Contrasting patterns of gene diversity between microsatellites and mitochondrial SNPs in farm and wild Atlantic salmon

Abstract

Levels of genetic variability at 12 microsatellite loci and 19 single nucleotide polymorphisms in mitochondrial DNA were studied in four farm strains and four wild populations of Atlantic salmon. Within populations, the farm strains showed significantly lower allelic richness and expected heterozygosity than wild populations at the 12 microsatellite loci, but a significantly higher genetic variability with respect to observed number of haplotypes and haplotype diversity in mtDNA. Significant differences in allele-and haplotype-frequencies were observed between farm strains and wild populations, as well as between different farm strains and between different wild populations. The large genetic differentiation at mitochondrial DNA between wild populations (F ST = 0.24), suggests that the farm strains attained a high mitochondrial genetic variability when created from different wild populations seven generations ago. A large proportion of this variability remains despite an expected lower effective population size for mitochondrial than nuclear DNA. This is best explained by the particular mating schemes in the breeding programmes, with 2-4 females per male. Our observations suggest that for some genetic polymorphisms farm populations might currently hold equal or higher genetic variability than wild populations, but lower overall genetic variability. In the short-term, genetic interactions between escaped farm salmon and wild salmon might increase genetic variability in wild populations, for some, but not most, genetic polymorphisms. In the long term, further losses of genetic variability in farm populations are expected for all genetic polymorphisms, and genetic variability in wild populations will be reduced if escapes of farm salmon continue.

Half a century of genetic interaction between farmed and wild Atlantic salmon: Status of knowledge and unanswered questions

“…An alternative is to include multiple farmed strains and/or wild populations to identify evidence of parallel evolution. While the former has been done in several studies (Debes & Hutchings, ; Einum & Fleming, ; Fleming, Agustsson, Finstad, Johnsson, & Bjornsson, ; Solberg et al., ; Thodesen, Grisdale‐Helland, Helland, & Gjerde, ), the latter is more resource demanding, although it has been carried out for several common‐garden studies (Fraser, Cook, Eddington, Bentzen, & Hutchings, ; Glover, Hamre, Skaala, & Nilsen, ; Harvey, Glover, Taylor, Creer, & Carvalho, ; Normandeau, Hutchings, Fraser, & Bernatchez, ; Solberg et al., ) and for studies of polymorphic genetic markers (Karlsson, Moen, & Hindar, ; Norris, Bradley, & Cunningham, ; Skaala et al., ). In addition, a few studies have combined both approaches by comparing multiple farmed and/or wild strains, while also including the major wild founding population (Harvey, Glover et al., ; Neregard et al., ; Solberg et al., ).…”

“…The effect of marker type on levels of genetic diversity within and among farmed strains and wild populations is further evidenced in studies of mtDNA. Analysis of mtDNA haplotypes in four Norwegian farmed strains and four Norwegian wild populations has revealed greater numbers of haplotypes in the farmed strains, even when the same strains simultaneously displayed reduced diversity in highly polymorphic markers (Karlsson et al., ). This result is counterintuitive given that the effective population size for mtDNA is normally lower than for nuclear loci, reflecting haploid and maternal inheritance of mtDNA.…”

Area use and movement patterns of wild and escaped farmed Atlantic salmon before and during spawning in a large Norwegian river

“…Wild salmon populations differ in genetic composition as a result of local adaptations to different eco-logical conditions (Garcia de Leaniz et al 2007). The farmed Atlantic salmon in Norway were founded by individuals from a few wild strains in the early 1970s, and have less genetic variation than the wild population due to domestication and selective breeding (Skaala et al 2005, Karlsson et al 2010. Consequently, crossbreeding between wild and farmed fish may lead to lower genetic variation and loss of local adaptability in wild Atlantic salmon populations (Ferguson et al 2007, Glover et al 2012, 2013.…”

Genetic structure and diversity in natural and stocked populations of the mandarin fish (Siniperca chuatsi) in China

“…Genetic diversity in the Amur River samples was very low, suggesting a serious decline of the species, possibly caused by recent habitat destruction and environmental degradation. The low genetic diversity we found in the hatchery populations (both in the central and southern areas) could be explained by several factors: 1) a relatively small effective population size; 2) the effects of genetic drift during the initial stages of transplanting; and 3) intensive directional selection in breeding programs (Doebley et al, 2006;Gross and Olsen, 2010;Karlsson et al, 2010). Therefore, for the genetic improvement of hatchery stocks it is necessary to construct a broad genetic base with a large effective population size, or to regularly introduce individuals from natural populations.…”