IIb-RAD-sequencing coupled with random forest classification indicates regional population structuring and sex-specific differentiation in salmon lice (Lepeophtheirus salmonis)

Abstract

The aquaculture industry has been dealing with salmon lice problems forming serious threats to salmonid farming. Several treatment approaches have been used to control the parasite. Treatment effectiveness must be optimized, and the systematic genetic differences between subpopulations must be studied to monitor louse species and enhance targeted control measures. We have used IIb-RAD sequencing in tandem with a random forest classification algorithm to detect the regional genetic structure of the Norwegian salmon lice and identify important markers for sex differentiation of this species. We identified 19,428 single nucleotide polymorphisms (SNPs) from 95 individuals of salmon lice. These SNPs, however, were not able to distinguish the differential structure of lice populations. Using the random forest algorithm, we selected 91 SNPs important for geographical classification and 14 SNPs important for sex classification. The geographically important SNP data substantially improved the genetic understanding of the population structure and classified regional demographic clusters along the Norwegian coast. We also uncovered SNP markers that could help determine the sex of the salmon louse. A large portion of the SNPs identified to be under directional selection was also ranked highly important by random forest. According to our findings, there is a regional population structure of salmon lice associated with the geographical location along the Norwegian coastline.

Keywords: Norway; geographical distribution; population genetics; salmon lice; sex.

FIGURE 1

Salmon lice adult life stage. Salmon louse adult male (above) and adult female (below). Adult female produces egg strings (not shown in the figure)

FIGURE 2

Geographical locations of lice sampling. The map shows all 12 sites of salmon lice collection. Each 3 sampling sites are grouped regionally RA: P01‐P03, VE: P04a‐P05, MD: P06‐P08, and NN: P09‐P12. The coordinates and full details of locations are included in Table S1. Map was plotted using R package ggmap

FIGURE 3

SNPs putatively under selection. (a) Output plot of BayeScan software where each dot represents one SNP out of 19428 SNPs. Black, red, and blue color represent balancing, diversifying, and neutral SNPs, respectively. The SNPs putatively under diversifying selection are annotated by contig number and position. (b) Detection of loci under selection from genome scans based on Fst simulations implemented in Arlequin. Red annotated dots represent loci under diversifying selection, and details of each locus under selection are listed in Table 3. Dotted yellow and blue lines indicate 50% and 95% quantiles, respectively

FIGURE 4

Geography‐based distinction and population structure in lice populations using Rf‐reduced datasets. (a) Heatmap showing pairwise Fst values based on Rf‐reduced (RfGeo) and full‐SNP dataset. Asterisk denotes the significant Fst values (FDR adjusted p < .05). The values above diagonal are the full‐SNP dataset, and the values below diagonal are the RfGeo dataset. (b) PCA plot of RfGeo dataset showing each sampling site. (c) UMAP projection of RfGeo, Euclidean distance metric, and 23 neighbors. Clusters are formed pertaining to each distinct geographical population. (d) The local populations are mixed within geographical regions clusters on C. RA: P01‐P03, VE: P04a‐P05, MD: P06‐P08, and NN: P09‐P12

FIGURE 5

Sex‐based distinction mapping of sex‐specific SNPs at the chromosomal level. (a) PCA biplot of RfSex dataset where blue dots represent male individuals and pink dots represent females. The arrows for each SNPs point in the direction of increasing values of that variable. (b) UMAP projection of RfSex, euclidean metrics, and 13 neighbors. Two distinct clusters are formed, one for each sex. (c) RfSex SNPs were mapped across the chromosomes using the IoA‐001 assembly. In the chromosomal assembly, 11 SNPs were mapped out of 14. Variant types are represented by distinct colors, and a number of mapped variants per chromosome are shown

FIGURE 6

The membership probability plot showing the probability of each individual being assigned to a population or sex. Membership probability plots for population assignment in geographical regions using DAPC, where each bar represents a single individual. Upper panel: Full‐SNP dataset (left) and important SNPs RfGeo (left). Membership probability plot for sex assignment, where each bar represents a single individual. Lower panel: Full‐SNP dataset (left) and important SNPs RfSex (right)