Second-generation PLINK: rising to the challenge of larger and richer datasets

Chang, Chris; Chow, Carson C.; Tellier, Laurent; Vattikuti, Shashaank; Purcell, Shaun; Lee, James J.

doi:10.1186/s13742-015-0047-8

Cited by 9,709 publications

(9,399 citation statements)

References 39 publications

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“…The input files for fastStructure were generated using PLINK v1.9 (Chang et al., 2015). We executed the program using the default settings with simple prior and tested multiple K values ranging from 1 to 6.…”

Section: Methodsmentioning

confidence: 99%

Capturing variation in Lens (Fabaceae): Development and utility of an exome capture array for lentil

et al. 2018

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Premise of the StudyLentil is an important legume crop with reduced genetic diversity caused by domestication bottlenecks. Due to its large and complex genome, tools for reduced representation sequencing are needed. We developed an exome capture array for use in various genetic diversity studies.MethodsBased on the CDC Redberry draft genome, we developed an exome capture array using multiple sources of transcript resources. The probes were designed to target not only the cultivated lentil, but also wild species. We assessed the utility of the developed method by applying the generated data set to population structure and phylogenetic analyses.ResultsThe data set includes 16 wild lentils and 22 cultivar accessions of lentil. Alignment rates were over 90%, and the genic regions were well represented in the capture array. After stringent filtering, 6.5 million high‐quality variants were called, and the data set was used to assess the interspecific relationships within the genus Lens.DiscussionThe developed exome capture array provides large amounts of genomic data to be used in many downstream analyses. The method will have useful applications in marker‐assisted breeding programs aiming to improve the quality of cultivated lentil.

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Section: Methodsmentioning

confidence: 99%

Capturing variation in Lens (Fabaceae): Development and utility of an exome capture array for lentil

et al. 2018

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“…Q‐values were visualized in R (R Core Team, 2016). To have an overall estimate on population divergence, we calculated in PLINK 1.9 (Chang et al., 2015) the average genomewide pairwise F ST (Weir & Cockerham, 1984) between A. m. iberiensis, A. m. carnica and A. m. ligustica and between A. m. iberiensis and combined A. m. carnica with A. m. ligustica (C‐lineage).…”

Section: Methodsmentioning

confidence: 99%

Developing reduced SNP assays from whole‐genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)

Henriques

Parejo

Vignal

et al. 2018

Evolutionary Applications

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The most important managed pollinator, the honeybee (Apis mellifera L.), has been subject to a growing number of threats. In western Europe, one such threat is large‐scale introductions of commercial strains (C‐lineage ancestry), which is leading to introgressive hybridization and even the local extinction of native honeybee populations (M‐lineage ancestry). Here, we developed reduced assays of highly informative SNPs from 176 whole genomes to estimate C‐lineage introgression in the most diverse and evolutionarily complex subspecies in Europe, the Iberian honeybee (Apis mellifera iberiensis). We started by evaluating the effects of sample size and sampling a geographically restricted area on the number of highly informative SNPs. We demonstrated that a bias in the number of fixed SNPs (FST = 1) is introduced when the sample size is small (N ≤ 10) and when sampling only captures a small fraction of a population's genetic diversity. These results underscore the importance of having a representative sample when developing reliable reduced SNP assays for organisms with complex genetic patterns. We used a training data set to design four independent SNP assays selected from pairwise FST between the Iberian and C‐lineage honeybees. The designed assays, which were validated in holdout and simulated hybrid data sets, proved to be highly accurate and can be readily used for monitoring populations not only in the native range of A. m. iberiensis in Iberia but also in the introduced range in the Balearic islands, Macaronesia and South America, in a time‐ and cost‐effective manner. While our approach used the Iberian honeybee as model system, it has a high value in a wide range of scenarios for the monitoring and conservation of potentially hybridized domestic and wildlife populations.

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“…We measured linkage disequilibrium by calculating the squared correlation coefficient between unphased genotypes, using PLINK version 1.90b3.45 (ref. 69 ). We started with three datasets: 'neutral' loci (a subsample of SNPs that showed no significant correlation with depth); 'type 1' outliers (the 9 SNPs that are differentiated between 1,000 m and 1,800 m, and which code for non-synonymous changes within coding genes); and 'type 2' outliers (the remaining 337 SNPs that are differentiated between 1,000 m and 1,800 m).…”

Section: Nature Ecology and Evolutionmentioning

confidence: 99%

Genomics of habitat choice and adaptive evolution in a deep-sea fish

et al. 2018

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W hile longitudinal and latitudinal habitat transitions have been proposed to define marine communities and promote intraspecific differentiation 1-3 , little is known about the importance of transitions along ocean depth gradients 4,5 , although substantial changes in species assemblages with depth have been recorded (for example, ref. 6 ), and relatively narrow depth ranges may distinguish closely related species (for example, refs 7,8 ). Understanding the relevant mechanisms will contribute significantly to our understanding of eco-evolutionary processes and the origin of marine biodiversity. We chose the roundnose grenadier (Coryphaenoides rupestris) as a model system because it is a widespread species that can inhabit a comparatively broad range of depths 9 from ~180 m to 2,600 m. It is a batch spawner, producing up to 69,000 pelagic eggs per female 10 . It has a spawning season peaking in autumn 11 (recent observations were in September at 1,500 m; ref. 12 ), preys on fish, cephalopods and invertebrates in both benthic and pelagic habitats 13 , and shows minor genetic differentiation across its geographic range [14][15][16] .Adaptation to habitat can occur among populations within a species, and if disruptive selection is associated with assortative mating has the potential to promote incipient speciation through ecological processes in sympatry 17 . When environmental change exposes new habitats and niche potential, adaptive radiations may rapidly generate a new lineage of species 18,19 . To the extent that differential selection can retain polymorphisms within or among populations, this may facilitate the process of adaptive radiation. Here, we focus on one of the key habitat transitions in the oceans-between the photic mesopelagic region and the aphotic regions below (together with the more contiguous changes associated with increasing depth). There is the potential for species (such as the roundnose grenadier), whose habitat range extends across this boundary or along the depth gradient, to experience differential selective pressures. We tested hypotheses about adaptation to these deep-sea habitats using genome sequence data together with data on the ecology and life history of the subject species. We found that juvenile fish of this species are found primarily in relatively shallow depths (near the transition between the mesopelagic and bathypelagic zones) and then migrate as they mature to different depths, and this is strongly associated with their genotype at a set of functional loci. In particular, all adults below ~1,800 m share the same homozygous genotype at each locus. There is evidence for strong selection maintaining this difference, but no clear evidence for differentiation driven by assortative mating. Results and discussionWe produced an annotated reference genome for C. rupestris with a total length of 0.829 gigabase pairs, a mean depth of 104× and an N50 of 159,738 (see Supplementary Methods for details). We used this draft genome to map 60 additional genomes sequenced to a mean depth ...

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Second-generation PLINK: rising to the challenge of larger and richer datasets

Cited by 9,709 publications

References 39 publications

Capturing variation in Lens (Fabaceae): Development and utility of an exome capture array for lentil

Capturing variation in Lens (Fabaceae): Development and utility of an exome capture array for lentil

Developing reduced SNP assays from whole‐genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)

Genomics of habitat choice and adaptive evolution in a deep-sea fish

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