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Breed population analyses:
some background,
a guide to the reports,
& some interesting examples.
Inbreeding defined as the mating of genetically related
individuals.
Inbreeding
2n ancestors where n = generations back
We all have
2 parents
4 grand parents
8 great grand parents
16 great great grand parents
etc…
10 generations ago was the 1700s
mainly
isolated
rural
communities
How many of us have 1024 unrelated ancestorsfrom this era?
25 generations ago was the 1300s
To be completely non-inbred we would need over 33½ million unrelated ancestors
Furthermore, the resemblance of relatives…
means selection will result in the mating of
individuals more closely related than average
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
Why? Inbred lines tend to die out…
time
It’s all about risk…
Alvarez et al (2009) PLoS ONE 4(4): e5174
What are the risks associated with inbreeding?
Why does inbreeding cause these problems?
CGT-CGT-CGT-CGT-TGA CGT-CGT-CGT-CAT-TGACGT-CGT-CGT-CGC-TGA
CGT-CGT-CGT-CGT-TGA CGT-CGT-CGT-CAT-TGACGT-CGT-CGT-CGC-TGA
Why does inbreeding cause these problems?
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)
Alvarez et al (2009) PLoS ONE 4(4): e5174
COI = 25.4%
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
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
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)
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
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
Paper detailing results now available:
http://www.cgejournal.org/
Breed analysis reports
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)
Table 1: sire statistics per year
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
Table 2: trends within 1980-2014
Figure 3: distribution of progeny per sire/dam
Broad trends and interesting examples…
The rate of inbreeding is (generally) slowing…
…although, not in all breeds…
Some rarer breeds are conserving diversity…
…but others are really struggling…
Drastic loss of genetic diversity in some breeds
Effective and actual popn size appear unrelated
Possible effect of ‘sub’ populations…
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
Thank you – and any questions?
With grateful acknowledgements to:
Dr Sarah Blott – University of Nottingham
Prof John Woolliams – Roslin Institute
Dr Tom [email protected]
