ArticleBMC bioinformatics2022
GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species.
Article in BMC bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it, 39 citations in OpenAlex.
- The practice and promise of temporal genomics for measuring evolutionary responses to global change.Molecular ecology resources · 2025Pooled it
- Museum Genomics of an Important Swedish Pollinator Reveals Population Stability Across Time.Molecular ecology · 2026Article
- Massive Genetic Diversity Loss Within Asian Elephant Subspecies: New Insights for Determining Conservation Priorities.Genome biology and evolution · 2026Article
- Ancient environmental genome reveals a migratory brown bear individual in Early Holocene Scandinavia.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Strengths and constraints in ivory provenance research: La Beleña (Córdoba, Spain) as a case study.Scientific reports · 2026Article
- Whole genomes reveal subpopulations and isolation-by-distance patterns in the Norwegian lemming.BMC biology · 2026Article
- Increased Genetic Load in Breed Chickens and Reduced Coding Content in Long ROH.Genome biology and evolution · 2026Article
- Genome Shows no Recent Inbreeding in Near-Extinction Woolly Rhinoceros Sample Found in Ancient Wolf's Stomach.Genome biology and evolution · 2026Article
- Framework for assessing genetic variation in livestock using demographic, pedigree, and genomic measures.Frontiers in genetics · 2026Review
- That's So Last Season: Unraveling the Genomic Consequences of Fur Farming in Arctic Foxes (Vulpes lagopus).Molecular ecology · 2025Article
- Paleogenomics Reveals a Loss of Bovine Lineages in Mid-latitude Asia Over the Last 200,000 Years.Genome biology and evolution · 2025Article
- The Genomic Basis of the Svalbard Reindeer's Adaptation to an Extreme Arctic Environment.Genome biology and evolution · 2025Article
- Genomic and morphological analysis reveals long-term mammoth hybridization in British Columbia, Canada.Biology letters · 2025Article
- Genome analyses suggest recent speciation and postglacial isolation in the Norwegian lemming.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Using sedimentary ancient DNA in coastal and marine contexts to explore past human-environmental interactions in Australia.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Potential risk of dipterocarps in the marginal Asian rainforests: low population size and high genomic erosion.BMC biology · 2025Article
- A High-Throughput Ancient DNA Extraction Method for Large-Scale Sample Screening.Molecular ecology resources · 2025Article
- Constraints to gene flow increase the risk of genome erosion in the Ngorongoro Crater lion population.Communications biology · 2025Article
- PopGLen-a Snakemake pipeline for performing population genomic analyses using genotype likelihood-based methods.Bioinformatics (Oxford, England) · 2025Article
- Heterochronous mitogenomes shed light on the Holocene history of the Scandinavian brown bear.Scientific reports · 2024Article
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundMany wild species have suffered drastic population size declines over the past centuries, which have led to 'genomic erosion' processes characterized by reduced genetic diversity, increased inbreeding, and accumulation of harmful mutations. Yet, genomic erosion estimates of modern-day populations often lack concordance with dwindling population sizes and conservation status of threatened species. One way to directly quantify the genomic consequences of population declines is to compare genome-wide data from pre-decline museum samples and modern samples. However, doing so requires computational data processing and analysis tools specifically adapted to comparative analyses of degraded, ancient or historical, DNA data with modern DNA data as well as personnel trained to perform such analyses.
resultsHere, we present a highly flexible, scalable, and modular pipeline to compare patterns of genomic erosion using samples from disparate time periods. The GenErode pipeline uses state-of-the-art bioinformatics tools to simultaneously process whole-genome re-sequencing data from ancient/historical and modern samples, and to produce comparable estimates of several genomic erosion indices. No programming knowledge is required to run the pipeline and all bioinformatic steps are well-documented, making the pipeline accessible to users with different backgrounds. GenErode is written in Snakemake and Python3 and uses Conda and Singularity containers to achieve reproducibility on high-performance compute clusters. The source code is freely available on GitHub ( https://github.com/NBISweden/GenErode ).
conclusionsGenErode is a user-friendly and reproducible pipeline that enables the standardization of genomic erosion indices from temporally sampled whole genome re-sequencing data.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.