Data from: Levels and spatial patterns of effective population sizes in the southern damselfly (Coenagrion mercuriale): On the need to carefully interpret single-point and temporal estimations to set conservation guidelines
Data files
Dec 12, 2024 version files 14.98 MB
Abstract
The effective population size (Ne) is a key parameter in conservation and evolutionary biology, reflecting the strength of genetic drift and inbreeding. While demographic estimations of Ne are logistically and time-consuming, genetic methods have become more widely used due to increasing data availability. Nonetheless, accurately estimating Ne remains challenging, with few studies comparing Ne estimates across molecular markers types and estimators such as single-sample methods based on linkage disequilibrium or sibship analyses versus methods based on temporal variance in allele frequencies. This study aims at bridging this gap by analysing single-sample and temporally-spaced populations in the southern damselfly (Coenagrion mercuriale), a bioindicator Odonata species of conservation concern found in southwestern Europe’s freshwater stream networks. 77 local populations were sampled from a semi-urbanised area located in eastern France near Strasbourg city, yielding 2,842 individuals that were genotyped with microsatellites, and 958 of which were also genotyped for 2,092 SNPs. Spatial genetic structure was stable over time, suggesting porosity between alternate-year cohorts. When accounting for spatial genetic structure, single-sample and temporal estimations of Ne were consistent for each set of molecular markers. Biologically meaningful results were obtained when the effect of migration was minimising by considering metapopulation Ne-estimates based on the level of genetic differentiation and population boundaries. In terms of applied conservation and management, most depicted metapopulations displayed large Ne, indicating no immediate need for conservation measures to mitigate anthropogenic pressures, provided that a continuous suitable freshwater network is maintained. However, urbanization negatively impacted Ne levels in populations close to Strasbourg city. Because Ne is used to inform conservation decisions, caution is crucial in interpreting Ne estimates, especially in continuously distributed populations undergoing migration. Altogether, our study highlights the challenge of obtaining robust Ne estimates and the necessity of careful interpretation to set relevant conservation guidelines.
README: Levels and spatial patterns of effective population sizes in the southern damselfly (Coenagrion mercuriale): on the need to carefully interpret single-point and temporal estimations to set conservation guidelines
https://doi.org/10.5061/dryad.83bk3jb34
Description of the data and file structure
-Microsatellite genotypes (samples locations and genotypes at 10 microsatellite loci)
-2092 SNPs genotypes (samples locations and genotypes at 2092 SNPs loci)
Files and variables
File: Southern_Damselfly_Sample_microsatellite_genotype_and_locations.xlsx
Description: Southern_Damselfly_Sample_microsatellite_genotype_and_locations.xlsx – File containing for each sample: the name of the individual (Sample_Name), the name of the site where it was sampled (ID_Site), the sampling year (Year), population location (Longitude_EPSG4326 [East], Latitude_EPSG4326 [North]), individual multilocus genotypes at 10 microsatellite loci.
All individual samples were genotyped using ten unlinked nuclear microsatellite loci named LIST002, LIST023, LIST034, LIST035, LIST037, LIST042, LIST062, LIST024, LIST063, and LIST066, with forward and reverse primers initially isolated and described in Watts, P. C., Wu, J. H., Westgarth, C., Thompson, D. J., & Kemp, S. J., (2004) A panel of microsatellite loci for the Southern Damselfly, Coenagrion mercuriale (Odonata : Coenagrionidae). Conservation Genetics, 5, 117-119).
PCR reactions were performed in two multiplexes described in Table S2. PCR reactions were conducted in a volume of 10 µL, using 3 µL of DNA (0.5-5 ng/mL), 5 µL Multiplex PCR Master Mix (QIAGEN) and a primer mix (each primer at a final concentration of 0.2 µM). PCR amplifications were as follows: (i) 15 min at 95°C, (ii) 30 cycles for whole individuals, and 32 cycles for legs of 30 s denaturation at 94°C, 90 s annealing 55°C, and 60 s elongation at 72°C, (iii) 30 min at 60°C. 1.5 µL of PCR products (1/10 diluted for whole individual samples) were pooled with 0.25 μL of RadiantDyTM 632 500 MOB size standard (Eurogentec, Seraing, Belgium) and 9.75 μL of formamide (Applied Biosystems, Foster City, CA), electrophoresed and sized with an ABI PRISM 3130XL sequencer (Applied Biosystems) and the software GeneMapper 5.0 software (Applied Biosystems).
There is no missing data in this file.
File: Southern_Damselfly_Sample_2092SNP_genotype_and_locations.xlsx
Description: Southern_Damselfly_Sample_2092SNP_genotype.xlsx – File containing for each sample: the name of the individual (Sample_Name), the name of the site where it was sampled (ID_Site), the sampling year (Year), its location (Longitude_EPSG4326 [East], Latitude_EPSG4326 [North]), its genotype at the 2092 SNPs loci extracted from a genind genotype format as a matrix. Each 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 data are encoded by "NA".