Family Trees

Genetics can be a minefield to the uninitiated (and that includes me), however, it can be intriguing. The use of genetic analysis in fisheries management has been used for many years enabling fishery managers to identify various stock components from different rivers and within rivers. It can identify traits within species, run timings and links with other species such as Freshwater pearl mussels. In addition, Environmental DNA analysis (eDNA) can identify the presence of species within our systems (Pink Salmon, Saprolegnia). It’s a tool that can give us insights into what is going on in our rivers.

Genetic analysis was a major tool utilised in the Upper Garry Restoration Project. For those of you unaware of this project I will give you some background information and as a result of the analysis an intriguing story!

The River Garry was once a prolific river, counts through the dams used to be in region of 1000 fish, all heading into the headwaters and burns to spawn. The abundance of salmon in the Upper River Garry has declined over the last fifty years and was showing little sign of recovery. Stocking undertaken as mitigation for loss of habitat following historical hydroelectric development, together with subsequent easing of fish passage, has proven to be unsuccessful. It is believed that the indigenous population may have been affected by non-native strains of salmon that may not be fully adapted to their environment. Initial baseline monitoring indicated that a remnant of the original native stock of salmon was still present.

Scottish Southern Energy, Ness Beauly Fisheries Trust, The Ness District Salmon Fishery Board, MOWI, Scottish Environment Protection Agency and Institute for Biodiversity & Freshwater Conservation ( previously River and Lochs Institute, University of the Highlands and Islands), came together to collaborate on the delivery of a project to restore a self – sustaining wild salmon population to the Upper River Garry. This included the implementation of carefully targeted, designed and linked enhancement initiatives, encompassing habitat improvement and stock rehabilitation through supportive breeding and supplementary stocking.

The River Kingie on the Upper Garry

The supportive breeding and supplementary stocking element of the project involved the capture of a proportion of the Upper Garry salmon smolts as they migrate downstream towards the sea between March and May These fish were then be grown on to maturity in captivity, enabling a sufficient number of eggs to be produced to have a meaningful impact on the system.

It was initially intended to stock these eggs to areas accessible to salmon upstream of Garry Dam in an attempt to “kick start” the population The project began in March 2014 and would last for at least 10 years The success of the work is still being monitored and evaluated on a regular basis.

All smolts captured for this project were measured and weighed, genetic samples were taken and analysed by the Institute for Biodiversity and Freshwater Conservation. This was to ensure that no ‘farmed fish’ (aquaculture escapees) were used and to identify any siblings and so allowing genetic integrity to remain. In addition, scale samples were taken to ascertain the ages of smolts. These smolts were PIT (Passive integrated Transponder) tagged to enable identification. Smolts would be grown on to the adult stage where they were stripped and the eggs stocked back into the river at pre-ordained sites, River Kingie, Allt Choire a’Bhalachain and Greenfield burn initially. Eggs were also stocked into the Gearr Garry towards the end of the project ( this is another story so watch this space).

Each smolt is fitted with a passive integrated transponder (PIT) so it can be identified and a tissue sample is taken allowing genetic profiling

Monitoring the success of this project involved electrofishing surveys in agreed locations throughout the Garry catchment to quantify changes in juvenile salmon populations alongside genetic analysis of returning adults and juveniles to assess the effectiveness of the restoration stocking. In addition, counting of returning adults using the SSE fish counter at Garry Dam (Although there has been issues regarding accuracy). Scale samples are also taken from rod caught adults; these scales are then genetically analysed.

Parr captured during electrofishing

In summary

• Kingie – Stocking took place 2018-2023. Fry densities increased post stocking and remain stable
• Allt Choire a’Bhalachain – Stocking took place 2018-2022. Redds observed in Autumn 2022 and fry captured in the following year meaning natural spawning had occurred. No redds observed in 2023 and fry absent in subsequent survey. Adult fish and redds observed in Autumn 2024. Surveys in 2025 had the highest densities recorded at both sites for fry meaning natural spawning had occurred.
• Greenfield – Stocking took place 2018-2023. Densities increased dramatically as a result of stocking. However, fry were absent at this site since stocking ceased. Greenfield has little or no suitable spawning areas, those present are limited to the lower reaches where fry were observed in 2025.
• Gearr Garry – Stocking took place in 2023 and 2024. Prior to this salmon were mainly absent. Fry were observed in 2025 suggesting this is the first time that natural spawning had taken place here.

As the Upper Garry stocking ended in 2024, all stocked fish are now parr, smolts or adults. But the story doesn’t end there.

Staff at the  Institute for Biodiversity and Freshwater Conservation led by Dr Victoria Pritchard have been working on genetic grandparent analysis, this means that samples taken from adult returning fish can be traced to back to grandparents, in this case potential stocked fish. This is a novel technique and we await a full report. However, we do have a story to tell.

On the 12^th May 2023, Mr Paul Eddington captured a salmon at Dochfour on the River Ness ably assisted by Cameron Chapman, a well known ghillie and fisherman (you can view the capture below). The fish was 740mm in length and weighed around 10lb. Scale reading analysis suggested the fish hatched in 2019 and spent two years in freshwater before migrating to sea in 2021. It spent a further two winters at sea returning to the river in 2023.

Genetics taken from the scale revealed some interesting information. This fish was of stocked origin. But it doesn’t end there, samples taken from fry in the Upper Kingie in the summer of 2024 revealed that this fish was a parent, and this was also revealed in parr samples taken in 2025. So, after capture, this fish successfully spawned in the River Kingie, we have the parent (A stocked fish) and its offspring.

But how do we know it was stocked? The answer of course is genetics and the fantastic work done by the  Institute for Biodiversity and Freshwater Conservation which has enabled us to identify the parents of this fish.

Rewind to April 2016. Our rotary screw trap was installed at the beginning of the month. Smolts were captured throughout the month and processed, tagged and sampled. On the 22^nd of April 38 smolts were captured. Fish number 63 was a female smolt measuring 138mm and was two years old, the mother of the Dochfour fish and grandmother of the fry/parr sampled in 2024/2025.

The following day 23^rd April, 31 smolts were captured. Fish number 106 was a male smolt measuring 142mm and was two years old. The father of the Dochfour fish and grandfather of the fry/parr sampled in 2024/2025. Both fish were stripped in the Autumn of 2018 and eggs stocked into the Kingie in early 2019.

Now, going back to the Dochfour fish, not only did it go on to spawn after being captured, sampled and released, it wasn’t the first time this fish had encountered capture and subsequent release although in this case not intentional. Photographs show that there was significant, fresh predator damage to the fish, probably as a result of an encounter with a seal, and yet miraculously it survived to produce offspring.

Genetic sampling is utilised throughout many catchments for a variety of purposes, yes it can be confusing (believe me) but the results can be fascinating, we have a few other stories resulting from genetics taken from adults/smolts/juveniles within our catchment and I will summarise here.

• Fish 1 was stocked out in 2018 and returned to spawn in Allt Choire a’Bhalachain in 2022, producing fry and parr that were sampled in 2023/24.
• Fish 2 was stocked out in Kingie in 2020, returning to spawn in Gear Garry in 2024, producing fry that were sampled in 2025. (More to come on the enigma that is the Gearr Garry)

Wild-spawned fish in the Garry also successfully returned to reproduce:

• Fish A hatched in the Upper Garry on 31^st March 2018 and was caught as an 18lb adult female in the River Garry in March 2023, and spawned in the Kingie to produce fry sampled in 2024. This fish had spent two years in freshwater migrating as a smolt in 2020 before returning in 2023.

And with regard to parr and smolts

• 6% (7/48) of the smolts captured in the Kingie smolt trap in 2025 had been stocked as eggs, the rest were wild-spawned fish.
• 6% (22/23) of the parr captured in the Gear Garry in 2025 were stocked
• 7% (7/9) of the parr captured in Greenfield Burn in 2025 were stocked
• 8% (1/21) of the parr captured in Kingie/Kinbreak in 2025 were stocked

Analysis of smolts collected in 2025 from the River Moriston smolt trap also reveals the fate of some adults captured in the river:

Two fish, both caught as 2.2 adults at Dochfour in May 2022, spawned together in the Moriston to produce an offspring caught in the smolt trap in 2025.

So, there we are, more information is to come as all the data gets analysed, as you can imagine it is a laborious, time-consuming process but fascinating nonetheless and all as a result of good science, good data collection and of course GENETICS!