STOCKING OF ATLANTIC SALMON

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

Genetics = molecular markers

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

- Functional divisions

The Individual The Breeding Population

Population Genetics
- the genetic processes relating to individuals within and among populations.

The Species

- like, computers, simple in concept but extremely complex in operation Mendelian Laws
A, a - green pea A, a - yellow pea
F e m a le P a r e n t M a le P a r e n t

Aa x Aa -> AA, Aa, aA, aa Aa x aA -> Aa, AA, aa, aA

n u c le a r genes m ito c h o n d r ia l genes mRNA

The Individual
Genetic Reality
100,000s of hard to define interacting functional DNA units
Fish scale 1cm

P r o te in s

2X human genome

Cell ~100 um

20 nm 10 m

58 chromosomes, 7 billion base pairs

Gentile et al. Nano Lett. 2012, 12, 64536458

- again workings in populations simple in concept but extremely complex in operation

Populations
- interactions between individuals within populations; between populations; between species; between populations and their environment, which affect their DNA

- 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

- four sources of understanding

Populations

Breeding studies Characterisation of traits and success of parents and offspring Analysis of DNA variation Mathematical modelling

- 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

Populations
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

- all individual salmon are genetically different; all breeding populations are genetically different

Population 1

Population 2

0.60 0.48
Proportion in Population

0.36 0.24 0.12 0.00

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.

a b c d e f g h

j (From k lVerspoor m n 1997) o p q r s

t u v w x

- genotype-environment interaction

Populations

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.

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

- genotype-environment interaction

Populations
Adaptation, fitness, abundance and viability

- adaptation, fitness and viability

Populations
If environmental change is too much or outside of niche limits

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

- adaptation, fitness and viability

Populations
If genetic change occurs that makes fitness differential too great

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.

- structuring into breeding populations

Populations

McGinnity et al. unpublished

Microsatellites

Ireland

DILLANE et al. (2008), Molecular Ecology, 17: 47864800. King et al. (2007).

- structuring into breeding populations

Populations
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.
Two tributaries

e.g. choice of Loci, Genetic Sampling: neutral vs adaptive variation

Unselected genes

No structure

- to resolve it all need to find the genome locations with highest levels of differentiation among locations

Selected gene

Structure

Gilbey et al. (1999). Aquat. Living Res.

- structuring into breeding populations

Populations

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

Summary

Reproductive isolation among these populations, even within river systems, may be complete or encompass regular or occasional migration and a meta-population dynamic
Each rivers structuring will be unique and conditioned by historical and contemporary factors

- adaptive differentiation of populations

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. Some examples but we have only opened door on its extent; studies of adaptive genetic differentiation are in their infancy

- adaptive differentiation of populations

Populations
Intensity of G. salaris infection
Comparision of Baltic & Norwegian stocks
Gyrodactylus salaris
80 70 60

ion MaximumIntensity of Infestat

50 40 30 20 10 0 Lorne Neva 0 7 14 21 28 35

Stock
M o d e rnD is trib u tio n o fW ildA tla n ticS a lm o n

Da ys Po st Ex po su re
(Bakke et al. 1990)

- adaptive differentiation of populations

Populations
High altitude

Adult Run Timing - River Tay

Low altitude

Stewart et al. 2002

- adaptive differentiation of populations

Populations
Example of genotype environment interaction
Egg Mortality
(Donaghy and Verspoor 1997)

50

Kyle of Sutherland river system resistance to acid water reciprocal transplant and common garden comparisons

40

30

20

10 Shin 0 Loth Shin Oykel

Oykel eggs show heritable resistance to acid flushes; Shin eggs do not.

Oykel
Hatchery

- Adaptation and Outbreeding depression

Populations
Change of variant frequencies or introduction of maladaptive variants
1.2 1 0.8 120

80 60 40 20 0

0.6 0.4 0.2 0

F1HyF

BC1F

McGinnity et al. 2003 Proc. Roy. Soc. B

F1HyW

BC1W

Cross type

F2Hy

Farm

Wild

Percent wild type alleles

100

Fitness

- Adaptation and Outbreeding depression

Populations
Loss of internal genomic coadaptation
Crossing of Scottish anadromous with Canadian non-anadromous salmon

Cauwelier et al. Conserv Genet (2012) 13:16651669

- Adaptation and inbreeding depression

Populations
Reduced variation; fitness effect; induced in supportive breeding programmes based on relatively few breeders
Expected but few studies as it is difficult to follow to assess impact at population level.

Recapture frequencies of stocked salmon relative to level of inbreeding.

Ryman, N. (1970) Hereditas 65, 159160.

Populations

- Adaptation differentiation, population structuring and salmon production

Sockeye salmon in Alaska

Having multiple, adaptively differentiated populations appears to increase and stabilize overall salmon production; the portfolio effect.

Atlantic salmon?

Schindler et al. 2010 Nature Letters

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!

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!