Population genetic structure of the parasitic copepod Lepeophtheirus salmonis throughout the Atlantic

Abstract

The parasitic copepod Lepeophtheirus salmonis is responsible for huge economic losses in the salmonid aquaculture industry, and has been linked with declines of wild salmonid populations. In order to elucidate population genetic structure throughout the Atlantic Ocean, 2495 lice representing 27 samples collected from 22 locations were analysed for 14 microsatellite loci. Significant overall genetic variation was observed (14 loci: global F ST = 0.0057, p < 0.0001), although this decreased slightly when an outlier locus (LsalSTA3), detected as a candidate for positive selection, was removed (13 neutral loci: global F ST = 0.0022, p < 0.0001). A relationship between physical and genetic distance was observed (R 2 = 0.179, p = 0.0013), but only when data from LsalSTA3 was included. No overall genetic variation was observed among the 19 samples collected in Norway (Norwegian global F ST < 0.0001, p = 0.6). None of the within-country (Canada, Ireland, Shetland and Faroe Islands) pairwise F ST values were statistically significant when analysing the 13 neutral loci and following Bonferroni correction. Samples taken at 5 Norwegian farms did not exhibit significant genetic differences before and after medicated treatment. We conclude that L. salmonis displays weak but nevertheless statistically significant population genetic variation throughout the Atlantic. Analysis of temporal samples, potentially combined with larger numbers of markers giving greater genome coverage, will be required to fully elucidate the biological significance of the observed variation.

How does sequence variability affectde novoassembly quality?

“…However, the increase in variability from the wild 24 × data set to the wild 36 × data set was surprisingly low considering that the wild 24 × data sets were generated from single localities whereas the wild 36 × data sets contained reads from all localities. This suggests that most of the variable sites are found throughout the North Atlantic, supporting earlier studies indicating that L. salmonis displays a high degree of gene-flow, consistent with a species that can disperse at both planktonic and adult stages (Glover et al 2011). The homogeneous level of sequence variability in the 36 × data sets compared with the smaller data sets, that all stem from single sequencing runs, is probably the result of the bootstrapping procedure averaging variability among sequencing runs, which in turn indicates that the error rate variation between sequencing runs is noticeable.…”

“…This appears to confirm the reduced sequence variation in the inbred strain reported earlier (Hamre et al 2009) and later supported by analyses using an expanded set of microsatellites (12 out of 13 microsatellites were fixed, the last had two alleles, data not shown) following methods previously reported (Glover et al 2011). The apparent large remaining sequence variability in the inbred strain seems surprising if microsatellite variability is a reliable proxy of genetic variation.…”

“…Four of these have been described previously (Glover et al 2011): C858 (Canada), S856 (Shetland), I852 (Ireland), N849 (northern Norway). The fifth sample consisting of eight females was collected in September 2008 from an emamectin-benzoate-desensitized population in Austevoll, western Norway.…”

Salmon lice (Lepeophtheirus salmonis) development times, body size, and reproductive outputs follow universal models of temperature dependence

“…On the other hand, the fit of our data to universal models of temperature dependence suggests that faster than expected development times to the infective stage may not have occurred yet, or the genetic change has not spread to all lice populations yet. However, the salmon louse has a huge spread potential, and evidence suggests a panmictic population (Glover et al 2011). Therefore, any genetic changes would spread within a few years (Besnier et al 2014).…”

A Review of Molecular Approaches for Investigating Patterns of Coevolution in Marine Host–Parasite Relationships

“…To gain insights into adaptive coevolutionary processes at ecological timescales and moreover to gain direct information on selective processes involving the interactions of individuals with their environment, higher resolution can often be achieved with functional markers that are under selection. Several studies have shown that the proportion of quantitative trait variation at the population level is much higher than it is for neutral markers (Conover et al, 2006;Glover et al, 2011;Hemmer-Hansen et al, 2007;Nielsen et al, 2009;Westgaard and Fevolden, 2007). Thus far, nonneutral markers have only been applied in potential fish host species; there are no data available on parasites.…”