ArticleMolecular ecology resources2017
Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation.
Article in Molecular ecology resources, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 171 papers, 1 of them a synthesis that pooled it.
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Who cites it
171 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Shortcomings of Phylogenetic Studies on Recent Radiated Insular Groups: A Meta-Analysis Using Cabo Verde Biodiversity.International journal of molecular sciences · 2019Pooled it
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- Development of High-Throughput Genomic Resources to Inform White-Tailed Deer Population and Disease Management.Molecular ecology resources · 2026Article
- Missing or Mis-Telling the Story? Trade-Offs for Restriction-Site Associated Compared to Whole Genome Sequencing.Molecular ecology · 2026Article
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- A novel sex-associated genomic region in Catostomus fish species.The Journal of heredity · 2025Article
- Landscape and Climate-Associated Selection in the Native and Widespread Bumblebee, Bombus terrestris.Molecular ecology · 2025Article
- vcfsim: flexible simulation of all-sites VCFs with missing data.bioRxiv : the preprint server for biology · 2025Article
- NewtCap: An Efficient Target Capture Approach to Boost Genomic Studies in Salamandridae (True Salamanders and Newts).Ecology and evolution · 2025Article
111 more citing papers are in PubMed but not listed here.
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7 authors.
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Abstract
Understanding how and why populations evolve is of fundamental importance to molecular ecology. Restriction site-associated DNA sequencing (RADseq), a popular reduced representation method, has ushered in a new era of genome-scale research for assessing population structure, hybridization, demographic history, phylogeography and migration. RADseq has also been widely used to conduct genome scans to detect loci involved in adaptive divergence among natural populations. Here, we examine the capacity of those RADseq-based genome scan studies to detect loci involved in local adaptation. To understand what proportion of the genome is missed by RADseq studies, we developed a simple model using different numbers of RAD-tags, genome sizes and extents of linkage disequilibrium (length of haplotype blocks). Under the best-case modelling scenario, we found that RADseq using six- or eight-base pair cutting restriction enzymes would fail to sample many regions of the genome, especially for species with short linkage disequilibrium. We then surveyed recent studies that have used RADseq for genome scans and found that the median density of markers across these studies was 4.08 RAD-tag markers per megabase (one marker per 245 kb). The length of linkage disequilibrium for many species is one to three orders of magnitude less than density of the typical recent RADseq study. Thus, we conclude that genome scans based on RADseq data alone, while useful for studies of neutral genetic variation and genetic population structure, will likely miss many loci under selection in studies of local adaptation.
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