ArticleFrontiers in genetics2019
Selecting RAD-Seq Data Analysis Parameters for Population Genetics: The More the Better?
Article in Frontiers in genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed, 74 citations in OpenAlex.
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- Hardy-Weinberg Equilibrium Filtering in Population Genomics: Empirical Review and Decision Framework for Improved Practice.Ecology and evolution · 2026Review
- Optimization and Evaluation of the bestRAD Sequencing Approach: Towards Ascertainment of the Invasion Routes of the Oriental Fruit Fly, Bactrocera dorsalis.Molecular ecology resources · 2025Article
- Genomic insights into the population structure and adaptive variation of Mullus barbatus in the Mediterranean Sea.BMC ecology and evolution · 2025Article
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- Scaling-up RADseq methods for large datasets of non-invasive samples: Lessons for library construction and data preprocessing.Molecular ecology resources · 2025Article
- Next-generation data filtering in the genomics era.Nature reviews. Genetics · 2024Review
- Conservation genetics and potential geographic distribution modeling of Corybas taliensis, a small 'sky Island' orchid species in China.BMC plant biology · 2024Article
- Sponge diversification in marine lakes: Implications for phylogeography and population genomic studies on sponges.Ecology and evolution · 2023Article
- Genetic and particle modelling approaches to assessing population connectivity in a deep sea lobster.Scientific reports · 2022Article
- Genome-wide species delimitation analyses of a silverside fish species complex in central Mexico indicate taxonomic over-splitting.BMC ecology and evolution · 2022Article
- Population genomic monitoring provides insight into conservation status but no correlation with demographic estimates of extinction risk in a threatened trout.Evolutionary applications · 2022Article
- Genomic data is missing for many highly invasive species, restricting our preparedness for escalating incursion rates.Scientific reports · 2022Article
- Breaking the reproductive barrier of divergent species to explore the genomic landscape.Frontiers in genetics · 2022Article
- Genomic signatures of inbreeding in a critically endangered parrot, the kākāpō.G3 (Bethesda, Md.) · 2021Article
- In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Animals : an open access journal from MDPI · 2021Article
- Base-substitution mutation rate across the nuclear genome of Alpheus snapping shrimp and the timing of isolation by the Isthmus of Panama.BMC ecology and evolution · 2021Article
- Potential of genomic technologies to improve disease resistance in molluscan aquaculture.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2021Review
- Low impact of different SNP panels from two building-loci pipelines on RAD-Seq population genomic metrics: case study on five diverse aquatic species.BMC genomics · 2021Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Restriction site-associated DNA sequencing (RAD-seq) has become a powerful and widely used tool in molecular ecology studies as it allows to cost-effectively recover thousands of polymorphic sites across individuals of non-model organisms. However, its successful implementation in population genetics relies on correct data processing that would minimize potential loci-assembly biases and consequent genotyping error rates. RAD-seq data processing when no reference genome is available involves the assembly of hundreds of thousands high-throughput sequencing reads into orthologous loci, for which various key parameter values need to be selected by the researcher. Previous studies exploring the effect of these parameter values found or assumed that a larger number of recovered polymorphic loci is associated with a better assembly. Here, using three RAD-seq datasets from different species, we explore the effect of read filtering, loci assembly and polymorphic site selection on number of markers obtained and genetic differentiation inferred using the Stacks software. We find (i) that recovery of higher numbers of polymorphic loci is not necessarily associated with higher genetic differentiation, (ii) that the presence of PCR duplicates, selected loci assembly parameters and selected SNP filtering parameters affect the number of recovered polymorphic loci and degree of genetic differentiation, and (iii) that this effect is different in each dataset, meaning that defining a systematic universal protocol for RAD-seq data analysis may lead to missing relevant information about population differentiation.
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