# README for Convergent genomic signatures of local adaptation across a continental-scale environmental gradient Lucas R. Moreira & Brian T. Smith 2023-03-07 This readme file describes the data files accompanying the above publication. For any further queries please contact Lucas Moreira at lr2767@columbia.edu Original RAW reads for each individual sample are available at SRA with Accession PRJNA917637. This repository includes the following data files: D.pubescens_T.guttata-pseudochromosomes.cds.gff - Gene annotation of Downy Woodpecker mapped to the pseudochromosome reference genome. ## Genotype-association analysis (ANGSD-asso) * Headers: "Chromosome": chromosome "win_start": window starting bp "win_end": window ending bp "win_mid": window midpoint "LRT_n": number of SNPs in window "LRT_median": median likelihood ratio test statistic (LRT) D.pubescens_candidates_windows_PC1T.csv - GEA significant windows for PC1 of temperature in D. pubescens D.pubescens_candidates_windows_PC2T.csv - GEA significant windows for PC2 of temperature in D. pubescens D.pubescens_candidates_windows_PC3T.csv - GEA significant windows for PC3 of temperature in D. pubescens D.pubescens_candidates_windows_PC1T.csv - GEA significant windows for PC1 of precipitation in D. pubescens D.pubescens_candidates_windows_PC2P.csv - GEA significant windows for PC2 of precipitation in D. pubescens D.pubescens_candidates_windows_PC3P.csv - GEA significant windows for PC3 of precipitation in D. pubescens D.pubescens_PC1T.rol_win - Per-window median LRT scores for the association with PC1 of temperature in D. pubescens D.pubescens_PC2T.rol_win - Per-window median LRT scores for the association with PC2 of temperature in D. pubescens D.pubescens_PC3T.rol_win - Per-window median LRT scores for the association with PC3 of temperature in D. pubescens D.pubescens_PC1T.rol_win - Per-window median LRT scores for the association with PC1 of precipitation in D. pubescens D.pubescens_PC2P.rol_win - Per-window median LRT scores for the association with PC2 of precipitation in D. pubescens D.pubescens_PC3P.rol_win - Per-window median LRT scores for the association with PC3 of precipitation in D. pubescens D.pubescens_PC1T.permutation.rol_win - Per-window median LRT scores for 200 random permutations of the association with PC1 of temperature in D. pubescens D.pubescens_PC2T.permutation.rol_win - Per-window median LRT scores for 200 random permutations of the association with PC2 of temperature in D. pubescens D.pubescens_PC3T.permutation.rol_win - Per-window median LRT scores for 200 random permutations of the association with PC3 of temperature in D. pubescens D.pubescens_PC1T.permutation.rol_win - Per-window median LRT scores for 200 random permutations of the association with PC1 of precipitation in D. pubescens D.pubescens_PC2P.permutation.rol_win - Per-window median LRT scores for 200 random permutations of the association with PC2 of precipitation in D. pubescens D.pubescens_PC3P.permutation.rol_win - Per-window median LRT scores for 200 random permutations of the association with PC3 of precipitation in D. pubescens D.villosus_candidates_windows_PC1T.csv - GEA significant windows for PC1 of temperature in D. villosus D.villosus_candidates_windows_PC2T.csv - GEA significant windows for PC2 of temperature in D. villosus D.villosus_candidates_windows_PC3T.csv - GEA significant windows for PC3 of temperature in D. villosus D.villosus_candidates_windows_PC1T.csv - GEA significant windows for PC1 of precipitation in D. villosus D.villosus_candidates_windows_PC2P.csv - GEA significant windows for PC2 of precipitation in D. villosus D.villosus_candidates_windows_PC3P.csv - GEA significant windows for PC3 of precipitation in D. villosus D.villosus_PC1T.rol_win - Per-window median LRT scores for the association with PC1 of temperature in D. villosus D.villosus_PC2T.rol_win - Per-window median LRT scores for the association with PC2 of temperature in D. villosus D.villosus_PC3T.rol_win - Per-window median LRT scores for the association with PC3 of temperature in D. villosus D.villosus_PC1T.rol_win - Per-window median LRT scores for the association with PC1 of precipitation in D. villosus D.villosus_PC2P.rol_win - Per-window median LRT scores for the association with PC2 of precipitation in D. villosus D.villosus_PC3P.rol_win - Per-window median LRT scores for the association with PC3 of precipitation in D. villosus D.villosus_PC1T.permutation.rol_win - Per-window median LRT scores for 200 random permutations of the association with PC1 of temperature in D. villosus D.villosus_PC2T.permutation.rol_win - Per-window median LRT scores for 200 random permutations of the association with PC2 of temperature in D. villosus D.villosus_PC3T.permutation.rol_win - Per-window median LRT scores for 200 random permutations of the association with PC3 of temperature in D. villosus D.villosus_PC1T.permutation.rol_win - Per-window median LRT scores for 200 random permutations of the association with PC1 of precipitation in D. villosus D.villosus_PC2P.permutation.rol_win - Per-window median LRT scores for 200 random permutations of the association with PC2 of precipitation in D. villosus D.villosus_PC3P.permutation.rol_win - Per-window median LRT scores for 200 random permutations of the association with PC3 of precipitation in D. villosus ## FST-outlier analysis (ANGSD) #D.pubescens_FST_comparisons.zip: PP--.50kb-10kbstep.pdf - Manhattan plot of Fst values estimated for 50kb windows (10 kb increments) comparing and in D. pubescens PP--.FST_histogram.pdf - Histogram of Fst values estimated for 50kb windows (10 kb increments) comparing and in D. pubescens PP--.fst_slidingwindow - Fst values estimated for 50kb windows (10 kb increments) comparing and in D. pubescens PP--.outliers_5sd.csv - Outlier Fst windows (>5 standard deviations) for the comparison between and in D. pubescens * Headers: "region": windows intervals "chr": chromosome "midPos": window midpoint "Nsites": total number of sites "fst": Fst value PP---candidates.csv - Candidate genes within outlier Fst windows (>5 standard deviations) for the comparison between and in D. pubescens * Headers: "ID": gene ID "chromosome": chromosome "first": first bp "last": last bp "ENSEMBL": ENSEMBL gene ID "gene_name": gene symbol #D.villosus_FST_comparisons.zip: PV--.50kb-10kbstep.pdf - Manhattan plot of Fst values estimated for 50kb windows (10 kb increments) comparing and in D. villosus PV--.FST_histogram.pdf - Histogram of Fst values estimated for 50kb windows (10 kb increments) comparing and in D. villosus PV--.fst_slidingwindow - Fst values estimated for 50kb windows (10 kb increments) comparing and in D. villosus PV--.outliers_5sd.csv - Outlier Fst windows (>5 standard deviations) for the comparison between and in D. villosus * Headers: "region": windows intervals "chr": chromosome "midPos": window midpoint "Nsites": total number of sites "fst": Fst value PV---candidates.csv - Candidate genes within outlier Fst windows (>5 standard deviations) for the comparison between and in D. villosus * Headers: "ID": gene ID "chromosome": chromosome "first": first bp "last": last bp "ENSEMBL": ENSEMBL gene ID "gene_name": gene symbol ## H-scan analysis * Headers: "chr": chromosome "win_start": window starting bp "win_end": window ending bp "win_mid": window midpoint "H_n": number of SNPs in window "H_median": median H score D.pubescens_AK_all_chr_Hscan.rol_win - Median H scores for 50 SNP windows (10 SNP increments) in the Alaska population of D. pubescens D.pubescens_E_all_chr_Hscan.rol_win - Median H scores for 50 SNP windows (10 SNP increments) in the East population of D. pubescens D.pubescens_R_all_chr_Hscan.rol_win - Median H scores for 50 SNP windows (10 SNP increments) in the Rockies population of D. pubescens D.pubescens_NW_all_chr_Hscan.rol_win - Median H scores for 50 SNP windows (10 SNP increments) in the Northwest population of D. pubescens D.villosus_AK_all_chr_Hscan.rol_win - Median H scores for 50 SNP windows (10 SNP increments) in the Alaska population of D. villosus D.villosus_E_all_chr_Hscan.rol_win - Median H scores for 50 SNP windows (10 SNP increments) in the East population of D. villosus D.villosus_R_all_chr_Hscan.rol_win - Median H scores for 50 SNP windows (10 SNP increments) in the Rockies population of D. villosus D.villosus_NW_all_chr_Hscan.rol_win - Median H scores for 50 SNP windows (10 SNP increments) in the Northwest population of D. villosus ## PCAdapt analysis * Headers: "chr": chromosome "win_start": window starting bp "win_end": window ending bp "win_mid": window midpoint "p.value_n": number of SNPs in window "p.value_median": median-value D.pubescens_PCAdapt.candidates.tsv - Candidate SNP windows for the PCAdapt analysis in D. pubescens D.pubescens_PCAdapt.rol_win - Median p-values of each 50 SNP windows (10 SNP increments) for the PCAdapt analysis in D. pubescens D.villosus_PCAdapt.candidates.tsv - Candidate SNP windows for the PCAdapt analysis in D. villosus D.villosus_PCAdapt.rol_win - Median p-values of each 50 SNP windows (10 SNP increments) for the PCAdapt analysis in D. villosus