Harnessing the power of RADseq for ecological and evolutionary genomics

Andrews, Kimberly R.; Good, Jeffrey M.; Miller, Michael R.; Luikart, Gordon; Hohenlohe, Paul A.

doi:10.1038/nrg.2015.28

Cited by 1,207 publications

(1,250 citation statements)

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“…Methods for producing reduced representation libraries, such as RAD‐seq, are rapidly evolving, and more than 15 methods exist with variations in data quality, genotyping errors, cost, and the number of loci discovered (reviewed in Andrews, Good, Miller, Luikart, & Hohenlohe, 2016). Furthermore, filtering choices (see figure 2 in Benestan et al., 2016) can greatly influence downstream summary statistics.…”

Section: Genotyping Error and Improving Data Qualitymentioning

confidence: 99%

Recent advances in conservation and population genomics data analysis

Hendricks

Anderson

Antão

et al. 2018

Evolutionary Applications

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New computational methods and next‐generation sequencing (NGS) approaches have enabled the use of thousands or hundreds of thousands of genetic markers to address previously intractable questions. The methods and massive marker sets present both new data analysis challenges and opportunities to visualize, understand, and apply population and conservation genomic data in novel ways. The large scale and complexity of NGS data also increases the expertise and effort required to thoroughly and thoughtfully analyze and interpret data. To aid in this endeavor, a recent workshop entitled “Population Genomic Data Analysis,” also known as “ConGen 2017,” was held at the University of Montana. The ConGen workshop brought 15 instructors together with knowledge in a wide range of topics including NGS data filtering, genome assembly, genomic monitoring of effective population size, migration modeling, detecting adaptive genomic variation, genomewide association analysis, inbreeding depression, and landscape genomics. Here, we summarize the major themes of the workshop and the important take‐home points that were offered to students throughout. We emphasize increasing participation by women in population and conservation genomics as a vital step for the advancement of science. Some important themes that emerged during the workshop included the need for data visualization and its importance in finding problematic data, the effects of data filtering choices on downstream population genomic analyses, the increasing availability of whole‐genome sequencing, and the new challenges it presents. Our goal here is to help motivate and educate a worldwide audience to improve population genomic data analysis and interpretation, and thereby advance the contribution of genomics to molecular ecology, evolutionary biology, and especially to the conservation of biodiversity.

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Section: Genotyping Error and Improving Data Qualitymentioning

confidence: 99%

Recent advances in conservation and population genomics data analysis

Hendricks

Anderson

Antão

et al. 2018

Evolutionary Applications

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“…Many recent studies have used RADseq for genome scans to detect locally adapted loci (reviewed in Arnold et al 2013;Tiffin & Ross-Ibarra 2014;Andrews et al 2016). However, RADseq presents a major challenge for genome scan studies because the approach usually samples only a small proportion of the genome, despite generating hundreds to thousands of polymorphic markers (Fig.…”

Section: -Mike Ehrmantraut Breaking Badmentioning

confidence: 99%

“…Table S1 Recent (January 2015 to April 2016) genome scan studies, which used RAD-seq for genotyping. Andrews et al (2016). Generally, RADseq methods produce DNA libraries for high-throughput sequencing using restriction enzymes that cut at specific motifs throughout the genome.…”

Section: Correction Notementioning

confidence: 99%

Breaking RAD: An evaluation of the utility of restriction site associated DNA sequencing for genome scans of adaptation

et al. 2016

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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 Correspondence: David B. Lowry, Fax: 517-353-1926; dlowry@msu.edu. Correction noteThe original advance online paper contained two errors associated with the calculation of the median density of RAD-seq tags in the survey of recent RAD-seq genome scan studies (Table S1). The first error was in the size of the assembled stickleback genome, which was reported as 0.53 Gbp, but should have been 0.46 Gbp. The second error was an accidental inversion of terms. These two mistakes contributed to an erroneous statement in the original abstract that the median density of RAD-tags across recent studies "was one marker per 3.96 megabases." The statement has been revised to read: "was 4.08 RAD-tag markers per megabase." Following these corrections, changes were made in the abstract and elsewhere in the paper to reflect a modified interpretation of the results, though we note the main arguments in the article are unaffected. Other minor modifications to the paper were made based upon suggestions by the editors of Molecular Ecology Resources. This version of the article, published as an "accepted article" on 12 November 2016 under DOI 10.1111/1755-0998.12635 replaces the original version of the article published on 12 September 2016 under DOI 10.1111/1755-0998.12596.The idea for the manuscript was conceived collectively by all authors during an NSF National Institute for Mathematical and Biological Synthesis (NIMBioS) working group. All authors contributed to the writing of the manuscript.Supporting Information Additional Supporting Information may be found in the online version of this article: Appendix S1 Supplementary R scripts for Breaking RAD. Table S1 Recent (January 2015 to April 2016) genome scan studies, which used RAD-seq for genotyping. Andrews et al. (2016). Generally, RADseq methods produce DNA libraries for high-throughput sequencing using restriction enzymes that cut at specific motifs throughout the genome. RADseq markers come in the form of RAD-tags, which are short-read sequences adjacent to restriction enzyme cut sites. Because many polymorphic markers are produced by RADseq, it has frequently been used successfully for population genetic analyses, including assessment of population structure, hybridization, demographic history, phylogeography and migration (Catchen et al. 2013;Cavender-Bares et al. 2015;Combosch & Vollmer 2015;Qi et al. 2015). Markers generated by RADseq have also been quite useful for constructing linkage maps and identifying quantitative trait loci (QTL;Pfender et al. 2011;Houston et al. 2012;Weber et al. 2013;Laporte et al. 2015...

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“…Additionally, generating microsatellite data that is comparable across laboratories is problematic, which can impede large-scale stock structure and MSA syntheses. In contrast, SNPs typically have lower power per locus relative to microsatellites, but hundreds to thousands of SNP loci can now be rapidly and reliably quantified across large numbers of individuals (Campbell et al, 2015;Ali et al, 2016;Andrews et al, 2016). Additionally, SNPs in coding regions can be used to understand genotype and phenotype linkages and identify loci under selection if adequate genomic and budget resources are available (Hoban et al, 2016;Todd et al, 2016).…”

Section: Expansion Of Molecular Markersmentioning

confidence: 99%

Advances in the Application of Genetics in Marine Turtle Biology and Conservation

et al. 2017

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Marine turtles migrate across long distances, exhibit complex life histories, and occupy habitats that are difficult to observe. These factors present substantial challenges to understanding fundamental aspects of their biology or assessing human impacts, many of which are important for the effective conservation of these threatened and endangered species. The early development and application of genetic tools made important contributions to understanding marine turtle population and evolutionary biology, such as providing evidence of regional natal homing by breeding adults, establishing connectivity between rookeries and foraging habitats, and determining phylogeography and broad scale stock structure for most marine turtle species. Recent innovations in molecular technologies, statistical methods, and creative application of genetic tools have significantly built upon this knowledge to address key questions in marine turtle biology and conservation management. Here, we evaluate the latest major advances and potential of marine turtle genetic applications, including improved resolution and large-scale syntheses of population structure, connectivity and phylogeography, estimation of key demographic rates such as age to maturity and operational or breeding sex ratios, insight into reproductive strategies and behavior, and assessment of differential human impacts among populations. We then discuss remaining challenges and emerging capabilities, such as rapid, multiplexed genotyping, and investigation of the genomic underpinnings of adaptive variation afforded by high-throughput sequencing technologies.

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Harnessing the power of RADseq for ecological and evolutionary genomics

Cited by 1,207 publications

References 121 publications

Recent advances in conservation and population genomics data analysis

Recent advances in conservation and population genomics data analysis

Breaking RAD: An evaluation of the utility of restriction site associated DNA sequencing for genome scans of adaptation

Advances in the Application of Genetics in Marine Turtle Biology and Conservation

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