Reduced genetic diversity and low effective size in peripheral northern European catfish Silurus glanis populations

Abstract

Using 10 polymorphic microsatellites and 1251 individual samples (some dating back to the early 1980s), genetic structure and effective population size in all native and introduced Swedish populations of the European wels catfish or Silurus glanis were studied. Levels of genetic variability and phylogeographic relationships were compared with data from a previous study of populations in other parts of Europe. The genetically distinct Swedish populations displayed comparably low levels of genetic variability and according to one-sample estimates based on linkage disequilibrium and sib ship-reconstruction, current local effective population sizes were lower than minimum levels recommended for short-term genetic conservation. In line with a previous suggestion of postglacial colonisation from a single refugium, all Swedish populations were assembled on a common branch in a star-shaped dendrogram together with other European populations. Two distinct subpopulations were detected in upper and lower habitats of River Emån, indicating that even minor dispersal barriers may restrict gene flow for wels in running waters. Genetic assignment of specimens encountered in the brackish Baltic Sea and in lakes where the species does not occur naturally indicated presence of long-distance sea dispersal and confirmed unauthorised translocations, respectively.

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

“…We found that the population of catfish from Emån displayed slightly higher estimates of genetic variation than the two other extant native Swedish populations of Båven and Möckeln, regardless of whether diversity was estimated as nucleotide diversity (π), heterozygosity (H) or proportion of polymorphic loci (P). This is in contrast to Palm et al ( 2019 ) who reported the highest diversity in Båven followed by Emån and then Möckeln. This difference may be indicative of the uncertainty of basing genetic diversity estimates on a few highly polymorphic loci when comparing populations.…”

“…Here, we show that many of the inferences made in a previous microsatellite-based analysis (Palm et al 2019 ) remain robust and are hence corroborated by our whole-genome re-sequencing approach. This is to our knowledge one of the first intraspecific comparisons of the same study populations in which traditional marker-based genetic study can be directly compared with genomic study.…”

“…This is especially true for inferences about possible past and present inbreeding, which can be made from resequencing data but are more obscure in a microsatellite study. Below we discuss our findings and discuss their resemblance and differences to the previously published microsatellite analyses (Palm et al 2019 ). This is no way in disregard of the quality of previous work but as an example how different methods and analytical tools may or may not arrive at different conclusions.…”

“…In addition, we use whole-genome resequencing of individuals from four Swedish populations (three native and one reintroduced) to make inferences on genetic diversity, differentiation, and estimates of inbreeding in Swedish catfish. We use our data to compare with similar estimates obtained in a previously published genetic study using microsatellites (Palm et al 2019 ) on the same populations, to determine whether our whole-genome approach yields additional population genetic inferences and conservation genetic recommendations.…”

“…Microsatellite markers applied in Triantafyllidis et al ( 2002 ) have recently been used to infer population substructure and diversity in Sweden (Palm et al 2019 ). Genetic diversity was among the lowest reported in Europe, and high levels of genetic differentiation were observed between the Swedish populations (Palm et al 2019 ). Among the three native populations, no substantial differences in genetic diversity were apparent.…”