1. Eric Verspoor Rivers and Lochs Institute, Inverness College University of the Highlands and Islands

2. trait inheritance from parents to offspring; a fundamental aspect of all living organisms controls the production of each new generation, its character, its abundance all biodiversity is fundamentally, genetic diversity underlies domestication and selective improvement farmed plants and animals. underpinned by DNA and its division into functional units (e.g. genes), through the control of cellular processes; encompasses variation among individuals, their organisation into breeding populations; modified by natural selection, chance, mutation, gene flow and the environment Genetics = molecular markers

3. The Individual The Breeding Population The Species - Functional divisions - the genetic processes relating to individuals within and among populations. Population Genetics

4. - like, computers, simple in concept but extremely complex in operation Aa ♂ x Aa♀ -> AA, Aa, aA, aaA, a - green pea A, a - yellow pea Aa ♂ x aA♀ -> Aa, AA, aa, aA Mendelian Laws 10 μm Fish scale – 1cm Cell ~100 um 20 nm Gentile et al. Nano Lett. 2012, 12, 6453−6458 Genetic Reality – 100,000s of hard to define interacting functional DNA units 58 chromosomes, 7 billion base pairs 2X human genome The Individual

5. - interactions between individuals within populations; between populations; between species; between populations and their environment, which affect their DNA - again workings in populations simple in concept but extremely complex in operation - basic concepts are clearly understood but detailed understanding of exactly how processes work is incomplete and what is known is described using many mathematical formulations in a myriad of thousands of scientific papers, some simple, some complex e.g. Genetics August 1, 2003 vol. 164 no. 4 1567-1587 Populations

6. - four sources of understanding Breeding studies Characterisation of traits and success of parents and offspring Analysis of DNA variation Mathematical modelling Populations

7. - key issues relevant to stocking Populations - Genetic variation among individuals within and among populations - genotype-environment interaction and adaptation - structuring of stocks into breeding populations - adaptive differentiation of populations

8. - all individual salmon are genetically different; all breeding populations are genetically different Populations (From Verspoor 1997) 3 genetic loci each with two variants = 27 genotypes If all variants occur in both populations but differ in frequency such for each variant is 0.9 in one population and 0.1 in the other, or visa versa then… But there are 10,000 of loci whose variant frequencies vary among populations e.g. genotype a is 500,000 times more likely to occur in population 1 than in population 2, and the converse for genotype #; given a finite population of a few thousand salmon, few if any genotypes will be shared between two populations.

9. - genotype-environment interaction Populations All salmon = interaction between inherited DNA from parents and life-time environment, including food eaten and conspecifics; determines their character and their fitness i.e. probability of survival and leaving offspring that survive and leave offspring; Differences in the DNA of individuals within populations and among populations DNA give rise to differences in character and fitness The fitness and character of a population, and thereby its abundance, are a function of the cumulative fitness of its constituent individuals and the amount of available habitat i.e. the environmental carrying capacity for the genotypes in the population.

10. - genotype-environment interaction Populations Adaptation, fitness, abundance and viability

11. If environmental change is too much or outside of niche limits - adaptation, fitness and viability Populations Stocking, in some circumstances could cause environmental change by increasing interspecific densities and competition for space and food resources, introducing pathogens e.g. G. salaris

12. Populations If genetic change occurs that makes fitness differential too great - adaptation, fitness and viability Stocking, in some circumstances could cause genetic change through outbreeding depression, by the use of adaptively different non-native populations or increasing inbreeding when using native fish and increasing the success of some families more than others.

13. Populations - structuring into breeding populations King et al. (2007). Ireland Microsatellites McGinnity et al. unpublished DILLANE et al. (2008), Molecular Ecology, 17: 4786–4800.

14. Populations - structuring into breeding populations e.g. choice of Loci, Genetic Sampling: neutral vs adaptive variation Gilbey et al. (1999). Aquat. Living Res. Understanding incomplete in regard to numbers, levels of genetic exchange; extent is likely to be underestimated due to only small number of loci surveyed and focus on non-adaptive variation, a view supported by more robust studies of other species such as cod Gadus morhua. Selected geneStructure Unselected genesNo structure Two tributaries - to resolve it all need to find the genome locations with highest levels of differentiation among locations

15. salmon stocks in most larger river systems will be composed of more than one breeding population and could be many tens in numbers. With over 2000 salmon rivers, it is likely that there are in excess of 10,000 populations across the species range Reproductive isolation among these populations, even within river systems, may be complete or encompass regular or occasional migration and a meta-population dynamic Each river’s structuring will be unique and conditioned by historical and contemporary factors Populations - structuring into breeding populations Summary

16. Populations - arises through natural selection in response to historical environmental differences, genetic drift and mutation supported by physical, behavioural or temporal isolation of breeding, and countered by gene flow. - adaptive differentiation of populations Some examples but we have only opened door on its extent; studies of adaptive genetic differentiation are in their infancy

17. Gyrodactylus salaris Populations - adaptive differentiation of populations

18. Populations - adaptive differentiation of populations Adult Run Timing - River Tay Stewart et al. 2002 High altitude Low altitude

19. Example of genotype environment interaction Kyle of Sutherland river system - resistance to acid water – reciprocal transplant and common garden comparisons Egg Mortality Shin Oykel Stock Shin Oykel Hatchery Environment Loth 0 10 20 30 40 50 % mortality (Donaghy and Verspoor 1997) Populations - adaptive differentiation of populations Oykel eggs show heritable resistance to acid flushes; Shin eggs do not.

20. Populations Change of variant frequencies or introduction of maladaptive variants - Adaptation and Outbreeding depression McGinnity et al. 2003 Proc. Roy. Soc. B

21. Populations Loss of internal genomic coadaptation - Adaptation and Outbreeding depression Crossing of Scottish anadromous with Canadian non-anadromous salmon Cauwelier et al. Conserv Genet (2012) 13:1665–1669

22. Populations Reduced variation; fitness effect; induced in supportive breeding programmes based on relatively few breeders - Adaptation and inbreeding depression Recapture frequencies of stocked salmon relative to level of inbreeding. Ryman, N. (1970) Hereditas 65, 159–160. Expected but few studies as it is difficult to follow to assess impact at population level.

23. Having multiple, adaptively differentiated populations appears to increase and stabilize overall salmon production; the “portfolio effect”. Populations - Adaptation differentiation, population structuring and salmon production Schindler et al. 2010 Nature Letters Sockeye salmon in Alaska Atlantic salmon?

24. Populations Current state of knowledge in relation to salmon What we know is just the tip of a very large iceberg of knowledge; we know its basic nature but only some of its detail!

25. …genetics is the ”elephant” in your programme, the unavoidable but largely hidden and uncertain factor! Genetics is complicated and largely hidden from view but underpins the character, abundance and viability of salmon stocks; it needs to be taken into account if management interventions are to be successful. … like gravity or magnetism in the physical world, genetic issues are an unavoidable reality in the world of stocking!