From the gene lab

PhD defence about genetic interactions between domesticated and wild trout

Wednesday 13 Dec 17

Time & Place

Thursday 14 December 2017, 1 p.m. 

DTU Aqua
8600 Silkeborg

The thesis

A copy of the thesis "Adaptive differences between wild and farmed trout: linking traits with genomic variation" is available for reading at DTU Aqua. Contact Rikke Hansen,

PhD Student Thomas Frank-Gopolos has produced experimental trout families with different levels of domestic-wild genetic ‘mixing’ and compared their fitness after some time. On 14 December he will defend his thesis based on the results 

There is increased concern about the perspectives of maintaining the genetic integrity of wild fish populations in the face of human impacts. A specific concern relates to the potentially detrimental effects of released and escaped fish of aquaculture origin, which may affect the gene pools and fitness of their wild counterparts. However, knowledge about direct effects of introgression with genes of aquaculture origin on fitness traits in the wild is at best scarce.

To expand the current knowledge, Thomas Frank-Gopolos, DTU Aqua has dedicated his PhD project to this subject, with specific attention to the potential adverse fitness consequences in native populations under contrasting environmental conditions. 

This was approached by producing experimental brown trout families representing different levels of domestic-wild genetic ‘mixing’ and comparing physical traits after short and long term periods of growth under standardized farming conditions. 

The results show that growth is generally enhanced in families with higher proportions of domesticated genes, demonstrating that interbreeding can potentially alter fitness traits in wild populations. The effect was stronger at high temperatures, suggesting that impact of domestic-wild interactions may increase under a future warmer climate. 

About the defence

Thomas Frank-Gopolos will defend his PhD thesis, "Adaptive differences between wild and farmed trout: linking traits with genomic variation” on 14 December 2017. The defence will take place at DTU Aqua, Vejlsøvej, 8600 Silkeborg, at 1 p.m. 


  • Principal supervisor: Senior Researcher Dorte Bekkevold, DTU Aqua
  • Co supervisor: Professor Einar Eg Nielsen, DTU Aqua


  • Senior Researcher Jakob Hemmer Hansen, DTU Aqua
  • Doctor Sarah J. Helyar, Queen’s University Belfast, Ireland
  • Environmental expert Lasse Fast Jensen, Vattenfall AB, Sweden

Chairperson at the defence

  • Deputy Director Anders Koed, DTU Aqua

Summary of the thesis

The overarching objective of the present PhD thesis was to expand the current knowledge on genetic interactions between domesticated and wild conspecifics in cultured fish species with specific attention to the potential adverse fitness consequences in native populations under contrasting environmental conditions.This was approached by producing experimental brown trout (Salmo trutta, L.) families representing a domestic-wild introgression gradient, i.e. pure wild and hatchery extremes as well as their hybrids and backcrosses, and testing fitness-related phenotypic traits using a common-garden design under standard hatchery conditions.

The experiments allowed us to study trait variations among families representing various stages of introgression and to apply QTL mapping for the association of diverging fitness traits with their coding regions in the trout genome. Results were envisioned to support management decisions and guide future research on topics within the fields of aquaculture and conservation.

Manuscript A reports on the temperature dependency of introgression effects on growth and survival under three temperatures (7 °C, 12 °C and 16 °C). Our results showed additive genetic effects of introgression level on growth traits at 12 °C and 16 °C with substantial growth enhancement even in families of lowest tested hatchery strain input. Conversely, condition and survival was not significantly associated with introgression level. These findings suggest that altered growth patterns and potential cascading effects are likely of greater importance to the severity of domestic/wild introgression than changes related to condition factor and survival, albeit this requires confirmation under natural conditions. Results also suggest that effects of introgression on life history traits may increase under warmer conditions, and global change of thermal profiles of rivers may hence influence introgression dynamics and ultimately determine the fate of afflicted wild populations.

Manuscript B reports on the underlying genetic architecture of fitness traits, which is key to understanding the genomic pathways of domestic/wild introgression. Based on a variance component mapping method using SNP markers, we identified quantitative trait loci (QTL) for fitness traits body length, body weight, condition factor, growth rate and age of maturation, measured at ages 1, 1.5 and 2.5 y. 27 genome-wide significant QTL were identified across 12 linkage groups with general contribution from parents of all three genetic backgrounds (wild, admixed and hatchery), indicating that QTL are polymorphic both in wild and hatchery strains. Within traits, QTL were not consistent across life stages but showed distinct ontogenetic shifts. Thus, the study identified genetic variation affecting several fitness traits in natural, admixed brown trout populations, corroborating the general conception that introgression may lead to altered functional trait composition.

Manuscript C reports on introgression effects on life-history traits maturation age and maturation phenology and their association with growth traits across juvenile, post-smolt and adult life history stages. Despite documented domestic-wild growth divergence among the experimental families used, our results showed no evidence of an additive genetic effect of introgression on maturation age and phenology, indicating little selective forcing on maturation traits during hatchery propagation of the partially domesticated strain used in experimental crosses. We, thus, do not expect stocking with the specific hatchery strain across Danish rivers during the 1980’es and 1990’es to have induced significant changes in these life-history traits. Also, our results did not add support to the notion that physical isolation of spawning contingents may offer introgression resistance in some wild populations.