Exploring the genetic basis of metal tolerance in populations of the brown trout (Salmo trutta L.)

Josephine Paris, Andrew King &

Jamie Stevens

Camel Fal Hayle Red RiverZinc (ug/l) 17 37 350 238

Copper (ug/l) 5 5 28 27Arsenic (ug/l) 4 4 9 86

Clean Metal

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.

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

Lower genetic diversity in heavy metal rivers

25 microsatellite loci 15 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

100

0.05

Analysis of trout microsatellite genotype profiles = highly structured

Distinct population structure

Hayle 1

Gannel 2 Fal

Camel 1 Camel 2

Gannel 1

Tresillian

Hayle 2

Crowlas

Trevaylor 1

Trevaylor 2

Hayle 3 Hayle 4

Red River 1

Red River 2

Coor

d. 2

: 19.

8%

Coord. 1: 45.2%

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.

Genetic Investigations on Brown Trout from the

Devon Avon R. Andrew King, Bruce Stockley & Jamie R. Stevens Exeter University & Westcountry Rivers Trust

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)

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)

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?

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

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

Q1 - Gene Diversity

Q1 - Allelic Richness

Q1 - Private Allelic Richness

Q2 – Genetic structure

Us Avon Dam Dam to Shipley

Shipley to

South Brent

Avonwick Bickham Bridge

US/DS Split Time

us Shipley ds Shipley

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)

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