Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations

Abstract

Recently, Lowry et al. addressed the ability of RADseq approaches to detect loci under selection in genome scans. While the authors raise important considerations, such as accounting for the extent of linkage disequilibrium in a study system, we strongly disagree with their overall view of the ability of RADseq to inform our understanding of the genetic basis of adaptation. The family of RADseq protocols has radically improved the field of population genomics, expanding by several orders of magnitude the number of markers available while substantially reducing the cost per marker. Researchers whose goal is to identify regions of the genome under selection must consider the LD of the experimental system; however, there is no magical LD cutoff below which researchers should refuse to use RADseq. Lowry et al. further made two major arguments: a theoretical argument that modeled the likelihood of detecting selective sweeps with RAD markers, and gross summaries based on an anecdotal collection of RAD studies. Unfortunately, their simulations were off by two orders of magnitude in the worst case, while their anecdotes merely showed that it is possible to get widely divergent densities of RAD tags for any particular experiment, either by design or due to experimental efficacy. We strongly argue that RADseq remains a powerful and efficient approach that provides sufficient marker density for studying selection in many natural populations. Given limited resources, we argue that researchers should consider a wide range of trade-offs among genomic techniques, in light of their study question and the power of different techniques to answer it.

Conservation of freshwater bivalves at the global scale: diversity, threats and research needs

“…Additionally, nextgeneration sequencing is now allowing for quicker and less expensive robust phylogenies using methods like whole-transcriptome and whole-mitogenome analyses with a wide range of markers (Guerra et al, 2017;Lopes-Lima et al, 2017c). 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).…”

Recent advances in conservation and population genomics data analysis

“…A recent study testing the impact of data processing on population genetic inferences using RAD‐seq data observed large differences between reference‐based and de novo approaches in population genetic summary statistics, particularly those based on the site frequency spectrum (Shafer et al., 2016). In addition, the recent debate over the effectiveness of RAD‐seq for discovering loci under selection (Catchen et al., 2017; Lowry et al., 2016; McKinney, Larson, Seeb, & Seeb, 2017) has highlighted the importance of testing the extent of linkage disequilibrium (LD) over the genome, whenever possible, in order to assess the power of genome scans to detect selected loci (e.g., Kardos, Taylor, Ellegren, Luikart, & Allendorf, 2016). …”

“…Focusing on the choice of sequencing method, a particular point of discussion at the ConGen 2017 workshop was the recent set of papers addressing the limitations of RADseq to illuminate the genetic basis of adaptation (Catchen et al., 2017; Lowry et al., 2016; McKinney et al., 2017). The primary criticism raised by Lowry et al.…”

“…The extent of LD can be directly estimated if a reference genome is available (Catchen et al., 2017), and it is recommended that LD should be estimated whenever possible in population genomic studies. Moreover, many conservation and population genomic questions can be answered without exhaustive sampling of the genome or detection of all functionally important loci, and alternative techniques such as WGS may impose substantial costs and other trade‐offs (Catchen et al., 2017). In particular, increasing the density of markers may necessitate reducing the number of individuals or populations sampled, and choosing methods that target candidate loci can bias against detecting selection at previously unknown loci.…”

Understanding the molecular basis of adaptation to freshwater environments by prawns in the genus Macrobrachium

“…To address fundamental questions about evolution, adaptation and phylogenetics, many studies now adopt a genomics approach, and it seems logical that the data generated will inevitably be applied to the independent field of ecology (Catchen et al, 2017). Availability of genome sequences and related genomics tools provide unprecedented opportunities for addressing many key questions in evolutionary ecology not previously addressed easily.…”