Human-induced evolution caught in action: SNP-array reveals rapid amphi-atlantic spread of pesticide resistance in the salmon ecotoparasite Lepeophtheirus salmonis

Abstract

Background: The salmon louse, Lepeophtheirus salmonis, is an ectoparasite of salmonids that causes huge economic losses in salmon farming, and has also been causatively linked with declines of wild salmonid populations. Lice control on farms is reliant upon a few groups of pesticides that have all shown time-limited efficiency due to resistance development. However, to date, this example of human-induced evolution is poorly documented at the population level due to the lack of molecular tools. As such, important evolutionary and management questions, linked to the development and dispersal of pesticide resistance in this parasite, remain unanswered. Here, we introduce the first Single Nucleotide Polymorphism (SNP) array for the salmon louse, which includes 6000 markers, and present a population genomic scan using this array on 576 lice from twelve farms distributed across the North Atlantic.

Results: Our results support the hypothesis of a single panmictic population of lice in the Atlantic, and importantly, revealed very strong selective sweeps on linkage groups 1 and 5. These sweeps included candidate genes potentially connected to pesticide resistance. After genotyping a further 576 lice from 12 full sibling families, a genome-wide association analysis established a highly significant association between the major sweep on linkage group 5 and resistance to emamectin benzoate, the most widely used pesticide in salmonid aquaculture for more than a decade.

Conclusions: The analysis of conserved haplotypes across samples from the Atlantic strongly suggests that emamectin benzoate resistance developed at a single source, and rapidly spread across the Atlantic within the period 1999 when the chemical was first introduced, to 2010 when samples for the present study were obtained. These results provide unique insights into the development and spread of pesticide resistance in the marine environment, and identify a small genomic region strongly linked to emamectin benzoate resistance. Finally, these results have highly significant implications for the way pesticide resistance is considered and managed within the aquaculture industry.

Figure 1

Lepeophtheirus salmonis sample locations throughout the Atlantic. The letter in front of a sample number indicates the source: C = Canada, F = Faroe Islands, I = Ireland, N = Norway, S = Shetland.

Figure 2

Distribution of SNPs relative to global inter–region F _ST value. A. barplot where SNPs are ranked on the x axis in decreasing order of F_ST value. The highest 10% values are represented with red bars. B. Distribution of the SNPs position on the linkage map. linkage groups 1 to 14 are represented as horizontal bars with length proportional to recombination frequencies in cM. Each SNP is represented as a vertical grey bar. SNPs displaying the highest 10% F_ST values are represented with red bars.

Figure 3

Distribution of SNPs under positive selection on the linkage map. Linkage groups from 1 to 14 are represented as horizontal bars with length proportional to recombination frequencies in cM. Each SNP is represented as a vertical grey bar. SNPs under positive selection are colored in red.

Figure 4

Pairwise linkage disequilibrium among SNPs on linkage group 5 in sample I852 (Ireland). Linkage map with SNP position in cM is represented on the diagonal of the LD matrix. SNPs under positive selection are colored in red. Black segments connect the SNP positions on the linkage map to the SNP positions on the LD matrix.

Figure 5

Genome scan of Shetland (S856) sample for selective sweeps. A and B represent respectively CLR calculated by SweeD and Omega statistic calculated by OmegaPlus on the y-axis, and the genome position in cM on the x-axis. Alternating grey and white areas separates linkage groups. C represents the joint plot of CLR and omega statistic. SNPs detected as outlier (p < 0.05) by both methods are in red.

Figure 6

Close-up of CLR scans for selective sweeps on linkage group 1 and linkage group 5 in S856 sample. A and B: Close up of CLR scan for selective sweep on linkage group 1 and 5 in S856 sample. C and D: haplotypes present with frequency >10% in the same two genomic regions, and individualized by color. Sampling sites are reported together with haplotype frequency in percent within sampling site. E and F: predicted genes under the same two genomic regions.

Figure 7

Genome scan for association between 3 consecutive SNPs haplotypes and resistance to EMB, in the F2 dataset (A), and F1 dataset (B). Cumulative genomic position is represented on the X axis with alternating grey and white areas to delimitate linkage groups. Dispersion parameter of the random genetic effect is reported on the Y axis. Areas corresponding to selective sweeps are colored in red. The 5% significance threshold is represented as horizontal dashed line.