The future is now: Amplicon sequencing and sequence capture usher in the conservation genomics era

Abstract

The genomics revolution has initiated a new era of population genetics where genome‐wide data are frequently used to understand complex patterns of population structure and selection. However, the application of genomic tools to inform management and conservation has been somewhat rare outside a few well studied species. Fortunately, two recently developed approaches, amplicon sequencing and sequence capture, have the potential to significantly advance the field of conservation genomics. Here, amplicon sequencing refers to highly multiplexed PCR followed by high‐throughput sequencing (e.g., GTseq), and sequence capture refers to using capture probes to isolate loci from reduced‐representation libraries (e.g., Rapture). Both approaches allow sequencing of thousands of individuals at relatively low costs, do not require any specialized equipment for library preparation, and generate data that can be analyzed without sophisticated computational infrastructure. Here, we discuss the advantages and disadvantages of each method and provide a decision framework for geneticists who are looking to integrate these methods into their research programme. While it will always be important to consider the specifics of the biological question and system, we believe that amplicon sequencing is best suited for projects aiming to genotype <500 loci on many individuals (>1,500) or for species where continued monitoring is anticipated (e.g., long‐term pedigrees). Sequence capture, on the other hand, is best applied to projects including fewer individuals or where >500 loci are required. Both of these techniques should smooth the transition from traditional genetic techniques to genomics, helping to usher in the conservation genomics era.

RAPTURE (RAD capture) panel facilitates analyses characterizing sea lamprey reproductive ecology and movement dynamics

“…Protocols that combine targeted sequence capture with restriction site-associated DNA sequencing (Ali et al, 2016;Hoffberg et al, 2016) and highly multiplexed amplicon sequencing protocols (GT-Seq; Campbell et al, 2015) are beginning to be widely used for conservation genomic applications (Meek & Larson, 2019). Greater understanding of sea lamprey mating ecology and movement dynamics of sibling groups prior to metamorphosis could greatly aid sea lamprey control efforts.…”

Leveraging targeted sequencing for non-model species: a step-by-step guide to obtain a reduced SNP set and a pipeline to automate data processing in the Antarctic Midge, Belgica antarctica

“…The step-by-step guide for marker discovery and the pipeline designed for amplicon-sequencing can be used to isolate informative SNPs and rapidly genotype any non-model species. Amplicon-sequencing can not only speed-up the genotyping of endangered species but also facilitate the transition from conservation genetics to genomics (Meek & Larson, 2019;Taylor et al, 2017). The pipeline is flexible enough for amplicon-sequencing with different degrees of amplicons and samples, and can also be used to prepare the data of low-coverage ampliconsequencing experiments that incorporate some error (e.g.…”

“…Most important information for population and conservation genetic studies can be achieved with traditional molecular methods that do not require whole genome sequencing of populations (Allendorf, 2017;Bowden et al, 2012;Fischer et al, 2017;Peterson et al, 2012). Targeted enrichment protocols are alternatives to whole-genome re-sequencing (WGR) (Henriques et al, 2018;Meek & Larson, 2019;Milano et al, 2013). These protocols enable amplification of specific genomic regions that contain previously discovered variation.…”

RAD‐Seq Refines Previous Estimates of Genetic Structure in Lake Erie Walleye

“…Collectively, these findings indicate that genomic approaches, such as RAD-seq, could be useful for identifying genetic differences between western and eastern basin Walleye populations. Once these differences are quantified, other, higher-throughput molecular resources (e.g., genotyping-in-thousands by sequencing [GT-seq] and RAD capture [Rapture] panels) could be developed to determine the relative contributions of western versus eastern basin stocks to Lake Erie's mixed-stock fisheries Ali et al 2016;Meek and Larson 2019).…”

“…Higher genomic coverage could be achieved by using alternate enzymes during RAD-seq preparation that increase the number of cut sites or by conducting full-genome resequencing (Fuentes-Pardo and Ruzzante 2017;McKinney et al 2017). Once the most informative loci for stock delineation are identified, they can be used to construct resources, such as GT-seq and Rapture panels, which can quickly and consistently genotype thousands of individuals and in turn greatly increase sample sizes and statistical confidence (Meek and Larson 2019). These panels could then be used independently (if the resolution is high enough) or in conjunction with other techniques, such as otolith microchemistry, to successfully delineate populations (Chen et al 2017).…”