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Microsatellite marker data for Chernobyl Daphnia populations

Citation

Auld, Stuart (2022), Microsatellite marker data for Chernobyl Daphnia populations, Dryad, Dataset, https://doi.org/10.5061/dryad.0cfxpnw48

Abstract

Populations experiencing varying levels of ionising radiation provide an excellent opportunity to study the fundamental drivers of evolution. Radiation can cause mutations, and thus supply genetic variation; it can also selectively remove individuals that are unable to cope with the physiological stresses associated with radiation exposure, or non-selectively cull swathes of the population, reducing genetic variation. Since the nuclear power plant explosion in 1986, the Chernobyl area has experienced a spatially heterogeneous exposure to varying levels of ionising radiation. We sampled Daphnia pulex (a freshwater crustacean) from lakes across the Chernobyl area, genotyped them at ten microsatellite loci, and also calculated the current radiation dose rates. We then investigated whether the pattern of genetic diversity was positively associated with radiation dose rates, consistent with radiation-mediated supply of de novo mutations, or negatively associated with radiation dose rates, as would be expected with strong radiation-mediated selection. We found that measures of genetic diversity, including expected heterozygosity and mean allelic richness (an unbiased indicator of diversity) were significantly higher in lakes that experienced the highest radiation dose rates. This suggests that mutation outweighs selection as the key evolutionary force in populations exposed to high radiation dose rates. We also found significant but weak population structure, indicative of low genetic drift, and clear evidence for isolation by distance between populations. This further suggests gene flow between nearby populations is eroding population structure, and that mutational input in high radiation lakes could, ultimately, supply genetic variation to lower radiation sites.

Methods

Genomic DNA was extracted from 205 whole Daphnia samples from the seven Chernobyl lake populations that varied in radiation dose rates. We used protocols provided in NucleoSpin Tissue XS (Machery Nagel). We successfully amplified eleven microsatellite markers for each Daphnia across two multiplexes, though one marker exceeded a 5% null allele rate and was thus excluded from further analysis. Multiplex PCR reactions consisted of 5 µL 2 ×Type-it Multiplex PCR Mastermix (Qiagen), 3 µL Nuclease Free H2O, 1 µL primer mix solution and 1 µL DNA to give a total volume of 10 µL per reaction. The PCR programme was as follows: 15 minutes at 95 ºC for Taq activation, followed by 30 cycles of 30 seconds at 94 ºC for denaturation of the DNA into separate strands, 90 seconds at 57 ºC for annealing of the DNA strands to template DNA and 90 seconds at 72 ºC for extension. The final extension was performed for 30 minutes at 60 ºC. The final PCR products were analysed with an ABI 3730XL DNA Analyzer (at the Protein Phosphorylation and Ubiquity-lation Unit, University of Dundee, UK) using the GeneScan-500 LIZ size standard (Applied Biosystems). Microsatellite band scoring was completed manually using GENEIOUS software (Biomatters, version 9.1.8). The strongest peak(s) within the loci were selected to determine allele size.

Funding

Natural Environment Research Council, Award: NE/L000369/1

Natural Environment Research Council, Award: NE/L011549/1