Genomic Signatures of Selection Are Enriched in Differentially Expressed Genes in Sticklebacks Adapting to Contrasting Environments.

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Paper

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The authors' code

Perl · 36 lines · 869 B · no license

#!/usr/bin/perl
my $usage= "
Prints out list of commands for launcher_creator.py
to bowtie2-map the trimmed 36b 2bRAD reads
Arguments:
1: glob to fastq files
2: reference to map to (basename of bowtie2 index file)
3: optional, the position of name-deriving string in the file name
if separated by underscores,
such as: input file Sample_RNA_2DVH_L002_R1.cat.fastq
specifying arg2 as \'3\' would create output file with a name \'2DVH.fastq'
";
if (!$ARGV[0]) { die $usage;}
my $glob=$ARGV[0];
if (!$ARGV[1]) { die $usage;}
my $ref=$ARGV[1];
opendir THIS, ".";
my @fqs=grep /$glob/,readdir THIS;
my $outname="";
foreach $fqf (@fqs) {
if ($ARGV[2]) {
my @parts=split('_',$fqf);
$outname=$parts[$ARGV[1]-1].".bt2.sam";
}
else { $outname=$fqf.".bt2.sam";}
print "bowtie2 --no-unal --score-min L,16,1 --local -L 16 -x $ref -U $fqf -S $outname\n";
}

2bRAD_bowtie2_launch.pl at commit 0c8a25f, no license · at the source

Overview

Authors: Alexander Kwakye^1,2, Natalie Dzikowski^3,4, Matthew A Wund⁵, Krishna R Veeramah¹

ORCID iDs: Alexander Kwakye, Natalie Dzikowski, Matthew A Wund, Krishna R Veeramah

Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
The Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
Department of Biology, The College of New Jersey, Ewing, NJ 08628, USA

Institutions: Stony Brook University (United States); Duke University (United States); The College of New Jersey (United States)

Journal: Genome biology and evolution, volume 18, issue 9, article evag222

Dates: accepted 23 August 2026; published online 30 August 2026; in print September 2026

Type: Research article · Language: English

License: CC BY

Identifiers: DOI 10.1093/gbe/evag222 · PMID 42668140 · PMCID PMC13583502 · OpenAlex W7131091932

Open access: gold, a free copy (OpenAlex)

Preprint: doi:10.64898/2026.02.22.707242

Status: code verified

Categories: genetics / omics (modality), other (organism), cellular / molecular (subfield)

Methods: Smoothing, state filtering, decompositions, Statistics

Keywords: Threespine stickleback (Gasterosteus aculeatus), Genotype–phenotype mapping, Differential gene expression, Freshwater adaptation, Cis-regulation

MeSH: Adaptation, Physiological*, Selection, Genetic*, Smegmamorpha*, Animals, Fresh Water, Gills, Polymorphism, Single Nucleotide, Transcriptome (* major topic)

Topic: Genetic diversity and population structure (Genetics, Biochemistry, Genetics and Molecular Biology), according to OpenAlex

Funding: NIGMS NIH HHS (R01GM124330, R01 GM124330)

Citations: not cited yet (Europe PMC); 130 references in the paper

Abstract

Whole genome scans have identified numerous adaptive alleles in many species; however, linking these alleles to specific phenotypes remains a major challenge. A promising alternative to direct genotype–phenotype mapping, particularly given the complexities introduced by epistasis, pleiotropy, and environmental variability, is to assess whether differentially expressed genes (DEGs) are enriched in regions of genetic divergence between populations adapted to contrasting environments. Here, we study gene expression patterns in threespine stickleback populations adapting to contrasting environments (marine vs. freshwater) and investigate signatures of selection associated with gene expression evolution during adaptation. We performed transcriptomic experiments of the brain and gill tissues of wild-caught sticklebacks sampled from one marine and two freshwater environments using TagSeq. We found that DEGs in the freshwater environments harbor single nucleotide polymorphisms (SNPs) previously identified to be involved in rapid adaptation and FST outliers. A majority of these SNPs were located in cis-regulatory regions of the genes with predicted low to moderate effects on protein function and structure, although we found a high-impact SNP in the gene col8a1b. Genes such as pvalb4 and acsl4a, involved in calcium regulation in the gill and fatty acid metabolism in the brain, respectively, were enriched with SNPs showing signatures of selection. By linking signatures of selection to tissue-specific gene expression patterns, our study bridges the gap between genomic divergence and the molecular mechanisms underlying physiological adaptation to new environments and identifies specific pathways that can be targeted for future functional studies.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above.

z0on/tag-based_RNAseq

License: none: the authors keep all their rights

State: the link answers, verified on 26 September 2026

Evidence: files inventoried

Commit: 0c8a25f81e7c0d35ef9c527d1f5a060db9c96b1f, 11 January 2021

Languages: Perl (20), R (6), Python (3)

Size: 38 files, 29 scripts

Software Heritage: not archived

Found in: the text, “Bioinformatic Processing”

Holds: README

Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation

Tools: NumPy (1 file), pheatmap (1 file)

Availability: 1 check, the latest on 26 September 2026: the link answers

26 September 2026: the link answers

30 files

2bRAD_bowtie2_launch.pl, Perl, 36 lines
countreads.pl, Perl, 21 lines
dna.mixing.R, R, 49 lines
dupCount.R, R, 27 lines
expression_compiler.pl, Perl, 47 lines
heatmapEveryWhichWay.R, R, 132 lines
iRNAseq_shrimpmap_SAM.pl, Perl, 42 lines
iRNAseq_trim_launch0.pl, Perl, 34 lines
isogroup_namer.pl, Perl, 67 lines
launcher_creator.py, Python, 536 lines
ls5_launcher_creator.py, Python, 460 lines
mix_illumina_qpcr.R, R, 66 lines
ngs_concat.pl, Perl, 41 lines
picogreen.R, R, 30 lines
rnaseq_clipper0.pl, Perl, 60 lines
rnaseq_clipper_fasta.pl, Perl, 50 lines
rnaseq_clipper_old.pl, Perl, 59 lines
samcount.pl, Perl, 134 lines
samcount_launch.pl, Perl, 34 lines
samcount_launch_bt2.pl, Perl, 25 lines
samcount_v.0.1.pl, Perl, 143 lines
selectFastaByHeader.pl, Perl, 38 lines
splitFastaByHeader.pl, Perl, 48 lines
tagseq_bowtie2map.pl, Perl, 42 lines
tagseq_clipper.pl, Perl, 96 lines
tagseq_trim_launch.pl, Perl, 42 lines
tagseq_trim_launch_bgi.pl, Perl, 31 lines
thetaByContig.py, Python, 148 lines
uniHeatmap.R, R, 89 lines
README.md, Text, 24 lines

At the source: github.com/z0on/tag-based_RNAseq

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
29 scripts, each with its path and the digest of its content;
no match between paragraphs and code yet;
neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Data links

ncbi.nlm.nih.gov/sra, NCBI; found in “Data Availability”

Data Availability

All sequenced raw reads have been deposited on Sequence Read Archive (www.ncbi.nlm.nih.gov/sra) under accession code PRJNA1427159.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 4 authors, 5 keywords, 8 MeSH terms, 1 funder, 120 references.

Cite

This paper

Kwakye, A., Dzikowski, N., Wund, M. A., & Veeramah, K. R. (2026). Genomic Signatures of Selection Are Enriched in Differentially Expressed Genes in Sticklebacks Adapting to Contrasting Environments. Genome biology and evolution, 18(9), evag222. https://doi.org/10.1093/gbe/evag222

BibTeX

@article{kwakye2026genomic, author = {Kwakye, Alexander and Dzikowski, Natalie and Wund, Matthew A and Veeramah, Krishna R}, title = {{Genomic Signatures of Selection Are Enriched in Differentially Expressed Genes in Sticklebacks Adapting to Contrasting Environments}}, journal = {Genome biology and evolution}, year = {2026}, month = sep, volume = {18}, number = {9}, pages = {evag222}, publisher = {Oxford University Press}, issn = {1759-6653}, doi = {10.1093/gbe/evag222}, url = {https://doi.org/10.1093/gbe/evag222}, pmid = {42668140}, pmcid = {PMC13583502} }

RIS

TY - JOUR AU - Kwakye, Alexander AU - Dzikowski, Natalie AU - Wund, Matthew A AU - Veeramah, Krishna R TI - Genomic Signatures of Selection Are Enriched in Differentially Expressed Genes in Sticklebacks Adapting to Contrasting Environments T2 - Genome biology and evolution J2 - Genome Biol Evol PY - 2026 DA - 2026/09/01 VL - 18 IS - 9 SP - evag222 SN - 1759-6653 PB - Oxford University Press DO - 10.1093/gbe/evag222 UR - https://doi.org/10.1093/gbe/evag222 LA - en ER -

CSL-JSON

{ "id": "10.1093/gbe/evag222", "type": "article-journal", "title": "Genomic Signatures of Selection Are Enriched in Differentially Expressed Genes in Sticklebacks Adapting to Contrasting Environments", "container-title": "Genome biology and evolution", "author": [ { "family": "Kwakye", "given": "Alexander" }, { "family": "Dzikowski", "given": "Natalie" }, { "family": "Wund", "given": "Matthew A" }, { "family": "Veeramah", "given": "Krishna R" } ], "container-title-short": "Genome Biol Evol", "volume": "18", "issue": "9", "page": "evag222", "DOI": "10.1093/gbe/evag222", "PMID": "42668140", "PMCID": "PMC13583502", "ISSN": "1759-6653", "publisher": "Oxford University Press", "URL": "https://doi.org/10.1093/gbe/evag222", "language": "en", "issued": { "date-parts": [ [ 2026, 9, 1 ] ] } }

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