7. Ecological genomics of the Northern krill: Genome-scale comparisons of adaptive divergence

Many analyses were performed in "chunks" (160 in total across both gene-rich and gene-poor sequences), which are described in a previous item. Population definitions Population definitions are the same as desribed in a different item: - "at vs. me" = Atlantic Ocean samples (n=67) vs. the Mediterranean (i.e. Barcelona) samples (n=7). - "we vs. ea" = South-West North Atlantic Ocean (n=20) vs. North-East North Atlantic Ocean (n=47).

In files using this contrast, sometimes the label "wa" is used instead of "we" for the South-West North Atlantic Ocean samples. Contents: - allele_freqs_fst.gene_rich_sequences.at_vs_me.tar, contains per-SNP estimates of allele frequencies and FST between "at" and "me" groups along gene-rich sequences. - allele_freqs_fst.gene_rich_sequences.we_vs_ea.tar, as above but between "we" and "ea" groups. - allele_freqs_fst.gene_poor_sequences.at_vs_me.tar, contains per-SNP estimates of allele frequencies and FST between "at" and "me" groups along gene-poor sequences. - allele_freqs_fst.gene_poor_sequences.we_vs_ea.tar, as above but for "we" and "ea" groups. - allele_freqs_fst.merged_sequences.at_vs_me.csv.gz, contains per-SNP estimates of allele frequencies and FST between "at" and "me" merged into a single TSV file. - allele_freqs_fst.merged_sequences.we_vs_ea.csv.gz, as above but for "we" and "ea". - allele_freqs_fst.gene_rich_sequences_windows.at_vs_me.tar.gz, contains per-window estimates of FST between "at" and "me" groups along gene-rich sequences. - allele_freqs_fst.gene_rich_sequences_windows.we_vs_ea.tar.gz, as above but for "we" and "ea" groups. - allele_freqs_fst.gene_poor_sequences_windows.at_vs_me.tar.gz, contains per-window estimates of FST between "at" and "me" groups along gene-poor sequences. - allele_freqs_fst.gene_poor_sequences_windows.we_vs_ea.tar.gz, as above but for "we" and "ea" groups. - selscan_xpnsl.gene_rich_sequences.tar.gz, contains per-SNP cross-population XP-nSL statistics for gene-rich sequences. - selscan_xpnsl.gene_poor_sequences.tar.gz, contains per-SNP cross-population XP-nSL statistics for gene-poor sequences. - selscan_xpnsl.gene_rich_sequences_windows.tar.gz, contains per-window cross-population XP-nSL statistics for gene-rich sequences. - selscan_xpnsl.gene_poor_sequences_windows.tar.gz, as above but for gene-poor sequences. - fst_vs_xpnsl.per_snp.at_vs_me.csv.gz, contains per-SNP FST, genomic region and XP-nSL values in a single file for the "at vs. me" contrast. - fst_vs_xpnsl.per_snp.we_vs_ea.csv.gz, contains per-SNP FST, genomic region and XP-nSL values in a single file for the "we vs. ea" contrast. - fst_vs_xpnsl_vs_diversity_vs_regions.merged_sequences.at_vs_me.tsv.tar.gz, integrates window-based statistics into a single file for the "at vs. me" contrast. - fst_vs_xpnsl_vs_diversity_vs_regions.merged_sequences.we_vs_ea.tsv.tar.gz, as above but for the "we vs. ea" contrast. allele_freqs_fst.gene_(rich|poor)_sequences.(at_vs_me|we_vs_ea).tar The TSV files in these archives contain per-SNP estimates of allele frequencies and FST, along with SNP annotations.