THE IMPORTANCE OF GENETICS

Eric VerspoorRivers and Lochs Institute,

Inverness College University of the Highlands and Islands

STOCKING OF ATLANTIC SALMON

• 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 markersGENETICS

The Individual

The Breeding Population

The Species

GENETICS - Functional divisions

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

Population Genetics

GENETICS - 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, aAMendelian Laws

10 μmFish scale – 1cm Cell ~100 um20 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 Individualm RNA

Proteins

nucleargenes

m itochondrialgenes

Fem ale Parent Male Parent

- 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

GENETICSPopulations

𝑯𝒂𝒓𝒅𝒚 −𝑾𝒆𝒊𝒏𝒃𝒆𝒓𝒈 :𝒑𝟐+𝟐𝒑𝒒+𝒒𝟐=𝟏

- four sources of understanding

• Breeding studies

• Characterisation of traits and success of parents and offspring

• Analysis of DNA variation

• Mathematical modelling

GENETICSPopulations

- key issues relevant to stockingGENETICSPopulations

- Genetic variation among individuals within and among populations

- genotype-environment interaction and adaptation

- structuring of stocks into breeding populations

- adaptive differentiation of populations

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

GENETICSPopulations

a b c d e f g h i j k l m n o p q r s t u v w x y z #

Genotype

0.00

0.12

0.24

0.36

0.48

0.60

Pro

po

rtio

n i

n P

op

ula

tio

n

Population 1 Population 2

(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.

- genotype-environment interactionGENETICSPopulations

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.

- genotype-environment interactionGENETICSPopulations

Adaptation, fitness, abundance and viability

If environmental change is too much or outside of niche limits

- adaptation, fitness and viabilityGENETICSPopulations

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

GENETICSPopulations

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.

GENETICSPopulations

- structuring into breeding populations

King et al. (2007).

IrelandMicrosatellitesMcGinnity et al.

unpublished

DILLANE et al. (2008), Molecular Ecology, 17: 4786–4800.

GENETICSPopulations

- 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 gene Structure

Unselected genes No structure

Two tributaries

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

• 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

GENETICSPopulations

- structuring into breeding populations

Summary

GENETICSPopulations

- 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

Gyrodactylus salaris

Modern Distributionof Wild Atlantic Salmon

Intensity of G. salaris infectionComparision of Baltic & Norwegian stocks

07

1421

28

35 Day

s Po

st E

xpos

ure

Lorne

NevaStock

0

10

20

30

40

50

60

70

80

Max

imum

Int

ensi

ty

of I

nfes

tati

on

(Bakke et al . 1990)

GENETICSPopulations

- adaptive differentiation of populations

GENETICSPopulations

- adaptive differentiation of populations

Adult Run Timing - River Tay

Stewart et al. 2002

High altitude

Low altitude

Example of genotype environment interaction

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

Egg Mortality

Shin

Oykel Stoc

k

ShinOykel

HatcheryEnvironment

Loth0

10

20

30

40

50

% m

ort

alit

y

(Donaghy and Verspoor 1997)

GENETICSPopulations

- adaptive differentiation of populations

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

GENETICSPopulationsChange of variant frequencies or introduction of maladaptive variants

- Adaptation and Outbreeding depression

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

0

0.2

0.4

0.6

0.8

1

1.2

Wild

BC

1W

F1H

yW

F1H

yF

F2H

y

BC

1F

Farm

Cross type

Fitness

0

20

40

60

80

100

120

Perc

ent

wild t

ype a

llele

s

GENETICSPopulationsLoss 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

GENETICSPopulationsReduced 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.

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

GENETICSPopulations

- Adaptation differentiation, population structuring and salmon production

Schindler et al. 2010 Nature Letters

Sockeye salmon in Alaska

Atlantic salmon?

GENETICSPopulations

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.

Thus when it comes to salmon and stocking…

… like gravity or magnetism in the physical world, genetic issues are an unavoidable reality in the world of stocking!

Thank you!