A cost‐and‐time effective procedure to develop SNP markers for multiple species: A support for community genetics

Abstract

Multispecies population genetics is an emerging field that provides insight relevant to conservation biology and community ecology. However, to date, this approach is limited to species with available genetic resources. The use of thousands of single‐nucleotide polymorphism (SNP) markers developed from recent genotyping‐by‐sequencing (GBS) technologies is a roadmap for the study of nonmodel species, but remains cost prohibitive when several, distantly related species are involved. We aimed to overcome this issue using a single HiSeq3000 run of restriction‐site associated DNA sequencing (RAD‐Seq) to retrieve SNP markers for 40 diverse species including plants, invertebrates, fish, and mammals. We developed a Python‐based pipeline to isolate c. 100–500 high‐quality SNP markers for each species that could be genotyped through classical PCR amplification methods. To assess the quality of these markers, we validated our approach on c. 160 of the characterized SNPs for each of 18 Neotropical fish species from the river Maroni (French Guiana, South America), using the MassARRAY iPLEX platform from Agena Bioscience (San Diego, CA, USA). A run of the pipeline applying stringent filtering parameters enabled the successful design of between 130 and 3,492 SNP markers for 30 of the 40 study species. Relaxing pipeline parameters allows for an increase in the number of detected SNPs. Across the 18 species from French Guiana, an average of 85% of markers were successfully amplified, polymorphic, and scored in ≥90% of individuals (c. 200 individuals per species). The great majority (>98%) of these markers were at Hardy–Weinberg equilibrium in each sampling site from the river Maroni. This SNP discovery was performed at the cost of c. $US110 for each of the 40 species. Genotyping was performed at the cost of c. $US6000 for each of the 18 fish species with an average of 200 individuals per species. This strategy was found cost‐and‐time efficient to develop hundreds of SNP markers for a large range of nonmodel species, which can be used to investigate ecological and evolutionary questions that do not require whole‐genome coverage.

A newly developed genetic sex marker and its application to understanding chemically induced feminisation in roach (Rutilus rutilus)

“…We acknowledge that potential genotyping and sex‐identification error can also be introduced by pooling males and females, and the biases in pooled approaches, especially in allele frequency determination, is well recognised (Gautier et al., 2013; Rellstab, Zoller, Tedder, Gugerli, & Fischer, 2013). However, pooled‐based approaches have shown great promise for delineating diversity in species lacking reference genomes (Kurland et al., 2019; Neethiraj, Hornett, Hill, & Wheat, 2017), and, moreover, pool‐RAD‐seq approaches have been used to successfully identify species‐specific SNPs across a range of species (Delord et al., 2018).…”

A river runs through it: The causes, consequences, and management of intraspecific diversity in river networks

“…We should aim to go bigger and characterize spatial patterns of intraspecific diversity at the whole riverscape metacommunity level. Recent advances in high‐throughput sequencing and bioinformatics allow conducting fast biodiversity assessments by massively sequencing molecular markers from multiple species at affordable costs (Delord et al, 2018; Lepais et al, 2019). It is thus becoming possible to rapidly identify species composing riverine communities while estimating the intraspecific (genetic) diversity of all the species forming these communities (e.g., using DNA metabarcoding techniques; Elbrecht, Vamos, Steinke, & Leese, 2018).…”

Genome-wide SNP analyses reveal population structure of Portunus pelagicus along Vietnam coastline

“…Population information including connectivity across species distribution range, exchange rate and source-sink dynamics are important for understanding potential impacts of bio-physical factors [28–31], human-induced fragmentation [32] and pollution [33,34], or overexploitation [35–37]. Among the wide-range of molecular approaches, restriction site-associated DNA sequencing (RADseq) is well known for its ability to identify and score thousands of single nucleotide polymorphisms (SNPs), which are randomly distributed across the target genomes using next generation sequencing [38–40]. RAD methods are being used and developed with many techniques such as mbRAD [41], 2b-RAD [42], ddRAD [38] and ezRAD [43].…”