assessment of salmon stocks in scotland: integrating genetics - mark coulson, rivers & lochs...

Assessment of Salmon Stocks in Scotland: Integrating Genetics

(AS3IG)

Mark Coulson Rivers and Lochs Institute

UHI Inverness College

Rivers and Lochs Institute

StudentsMatt Curran Part-time PhD Evan Roderick M by ResDara Vaughn Full-time PhD

Supporting the sustainable management of Scotland’s

freshwater biodiversity

Biodiversity Management Applied GenomicsBioMAG Laboratory

Current Demographic Assessment Metrics

Retain

Main river counters

Angling records+

Mark-recapture

Catch Release

Tributary counters

Redd Counts

Juvenile surveys

Smolt Counters

Number, size, timing, age

Number, size, timing, age

Number, size, timing, age

Logistic and Analytical Challenges in using this information to achieve

conservation/exploitation objectives

Retain

Main river counters

Angling records+

Mark-recapture

Catch

Release

Tributary counters

Redd Counts

Juvenile surveys

Smolt Counters

Number, size, timing, age

Number, size, timing, age

Number, size, timing, age

Numbers of breedersgenetic diversitypopulation membership phenotype (e.g. run timing)

Current Demographic Assessment Metrics + Genetics

Optimisation of

genotyping and data

processing

UHI-SME Collaboration

Fisheries Management

Delivery of stock assessment framework

Delivery of genetic analysis service

AS3IG Project(Assessment of Salmon Stocks in Scotland: Integrating Genetics)

FundingSSE

UHI/ICNess DSFB

Spey Foundation

Dara Evan

River Carron 2012 juvenile sample

Identified 10 groups as most likely

Individuals sorted by group membership

stocked? wild? stocked/wild? wild? stocked?

Group % related Nb # full-sib families

1 100 7 (1 + 6) 62 100 6 (1 + 5) 53 3 92 (45 + 47) 694 6 57 (27 + 30) 425 47 5 (2 + 3) 36 14 18 (8 + 10) 107 3 95 (45 + 40) 688 18 14 (6 + 8) 139 77 10 (7 + 3) 8

10 100 4 (1 + 3) 3

stocked? wild? stocked/wild? wild? stocked?

River Carron - estimating number of breeders

Sample of juveniles

4

4

Resolving family relationships

Sample of juveniles(n = 10)

4

4

Resolving family relationships

No. breeders = 8

Max. No. breeders = 20

Nb/Max. Nb = 8/20 = 0.4

BUT

Site Sample size No. Breeders Max. Breed Ratio

Whiteadder 50 68 100 0.68

Till - Twizel Mill 32 44 64 0.69

Till - Lilburn 50 65 100 0.65

Teviot Ale Water 31 51 62 0.82

Middle Tweed Gledswood 50 77 100 0.77

Ettrick lowest 51 74 102 0.73

Ettrick - middle 50 64 100 0.64

Ettrick – middle 32 45 64 0.70

Ettrick Rankle Burn 65 77 130 0.59

Ettrick- upper 46 51 92 0.55

Yarrow lower 48 61 96 0.64

Yarrow Douglas Burn 32 50 64 0.78

Yarrow upper 50 59 100 0.59

Upper Tweed Elibank 32 54 64 0.84

Manor Water3 43 59 86 0.69

Upper Tweed – Drumelzier 50 69 100 0.69

Upper Tweed – Fruid 32 45 64 0.70

River Tweed (FASMOP report)

• Barriers?• Fry/parr electrofishing surveys• Stream order/elevation/distance upstream. . .

Courtesy: James Hunt

Nb/Nratio

UnequalSex ratio

Variance in Reproductive

success

FluctuatingPopulation size-

- -Photo from: Moore & Fraser (2013)

Annual total adult run size (N)Annual number large (>63 cm) adultsNb estimate (lower 95% CL)

+precocious parr

Genetic Assessment Sampling Challenges

Sampling requirements for specific of river stock conditioned by e.g.• population structuring• number of populations • spatial distribution of populations• need for population specific or overall river

stock information• costs of genetic typing of individual loci• confidence limits needed around Nb

Sampling requirements for genome conditioned by e.g.• variability of loci i.e. number of alleles• linkage relationships among loci i.e.

unlinked is best • confidence limits needed around Nb

• costs of genetic typing of individual loci

10 km

Sampling requirements for short simple systems (e.g. Evelix) will be different than for long branching systems (e.g. Oykel-Casseley) and in turn than for long systems with lochs (e.g. Shin system)

Optimisation of

genotyping and data

processing

UHI-SME Collaboration

Fisheries Management

Delivery of stock assessment framework

Delivery of genetic analysis service

AS3IG Project(Assessment of Salmon Stocks in Scotland: Integrating Genetics)

case

stud

ies

Retain

Main river counters

Angling records+

Mark-recapture

Catch

Release

Tributary counters

Redd Counts

Juvenile surveys

Smolt Counters

Number, size, timing, age

Number, size, timing, age

Number, size, timing, age

Numbers of breedersgenetic diversitypopulation membership phenotype (e.g. run timing)

Current Demographic Assessment Metrics + Genetics