DOI: 10.5061/dryad.vq83bk446
title: Development of a panel of SNP loci in the emblematic southern damselfly (Coenagrion mercuriale) using a hybrid method: Pitfalls and recommendations for large-scale SNP genotyping in a non-model endangered species

description: Genomic markers are essential tools for studying species of conservation
 concern, yet non-model species often lack a reference genome. Here we
 describe a methodology for identifying and genotyping thousands of SNP
 loci in the southern damselfly (Coenagrion mercuriale), a bioindicator of
 freshwater stream quality classified as near-threatened, with locally
 declining populations. We used a hybrid approach combining reduced
 representation sequencing and target enrichment. First, we identified
 putative SNP loci using ddRADseq and de novo assembly. Then, single primer
 enrichment technology targeted 6,000 of these SNPs across 1,920
 individuals. Challenges encountered included sequence recapture failure,
 coverage depth discrepancies, and aberrant FIS values. We provide
 recommendations to address such issues. After multiple filtering steps,
 2,092 SNPs were retained and used to analyse the genetic structure of 131
 individuals belonging to 11 populations in France, comparing central and
 marginal populations. Genetic differentiation was lower among central
 populations, with no sign of inbreeding. As compared to microsatellite
 loci, SNPs exhibited greater resolution in detecting fine-scaled genetic
 structure, identifying putative hybrids in adjacent populations. In this
 study, we emphasise the difficulties of large-scale SNP genotyping in
 non-model species via a hybrid method that ultimately did not offer the
 expected cost and time saving compared to classical ddRAD approaches.
 However, SNPs showed greater power than previously available markers in
 identifying conservation units or admixture events, and the panel of
 reusable probes we describe here offers the potential to improve
 conservation efforts through future diachronic studies or finer
 estimations of key parameters like effective population size. 
description: # Development of a panel of SNP loci in the emblematic southern damselfly
 (Coenagrion mercuriale) using a hybrid method: Pitfalls and
 recommendations for large-scale SNP genotyping in a non-model endangered
 species
 [https://doi.org/10.5061/dryad.vq83bk446](https://doi.org/10.5061/dryad.vq83bk446) ## Description of the data and file structure ### Files and variables #### File: SNP\_genotypes\_131indv.txt **Description:** this file contains for each population sample: the name of the geographical location where population was sampled (Population), the name of the collected individual (Individual), the geographical coordinates of each sampled population (xcoord_WGS84.EPSG4326, ycoord_WGS84.EPSG4326), the individual genotypes at the 2092 SNPs loci using a genind genotype format. Each individual sample is represented by a row, and each biallelic locus is encoded by two columns indicating the variant, with integers indicating the number of each allele, and summing up to the individuals' ploidy (2). Missing genotypes are encoded with NAs. #### File: 135468\_RADloci\_sequence.fa **Description:** a fasta file containing the sequences of the 135,468 RADloci built at the end of the ddRADseq data analyses with STACKS software #### File: ddRADg\_genotypes\_20individuals.vcf **Description:** a vcf file showing the genotypes on 758,786 SNPs of 20 individuals at the end of the ddRADseq data analyses with STACKS software.