In December 2014 WRT held a Catchment Based Approach and Catchment Restoration Fund Conference in Exeter. The University of Exeter's Andy King and Jamie Stevens gave an overview of their work on fish genetics.

1. Exploring the genetic basis of metal
tolerance in populations of the
brown trout (Salmo trutta L.)
Josephine Paris, Andrew King &
Jamie Stevens

2. Camel Fal Hayle Red River
Zinc (ug/l) 17 37 350 238
Copper (ug/l) 5 5 28 27
Arsenic (ug/l) 4 4 9 86
Clean Metal

3. For example, the River Hayle
• Essentially copper
producing mines
• Record production
approaching 160,000 tons
of concentrates.
• Small amounts of zinc and
lead, plus some silver.
• Tin is recorded from only
three of the mines and
outputs are insignificant.

4. What we’ve found
Each trout metal population has a different genetic profile
compared to trout from clean rivers, and other metal
populations
We have timed the generation of each distinct heavy metal
population to historical events relating to mining activity
Metal-impacted populations have lower genetic diversity
compared to reference ‘clean’ rivers… evidence of population
bottlenecks & local adaptation
15 populations
641 individuals
25 microsatellite loci
9 potentially under
selection

5. Lower genetic diversity in heavy metal rivers
25 microsatellite loci15 populations
641 individuals
5.50
6.50
7.50
8.50
9.50
10.50
AR
0.55
0.60
0.65
0.70
0.75
0.80
He
0.55
0.60
0.65
0.70
0.75
0.80
Ho

6. 100
0.05
Analysis of trout microsatellite genotype profiles = highly structured

7. Distinct population structure
Hayle 1
Gannel 2
Fal
Camel 1
Camel 2
Gannel 1
Tresillian
Hayle 2
Crowlas
Trevaylor 1
Trevaylor 2
Hayle 3Hayle 4
Red River 1
Red River 2
Coord.2:19.8%
Coord. 1: 45.2%

8. Next step:
RAD-seq-based SNP discovery
• Allows for rapid genome-wide screening for fine-scale
(inter-population) variation
• Allows for detection of genetic markers (SNPs) associated
with adaptive traits (= identification of non-neutral
genetic loci)
• Preliminary analysis identifies SNPs (polymorphisms)
associated with survival in metal impacted waters; some
of these SNPs are in areas of the genome associated with
metal processing, e.g. metallothionein.

9. Genetic Investigations on
Brown Trout from the
Devon Avon
R. Andrew King, Bruce Stockley & Jamie R. Stevens
Exeter University & Westcountry Rivers Trust

10. Devon Avon
• Also known as the River Aune
• Catchment is in the South Hams district of Devon
• River is approx. 35km in length and 105km2, rising
on Dartmoor and entering the sea at Bigbury-on-Sea
• Catchment is included, along with the Erme and
Yealm, in the CRF South Hams River Improvement
Project (SHRImP)

11. WFD Failures
• EA report published January 2011
• Upper Avon is failing Water
Framework Directive (WFD) for fish
and acidity
• Section downstream of the Avon
Dam is notable for the absence of
salmon and eels, but trout are
present
• This was suspected as being due to
the combined influence of the Avon
Dam (1957) and low acidity (post-
Industrial Revolution)

12. WRT Management Questions
• Q1 - Is the Avon Dam having a genetic affect on
the trout populations downstream of the dam?
• Q2 - Are there genetic differences between the
trout populations above and below the Avon
Dam?

13. Genetic Analyses
• Samples collected from multiple sites along the river by
Environment Agency and Westcountry Rivers Trust staff during
routine electrofishing surveys
• Total sample of 236 fish
• Grouped into five ‘populations’
• Us Avon Dam
• Avon Dam to Shipley
• Shipley to South Brent
• Avonwick
• Bickham Bridge
• Screened for variation at 19 putatively neutral
microsatellite loci used during the AARC Project
• Basic measures of genetic diversity calculated and
genetic structuring investigated

14. Bickham Br
2012 - N=29
Avonwick
2011 - N=44
N=number collected
us Avon Dam
2013 - N=76
Dam to Shipley
2013 - N=14
2014 - N=36
Shipley to South Brent
2013 - N=10
2014 - N=29

15. Q1 - Gene Diversity

16. Q1 - Allelic Richness

17. Q1 - Private Allelic Richness

18. Q2 – Genetic structure
Us Avon Dam Dam to
Shipley
Shipley
to
South Brent
Avonwick Bickham
Bridge

19. US/DS Split Time
us Shipley ds Shipley

20. Conclusions
• We can give answers to WRT’s management questions
• The Avon Dam has had an affect on the levels of genetic
diversity in brown trout in the reaches downstream of
the dam
• There are two distinct genetic groups of brown trout in
the Devon Avon, but the boundary between the two is
not coincident with the dam
• Divergence time of the two groups suggests that the split
is not recent and that the trout population in the upper
Avon has been isolated above Shipley Falls for at least
3500 years
• This would suggest that the WFD failures for salmon
and eel are due to Shipley Falls acting as a natural
migration barrier (also for sea trout)

21. Acknowledgments
• Project was funded by the Westcountry Rivers
Trust and by the EU INTERREG AARC project
• Karensa Lawrie, Giles Rickard and Scott West
• Environment Agency Devon electrofishing teams
Investing in our common future