ArticleMethods in molecular biology (Clifton, N.J.)2022
Population Genomics Analysis with RAD, Reprised: Stacks 2.
Article in Methods in molecular biology (Clifton, N.J.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
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- Population genomics identifies genetic structure and admixture in the endangered Beale's Eyed Turtle (Marine life science & technology · 2026Article
- Not Just a Matter of Space: Integrating Ecological Niche Modeling With Genotype-Environment Associations Suggests High Maladaptation Risks Under Climate Change for a Microendemic Malagasy Frog.Ecology and evolution · 2026Article
- Genetic Diversity, Population Structure and Differentiation of Farmed and Wild African Catfish (Evolutionary applications · 2026Article
- Genomic and biogeographic patterns of endemic geckos in the Galapagos Islands reveal population structure and species delimitation on inhabited islands.Scientific reports · 2025Article
- RAD-Seq-derived SNPs reveal no local population structure in the commercially important deep-sea queen snapper (Marine life science & technology · 2025Article
- Genetic Analysis of Recently Discovered Least Chub Populations in the Upper Snake River and Bonneville Drainages.Ecology and evolution · 2025Article
- A reference genome enhances the power to detect signatures of recent anthropogenic impact in genomic data: a lesson learned from a stag beetle system.BMC biology · 2025Article
- Conservation Genomics for Threatened New ZealandEcology and evolution · 2025Article
- Genomic signature and evolutionary history of completely cleistogamous lineages in the non-photosynthetic orchidProceedings. Biological sciences · 2025Article
- Genomic Insights From Natural History Collections Reveal Cryptic Speciation in Coral Guard Crabs (Family:Ecology and evolution · 2025Article
- How many species are there? Lineage diversification and hidden speciation in Solanaceae from highland grasslands in southern South America.Annals of botany · 2024Article
- Habitat Association Predicts Population Connectivity and Persistence in Flightless Beetles: A Population Genomics Approach Within a Dynamic Archipelago.Molecular ecology · 2024Article
- Simulating Genetic Mixing in Strongly Structured Populations of the Threatened Southern Brown Bandicoot (Evolutionary applications · 2024Article
- Seascape Genomics of the Smooth Hammerhead SharkEcology and evolution · 2024Article
- Population connectivity and size reductions in the Anthropocene: the consequence of landscapes and historical bottlenecks in white forsythia fragmented habitats.BMC ecology and evolution · 2024Article
- FecalSeq enrichment with RAD Sequencing from non-invasive environmental samples holds promise for genetic monitoring of an imperiled lagomorph.Scientific reports · 2024Article
- Effects of inbreeding on reproductive success in endangered North Atlantic right whales.Royal Society open science · 2024Article
- Post-meiotic mechanism of facultative parthenogenesis in gonochoristic whiptail lizard species.eLife · 2024Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Restriction enzymes have been one of the primary tools in the population genetics toolkit for 50 years, being coupled with each new generation of technology to provide a more detailed view into the genetics of natural populations. Restriction site-Associated DNA protocols, which joined enzymes with short-read sequencing technology, have democratized the field of population genomics, providing a means to assay the underlying alleles in scores of populations. More than 10 years on, the technique has been widely applied across the tree of life and served as the basis for many different analysis techniques. Here, we provide a detailed protocol to conduct a RAD analysis from experimental design to de novo analysis-including parameter optimization-as well as reference-based analysis, all in Stacks version 2, which is designed to work with paired-end reads to assemble RAD loci up to 1000 nucleotides in length. The protocol focuses on major points of friction in the molecular approaches and downstream analysis, with special attention given to validating experimental analyses. Finally, the protocol provides several points of departure for further analysis.
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