Is increased mutation driving genetic diversity in dogs within the Chornobyl exclusion zone?

Abstract

Environmental contamination can have lasting impacts on surrounding communities, though the long-term impacts can be difficult to ascertain. The disaster at the Chornobyl Nuclear Power Plant in 1986 and subsequent remediation efforts resulted in contamination of the local environment with radioactive material, heavy metals, and additional environmental toxicants. Many of these are mutagenic in nature, and the full effect of these exposures on local flora and fauna has yet to be understood. Several hundred free-roaming dogs occupy the contaminated area surrounding the Chornobyl Nuclear Power Plant, and previous studies have highlighted a striking level of genetic differentiation between two geographically close populations of these dogs. With this work, we investigate mutation as a possible driver of this genetic differentiation. First, we consider large-scale mutation by assessing the karyotypic architecture of these dogs. We then search for evidence of mutation through short tandem repeat/microsatellite diversity analyses and by calculating the proportion of recently derived alleles in individuals in both populations. Through these analyses, we do not find evidence of differential mutation accumulation for these populations. Thus, we find no evidence that an increased mutation rate is driving the genetic differentiation between these two Chornobyl populations. The dog populations at Chornobyl present a unique opportunity for studying the genetic effects of the long-term exposures they have encountered, and this study expands and builds on previous work done in the area.

Fig 1. Derived allele analysis pipeline.

The analysis involves setting the basenjis as ancestor (Phase 1), counts and proportion calculations for each individual (Phase 2), and summary of the combinatorial pairings for the analysis (Phase 3). CC represents Chornobyl City, NPP represents the Nuclear Power Plant. A simplified representation of derived allele analysis at the single locus level is featured in the lower right, where the ancestor represented here is the basenji. In the derived allele analyses, we scan the genome for instances such as these, where either the PP individual shows evidence of the derived allele (left) or the CC individual contains the derived allele (right) when compared to the ancestor (basenji).

Fig 2. DAPI banded chromosomes of a lymphocyte from a free ranging female dog from the Chornobyl Nuclear Power Plant population.

This cell contains 76 autosomes and two X chromosomes, as expected from a domestic dog. (A) and (B) show a DAPI banded metaphase spread and associated karyotype, respectively, tinted to highlight chromosome pairs. (C) and (D) show the DAPI-banded metaphase spread and associated karyotype, respectively, with tinting removed to allow gross cytogenetic evaluation. All cells evaluated had no evidence of gross structural or numerical changes. Tinted metaphases and karyotypes were generated using SmartType v 3.4.12 (Digital Scientific, Cambridge, UK).

Fig 3. Genetic differentiation analyses for Chornobyl and Eastern European free-breeding dog populations.

(A) Pairwise F_ST measures between all five populations, color scales from low F_ST (white) to high F_ST (blue). All F_ST values are significant based on bootstrapping to 99% confidence interval. (B) Cluster analysis and subsequent discriminant analysis of principal components, where cluster two (blue) is entirely Nuclear Power Plant individuals and cluster one (gold) contains the other four groups.

Fig 4. Representative selection of allele frequency distributions for three loci.

Included here are (A) AHTk253, (B) CDH4, (C) VGL2409. Chornobyl City frequencies indicated in gold, Nuclear Power Plant in blue. More plots are available in S1 Fig.

Fig 5. Summary of derived allele proportions for all 25 possible pairs of Nuclear Power Plant (NPP) and Chornobyl City (CC) individuals for all three analyses.

These plots depict Replicate one and Replicate two, with basenji as the common ancestor, and the final trial with gray wolf serving as the ancestor. Box plots highlight lower quartile, median, and upper quartile, and the whiskers extend to the most extreme values but not further than 1.5 * inter-quartile range (IQR) from the hinge. Points indicate the true proportions taken for each comparison.