John Gilbey - The use of scales for genetics

The use of scales for geneticsJohn Gilbey

Freshwater Fisheries Laboratory

• The use of scales

– Why use them?

– How DNA is obtained

– DNA quality

• For genetics

– What have they been used for?

– What are they being used for now?

The use of scales for genetics

• Easy to collect

– Non-invasive (or low-invasive)

– No special equipment

– Storage media paper envelopes (no ethanol)

– However, still require HO license if collected for scientific purposes

• Availability

– Available from many systems

– In many cases cover long time series

Why use them?

Extracted as with any other tissue

• dried dermis & epidermis

• dried mucus layer

• Destructive

How is DNA obtained?

• Storage conditions

– KEEP THEM DRY!!

DNA quality

Degrade over time

– But still may be of use

Microsatellites – 100’s of bp

SNP’s – Single bp (+ flanking)

DNA quality

• Can be used in the same way as DNA from any other

source

– e.g.

• Population analysis

• Mixed stock fisheries

• Sex determination (on the way?!)

• Hatchery influences

• Pedigree analysis

• etc.

• Often of great help in addressing the above due to the

large number of rivers/sites available

• Scales often provide unique opportunities to

investigate various issues due to the time series they

represent

Uses of DNA from scales

• Sex determination

– Unambiguous genetic test to show the sex of salmon of any age

Applications and case stories

• Identification of native populations

– The preservation of native populations is one of the main goals in

conservation biology of salmonid fishes

– However, in many areas populations may have experienced some

kind of influence by straying, escapes or stocking

– Consequently, it is of primary importance to identify populations

with limited or no introgression from foreign conspecifics in order to

ensure a high level of protection for these populations

Applications and case stories

– Skjern River - Catches decreased

– Were remainder native or from

strayers from nearby systems or

stocking that was done

– Analysed scale samples from the

30’s, 50’s and contemporary from

before and after stocking together

with samples from nearby rivers

Applications and case stories

– Found that is was highly probably that the salmon population in the river

today were descended from the original population that had persisted in

the river

– This finding had a “profound impact” on the protection status of the

population, with it becoming “probably the best protected” in Denmark.

• Examination of historical and contemporary population

structure

– Understanding the dynamics of geneflow, genetic drift and selection is of

great help in defining population structure which in turn can aid management

and conservation of stocks

– These relationships may be difficult to establish in contemporary populations

due to human impacts

– Authors examined scales from 1913 – 1989 (some from extinct populations)

– Found relationships in older samples not seen in more modern ones

Applications and case stories

Girnock burn pedigree analysis

Ongoing investigations using scales

– Trap operated in the Girnock burn on the Dee since 1966

– Have scale samples from parr, smolts and adults throughout this period

– International collaboration started in 2013

• Marine Scotland

• Institute of Marine Research, Ireland

• University of Belfast, NI

• University of Turku, Finland

Girnock burn pedigree analysis

Ongoing investigations using scales

– Genetic analysis (microsatellites) underway

→ pedigree

– Examine: trait heritabilities, assortative mating,

precocious parr input

– Focus on Ne determination (effective

population size) and examine its potential as a

management tool

Spring fish

Ongoing investigations using scales

– Interested in being able to differentiate between spring and later running fish

– Will allow investigations into spatial use with a river, survival at sea,

exploitation, and hence aid conservation of this stock component

– Using samples, including scale samples from a number of rivers across

Scotland – including the Tweed.

• Screen at a large number of SNPs

• Identify those linked to trait, and produce panel for screening

Have just received data for

~550 fish at 220,000 SNPs

Scales from 70s –

Scales from 80s –

Scales from 90s –

~

• Scales are very useful for many types of genetic analysis

– Geographic coverage

– Temporal coverage

• May allow unique analysis not possible using any other means

• However – destructive so care must be taken as to when to

use them

• Storage of critical importance – keep them dry!

Summary