Local adaptation in the Patagonian foundation tree species Nothofagus pumilio

<p><strong>Npumilio_specific_candidate_genes.xlsx&nbsp;</strong></p><ul><li>Study-specific candidate genes. For annotation information on the 1,789 candidate genes from orthogroups, see Milesi at al 2023 (https://doi.org/10.1101/2023.01.05.522822 and Supplemental Tables S12-S14).</li><li>Contains contig, Uniprot-TAIR code and original species, and reason for inclusion in the candidate list (e.g. upregulated or downregulated in the heat stress-transcriptome study (https://doi.org/10.1371/journal.pone.0246615), or of interest for wood growth)</li><li>The list includes some duplicate contigs that are contained in the candidate gene set; they were left in for the "Reason" information</li></ul><p><strong>N_pumilio_06Nov2019_probe_coverage.txt</strong></p><ul><li>Probe design file as provided by IGA Technology Services</li></ul><p>All called SNP variants. Data for 502 individual tree samples are included: 496 adult trees + 6 replicates.</p><ul><li><strong>variants-gatk_haplotypecaller_SNP_raw.vcf.gz</strong> are raw called variants.</li><li><strong>variants-gatk_haplotypecaller_SNP.vcf.gz</strong> are coarsely quality-filtered and are the starting datasets for our downstream analyses.</li></ul><p><strong>Npumilio_IDs_vcforder_all_info.xlsx</strong></p><ul><li>Metadata for all samples in the .vcf files (in the same order), including site name, geographic coordinates and elevation</li></ul><p><strong>Npumilio_orthogroups.csv</strong></p><ul><li>Orthogroups, TAIR codes, and best-hit Nothofagus contigs for cross-referencing with orthogroup candidate gene set (Milesi at al 2023 (https://doi.org/10.1101/2023.01.05.522822 and Supplemental Tables S12-S14)).</li></ul><p>&nbsp;</p>