Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations
Citations
479 citations
Cites background from "Unbroken: RADseq remains a powerful..."
...Often, the differences between these studies generated substantial discussion in the community (Catchen et al., 2017; Lowry et al., 2017; McKinney, Larson, Seeb, & Seeb, 2017) and a lot of speculation as to the inherent limitations of reduced repre‐ sentation sequencing....
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223 citations
Cites methods from "Unbroken: RADseq remains a powerful..."
...Furthermore, using reduced genome representations or snip analyses, it is now possible to get more information on the phylogeographic patterns of species and on the definition of conservation units (Catchen et al., 2017; Desalle & Amato, 2017)....
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191 citations
Cites background or methods from "Unbroken: RADseq remains a powerful..."
...In addition, Catchen et al. (2017) argue that even with short LD blocks, RAD-seq has been successful at detecting adaptive loci (e.g., the Eda locus in three-spine sticklebacks), and that endangered species usually exhibit small effective population sizes for which large LD blocks should be…...
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...A higher marker density (and thus genome coverage) can be achieved with the use of frequent cutter enzymes (McKinney, Larson, Seeb, & Seeb, 2017; Catchen et al., 2017); however, the target marker density should be informed by the genetic architecture of phenotypic traits of interest (i.e., the…...
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...Although previous knowledge on the extend of LD decay or recombination rate is generally lacking for nonmodel species, LD block size can be estimated from a dense genetic map or from RAD-seq data with a reference genome (Catchen et al., 2017)....
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...In the absence of reference genome, RAD-seq is an affordable alternative for the screening of neutral and putatively adaptive variation in a fraction of the genome (McKinney et al., 2017; Catchen et al., 2017) with some limitations (Hoban et al., 2016; Lowry et al., 2017a,b)....
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160 citations
Cites methods from "Unbroken: RADseq remains a powerful..."
...For de novo analyses, the core of the Stacks clustering algorithm (ustackscstacks-sstacks), which builds loci out of the single-end reads, remains as previously described [Catchen2011, Catchen2013], but has received a number of improvements and optimizations. Stacks has been capable of gapped assemblies since version 1.38 (2016), when Needleman-Wunch comparisons between stacks sharing many k-mers were added, and in Stacks v2 this capability has been refined and has become the default....
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...Individuals could then be matched to the metapopulation data contained in the catalog with sstacks [Catchen2011]. Availability of computational resources undergirded this design decision as the pipeline needed to process potentially thousands of individual samples, each with millions of raw reads. This architecture prevented population-level information, such as presence of a polymorphic site, from being incorporated into individual genotype calls. To incorporate this population-level information, version 1.10 of Stacks (2013) incorporated the rxstacks program to make population-level corrections retrospectively, after the core pipeline had executed....
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157 citations
Cites background from "Unbroken: RADseq remains a powerful..."
...Alternate genomic data sets have different advantages and disadvantages (e.g., Catchen et al., 2017; Josephs, Stinchcombe, & Wright, 2017; Lowry et al., 2017; McKinney, Larson, Seeb, & Seeb, 2017)....
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References
1,557 citations
"Unbroken: RADseq remains a powerful..." refers background in this paper
...Whole-genome resequencing samples a much smaller number of individuals for a given total sequencing effort, so while it can sample all LD blocks, it relies heavily on assumptions that the individuals sampled are representative of the populations under study (e.g. Jones et al. (2012))....
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1,406 citations
"Unbroken: RADseq remains a powerful..." refers background in this paper
...…the Eda locus in threespine stickleback has been repeatedly identified as a strong target of divergent selection in many independent RADSeq studies (Hohenlohe et al. 2010; Roesti et al. 2012; Ferchaud & Hansen 2016) – using less frequent cutters (SbfI, 8 bp) than Lowry et al. deem workable....
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...For example, the Eda locus in threespine stickleback has been repeatedly identified as a strong target of divergent selection in many independent RADSeq studies (Hohenlohe et al. 2010; Roesti et al. 2012; Ferchaud & Hansen 2016) – using less frequent cutters (SbfI, 8 bp) than Lowry et al....
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1,102 citations
"Unbroken: RADseq remains a powerful..." refers background in this paper
...In particular, RADseq protocols have a large degree of flexibility for tailoring sampling and study design for particular systems (Andrews et al. 2016), and accounting for factors such as LD, and they have demonstrated their potential to identify genetic signatures of selection in nature....
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...Pooled sequencing of various library types, while cost-efficient, carries inherent risks and limitations, particularly in the absence of a well-characterized genome (Schlotterer et al. 2014; Andrews et al. 2016)....
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953 citations
"Unbroken: RADseq remains a powerful..." refers background in this paper
...While the relative contribution of coding vs. regulatory regions still remains an open question (Hoekstra & Coyne 2007), biasing the genomic sampling a priori simply cannot address this question and may actually provide a biased view of the genomic determinants of evolutionary change....
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