Genetic Analysis Projects

Genetic Analysis Projects

Analysis of the DNA of salmon and trout is a valuable technique that is helping to answer a number of fundamental questions about these fish. These include population structures, and the extent to which stocks of salmon and trout form genetically distinct populations; determining the sex of fish without killing them and distinguishing between farmed and stocked fish.

This work has been greatly assisted by three major EU funded projects that among other things, analysed sea trout population structures in the Irish and Celtic seas[1], the North Sea[2] and the Channel[3]

Cornish Small Streams Project

The project analysed the genetic profiles of trout population in six small streams in Cornwall, three of them coastal streams and three tributaries of the Fowey. The results were supplemented by samples from 20 populations from 13 rivers/streams, part of the genetic baseline produced for the EU-funded Atlantic Aquatic Resource Conservation project (AARC), which analysed resident trout populations in sea trout rivers across southern England.

The results demonstrated contrasting patterns of genetic structuring between a number of small coastal streams and larger catchments. The latter, such as the Fowey and associated rivers, tend to contain very closely related populations with higher levels of genetic diversity, the result of straying between streams within the catchments. Some of the small coastal streams, on the other hand, are genetically distinct and appear to be isolated from each other and the larger catchments; they are also characterised by low levels of genetic diversity.

There appear to be a number of reasons why these small coastal streams are so distinct. One of the main causes seems to be barriers to upstream migration. This isolation of fish above barriers has produced populations with highly distinctive genetic profiles. However, the low level of genetic diversity in these populations potentially reduces their ability to adapt to changing environmental conditions and substantially increases their risks of extinction.

Where there are no barriers to sea trout movement, small coastal streams have levels of diversity comparable to that found in large catchments. The Caerhays, for example, is a small stream to the west of Carrick Roads and is genetically similar to the neighbouring rivers flowing into the Fal estuary, fitting in with the patterns of genetic diversity and population structure in south Cornwall.

Overall, while the project identifies genetically distinct populations in a number of small coastal streams, it suggests that this is largely due to the impact of human activities, such as the erection of barriers and industrial activity; these also reduce the genetic diversity of the surviving population. This highlights the vulnerability of small stream populations and the need, wherever possible, to restore natural ecosystems and to remover barriers to movement and migration.

Partners: West Country Rivers Trust; Exeter University; Atlantic Salmon Trust

AST Funding: £10,800 in 2014

Sea Trout Sex Ratios in the River Tamar

This is a two year project, the overall objective of which is to establish the sex ratios of sea trout entering and leaving the river Tamar. This will contribute to development of Biological Reference Points for sea trout and will improve our understanding of anadromy in trout. Specific objectives will be to establish the proportion of female fish within each age class, whether the sex ratio is consistent for different sea age classes, and whether the sex ratio changes with timing of river entry. The project uses genetic techniques to determine the sex of the fish. Smolts are caught for sampling in a screw trap on their downstream migration, and returning Finnock (school peal) and adult sea trout are taken in a trap at the weir at Gunnislake, at the tidal limit of the Tamar.

In 2015, the first year of the project, results were obtained from 300 smolts, 197 finnock and 205 sea trout. These showed that 80% of smolts were female, falling to 70% for finnock and one year old sea trout. Nearly all the latter had spawned first as finnock. For sea trout that had spawned first as finnock and were two years old and more, the proportion of females fell to 45%, although the sample was relatively small (31 fish). Interestingly, for sea trout which spawned first after spending a winter at sea, including those that had spawned more than once, the percentage of females (67%), was close to that for finnock and one year old fish, although the sample here was even smaller (12 fish). It remains to be seen whether these results will be replicated in 2016.

The high proportion of female smolts is in line with the preponderance of females in many sea trout stocks. However, the fall in the percentage of females in returning finnock, and presumably the higher mortality of female smolts, was unexpected, as was the apparent preponderance of males among older fish. Again, it remains to be seen whether these results will be replicated in 2016.

Partners: Environment Agency; Exeter University and Atlantic Salmon Trust

AST Funding: £5,500 in 2015 and £5,000 in 2016

Shetland Sea Trout  

This project sought to establish the contribution stocking has made to Shetland sea trout stocks. Burns in Shetland have been stocked over the past 10 years with trout of farmed origin, and sea trout catches have seen a significant improvement, from an annual average of around 10 fish in the 1990s to one of approximately 800 fish over the last 10 years. The project therefore sought to answer the two following questions:

  • Genetically, are there two groups of trout in the burns of Shetland – one corresponding to wild fish and the other to stocked fish?
  • If this is the case, are sea trout caught in the marine environment of wild or stocked origins?

To do this, trout from three sources were sampled for genetic analysis at Exeter: 1) fry were electro-fished from burns, 2) tissue samples were taken from farm broodstock, and 3) tissues samples were taken from adult sea trout. In total, 356 fish, comprising 267 resident fish (fry/parr), 50 SAA broodstock (25 cocks and 25 hens) and 39 sea trout were analysed.

Although some sample sizes were relatively small, the results were clear:

  • There is a very clear genetic difference between fish of stocked and wild origin;
  • Fry were predominantly of wild origin, even in burns with a long history of stocking
  • The highest proportion of fry of stocked origin was 32% in one burn, but this has only a very small area of spawning gravels on the outflow of a small loch.
  • Only one adult sea trout was of stocked origin, with a small number being stocked x wild hybrids. The vast majority of adult sea trout were of wild origin.

From the evidence from this project, it seems evident that stocking is having a very limited impact on sea trout numbers in Shetland.

Partners: Exeter University and Atlantic Salmon Trust

AST Funding: £7,500 in 2015

Why does a ‘brown’ trout become a ‘sea’ trout?

The aim of this project, undertaken as a PhD, funded under the IBIS Interreg programme, was to examine the population structuring of brown trout (Salmo trutta) (referred to as trout hereafter) across the Foyle catchment, Ireland. The three main questions addressed were:

1) do coexisting freshwater resident trout (brown trout) and anadromous trout (sea trout) originate from the same gene pool?

2) do trout in the Foyle catchment comprise multiple separate genepools with limited interbreeding?

3) which tributaries of the River Faughan (Foyle catchment) produce the sea trout?.

On the first question: the study identified five populations from three rivers, with co-existing brown trout and sea trout. All five of these populations produced both brown trout and sea trout indicating that there is no genetic differentiation between co-existing brown trout and sea trout within populations.

On the second question: analysis of trout from 30 sampling sites across six sub-catchments of the Foyle showed three major genetic groups, with two genetic groups dividing the north and south of the Foyle catchment. Further, more detailed analysis revealed 19 genetically distinct populations with structuring evident between tributaries within sub-catchments and, on occasion, between sampling sites within tributaries (Figure 1).

tributaries 1.River Burntollet
2.River Roe
3.Killen Burn
4.River Muff A
5.River Muff B
6.River Camowen
7.River Drumnakilly
8.River Owenreagh B
9.River Owenreagh
10.Routing Burn
12.River Castle
13.River Foreglen
14.River Owenbeg
16.River Faughan A
17.River Faughan
18.River Glenrandal
19.Bonds Glen


Figure 1: This map illustrates the complex population structuring of brown trout in the Foyle catchment based on 20 neutral microsatellite markers. Each coloured and numbered point on the map indicates a population.  

The third question was designed to assist the Loughs Agency (the managing body for the Foyle catchment – develop a strategy for sea trout management and conservation. The River Foyle catchment was well known historically for its sea trout runs.  However, like elsewhere in Britain and Ireland the number of sea trout has declined dramatically over recent years.  To assist with the process of developing an index of sea trout rivers in the system a genetic based survey was used to determine which tributaries are contributing to the production of sea trout. As proof of concept, the River Faughan, considered one of the best sea trout rivers on the Foyle system, was selected for a more detailed investigation. A rotary screw trap was placed at the mouth of the River Faughan to collect genetic samples from sea trout as they migrated to sea. A genetic baseline was then created by collecting genetic samples from juvenile trout taken from across the Faughan catchment Figure 1). The genetic samples from the sea trout were then compared with the genetic baseline to establish which rivers were contributing to the production of sea trout. The results showed that 88% of the smolts analysed on their downstream migration could be assigned to 5 of the 7 genetic groups found in the Faughan and its tributaries (of the two groups not detected, one is located above an impassable falls). The majority of the remaining 12% assigned to rivers close to the Faughan, suggesting some straying between the Faughan and neighbouring rivers (Table1).

Population Population ID (figure 1) River Catchment Proportion of individuals assigned (%)
Burngibbagh 15 Faughan 19.4
River Faughan A 16 Faughan 2.9
River Faughan 17 Faughan 47.5
Glenrandal 18 Faughan 12
Bonds Glen 19 Faughan 4.9
Owenbeg 14 Roe 7.9
Roe 2 Roe 0.8
Killen Burn 3 Derg 3.6
Routing Burn 10 Owenreagh 0.3
Owenreagh 9 Owenreagh 0.2
River Muff A 4 River Muff 0.3

Table 1: The percentage of individuals assigned to each population.

Partners: Glasgow University; Atlantic Salmon Trust; Queens University, Belfast; Loughs Agency; Funded by Interreg 4A project 2859

AST Funding: £2,000 each year in 2013, 2014 and 2015

The Celtic Sea Trout Project –

The Living North Sea Project  –

The AARC Project –