Atlantic salmon - determining run timing proportions: report

Background

While Atlantic salmon (Salmo salar L.) spawn in late autumn/early winter, their return migration to freshwater from the sea can occur at any time during the year (Juanes et al. 2004; Quinn et al. 2006; Shearer 1990). Both one-sea-winter grilse and multi-sea-winter (MSW) salmon occur in both early (pre-July) and late (post-June) seasonal runs, although the ratio of their proportions differs between these runs (Gurney et al. 2012). The late run consists of significant numbers of both grilse and MSW fish and predominantly of spawners returning to locations lower down the river systems (Smith et al. 1998; Webb 1992). In contrast, the early run is dominated by MSW fish, with small numbers of grilse and early running fish mostly spawn higher up in the river systems (Laughton and Smith 1992; Smith and Johnstone 1996). Although these general patterns are often seen, it is unknown how extensive they actually are, and if they are the same across different rivers.

In order to maintain the wide diversity observed in salmon fisheries, it is important to maintain the diversity of the populations that underpin them (e.g. Hilborn et al. 2003; Potter et al. 2003; Schindler et al. 2010). However, achieving this management aim is only possible if the biological structure of the resource is known. The large variation in run timing present in some rivers produces an elongated fishing season; the components of which are known to show different trends in abundance and may therefore have different conservation needs (Anon 2016; Quinn et al. 2016; Youngson et al. 2003). However, at present, salmon are often managed at the river-level, due to the difficulties in defining and accounting for within-river structuring (Potter et al. 2003). The ability to characterise areas of the catchment associated with differences in run timing characteristics will allow better understanding of the adaptive genetic structure of the stocks and may aid in the management of specific run timing components at the sub-catchment level.

Recently, a region of the Atlantic salmon chromosome Ssa09 was identified that was strongly associated with run timing and that contained a gene or a linked gene complex explaining ~24% of the trait variance (Cauwelier et al., 2018). A number of single nucleotide polymorphic (SNP) genetic markers were identified within this region, thus raising the possibility of developing these into a panel that could be used to screen juvenile salmon and characterise stocks according to their run timing composition. The development and calibration of this tool is described below.