Harnessing the Power of RADseq for Ecological and Evolutionary Genomics

Overview

Journal Nat Rev Genet

Specialty Genetics

Date 2016 Jan 6

PMID 26729255

Citations 411

Authors

Kimberly R Andrews

Jeffrey M Good

Michael R Miller

Gordon Luikart

Paul A Hohenlohe

Affiliations

Soon will be listed here.

Abstract

High-throughput techniques based on restriction site-associated DNA sequencing (RADseq) are enabling the low-cost discovery and genotyping of thousands of genetic markers for any species, including non-model organisms, which is revolutionizing ecological, evolutionary and conservation genetics. Technical differences among these methods lead to important considerations for all steps of genomics studies, from the specific scientific questions that can be addressed, and the costs of library preparation and sequencing, to the types of bias and error inherent in the resulting data. In this Review, we provide a comprehensive discussion of RADseq methods to aid researchers in choosing among the many different approaches and avoiding erroneous scientific conclusions from RADseq data, a problem that has plagued other genetic marker types in the past.

Citing Articles

Genomic insights into Mediterranean pepper diversity using ddRADSeq.

Toker T, Ulusoy D, Dogan B, Kasapoglu S, Hakan F, Reddy U PLoS One. 2025; 20(3):e0318105.

PMID: 40063634 PMC: 11892853. DOI: 10.1371/journal.pone.0318105.

Comprehensive review of : pathogenesis, pathotype diversity, and integrated control methods.

Xu X, Wu C, Zhang F, Yao J, Fan L, Liu Z Front Microbiol. 2025; 16:1531393.

PMID: 39980695 PMC: 11840573. DOI: 10.3389/fmicb.2025.1531393.

Using RAD-seq to identify and differentiate the medicinal herb Scrophularia ningpoensis and its adulterants.

Guo L, Wang X, Li H, Zhou M, Liu L, Wang R BMC Genomics. 2025; 26(1):109.

PMID: 39905289 PMC: 11796183. DOI: 10.1186/s12864-025-11304-7.

Reduced Representation and Whole-Genome Sequencing Approaches Highlight Beluga Whale Populations Associated to Eastern Canada Summer Aggregations.

Montana L, Bringloe T, Bourret A, Sauve C, Mosnier A, Ferguson S Evol Appl. 2024; 17(12):e70058.

PMID: 39703673 PMC: 11655672. DOI: 10.1111/eva.70058.

A Tale of Two Lakes: Divergent Evolutionary Trajectories of Two Populations Experiencing Distinct Environments.

Wersebe M, Gunther T, Morton P, Weider L, Frisch D Ecol Evol. 2024; 14(12):e70434.

PMID: 39691432 PMC: 11651911. DOI: 10.1002/ece3.70434.

References

Ferretti L, Ramos-Onsins S, Perez-Enciso M . Population genomics from pool sequencing. Mol Ecol. 2013; 22(22):5561-76. DOI: 10.1111/mec.12522. View

Elshire R, Glaubitz J, Sun Q, Poland J, Kawamoto K, Buckler E . A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One. 2011; 6(5):e19379. PMC: 3087801. DOI: 10.1371/journal.pone.0019379. View

Combosch D, Vollmer S . Trans-Pacific RAD-Seq population genomics confirms introgressive hybridization in Eastern Pacific Pocillopora corals. Mol Phylogenet Evol. 2015; 88:154-62. DOI: 10.1016/j.ympev.2015.03.022. View

Hedtke S, Morgan M, Cannatella D, Hillis D . Targeted enrichment: maximizing orthologous gene comparisons across deep evolutionary time. PLoS One. 2013; 8(7):e67908. PMC: 3699465. DOI: 10.1371/journal.pone.0067908. View

Schweyen H, Rozenberg A, Leese F . Detection and removal of PCR duplicates in population genomic ddRAD studies by addition of a degenerate base region (DBR) in sequencing adapters. Biol Bull. 2014; 227(2):146-60. DOI: 10.1086/BBLv227n2p146. View

Gautier M, Gharbi K, Cezard T, Foucaud J, Kerdelhue C, Pudlo P . The effect of RAD allele dropout on the estimation of genetic variation within and between populations. Mol Ecol. 2012; 22(11):3165-78. DOI: 10.1111/mec.12089. View

Andrews K, Hohenlohe P, Miller M, Hand B, Seeb J, Luikart G . Trade-offs and utility of alternative RADseq methods: reply to Puritz et al. Mol Ecol. 2014; 23(24):5943-6. DOI: 10.1111/mec.12964. View

Lu F, Lipka A, Glaubitz J, Elshire R, Cherney J, Casler M . Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genet. 2013; 9(1):e1003215. PMC: 3547862. DOI: 10.1371/journal.pgen.1003215. View

Leache A, Chavez A, Jones L, Grummer J, Gottscho A, Linkem C . Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing. Genome Biol Evol. 2015; 7(3):706-19. PMC: 5322549. DOI: 10.1093/gbe/evv026. View

10.

Wang Z, Gerstein M, Snyder M . RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2008; 10(1):57-63. PMC: 2949280. DOI: 10.1038/nrg2484. View

11.

Candy J, Campbell N, Grinnell M, Beacham T, Larson W, Narum S . Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt. Mol Ecol Resour. 2015; 15(6):1421-34. DOI: 10.1111/1755-0998.12400. View

12.

Pukk L, Ahmad F, Hasan S, Kisand V, Gross R, Vasemagi A . Less is more: extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology. Mol Ecol Resour. 2015; 15(5):1145-52. DOI: 10.1111/1755-0998.12392. View

13.

Perez T, Albornoz J, Dominguez A . An evaluation of RAPD fragment reproducibility and nature. Mol Ecol. 1998; 7(10):1347-57. DOI: 10.1046/j.1365-294x.1998.00484.x. View

14.

Cruaud A, Gautier M, Galan M, Foucaud J, Saune L, Genson G . Empirical assessment of RAD sequencing for interspecific phylogeny. Mol Biol Evol. 2014; 31(5):1272-4. DOI: 10.1093/molbev/msu063. View

15.

Pritchard J, Stephens M, Donnelly P . Inference of population structure using multilocus genotype data. Genetics. 2000; 155(2):945-59. PMC: 1461096. DOI: 10.1093/genetics/155.2.945. View

16.

Ilut D, Nydam M, Hare M . Defining loci in restriction-based reduced representation genomic data from nonmodel species: sources of bias and diagnostics for optimal clustering. Biomed Res Int. 2014; 2014:675158. PMC: 4095725. DOI: 10.1155/2014/675158. View

17.

Waples R, Seeb L, Seeb J . Linkage mapping with paralogs exposes regions of residual tetrasomic inheritance in chum salmon (Oncorhynchus keta). Mol Ecol Resour. 2015; 16(1):17-28. DOI: 10.1111/1755-0998.12394. View

18.

Anderson E, Skaug H, Barshis D . Next-generation sequencing for molecular ecology: a caveat regarding pooled samples. Mol Ecol. 2013; 23(3):502-12. DOI: 10.1111/mec.12609. View

19.

Kardos M, Luikart G, Allendorf F . Measuring individual inbreeding in the age of genomics: marker-based measures are better than pedigrees. Heredity (Edinb). 2015; 115(1):63-72. PMC: 4815495. DOI: 10.1038/hdy.2015.17. View

20.

Henning F, Lee H, Franchini P, Meyer A . Genetic mapping of horizontal stripes in Lake Victoria cichlid fishes: benefits and pitfalls of using RAD markers for dense linkage mapping. Mol Ecol. 2014; 23(21):5224-40. DOI: 10.1111/mec.12860. View