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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
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