DOI: 10.17044/scilifelab.22817410
title: 7. Ecological genomics of the Northern krill: Genome-scale comparisons of adaptive divergence

description: This item holds multiple tar archives with genome-scale comparisons of divergence between Northern krill populations, including estimated allele-frequencies and divergence (e.g. <em>F</em><sub>ST</sub>) , and extended haplotype signatures (XP-nSL estimates). Many analyses were performed in "chunks" (160 in total across both gene-rich and gene-poor sequences), which are described in a previous item.
<strong>Population definitions</strong>
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.

<strong>Contents:</strong>

 allele_freqs_fst.gene_rich_sequences.at_vs_me.tar, contains per-SNP estimates of allele frequencies and <em>F</em><sub>ST</sub> 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 <em>F</em><sub>ST</sub> 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 <em>F</em><sub>ST</sub> 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 <em>F</em><sub>ST</sub> 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 <em>F</em><sub>ST</sub> 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 <em>F</em><sub>ST</sub>, 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 <em>F</em><sub>ST</sub>, 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.

<strong>allele_freqs_fst.gene_(rich|poor)_sequences.(at_vs_me|we_vs_ea).tar</strong>
The TSV files in these archives contain per-SNP estimates of allele frequencies and <em>F</em><sub>ST</sub>, along with SNP annotations. There are nine main fields/columns with overlapping/redundant information to accommodate flexible parsing. Large fields have nested subfields that are separated by "|" (first level) or ":" (second level).

 name of sequence (e.g. "seq_s_1")
 position of SNP (e.g. "448878")
 reference allele (e.g. "A")
 alternate allele (e.g. "G")
 major column with <em>F</em><sub>ST</sub> value and allele frequency and other data for each population. It is described below.
 type of SNP (e.g. intron, synonymous, missense, intergenic, ...) and label of associated gene (e.g. missense|REF_STRG_1_4_XLOC_012878)
 <em>F</em><sub>ST</sub> tag and value (e.g. fst|0.0653)
 region, type of SNP and gene label (e.g. region|missense|REF_STRG_1_4_XLOC_012878)
 gene annotation derived from EnTAP annotations and <em>Drosophila</em> homologs, which are described below. Uses comma-separated sub-fields.

<em><strong>Subfields in field 5:</strong></em>
Example:
at/me:0.0653:148:1.0000:1.0000:1.0000|at,134,133.0000,1.0000,0.9925,0.0075|me,14,13.0000,1.0000,0.9286,0.0714
This field splits into three major subfields on "|": one about the pairwise comparison and two with metadata about each population.
<em>1st subfield</em> (at/me:0.0653:148:1.0000:1.0000:1.0000)

 name of contrast (at/me)
 <em>F</em><sub>ST</sub> of SNP (0.0653)
 Sample size (148)
 Proportion of observed data given overall sample size (1.0000), &lt;1 if there are missing genotypes.
 Proportion of observed data given sample size of population 1 (1.0000)
 As above but for population 2 (1.0000)

<em>2nd and 3rd subfields</em> (at,134,133.0000,1.0000,0.9925,0.0075 and me,14,13.0000,1.0000,0.9286,0.0714)

 name of population
 sample size
 number of observed reference alleles
 number of observed alternate alleles
 frequency of reference allele
 frequency of alternate allele

<em><strong>Subfields in field 9</strong></em>:
Example: annotation|entap,XP_037775362.1 uncharacterized protein LOC119572362 [Penaeus monodon]|blast,FBgn0002526,FBtr0077014,CG10236,LanA,Laminin

 annotation tag
 entap annotation (comma separated sub-fields)
 blast annotation (comma separated sub-fields)

These datasets are provided for each chunk and in a single merged TSV file for each contrast.
<strong>allele_freqs_fst.gene_(rich|poor)_sequences_windows.(at_vs_me|we_vs_ea).tar.gz</strong>
The TSV files in these archives contain <em>F</em><sub>ST</sub> estimates across 100 bp or 1,000 bp non-overlapping windows. Each TSV file has four fields:

 CHROM = name of sequence
 POS = window start position
 N_(contrast) = number of SNPs in the window
 FST_(contrast) = average Reynold's <em>F</em><sub>ST</sub> of the window.

<strong>selscan_xpnsl.gene_rich_sequences.tar.gz</strong> and <strong>selscan_xpnsl.gene_poor_sequences.tar.gz</strong>
The TSV files in these archives contain raw and normalized per-SNP cross-population XP-nSL output from selscan, which was used to test for selective sweeps. The format and meaning of the fields are documented with the original tool selscan: https://github.com/szpiech/selscan
<strong>selscan_xpnsl.gene_rich_sequences_windows.tar.gz</strong> and <strong>selscan_xpnsl.gene_poor_sequences_windows.tar.gz</strong>
The TSV files in these archives contain per-window average XP-nSL computed from the normalized SNP-estimates at 1,000 or 10,000 bp resolution. The TSV files have the following headers:

 CHROM = name of sequence
 START = start of window
 STOP = stop of window
 N = number of SNPs with XP-nSL estimates
 N_CRIT = number of SNPs with critical XP-nSL estimates (&gt;=2 or &lt;=-2)
 PROP_CRIT = proportion of critical SNPs
 MIN = minimal XP-nSL value in window
 MAX = maximal XP-nSL value in window
 MEAN = mean XP-nSL value in window

<strong>fst_vs_xpnsl.per_snp.at_vs_me.csv.gz</strong> and <strong>fst_vs_xpnsl.per_snp.we_vs_ea.csv.gz</strong>
Per-SNP <em>F</em><sub>ST</sub> and XP-nSL data that have been merged into a single TSV file. Fields:

 name of sequence
 position of SNP
 FST of SNP
 gene region
 XP-nSL

<strong>fst_vs_xpnsl_vs_diversity_vs_regions.merged_sequences.(at_vs_me|we_vs_ea).tsv.tar.gz</strong>
Merged TSV files that integrates window-based <em>F</em><sub>ST</sub>, XP-nSL variation genomic region data at 1,000 bp resolution. Fields in the TSV files are:

 CHROM = name of sequence
 START = start of window
 N_at_vs_me = number of SNPs
 FST_at_vs_me = average <em>F</em><sub>ST</sub> .
 MEAN = mean XP-nSL.
 LENGTH = length of window
 COVERED = accessible bases
 COVERED_PROP = proportion of accessible bases
 all_THETA = Watterson's theta all data
 all_PI = Pi all data
 all_TD = Tajima's D all data
 pop1_VARIABLE = polymorphic sites population 1
 pop1_THETA = Watterson's theta population 1
 pop1_PI = as above
 pop1_TD = as above
 pop2_VARIABLE = polymorphic sites population 2
 pop2_THETA = Watterson's theta population 2
 pop2_PI = as above
 pop2_TD = as above
 intergenic_COVERED = accessible sites of this region
 intergenic_all_THETA = theta for this region across all data
 five_prime_utr_COVERED
 five_prime_utr_all_THETA
 cds_COVERED cds_all_THETA
 intron_COVERED
 intron_all_THETA
 three_prime_utr_COVERED
 three_prime_utr_all_THETA