值得分（Q），以及基于后验概率≥0.8的样本聚类结果：K=2时，N为北部种群、S为南部种群、Adx为混合种群；K=3时，N为北部种群、SC为南部沿海种群、SI为南部内陆种群、Adx为混合种群。 表S2 用于筛查线粒体基因组（mitogenome）变异的样本集（N=32）。各字段说明如下：Sample为样本标识符；mtDNA为线粒体谱系；Mitogenome accession为线粒体基因组序列的NCBI登录号。 Hybrid_capture_probes.fasta：FASTA格式的捕获探针设计序列文件 Alignments：比对文件目录 RawData：相位化处理后生成的原始比对文件集 IMa_alignments：经IMgc软件清理歧义序列并修剪为单个连锁非重组单元的比对文件，从中随机选取400份用于IMa分析 BLAST_OUTPUT.txt：BLAST输出文件 SNP数据： SNP_STRUCTURE_MAF0.05_MissingData_10.str：异常位点过滤前的STRUCTURE格式SNP文件 NEUTRAL_SNPs_MAF0.05_MissingData_10.str：经异常位点过滤后用于判别主成分分析（DAPC）的SNP文件 RANDOM_NEUTRAL_SNP_MAF0.05_MissingData_10.str：经异常位点过滤后，每个捕获探针仅保留一个SNP的SNP文件，用于STRUCTURE分析