Genomic signatures and correlates of widespread population declines in salmon

Abstract

Global losses of biodiversity are occurring at an unprecedented rate, but causes are often unidentified. Genomic data provide an opportunity to isolate drivers of change and even predict future vulnerabilities. Atlantic salmon ( Salmo salar ) populations have declined range-wide, but factors responsible are poorly understood. Here, we reconstruct changes in effective population size ( N e ) in recent decades for 172 range-wide populations using a linkage-based method. Across the North Atlantic, N e has significantly declined in >60% of populations and declines are consistently temperature-associated. We identify significant polygenic associations with decline, involving genomic regions related to metabolic, developmental, and physiological processes. These regions exhibit changes in presumably adaptive diversity in declining populations consistent with contemporary shifts in body size and phenology. Genomic signatures of widespread population decline and associated risk scores allow direct and potentially predictive links between population fitness and genotype, highlighting the power of genomic resources to assess population vulnerability.

Mortality of Atlantic salmon after catch and release angling: assessment of a recreational Atlantic salmon fishery in a changing climate

“…Atlantic salmon abundance has declined across much of the North Atlantic despite closures and (or) restrictions of fisheries (Parrish et al 1998;Chaput 2012;Lehnert et al 2019). While retention fisheries still occur, which target salmon during their upstream spawning migration, voluntary and mandatory release of caught salmon is increasing (ICES 2019).…”

“…Among fisheries managers and conservation organizations, catch and release has been accepted as a management tool (Brownscombe et al 2017) allowing for the recreational fishery and associated social and economic benefits to continue, even when stock abundance is low, based on past evidence of minimal mortality of fish after release (Tufts et al 1991;Wilkie et al 1996;Lennox et al 2017a). Yet given the high numbers of caught and released fish (ICES 2019) and the declining abundance of Atlantic salmon (Lehnert et al 2019), the use of catch and release as a management tool is sometimes challenged and re-evaluated (Dempson et al 2002; Bartholomew and Bohnsack 2005;Arlinghaus et al 2007).…”

Effects of global warming on sex ratios in fishes

“…Lehnert et al . (2019) reported a strong association between the decline of more than half of 172 Atlantic salmon Salmo salar L. populations over recent decades and the decline of their respective N e . A strong correlate of these declines seemed to be increased winter temperatures and their effects on development of early developmental stages, but it remains unclear whether and how these temperature changes affected sex ratios.…”

Genome-wide genetic diversity yields insights into genomic responses of candidate climate-selected loci in an Andean wetland plant

“…Since they fuel all genetic variation (be it neutral or adaptive) and can cause its loss 4 , neutral and demographic processes determine the availability of and population capacity to produce new genetic material for selection to act upon. In addition, they can also limit evolutionary adaptive responses even in the presence of substantial adaptive genetic variation 38 , which may occur in the event of demographic constraints 38 linked, for instance, to small population size, or where gene flow is extensive and outweighs selection effects 19,39,40 . In discrete ecosystems such as high Andean wetlands, neutral processes can strongly impact species and genetic diversity due to greater potential for drift, demographic stochasticity and limited opportunity for dispersal 41 .…”