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 LewisTom.Lewis@thekennelclub.org.uk