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Inbreeding
Inbreeding
inbreeding coefficient F – probability that given alleles are identical by descent
- note: homozygotes may arise in population from unrelated parents
but: generally will have less overall homozygosity by random chance than from inbreeding
Inbreeding
Result of inbreeding is inbreeding depression:
- loss of fitness due to deficient heterozygosity
- recessive traits are expressed
Inbreeding
inbreeding coefficient F
F = 1 – H F is a function of the ratio
2pq of observed over expected H (# heterozygotes)
H = observed frequency of heterozygotes in the population p = frequency of one allele in the population q = frequency of alternate allele, or 1-p 2pq = expected frequency of heterozygotes in the population
Inbreeding
inbreeding coefficient F
F = 1 – H F is a function of the ratio
2pq of observed over expected H
example: p = 0.5, therefore q = 0.5 2pq = 0.5
Inbreeding
inbreeding coefficient F
F = 1 – H F is a function of the ratio
2pq of observed over expected H
example: p = 0.5, therefore q = 0.5 2pq = 0.5
if in H-W equilibrium, H = 0.5 so F = 0 = random matingif no heterozygotes, H = 0 F = 1 = complete inbreeding
Inbreedingselfing: F = 0.5 (loss of 50% of total variation per generation)
Inbreedingselfing: F = 0.5 (loss of 50% of total variation per generation)
AA Aa aa p q 1.0 0.5 0.5
0.250 0.500 0.250 0.5 0.5G
ener
atio
n
Inbreedingselfing: F = 0.5 (loss of 50% of total variation per generation)
AA Aa aa p q 1.0 0.5 0.5
0.250 0.500 0.250 0.5 0.5
0.250 0.250
Gen
erat
ion
Inbreedingselfing: F = 0.5 (loss of 50% of total variation per generation)
AA Aa aa p q 1.0 0.5 0.5
0.250 0.500 0.250 0.5 0.5
0.250 0.250
0.125 0.250 0.125
Gen
erat
ion
Inbreedingselfing: F = 0.5 (loss of 50% of total variation per generation)
AA Aa aa p q 1.0 0.5 0.5
0.250 0.500 0.250 0.5 0.50.375 0.250 0.375 0.5 0.5
Gen
erat
ion
Inbreedingselfing: F = 0.5 (loss of 50% of total variation per generation)
AA Aa aa p q 1.0 0.5 0.5
0.250 0.500 0.250 0.5 0.50.375 0.250 0.375 0.5 0.5
= ½ of het.frequency
= 1 x hom. frequency+ ¼ of het. frequency
Gen
erat
ion
Inbreedingselfing: F = 0.5 (loss of 50% of total variation per generation)
AA Aa aa p q 1.0 0.5 0.5
0.250 0.500 0.250 0.5 0.50.375 0.250 0.375 0.5 0.50.438 0.125 0.438 0.5 0.50.469 0.063 0.469 0.5 0.50.484 0.031 0.484 0.5 0.50.492 0.016 0.492 0.5 0.50.496 0.008 0.496 0.5 0.50.498 0.004 0.498 0.5 0.50.499 0.002 0.499 0.5 0.50.500 0.001 0.500 0.5 0.50.500 0.000 0.500 0.5 0.5
Gen
erat
ion
= ½ of het.frequency
= 1 x hom. frequency+ ¼ of het. frequency
Inbreedingselfing: F = 0.5 (loss of 50% of total variation per generation)
AA Aa aa p q 1.0 0.5 0.5
0.250 0.500 0.250 0.5 0.50.375 0.250 0.375 0.5 0.50.438 0.125 0.438 0.5 0.50.469 0.063 0.469 0.5 0.50.484 0.031 0.484 0.5 0.50.492 0.016 0.492 0.5 0.50.496 0.008 0.496 0.5 0.50.498 0.004 0.498 0.5 0.50.499 0.002 0.499 0.5 0.50.500 0.001 0.500 0.5 0.50.500 0.000 0.500 0.5 0.5
Gen
erat
ion
= ½ of het.frequency
= 1 x hom. frequency+ ¼ of het. frequency
If there is a recessive deleterious allele, the population is in trouble….
Inbreeding part 2 – or, how to predict the changes in genotype frequencies
F = 1 – H 2pq
H = observed frequency of heterozygotes in the population2pq = expected frequency of heterozygotes
Inbreeding
F = 1 – H 2pq
H = observed frequency of heterozygotes in the population2pq = expected frequency of heterozygotes
Define H = # heterozygotes (freq Aa) = 2pq –F2pq D = # homozygotes (freq AA)
R = # alternate homozygotes (freq aa)
Inbreedingselfing: F = 0.5 (loss of 50% of total variation per generation)
AA Aa aa p q 1.0 0.5 0.5
0.250 0.500 0.250 0.5 0.50.375 0.250 0.375 0.5 0.50.438 0.125 0.438 0.5 0.50.469 0.063 0.469 0.5 0.50.484 0.031 0.484 0.5 0.50.492 0.016 0.492 0.5 0.50.496 0.008 0.496 0.5 0.50.498 0.004 0.498 0.5 0.50.499 0.002 0.499 0.5 0.50.500 0.001 0.500 0.5 0.50.500 0.000 0.500 0.5 0.5
Gen
erat
ion
heterozygote freq. decreased by F
homozygote freq.increased by ½ F
Inbreeding
Thus, the impact of inbreeding on each genotype is:
freq (AA) = D = p2 + Fpq
freq (Aa) = H = 2pq – 2Fpq
freq (aa) = R = q2 + Fpq
(remember F = 1 is the result of complete inbreeding, no heterozygotes)
Inbreeding
Example of the impact of inbreeding:
p = 0.6, q = 0.4, 2pq = 0.48
F = 0
D = p2 + Fpq 0.36
H = 2pq – 2Fpq 0.48
R = q2 + Fpq 0.16
i.e., no inbreeding, population is in Hardy-Weinberg equilibrium, genotypes are predictable based H-W equation, p2 + 2pq + q2
Inbreeding
Example of the impact of inbreeding:
p = 0.6, q = 0.4, 2pq = 0.48
F = 0 F = 0.5
D = p2 + Fpq 0.36 0.48
H = 2pq – 2Fpq 0.48 0.24
R = q2 + Fpq 0.16 0.28
heterozygotes have decreased by ½ of 0.24; homozygotes have increased by ¼ of 0.24
Inbreeding
Example of the impact of inbreeding:
p = 0.6, q = 0.4, 2pq = 0.48
F = 0 F = 0.5 F = 1
D = p2 + Fpq 0.36 0.48 0.60
H = 2pq – 2Fpq 0.48 0.24 0.0
R = q2 + Fpq 0.16 0.28 0.40
heterozygotes have decreased by all of 0.24; homozygotes have increased by ½ of 0.24
Inbreeding
How much inbreeding is acceptable?Slow increase in inbreeding results in less inbreeding depression than rapid inbreeding– slow purging of deleterious alleles
Inbreeding
How much inbreeding is acceptable?Slow increase in inbreeding results in less inbreeding depression than rapid inbreeding
– slow purging of deleterious alleles
Low genetic variability is much less important than loss of variability
Inbreeding
Deliberate use of inbreeding
- breed out deleterious alleles
- temporary reduction in fitness, then stabilizes
- increase fitness by crossing inbred lines
Inbreeding
Examples?
Beware of file drawer effect/publication bias!- In stable populations, low variation is uninteresting
- In small populations, high variation is uninteresting
Small populations do not evolve
Forces that change neutral genes among sub-populationsfounder effect > reduced diversitygenetic drift > changes in allelic frequency
“Smallness and randomness are inseparable.”M. Soulé (1985)
How big does a population need to be to avoid loss of genetic variation?
What is a ‘small’ population?
Effective population size (Ne)
Ne reflects the probability that genetic variation will not be lost by random chance
Effective population size (Ne)
Ne reflects the probability that genetic variation will not be lost by random chance
Ideal:• 1:1 sex ratio
• all individuals live to maturity and breed
• all adults have equal chances of mating with each other
• all individuals or pairs contribute equal numbers of offspring
• all of the offspring live
Effective population size (Ne) = N only if all of these are true
Effective population size - evidence
Not all individuals can mate with each other:
• 1,000 grizzly bears left in US. (1980s)
• less than 1% of range still occupied
• species now present in 6 isolated subpopulations
• estimated effective population size ~ 25% of census size
(Allendorf et al. 1991)
Effective population size - evidence
Not all parents contribute equally to next generation:
Social structure with mate competition• harem-polygynous species, e.g., lions, some bats• 5.4% of spawning male smallmouth bass
produce 54.7% of progeny (Gross & Kapuscinski 1997)
Sperm competition• mass spawning of 2,000 rainbow trout genetically equiv. to 88.5 spawners• mass spawning of 10,000 Chinook salmon equiv. to 132.5 spawners
(K. Scribner and others)
Effect of sex ratio on Ne
Ne – taking sex ratio (only) into account
Ne = 4Nm Nf
Nm + Nf
Effect of sex ratio on Ne
Ne = 4Nm Nf for 25 of each sex, 4*25*25 = 2,500 = 50Nm + Nf 25 + 25 50
Effect of sex ratio on Ne
Ne = 4Nm Nf for 25 of each sex, 4*25*25 = 2,500 = 50Nm + Nf 25 + 25 50
BUT for 40 males, 10 females
4*40*10 = 1600 =
32 40 + 10 50
Effect of sex ratio on Ne
25:25 Ne = 50
40:10 Ne = 32
49:1 Ne = 3.9
Effect of fluctuating populations on Ne
Calculate Ne as harmonic mean* over several generations
Ne = t (1/Nt)
t = generation (population sample)Nt = number of individuals in generation t
* gives greater weight to small numbers
Effect of fluctuating populations on Ne
Example:Gen. (t) Pop. Size (Nt) 1/Nt
1 500 0.002 2 500 0.002 3 500 0.002 4 500 0.002 5 500 0.002 6 50 0.02 7 500 0.002 8 500 0.002 9 500 0.002 10 500 0.002
Arithmetic Ne Mean
455 263
Effect of fluctuating populations on Ne
Example:Gen. (t) Pop. Size (Nt) 1/Nt
1 500 0.002 2 50 0.02 3 500 0.002 4 50 0.02 5 500 0.002 6 50 0.02 7 50 0.02 8 50 0.02 9 500 0.002 10 500 0.002
Arithmetic Ne Mean
275 91
Effect of family size on NeEffect of family size on Ne
Neur = k(Nk – 1) Vk + k(k -1)
ur = unequal reproductive outputk = mean number of surviving progenyVk = variance in family sizeN = total progeny
Effect of family size on NeEffect of family size on Ne
Neur = k(Nk – 1) Vk + k(k -1)
ur = unequal reproductive outputk = mean number of surviving progenyVk = variance in family sizeN = total progeny
40 34 40 51 40 62 40 26 40 3 40 99 40 5
Av 40 40N 280 280Ne 287 165
Inbreeding and Ne
rate of inbreeding F = rate at which heterozygosity is lost (or fixation occurs)
1
F = 2Ne
Inbreeding and Ne
effect of changes in sex ratio:
25:25 Ne=50 F = 1/100 = 1%
40:10 Ne=32 F = 1/64 = 1.6%
49:1 Ne=3.9 F = 1/7.8 = 12.8%
1:1 Ne=2 F = 1/4 = 25%
Retention of genetic variation in a small population
# generations Ne 1 5 10 1002 75 24 6 <<16 91.7 65 42 <<110 95 77 60 <120 97.5 88 78 850 99 95 90 36
100 99.5 97.5 95 60
N = 50, M=25, F=25
Assume a population of N = 50As sex ratio changes, equivalent Ne changes
Retention of genetic variation in a small population
# generations Ne 1 5 10 1002 75 24 6 <<16 91.7 65 42 <<110 95 77 60 <120 97.5 88 78 850 99 95 90 36
100 99.5 97.5 95 60
N = 50, M=5, F=45
Retention of genetic variation in a small population
# generations Ne 1 5 10 1002 75 24 6 <<16 91.7 65 42 <<110 95 77 60 <120 97.5 88 78 850 99 95 90 36
100 99.5 97.5 95 60
N = 50, M=3, F=47
Inbreeding
How much inbreeding is acceptable?• 1-3% per generation – 1% preferred• recommended Ne = 50, to maintain inbreeding at <1%
Inbreeding
How much inbreeding is acceptable?• 1-3% per generation – 1% preferred• recommended Ne = 50, to maintain inbreeding at <1%
BUTgenerally only 1/3 to ¼ of popn contributes to next generation
- so N should be 150-200
Small populations: founder effect/bottlenecks, drift, inbreeding
Minimal founder population for captive breeding: 50(M. Soulé 1980)
For long-term breeding, minimal population: 500(J. Franklin 1980 )
the “50/500 rule”
Franklin, I.R. 1980. Evolutionary change in small populations, in Conservation Biology: An evolutionary-ecological perspective. M.E. Soulé and B.A. Wilcox (eds). Sinauer, MA Soulé, M.E. 1980. Thresholds for survival: maintaining fitness and evolutionary potential, in Conservation Biology: An evolutionary-ecological perspective. M.E. Soulé and B.A. Wilcox (eds). Sinauer, MA
Small populations: founder effect/bottlenecks, drift, inbreeding
Minimal founder population for captive breeding: 50(M. Soulé 1980)
For long-term breeding, minimal population: 500(J. Franklin 1980 )
To balance mutation and drift: 5,000(R. Lande 1995)
Franklin, I.R. 1980. Evolutionary change in small populations, in Conservation Biology: An evolutionary-ecological perspective. M.E. Soulé and B.A. Wilcox (eds). Sinauer, MA Soulé, M.E. 1980. Thresholds for survival: maintaining fitness and evolutionary potential, in Conservation Biology: An evolutionary-ecological perspective. M.E. Soulé and B.A. Wilcox (eds). Sinauer, MALande, R. 1995. Mutation and conservation. Conservation Biology 9:782-791.
Inbreeding
When is population size too small (hopeless)?Przewalski’s horse 13 Guam rail 10 black-footed ferret 6 European bison 6 Speke’s gazelle 4 dusky seaside sparrow 2…1..…0
note: these are all captive (regulated) populations….