Atlantic salmon from large Scottish east coast rivers - genetic stock identification: report

Introduction

Continuing declines in Atlantic salmon numbers across Scotland have been associated with an increased mortality in the marine environment (Friedland, 1998; Potter & Crozier, 2000). Trends in mortality appear to vary among rivers, possibly because different populations of salmon use the marine environment in different ways (Davidson et al., 2009; Thorstad et al., 2011, Gilbey et al., 2021). Understanding this variation is important for conservation efforts and will inform local managers, recreational and commercial fisheries and, at a national level, both marine renewables planning and climate change mitigation.

A number of projects are currently underway to understand the migratory routes of post-smolt salmon around Scotland, including acoustic tracking of movements and identification of distributions by trawling fish. The information gained can be used to inform plans for marine renewable energy developments and help mitigate against the impacts of other anthropogenic pressures. Further research is being carried out in the Norwegian Sea and near western Greenland in relation to impacts of climate change and ecosystem disruptions in these distant but important feeding areas for salmon. These projects include the Norwegian led ‘SeaSalar’ project which focuses on salmon in the Norwegian and Barents Seas, Canadian investigations of salmon around west Greenland and Marine Scotland surveys off the east coast of Scotland and Moray Firth. In each of these cases, genetic markers are being used to determine the origin of salmon in the areas to examine impacts at a regional and/or river-specific level.

Genetic stock identification (GSI) is an integral component of modern fisheries management (Begg et al., 1999; Beacham et al., 2021). To manage fish species successfully, it is important to understand the genetic structure underlying the various populations that make up a stock. Advances in DNA profiling and associated analytical techniques have allowed the development of GSI using different types of genetic markers (Waples et al., 1990, 2008). Initially, allozymes and mitochondrial DNA were successfully used for stock identification in salmonids (Shaklee et al., 1999; Moriya et al., 2007; Koljonen & McKinnell, 1996). More recently, panels of highly polymorphic microsatellite markers and single nucleotide polymorphisms (SNPs) have allowed stock identification to be successfully performed with Atlantic salmon at a number of geographic scales, from inter-continental to intra-river (Gilbey et al., 2005; Griffiths et al., 2010, 2011; Vähä et al., 2011). In Scotland, both a microsatellite baseline (Gilbey et al., 2018) and a single nucleotide polymorphism (SNP) baseline (Gilbey et al., 2016a) have been developed, both of which allowed accurate assignment to regions. However, in most cases these lack the resolution needed to allow reliable assignment to the individual river level.

The development of new marker types and the advancement of analytical tools have resulted in increased geographic resolution of assignment. For example, in Scotland, the 288 SNP panel showed higher geographic resolution compared to the 14 microsatellite markers previously used (Gilbey et al., 2016a, 2018). The assignment units defined by the latter, developed to encompass all eastern Atlantic Ocean countries harbouring Atlantic salmon populations, could, at the lowest level, distinguish between five regions in Scotland (Central, Cromarty Firth, NE, NW and West Central), as well as the individual River Leven and Water of Luce (Gilbey, et al., 2018). The SNP baseline, on the other hand, identified thirteen assignment units, in some cases further subdividing the units identified by the microsatellites. However, a number of assignment units still encompassed large geographic areas, most notably the East coast and North and West regions (Gilbey et al., 2016a).

In Gilbey et al. (2016a), the North and West assignment region of Scotland covered a large proportion of the country. However, river coverage was limited and the west coast is typified by a large number of relatively small rivers. The East coast assignment unit, on the other hand, included many of the largest rivers in the country and those rivers are the major contributors (~60%) to the overall Scottish wild salmon production (based on 2020 rod catch returns – Marine Scotland Science) and include nine of the seventeen Special Areas for Conservation (SACs) for the species in Scotland, under the EU Habitats Directive. A mixed stock fishery analysis of adult salmon caught in the coastal nets along the English NE coast revealed that approximately 40% of these fish were assigned to the Scottish NE region (Gilbey et al., 2016b), whilst this varied between ~20% and ~40% of returning adults captured at Armadale in the far north (Cauwelier et al., 2016; Armstrong et al., 2018). Given both the importance of large Scottish East coast rivers towards salmon productivity and conservation (including those designated as SACs) and the ongoing development of this coastal area for marine renewable energy, it is highly desirable to be able to distinguish salmon populations from the different rivers within this region in order to obtain more accurate GSI results and, thus, allowing patterns of ocean utilisation to be examined at the river level.

Recently, a new panel of 101 microsatellite markers has been developed and successfully utilised in Canada (Bradbury et al., 2018; Sylvester et al., 2018) to obtain river-level resolution of Atlantic salmon, where previous marker sets identified larger regions.

The aim of this project was to establish the utility of this panel in a Scottish context, focusing on developing the panel along the East coast of Scotland. The goal was to establish a new genetic reference baseline and develop improved GSI resolution. The baseline was built with samples collected as part of the National Electrofishing Programme for Scotland (NEPS) project (Malcolm et al., 2020). If higher robust assignments at an increased resolution could be obtained with this panel, then it would be used on contemporary samples of smolts caught by trawling off the Scottish east coast by Marine Scotland during the period 2017-19 for planning Marine Renewable developments. If possible, the analysis of the results of this screening would allow stock-specific patterns of migration and feeding to be examined and, hence, would provide invaluable information on ocean utilisation in the individual river stocks.