<i>Stacks</i>: Building and Genotyping Loci <i>De Novo</i> From Short-Read Sequences

Catchen, Julian M.; Amores, Angel; Hohenlohe, Paul A.; Cresko, William A.; Postlethwait, John H.

doi:10.1534/g3.111.000240

Cited by 1,776 publications

(1,849 citation statements)

References 40 publications

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“…For comparison, RAD‐seq data were also clustered using Stacks (Catchen, Amores, Hohenlohe, Cresko, & Postlethwait, 2011; Catchen, Hohenlohe, Bassham, Amores, & Cresko, 2013). Barcodes were first removed using gawk prior to filtering out low‐quality reads with the “process_radtags” module of Stacks (Catchen et al., 2011, 2013).…”

Section: Methodsmentioning

confidence: 99%

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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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Section: Methodsmentioning

confidence: 99%

“…Barcodes were first removed using gawk prior to filtering out low‐quality reads with the “process_radtags” module of Stacks (Catchen et al., 2011, 2013). The wrapper program “denovo_map.pl” provided by Stacks was used to perform de novo assembly of RAD‐seq.…”

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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“…Resulting sequences were processed with Stacks v1.21 (Catchen, Amores, Hohenlohe, Cresko, & Postlethwait, 2011) to identify and genotype SNPs de novo (without a reference genome). Sequences were first filtered for quality (minimum average phred score of 10 across 8‐bp sliding window; no sequencing errors in the barcode or restriction enzyme site) and demultiplexed by P2 index and P1 barcode.…”

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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“…Genotype‐calling software programs use either maximum‐likelihood (e.g., Stacks; Catchen et al., 2011) or Bayesian models (e.g., GATK; McKenna et al., 2010; dePristo et al., 2011; Van der Auwera et al., 2013) to assign individuals with genotypes. These models often incorporate some element of sequencing error, but the primary determinant of whether individuals are accurately genotyped as heterozygous or homozygous is the number of reads assigned to each individual.…”

Section: Design and Implement: Assessmentmentioning

confidence: 99%

Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservation

Flanagan

Forester

Latch

et al. 2017

Evolutionary Applications

198

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Identifying and monitoring locally adaptive genetic variation can have direct utility for conserving species at risk, especially when management may include actions such as translocations for restoration, genetic rescue, or assisted gene flow. However, genomic studies of local adaptation require careful planning to be successful, and in some cases may not be a worthwhile use of resources. Here, we offer an adaptive management framework to help conservation biologists and managers decide when genomics is likely to be effective in detecting local adaptation, and how to plan assessment and monitoring of adaptive variation to address conservation objectives. Studies of adaptive variation using genomic tools will inform conservation actions in many cases, including applications such as assisted gene flow and identifying conservation units. In others, assessing genetic diversity, inbreeding, and demographics using selectively neutral genetic markers may be most useful. And in some cases, local adaptation may be assessed more efficiently using alternative approaches such as common garden experiments. Here, we identify key considerations of genomics studies of locally adaptive variation, provide a road map for successful collaborations with genomics experts including key issues for study design and data analysis, and offer guidelines for interpreting and using results from genomic assessments to inform monitoring programs and conservation actions.

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Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences

Cited by 1,776 publications

References 40 publications

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

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

Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservation

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