<scp><i>dartR</i></scp> v2: An accessible genetic analysis platform for conservation, ecology and agriculture

Mijangos, Jose Luis; Gruber, Bernd; Berry, Oliver; Pacioni, Carlo; Georges, Arthur

doi:10.1111/2041-210x.13918

Cited by 68 publications

(51 citation statements)

References 42 publications

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“…The chickpea SNP data set [ 23 ] was provided in HapMap format and was converted to VCF format using TASSEL 5 Standalone ([ 29 ]; see the processing pipeline described in Supplementary Materials D3 Additional File. Hexaploid, tetraploid, and wild wheat SNP data files [ 22 ] were provided in DArT format [ 30 ]. These files were subdivided based on the provided passport information, with monomorphic loci removed, and then converted directly to GBS format, retaining only bi-allelic SNP loci, using the dartR R package (See the processing procedures described in Supplementary Materials D2 Additional File).…”

Section: Methodsmentioning

confidence: 99%

Assessing Genetic Distinctness and Redundancy of Plant Germplasm Conserved Ex Situ Based on Published Genomic SNP Data

2023

Plants

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Assessing genetic distinctness and redundancy is an important part of plant germplasm characterization. Over the last decade, such assessment has become more feasible and informative, thanks to the advances in genomic analysis. An attempt was made here to search for genebank germplasm with published genomic data and to assess their genetic distinctness and redundancy based on average pairwise dissimilarity (APD). The effort acquired 12 published genomic data sets from CIMMYT, IPK, USDA-ARS, IRRI, and ICRISAT genebanks. The characterized collections consisted of 661 to 55,879 accessions with up to 2.4 million genome-wide SNPs. The assessment generated an APD estimate for each sample. As a higher or lower APD is indicative of more genetic distinctness or redundance for an accession, respectively, these APD estimates helped to identify the most genetically distinct and redundant groups of 100 accessions each and a genetic outlier group with APD estimates larger than five standard deviations in each data set. An APD-based grouping of the conserved germplasm in each data set revealed among-group variances ranging from 1.5 to 53.4% across all data sets. Additional analyses showed that these APD estimations were more sensitive to SNP number, minor allele frequency, and missing data. Generally, 5000 to 10,000 genome-wide SNPs were required for an effective APD analysis. These findings together are encouraging and useful for germplasm management, utilization, and conservation, particularly in the genetic categorization of conserved germplasm.

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Section: Methodsmentioning

confidence: 99%

Assessing Genetic Distinctness and Redundancy of Plant Germplasm Conserved Ex Situ Based on Published Genomic SNP Data

2023

Plants

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“…Principal Components Analysis was undertaken using the glPCA function of the R adegenet package (as implemented in dartR, Gruber et al, 2018; Jombart, 2008; Jombart & Ahmed, 2011). Principal Coordinates Analysis was undertaken using the pcoa function in R package ape (Paradis & Schliep, 2019) implemented in dartR Version 2 (Mijangos et al, 2022).…”

Section: Methodsmentioning

confidence: 99%

“…The algorithms discussed in this paper form the basis of the distance analysis implemented in R software package dartR (Gruber et al, 2018; Mijangos et al, 2022).…”

Section: Methodsmentioning

confidence: 99%

“…Various software packages can display the results in three dimensions and allow rotation of the three axes to provide the best perspective (e.g. dartR, Gruber et al, 2018; Mijangos et al, 2022). Higher dimensions can be visualized by plotting the set of largest components in pairwise fashion.…”

Section: Methodsmentioning

confidence: 99%

“…To exemplify the effect of missing values on SNP visualisation using PCA (Figure 6), we performed computer simulations in dartR Version 2.0.3 (Mijangos et al, 2022). Ten simulated populations reproducing over 200 non-overlapping generations were placed in a linear series with low dispersal between adjacent populations (one disperser every ten generations).…”

Section: Methodsmentioning

confidence: 99%

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Distances and their visualization in studies of spatial-temporal genetic variation using single nucleotide polymorphisms (SNPs)

Georges

Mijangos

Patel

et al. 2023

Preprint

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Distance measures are widely used for examining genetic structure in datasets that comprise many individuals scored for a very large number of attributes. Genotype datasets composed of single nucleotide polymorphisms (SNPs) typically contain bi-allelic scores for tens of thousands if not hundreds of thousands of loci. We examine the application of distance measures to SNP data (both genotypes and sequence tag presence-absence) and use real datasets and simulated data to illustrate pitfalls in the application of genetic distances and their visualization. Missing values arise from ascertainment biases in the SNP discovery process (null alleles in the case of SNP genotyping; true missing data in the case of sequence tag presence-absence data). Missing values can cause displacement of affected individuals from their natural groupings and artificial inflation of confidence envelopes, leading to potential misinterpretation. Failure of a distance measure to conform to metric and Euclidean properties is important but only likely to create unacceptable outcomes in extreme cases. Lack of randomness in the selection of individuals and lack of independence of both individuals and loci (e.g. polymorphic haploblocks), can lead to substantial and otherwise inexplicable distortions of the visual representations and again, potential misinterpretation. Euclidean Distance is the metric of choice in many distance studies. However, other measures may be preferable because of underlying models of divergence, population demographic history, linkage disequilibrium, because it is desirable to down-weight joint absences, or because of other characteristics specific to the data or analyses. Distance measures for SNP genotype data depend on the arbitrary choice of reference and alternate alleles (e.g. Bray-Curtis distance) should be avoided. Careful consideration should be given to which state is scored zero when applying binary distance measures to fragment presence-absence data (e.g. Jaccard distance). Filtering on missing values then imputing those that remain avoids distortion in visual representations. Presence of closely related individuals or polymorphic haploblocks in the genomes of target species with limited genomic information occasionally emerge as challenges that need to be managed.

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Growth, drought response, and climate‐associated genomic structure in whitebark pine in the Sierra Nevada of California

Mantgem

Milano

Dudney

et al. 2023

Ecology and Evolution

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Whitebark pine (Pinus albicaulis Engelm.) has experienced rapid population declines and is listed as threatened under the Endangered Species Act in the United States.Whitebark pine in the Sierra Nevada of California represents the southernmost end of the species' distribution and, like other portions of its range, faces threats from an introduced pathogen, native bark beetles, and a rapidly warming climate. Beyond these chronic stressors, there is also concern about how this species will respond to acute stressors, such as drought. We present patterns of stem growth from 766 large (average diameter at breast height >25 cm), disease-free whitebark pine across the Sierra Nevada before and during a recent period of drought. We contextualize growth patterns using population genomic diversity and structure from a subset of 327 trees. Sampled whitebark pine generally had positive to neutral stem growth trends from 1970 to 2011, which was positively correlated with minimum temperature and precipitation. Indices of stem growth during drought years (2012 to 2015) relative to a predrought interval were mostly positive to neutral at our sampled sites. Individual tree growth response phenotypes appeared to be linked to genotypic variation in climate-associated loci, suggesting that some genotypes can take better advantage of local climatic conditions than others. We speculate that reduced snowpack during the 2012 to 2015 drought years may have lengthened the growing season while retaining sufficient moisture to maintain growth at most study sites. Growth responses may differ under future warming, however, particularly if drought severity increases and modifies interactions with pests and pathogens.

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dartR v2: An accessible genetic analysis platform for conservation, ecology and agriculture

Cited by 68 publications

References 42 publications

Assessing Genetic Distinctness and Redundancy of Plant Germplasm Conserved Ex Situ Based on Published Genomic SNP Data

Assessing Genetic Distinctness and Redundancy of Plant Germplasm Conserved Ex Situ Based on Published Genomic SNP Data

Distances and their visualization in studies of spatial-temporal genetic variation using single nucleotide polymorphisms (SNPs)

Growth, drought response, and climate‐associated genomic structure in whitebark pine in the Sierra Nevada of California

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