Genetic parentage analysis of hatchery contribution of Atlantic salmon on the River Spey

Mark Coulson
Rivers and Fisheries Trusts of Scotland (RAFTS)

IBIS/AST Atlantic Salmon Stocking Conference 27th-28th November, 2013 Glasgow, UK

Acknowledgements
Co-authors:
R Laughton, B Shaw (Spey Foundation) A Armstrong (RAFTS) E Verspoor (MSS / UHI)

Spey Foundation / Spey Research Board J Woods, D McPherson, R Knight

RAFTS Callum Sinclair (Director)

Marine Scotland Science

Hatcheries
(Cross et al. 2007)

Scenarios for stocking include

reintroduction rehabilitation enhancement mitigation

Genetic considerations? Genotyping of broodstock would allow:

Evaluation of stocking success Identification of siblings (inbreeding avoidance)

The River Spey Hatchery

Known salmon distribution

One of the largest rivers in Scotland ~170 km of mainstem ~900 km of tributaries

stock enhancement policy (2003)

targets under-populated areas above obstacles & accessible areas Aim: To boost the natural smolt man-made output from the Spey proven to be under-stocked catchment and hence adult returns. In turn, extra fish may be

caught in the rod fishery, and additional spawners may be suitable habitat above obstructions present within the accessible area>1,000,000 each autumn. m2
hatchery capacity ~ 1.2 million eggs; previously ~ 2.2 million juvenile fish planted into same area of the catchment as from where their parents originated

Hatchery operation

2
3

X X X

1 2 3

Spey salmon stocking 2007

Spey salmon stocking 2004

Spey salmon stocking 2010

Spey salmon stocking 2005

Spey salmon stocking 2008

Spey salmon stocking 2011

Spey salmon stocking 2006

Spey salmon stocking 2009

Spey salmon stocking 2012

Spey hatchery stocking summary by life stage

Rod catch (all years)

Q: What proportion of the rod-catch can be attributed to the hatchery?

Individual identification (DNA)

Each individual carries a unique DNA fingerprint Cases of genetic paternity Related individuals Forensics

Parentage assignment
Single genetic marker
Each parent passes on 1 of their 2 copies Offspring gets 1 copy from mother + 1 copy from father
Offspring

Applied across multiple markers makes most parents VERY unlikely

Assigning genetic parentage

Sample of adult males (broodstock)

M1 M4 M3 M2 M5

F1
F4

F2

?
Sample of potential offspring (rod-catch)

F5

F3

Sample of adult females (broodstock)

Assigning genetic parentage

Hatchery breeding records
F1

M1

F2

?
F3 F4

X
X X

M2

M3

M4

F5

M5

Sample of potential offspring (rod-catch)

Sample of broodstock

Assigning genetic parentage

Sample of adult males

F1

X X X

M1

F2

M2

F3

M3

F4

X
X

M4

F5

M5

Sample of juveniles

confirm with breeding records!!! Sample of adult females

The dataset
Marker Number of variants

SP2201
SP2210 SPG7 Ssa202

35
13 26 16

SsaD144
SsaD157 SP1605 SP1608 SP2216 Ssa171 Ssa14 Ssa289 SP3016 Ssa197 SsaD48 SsaD71 SsaF43

38
35 12 59 20 27 4 9 18 29 66 55 12

Error rate in generating genetic fingerprint ( < ~2%)

double-blind samples

4,183 salmon screened 36 cases (0.8%) of identical genotypes 4,155 distinct genetic profiles 114 (2.7%) removed due to insufficient profiles 4,041 individuals for analysis Breeding records: ~8% of cases unknown

Sample summary
Year Rod-catch Broodstock (male) Broodstock (female)

2004 - fish as possible 241 284 1,090 rod-caught hatchery origin 2005 240 868 broodstock as possible hatchery origin 2006 234 1,958 possible hatchery offspring 2007 163 252
2008 2009 2010 2011 2012 TOTAL 299 257 113 217 204 1253 156 108 150 1381

189
261 234 164 118 172 1422

1,958 possible hatchery offspring

1,931
hatchery parents

10

17

OR
offspring

>98% accuracy of parentage assignment with 7 (out of 17) genetic markers

Two hatchery parents

Broodstock

Rod caught fish

Two hatchery parents

Year Sample size Assigned both parents (hatchery) % sample attributed to hatchery

Rod-catch 2008 299 1 0.3%

2009
2010 (rod) Spey Dam 2011 2012

257
80 33 217 204

1
0 0 4 3

0.4%
0% 0% 1.8% 1.5%

Broodstock (as offspring) 2008 2009 320 226 1 7 0.3% 3.1%

2010

322

0%

One hatchery parent

Broodstock

OR

Rod caught fish

One hatchery parent

Year Sample size Assigned one parent (hatchery)

false positive
Human error

Rod-catch 2008 2009 2010 (rod) Spey Dam 2011 2012 299 257 80 33 217 204 Broodstock (as offspring) 2008 2009 2010 320 226 322 1 0 4 2 2 0 0 1 0

Other explanations pre/post hatchery spawning Precocious parr? Repeat spawners?

Close relatives

Spey Dam

Juveniles sampled above dam = 46/55 (83%) hatchery-origin

Family size 1 2 3 4 5
Broodstock = sourced from various parts of the upper river
Number of salmon above dam in 1990s ~100

occurrence 7 7 2 2 1 1

Have stocked 200,000-400,000 fry above dam

Adults returning sampled returning below dam (0/33)

Heavily targeted due to low population densities

Summary
Powerful tool for tracing hatchery origin
0%-1.8% of rod-caught fish could be traced to hatchery in any given year Importance of breeding records! Provides an example of sampling strategy to monitor effectiveness of hatchery practice Can be used to refine practices and target specific areas for restocking

Thank You!