breed population analyses: some background, a guide to the reports, & some interesting examples
TRANSCRIPT
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Breed population analyses:
some background,
a guide to the reports,
& some interesting examples.
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Inbreeding defined as the mating of genetically related
individuals.
Inbreeding
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2n ancestors where n = generations back
We all have
2 parents
4 grand parents
8 great grand parents
16 great great grand parents
etc…
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10 generations ago was the 1700s
mainly
isolated
rural
communities
How many of us have 1024 unrelated ancestorsfrom this era?
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25 generations ago was the 1300s
To be completely non-inbred we would need over 33½ million unrelated ancestors
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Furthermore, the resemblance of relatives…
means selection will result in the mating of
individuals more closely related than average
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Inbreeding defined as the mating of genetically related
individuals.
So, inbreeding is impossible to avoid (to some degree & if
you go back far enough)
However, most of the problems associated with
inbreeding come from more recent ancestral generations
– why?
Inbreeding
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Why? Inbred lines tend to die out…
time
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It’s all about risk…
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Alvarez et al (2009) PLoS ONE 4(4): e5174
What are the risks associated with inbreeding?
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Why does inbreeding cause these problems?
CGT-CGT-CGT-CGT-TGA CGT-CGT-CGT-CAT-TGACGT-CGT-CGT-CGC-TGA
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CGT-CGT-CGT-CGT-TGA CGT-CGT-CGT-CAT-TGACGT-CGT-CGT-CGC-TGA
Why does inbreeding cause these problems?
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COI is a probability that the 2 copies of a
gene are Identical By Descent (IBD)
• 25% for offspring of a full sib mating or a parent/offspring mating
• 12.5% for offspring of a half sib mating
• 6.25% for offspring of 1st cousins
Coefficient of inbreeding (COI)
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Alvarez et al (2009) PLoS ONE 4(4): e5174
COI = 25.4%
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Breed mean COI
(2014 born dogs)
German Shepherd Dog 3.2%
Norwegian Elkhound 4.4%
Cavalier King Charles Spaniel 5.5%
Labrador 6.5%
Bloodhound 7.0%
Tibetan Terrier 7.8%
Welsh Corgi (Cardigan) 9.9%
English Springer Spaniel 9.9%
Manchester Terrier 15.1%
Breed average COI
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COI = 0% * *…(using 3 generations of pedigree only, actual COI may be considerably higher. When using 5 generations of pedigree, COI = 17%)
Number of generations is all important
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20%
15%
10%
5%
Avera
ge C
OI
Generations / time
Rate of inbreeding (ΔF)
rate of inbreeding (ΔF) = change in average COI over time (or generations)
Usually quoted as the Effective population size (Ne)
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Pr = 0.06
Pr = 0.0004
f(g) = 0.05 f(g) = 0.15
Pr = 0.045
Pr = 0.0003
f(g) = 0.30(1 in 20 green) (3 in 20 green) (6 in 20 green)
(6/100) (45/1000)
(4/10,000) (3/10,000)
Genetic drift
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Inbreeding/drift summary
Inbreeding unavoidable in the long term
COI describes the probability of IBD, and so risk
Rate of inbreeding the important measure for breed/population
Inbreeding and drift act on allele frequencies
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Paper detailing results now available:
http://www.cgejournal.org/
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Breed analysis reports
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Figure 1: registrations by year of birth
Trend of registrations over year of birth (1980-2014) = 194.77 per year (with a 95% confidence interval of 143.33 to 246.21)
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Table 1: sire statistics per year
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Figure 2: rate of inbreeding
Estimated effective population size= 81.7 NB - this estimate is made using the rate of inbreeding over the whole period 1980-2014
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Table 2: trends within 1980-2014
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Figure 3: distribution of progeny per sire/dam
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Broad trends and interesting examples…
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The rate of inbreeding is (generally) slowing…
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…although, not in all breeds…
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Some rarer breeds are conserving diversity…
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…but others are really struggling…
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Drastic loss of genetic diversity in some breeds
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Effective and actual popn size appear unrelated
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Possible effect of ‘sub’ populations…
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Summary
General trend across breeds is a declining rate of inbreeding
Effective population size is over whole period 1980-2014
Be aware of changing trends within the whole period
No simple relationship between actual and effective population size
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Thank you – and any questions?
With grateful acknowledgements to:
Dr Sarah Blott – University of Nottingham
Prof John Woolliams – Roslin Institute
Dr Tom [email protected]