Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish

Abstract

The use of genetic markers in the context of conservation is largely being outcompeted by whole-genome data. Comparative studies between the two are sparse, and the knowledge about potential effects of this methodology shift is limited. Here, we used whole-genome sequencing data to assess the genetic status of peripheral populations of the wels catfish (Silurus glanis), and discuss the results in light of a recent microsatellite study of the same populations. The Swedish populations of the wels catfish have suffered from severe declines during the last centuries and persists in only a few isolated water systems. Fragmented populations generally are at greater risk of extinction, for example due to loss of genetic diversity, and may thus require conservation actions. We sequenced individuals from the three remaining native populations (Båven, Emån, and Möckeln) and one reintroduced population of admixed origin (Helge å), and found that genetic diversity was highest in Emån but low overall, with strong differentiation among the populations. No signature of recent inbreeding was found, but a considerable number of short runs of homozygosity were present in all populations, likely linked to historically small population sizes and bottleneck events. Genetic substructure within any of the native populations was at best weak. Individuals from the admixed population Helge å shared most genetic ancestry with the Båven population (72%). Our results are largely in agreement with the microsatellite study, and stresses the need to protect these isolated populations at the northern edge of the distribution of the species.

Exceptional longevity in northern peripheral populations of Wels catfish (Silurus glanis)

“…certain years) offer thermal conditions (> 22 °C) that allow for successful reproduction 18 , 43 . This is also supported by previous genetic studies showing very low effective population sizes in all three peripheral populations of catfish in Sweden 19 , 20 . Under such circumstances, natural selection should favor a longer reproductive lifespan to maximize the reproductive opportunity 1 , 2 but further studies are required to evaluate whether and how peripheral populations of catfish harbor unique adaptive variation that impacts growth rates, age-at-maturity and longevity.…”

“…However, it is equally possible that these peripheral populations have evolved local adaptations in growth trajectories and age-at-maturity that impact longevity 1 – 3 . These populations are geographically isolated and genetically differentiated from the ones in the core distribution area 19 , 20 and reside in habitats that only sporadically (i.e. certain years) offer thermal conditions (> 22 °C) that allow for successful reproduction 18 , 43 .…”

“…The northern peripheral populations of catfish were established in Sweden during warmer post glacial ages, 9500 to 8000 years ago, when the Baltic Sea was a freshwater lake (the Ancylus Lake). Today, these populations show pronounced genetic differentiation and low allelic diversity compared to the larger populations in central and eastern Europe 19 , 20 . Microsatellite and single nucleotide polymorphism (SNP) analysis reveals that the Swedish populations not only differ from other European populations, but to a lesser extent also from each other.…”

“…Microsatellite and single nucleotide polymorphism (SNP) analysis reveals that the Swedish populations not only differ from other European populations, but to a lesser extent also from each other. Moreover, genetic analyses also suggest that the effective population sizes are very low in all Swedish populations 19 , 20 which, together with the fragmented and sparse distribution, have contributed to catfish being considered endangered in this peripheral habitat and of high conservation status including complete protection from fishing.…”

Analysis of Autozygosity Using Whole-Genome Sequence Data of Full-Sib Families in Pikeperch (Sander lucioperca)

“…The observed nucleotide diversity was very low compared to mammals, such as cattle (Zhang et al, 2015b) or pigs (Bosse et al, 2012). Such low values have also been observed in other fish species, for instance, salmon (Kijas et al, 2018) and catfish (Jensen et al, 2021). Based on the relationship π 4 N e ν with a mutation rate ν per sequence (Nei and Takahata, 1993), this outcome also strengthens the indication that past N e size must have been rather small in pikeperch.…”