1. Methods of studying wild-reared interactions
T. F. Cross
Department of Zoology, Ecology & Plant Science
National University of Ireland, Cork, Ireland

2. The problem: Cultured fish inadvertently escape
from farms or wander from ranching exercises OR
are deliberately introduced by stocking
ALL OF THESE SOURCES CAN BE
EQUALLY DAMAGING

3. Cultured species breed with wild
conspecifics or closely-related species.
Offspring have reduced fitness compared with
wild populations or species, but in some cases
replace them
Cultured strains may out-compete wild
populations, or can transfer diseases,
so leading to reduced Ne
PRODUCTIVITY DECLINES (carrying capacity)

4. Direct and indirect genetic effects
Interbreeding with wild conspecific
populations or with closely related species
(most studied aspects to date)
Indirect
Cultured organisms compete successfully
with wild individuals, and so lead to population
decline (reduced Ne)
Disease transfer from cultured to wild organisms

5. Definition: fitness = reproductive fitness
Most European experiments have concentrated
on Atlantic salmon
These have generally shown reduced fitness in
reared and/or translocated salmon, compared
with natives
WHY?

6. Loss of genetic variability due to use of
small numbers of broodstock (so-called inbreeding
effects, also leading to loss of local adaptation).
2. Introduced organisms maladapted in
non-native area (breakdown of co-adapted gene
complexes/ genetic architecture; outbreeding
depression in subsequent generations).
Must be major factor in translocations without
rearing?
3. Domestication selection (relaxation of natural
selection/hatchery selection)
Only a factor where rearing involved but seems to
happen quickly!

7. Are there likely to be similar problems with other
European species?
Taking cod as an example:
Wild stocks are overfished
Genetic variability often much lower in cultured
strains than wild progenitors (Bekkevold et al.)
BUT not enough known of wild population
structure, extent of philopatry and local
adaptation (Norwegian & Danish examples?)
Also about domestication in reared cod

8. With reared cod Some knowledge of fate of deliberate releases
Farm escapes occur (eggs, net chewing)
Do they interbreed with wild conspecifics?
What is the relative fitness of progeny?

9. Potential for loss of genetic variability!
Armitage, with SAMS Ardtoe
Seven females & seven males in mass spawning M1 M2 M3 M4 M5 M6 M7
SIRE F1 2 13 1 24 40 F2 F3 3 6 F4 F5 7 11 F6 F7
DAM 17 32 57
Potential for loss of genetic variability!

10. Opportunist situations
Where escape or stocking/ranching exercise
has occurred and interactions are in progress
e.g. Clifford et al. in Donegal, Ireland
Escapes from big freshwater farm and from
sea cages
ID with mtDNA and minisatellites
Evidence for breeding in the wild
Reduction of cultured influence over time
Effects not quantifiable

11. Highly variable loci best-microsatellites (or many
SNP loci, chosen to give the greatest degree of
ascertainment)
Use individual assignment methods to allocate
individuals.
Based on genotypes thus giving more power than
methods based on allele frequencies (two alleles,
three genotypes; three alleles, five genotypes etc.)
The more loci used the more accurate (less error)
in the assignment (typically microsatellites)

12. Microsatellite locus

13. Manipulated situations
Common-garden field experiments (Burrishoole)
Know actual parents so can use parental assignment
which is more accurate than individual assignment
(exclusion methods like PAPA or FAP-Arden &
Jones)
Accuracy improves to near 100% as number of loci
is increased
Usually about six loci are optimal
Can then look at morphological traits of identified
individuals, since environment “common”

14. FIELD EXPERIMENT Assessing the potential impact on native salmon from farmed escapes in Ireland (McGinnity et al. 1997, 2003)

15. How general are Irish salmon findings?
AIR project had Scottish and Spanish
components-performance of natives better
than non-natives
“Common-garden” comparison in Ireland
of native versus non-native wild progeny,
showed significantly higher survival of former
Similarly in Imsa study in Norway (Fleming
et al.)

16. INDIRECT EFFECTS: Disease from cultured salmon affecting wild
salmonids
EU SALIMPACT-Neth, UK, Nor, Irl
Major Histocompatibility Complex investigated

17. Examining temporal samples of sea trout from a river in the west of Ireland with a history of aquaculture
Burrishoole – freshwater Atlantic salmon hatchery, ranching and sea cages

18. Burrishoole Upstream from Furnace Downstream from Feeagh
Salmon Leap trap

19. Aquaculture activity- Atlantic salmon (hatchery and ranching c1960)
MI smolt unit

20. Allelic richness
Significant loss of allelic richness/genetic
diversity at MHC I after 1958 but subsequent recovery
Relative stability at neutral loci

21. Putative agent of selection
Furunculosis associated with development of smolt release programme - reducing genetic variability at MHC
Aquaculture activities can cause changes at immune response genes in cohabiting salmonid species, in addition to changes caused by interbreeding, either within or between species

22. Marine species differ from salmon:
Census populations much larger (low drift)
Population (“stock”) structure far less defined
Is gene flow high?
Reduced interpopulation differences in latter
group often attributed to far greater gene flow
(poor natal homing)
Might also (or instead) be due to far less genetic
drift?

23. Known that salmon home natally and are locally
adapted.
Are marine species?
“Walls in ocean?”
Gyral retention of larvae
Heterogeneity of spawning habitat
Hybrid zones (Baltic/Atlantic-Nielsen et al.)

24. Challenge to study in “open” system
Maybe, invoke genetic “tagging” (breeding
for genotype that is rare in wild, but
functionally equivalent to other genotypes)
May have to use opportunist situations,
since experimental systems in ocean likely
to be too costly and uncontrollable (except
in semi-isolated habitats/Borgenfjord)

25. How can aquaculture grow without
further impinging on wild populations,
themselves threatened by overfishing,
pollution, habitat destruction and
climate change?

26. “When elements of a species are domesticated, the remaining wild
To quote a distinguished mammalologist:
“When elements of a species are
domesticated, the remaining wild
populations quickly go extinct”
Can we prevent this with aquatic
species?

27. Thank you!