Genome Scans Reveal Species-Specific Selection in the Genus Lynx.
The 2 matches · all tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
- [1] § Methods › Selection Scans and Candidate Regions ↔ exec/chr_lassi.sh, the whole file · a weak match · score 0.63 · saltiLASSI, calc, spec, unphased, winsize, winstep
- [2] § Methods › Sampling, DNA Extraction, Sequencing and Read Alignment ↔ exec/chr_lassi.sh, the whole file · a weak match · score 0.51 · Felis catus, reference genome, mapping, Gb, mem, DNA
Paper
Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC
The paper is loaded when this pane is shown.
The authors' code
Shell · 29 lines · 727 B · no license · 2 matches
- #!/bin/bash
- #SBATCH --time=3-00:00:00
- #SBATCH --mem=10GB
- #name variables
- sp=($(echo $1))
- chr=($(echo $2))
- INPUT=$STORE/saltilassi/${chr}_${sp}_goodsamples_filtered_polarized_variants_header_cat_ref.vcf
- #MAP=$STORE2/reference_genomes/Felis_catus_Ref/Felis_catus.Felis_catus_9.0.dna.toplevel.fa.fai
- #POP=$LUSTRE/selection_scan/${sp}_ind.txt
- #OUT=$LUSTRE/selection_scan/saltiLASSI/${chr}_${sp}_salti
- #load dependencies
- module load lassip
- #run lassi
- echo "running salti-lassi in $chr"
- lassip \
- --vcf INPUT \
- --unphased \
- --calc-spec \
- --hapstats \
- --salti \
- --map MAP \
- --winsize 101 \
- --winstep 50 \
- --pop POP \
- --out OUT
chr_lassi.sh at commit 6d06ed7, no license · at the source
Overview
- Department of Ecology and Evolution, Doñana Biological Station, CSIC, Seville, Spain
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources, Peterborough, ON K9J 7B8, Canada
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
- Texas A&M University, Veterinary Integrative Biosciences, College Station, TX 77843, USA
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
Abstract
Understanding the genetic basis of adaptation is essential for reconstructing evolutionary processes, and this can be accomplished particularly by studying closely related species occupying diverse ecological niches. In this study, we performed genome-wide scans for recent selective sweeps in the four extant species of the Lynx genus—Lynx canadensis (Canada lynx), Lynx rufus (bobcat), Lynx lynx (Eurasian lynx), and Lynx pardinus (Iberian lynx)—using a composite likelihood ratio test based on genotype frequency spectrum. Analyzing whole-genome sequences from 80 individuals, we identified species-specific selective sweeps and conducted functional enrichment analyses to explore biological processes under selection. Results revealed distinct adaptive mechanisms shaped by ecological specialization and demographic histories of different species. In Canada lynx, enriched functions include olfactory signaling and pigmentation-related processes; the Eurasian lynx showed signals related to cardiac and neural development; the Iberian lynx exhibited enrichment in immune-related pathways, potentially reflecting pathogen-mediated selection under strong genetic drift; and the bobcat displayed functional signals in reproductive and metabolic regulation. Our study revealed the species-specific nature of recent signatures of ecological differentiation in the genomes of closely related species of the genus Lynx, with minimal overlap, illustrating their diverse evolutionary trajectories and shedding light into the mechanism of adaptation among highly specialized carnivores.
Reproduced under the paper's license (CC BY), from the paper cited above.
Repository
Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.
lorenalorenzo/selection_scan_lynx
6d06ed794bd78cfc774cc1c668908c2811f54291, 17 June 2025Availability: 1 check, the latest on 28 September 2026: the link answers
- 28 September 2026: the link answers
5 files
- exec/
chr_lassi.sh , Shell, 29 lines, 2 matches - exec/
overlap_merge.py , Python, 24 lines - exec/
pre-steps.sh , Shell, 22 lines - exec/
sp_lassi.sh , Shell, 11 lines - README.md, Text, 6 lines
The paper's code and data availability statement is in the Data section.
Tracing map
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- 4 scripts, each with its path and the digest of its content;
- 2 matches between paragraphs of the paper and lines of the code (method lexical-v1);
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Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
No dataset and no data link were found in the paper.
Data Availability
Sequences analyzed in this study are available on the European Nucleotide Archive under the primary accession numbers: PRJEB109976 (current study), PRJEB48088 (Bazzicalupo et al. 2022), PRJEB28038 (Lucena-Perez et al. 2020) and PRJEB12609 (Abascal et al. 2016).
Scripts used for bioinformatics analyses are available in: https://
Reproduced under the paper's license (CC BY), from the paper cited above.
Versions
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Version 1, 28 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 7 authors, 5 keywords, 6 MeSH terms, 103 references.
Cite
This paper
Lorenzo-Fernández, L., Bazzicalupo, E., Koen, E. L., Janecka, J. E., Murphy, W. J., Schmidt, K., & Godoy, J. A. (2026). Genome Scans Reveal Species-Specific Selection in the Genus Lynx. Genome biology and evolution, 18(4), evag086. https://
BibTeX
@article{lorenzofernande
author = {Lorenzo-Fernández, Lorena and Bazzicalupo, Enrico and Koen, Erin L and Janecka, Jan E and Murphy, William J and Schmidt, Krzysztof and Godoy, José A},
title = {{Genome Scans Reveal Species-Specific Selection in the Genus Lynx}},
journal = {Genome biology and evolution},
year = {2026},
month = apr,
volume = {18},
number = {4},
pages = {evag086},
publisher = {Oxford University Press},
issn = {1759-6653},
doi = {10.1093/
url = {https://
pmid = {41983803},
pmcid = {PMC13092354}
}
RIS
TY - JOUR
AU - Lorenzo-Fernández, Lorena
AU - Bazzicalupo, Enrico
AU - Koen, Erin L
AU - Janecka, Jan E
AU - Murphy, William J
AU - Schmidt, Krzysztof
AU - Godoy, José A
TI - Genome Scans Reveal Species-Specific Selection in the Genus Lynx
T2 - Genome biology and evolution
J2 - Genome Biol Evol
PY - 2026
DA - 2026/
VL - 18
IS - 4
SP - evag086
SN - 1759-6653
PB - Oxford University Press
DO - 10.1093/
UR - https://
LA - en
ER -
CSL-JSON
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