Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

Baird, Nathan A.; Etter, Paul D.; Atwood, Tressa S.; Currey, Mark; Shiver, Anthony L.; Lewis, Zachary A.; Selker, Eric U.; Cresko, William A.; Johnson, Eric A.

doi:10.1371/journal.pone.0003376

Cited by 3,085 publications

(3,082 citation statements)

References 17 publications

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“…RAD libraries were prepared, including Sbf I restriction enzyme digestion, adapter ligation, shearing, and PCR amplifications using 500 ng DNA per fish according to Baird et al. (2008) and Hohenlohe, Amish, Catchen, Allendorf, and Luikart (2011), with modification to include Agencourt AMPure XP SPRI beads (Beckman Coulter, Inc., Pasadena, CA) for size selection/exclusion and purification (P.D. Etter, University of Oregon, personal communication ).…”

Section: Methodsmentioning

confidence: 99%

Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)

Drinan

Gruenthal

Canino

et al. 2018

Evolutionary Applications

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The discernment of populations as management units is a fundamental prerequisite for sustainable exploitation of species. A lack of clear stock boundaries complicates not only the identification of spatial management units, but also the assessment of mixed fisheries by population assignment and mixed stock analysis. Many marine species, such as Pacific cod, are characterized by isolation by distance, showing significant differentiation but no clear stock boundaries. Here, we used restriction‐site‐associated DNA (RAD) sequencing to investigate population structure and assess power to genetically assign Pacific cod to putative populations of origin. Samples were collected across the species range in the eastern Pacific Ocean, from the Salish Sea to the Aleutian Islands. A total of 6,425 putative biallelic single nucleotide polymorphisms were identified from 276 individuals. We found a strong isolation‐by‐distance signal along coastlines that mirrored previous microsatellite results and pronounced genetic differentiation between coastal samples and those from the inland waters of the Salish Sea, with no evidence for hybridization between these two populations. Individual assignment success based on two methods was high overall (≥84%) but decreased from south to north. Assignment to geographic location of origin also was successful, with average distance between capture and assignment location of 220 km. Outlier analyses identified more loci potentially under selection along the coast than between Salish Sea and coastal samples, suggesting more diverse adaptation to latitudinal environmental factors than inshore vs. offshore environments. Our results confirm previous observations of sharp genetic differentiation of the Salish Sea population and isolation by distance along the coast, but also highlight the feasibility of using modern genomic techniques to inform stock boundaries and fisheries management in a low F ST marine species.

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Section: Methodsmentioning

confidence: 99%

Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)

Drinan

Gruenthal

Canino

et al. 2018

Evolutionary Applications

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“…RAD sequencing library preparation was conducted at Floragenex, Inc. (Portland, OR, USA) following the methods of Baird et al. (2008) with Pst I as the restriction enzyme. RAD libraries were barcoded by individual and multiplexed on an Illumina Genome Analyzer IIx or on Illumina HiSeq 2000.…”

Section: Methodsmentioning

confidence: 99%

A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting

Fitzek

Delcamp

Guichoux

et al. 2018

Ecology and Evolution

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DNA barcoding has proved difficult in a number of woody plant genera, including the ecologically important oak genus Quercus. In this study, we utilized restrictionsite‐associated DNA sequencing (RAD‐seq) to develop an economical single nucleotide polymorphism (SNP) DNA barcoding system that suffices to distinguish eight common, sympatric eastern North American white oak species. Two de novo clustering pipelines, PyRAD and Stacks, were used in combination with postclustering bioinformatic tools to generate a list of 291 potential SNPs, 80 of which were included in a barcoding toolkit that is easily implemented using MassARRAY mass spectrometry technology. As a proof‐of‐concept, we used the genotyping toolkit to infer potential hybridization between North American white oaks transplanted outside of their native range (Q. michauxii, Q. montana, Q muehlenbergii/Q. prinoides, and Q. stellata) into a horticultural collection surrounded by natural forests of locally native trees (Q. alba and Q. macrocarpa) in the living collection at The Morton Arboretum (Lisle, IL, USA). Phylogenetic and clustering analyses suggested low rates of hybridization between cultivated and native species, with the exception of one Q. michauxii mother tree, the acorns of which exhibited high admixture from either Q. alba or Q. stellata and Q. macrocarpa, and a hybrid between Q. stellata that appears to have backcrossed almost exclusively to Q. alba. Together, RAD‐seq and MassARRAY technologies allow for efficient development and implementation of a multispecies barcode for one of the more challenging forest tree genera.

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“…In contrast to the original RAD protocol (Baird et al., 2008), ddRAD does not require manual shearing of the DNA and produces generally fewer loci per genome, which was preferable for laboratory and analytical efficiency with large sample sizes. Restriction enzymes SBfI‐HF and MspI were selected for DNA digestion to sequence approximately 100,000 loci per genome, estimated via an in silico digest of the closely related Weddell seal ( Leptonychotes weddellii) genome, LepWed1.0 (Assembly GCF_000349705.1), using a wide size range (150–500 bp) to reflect size selection by 1.5× magnetic beads.…”

Section: Methodsmentioning

confidence: 99%

Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds

Cammen

Schultz

Bowen

et al. 2018

Ecology and Evolution

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Population increases over the past several decades provide natural settings in which to study the evolutionary processes that occur during bottleneck, growth, and spatial expansion. We used parallel natural experiments of historical decline and subsequent recovery in two sympatric pinniped species in the Northwest Atlantic, the gray seal (Halichoerus grypus atlantica) and harbor seal (Phoca vitulina vitulina), to study the impact of recent demographic change in genomic diversity. Using restriction site‐associated DNA sequencing, we assessed genomic diversity at over 8,700 polymorphic gray seal loci and 3,700 polymorphic harbor seal loci in samples from multiple cohorts collected throughout recovery over the past half‐century. Despite significant differences in the degree of genetic diversity assessed in the two species, we found signatures of historical bottlenecks in the contemporary genomes of both gray and harbor seals. We evaluated temporal trends in diversity across cohorts, as well as compared samples from sites at both the center and edge of a recent gray seal range expansion, but found no significant change in genomewide diversity following recovery. We did, however, find that the variance and degree of allele frequency change measured over the past several decades were significantly different from neutral expectations of drift under population growth. These two cases of well‐described demographic history provide opportunities for critical evaluation of current approaches to simulating and understanding the genetic effects of historical demographic change in natural populations.

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Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

Cited by 3,085 publications

References 17 publications

Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)

Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)

A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting

Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds

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