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bioRxiv2024

Contrasting patterns of spatial genetic structure in endangered southern damselfly (Coenagrion mercuriale) populations facing habitat fragmentation and urbanisation.

AimHuman-induced environmental changes result in habitat loss and fragmentation, impacting wildlife population genetic structure and evolution. Urbanised and geographically peripheral areas often represent unfavourable environments, reducing connectivity among populations and causing higher population genetic differentiation and lower intra-population genetic diversity. We examined how geographic peripherality and anthropogenic pressures affect genetic diversity and genetic differentiation in the protected southern damselfly (Coenagrion mercuriale, Odonata), which has low dispersal capabilities and specific habitat requirements and whose populations are declining. LocationWe studied two areas: one in semi-natural habitats at the periphery of the species geographic range (northern France) and the other more central to the species range, in an urbanised area surrounding the city of Strasbourg (Alsace, eastern France). MethodsWe genotyped 2743 individuals from 128 populations using eleven microsatellite loci. We analysed the spatial distribution of neutral genetic diversity (allelic richness, heterozygosity, levels of inbreeding, genetic relatedness), the extent of genetic differentiation, and population affiliations (sPCA analyses) within the two areas. We also examined fine-scale patterns of gene flow in the urbanised area of Alsace by investigating patterns of isolation by distance and estimating effective migration surfaces (EEMS method). ResultsNorthern peripheral populations showed lower levels of genetic diversity and higher levels of genetic differentiation than central Alsacian populations. Although located in anthropised habitats, geographically central Alsacian populations showed high levels of gene flow, with dispersal events mainly occurring overland and not restricted to watercourses. However, the highly urbanised city of Strasbourg negatively impacted nearby populations by reducing levels of genetic diversity and increasing population genetic differentiation. Main conclusionsThese results showed the need for management action by restoring breeding sites and creating migratory corridors for peripheral southern damselfly populations. However, our results also highlighted the resilience of southern damselfly in central range populations facing strong urbanisation pressures.

evolutionary biology↗

bioRxiv2024

Pitfalls and recommendations for large-scale SNP genotyping in a non-model endangered species: the southern damselflies (Coenagrion mercuriale) as a case study.

Genomic markers are essential tools for studying species of conservation concern, yet non-model species often lack a genome reference. 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, we retained 2,092 SNPs. We used them to characterise rear-edge populations of the southern damselfly in Northern France, a region where populations are sparsely distributed. Previous surveys utilising microsatellite markers allowed comparison of genetic diversity and differentiation estimates. Consistent with prior findings, genetic diversity estimates were similar across the studied populations that showed no sign of inbreeding. SNP markers exhibited greater resolution in detecting fine-scaled genetic structure, identifying two putative hybrids in adjacent populations, a feat unattainable with microsatellite loci. Altogether, this study highlighted the ongoing challenge of large-scale SNP genotyping using target sequencing techniques in non-model species to set conservation guidelines. Nonetheless, these new markers showed greater statistical power in identifying conservation units and offered the promise of greater precision in the identification of admixture events or the estimation of key population parameters such as effective population size.

evolutionary biology↗