Week 3: fri: Genetics and extinction I: inbreeding depression

Inbreeding depression

A decrease in fitness (e.g. survival

Genetic mechanism of inbreeding depression

Inbreeding reduces heterozygosity leading to more homozygous deleterious alleles being expressed and lowering fitness

Role of heterozygotes (Aa)

They mask harmful recessive alleles and therefore maintain higher fitness

Why inbreeding decreases mean performance

It converts heterozygotes into homozygotes and increases harmful aa individuals which lowers average fitness

Identifying dominance from graphs

Look at where Aa lies relative to AA and aa

Overdominance

Aa has the highest fitness compared to both AA and aa

Complete dominance

Aa has the same fitness as AA so the recessive allele is fully masked

Partial dominance

Aa has intermediate fitness but closer to AA than aa

Additive (no dominance)

Aa is exactly halfway between AA and aa

Why dominance matters for inbreeding depression

Inbreeding removes beneficial heterozygotes so fitness decreases if Aa is advantageous

Partial dominance hypothesis

Inbreeding depression is caused by recessive deleterious alleles becoming homozygous

Overdominance hypothesis

Inbreeding depression is caused by loss of high-fitness heterozygotes

Main mechanism of inbreeding depression

Partial dominance involving many small-effect recessive deleterious alleles

Direction of dominance effects

Whether the heterozygote performs better or worse than expected

When inbreeding depression is strongest (direction)

When dominance is favourable and heterozygotes have high fitness

Size of dominance effects

The magnitude of the difference between Aa and aa

When inbreeding depression is strongest (size)

When aa is much worse than Aa

Single locus effect of inbreeding

Inbreeding increases homozygous deleterious genotypes and reduces mean survival

Additive combination of loci

Effects of different loci sum together for traits like size or production (Phenotype = locus1 + locus2 + …)

Multiplicative combination of loci

Effects of loci multiply together for fitness traits like survival (Fitness = locus1 × locus2 × …)

Linear decrease in additive traits

Phenotype declines linearly with F because each locus contributes independently

Linear regression formula

P = a + bF

Regression coefficient b

The slope describing change in a trait per unit increase in inbreeding

Exponential decline in survival

Survival decreases exponentially with inbreeding because effects multiply across loci

Exponential model of survival

S = e^(-A - BF)

Log transformation of survival

ln(S) = -A - BF

Why take ln(S)

To linearize the exponential relationship and estimate parameters

Lethal equivalents (B)

A measure of the strength of inbreeding depression on survival

Interpretation of B

A higher B indicates stronger reduction in survival due to inbreeding

Relative survival with inbreeding

SF / S0 = e^(-BF)

Meaning of relative survival

Survival at inbreeding level F relative to outbred individuals

Delta (δ)

The proportional reduction in fitness of inbred individuals compared to outbred individuals

Delta formula

δ = 1 - (SF / S0)

Interpretation of δ

A value representing how much fitness is reduced in inbred individuals

Effect of inbreeding on population growth

Inbreeding reduces survival and reproduction leading to lower population growth rate

Inbreeding and extinction risk

Reduced fitness due to inbreeding increases the likelihood of extinction

Variation in inbreeding depression

It differs across species populations traits and environments

Environmental effect on inbreeding depression

Inbreeding depression is stronger in stressful or poor environments

Why stress increases inbreeding depression

Stress exposes hidden genetic weaknesses

Purging

Removal of deleterious alleles when they are exposed in homozygous individuals

When purging is effective

For strongly deleterious recessive alleles

Why purging is ineffective

Most deleterious alleles have small effects and are difficult to remove by selection

Overdominance and purging

Overdominance prevents purging because both alleles are maintained by selection

Delta F (ΔF)

The rate of increase in inbreeding per generation

Why high ΔF is dangerous

It increases genetic drift and homozygosity

Interaction of drift and inbreeding

Drift increases harmful allele frequencies and inbreeding exposes them leading to fitness decline

Why limit ΔF

To prevent harmful alleles from increasing and causing strong inbreeding depression

Pedigree-based inbreeding coefficient F

F = Σ (1/2)^(n1 + n2 + 1) where n1 and n2 are steps from each parent to the common ancestor

Meaning of F

Probability that two alleles are identical by descent

Genomic F

Realized inbreeding measured from DNA homozygosity

Advantage of genomic measures

They provide more accurate estimates and do not require pedigrees

Why F measures are not directly comparable

Different methods measure different aspects of inbreeding

Big picture of inbreeding depression

Inbreeding increases F reduces heterozygosity exposes deleterious alleles lowers fitness reduces population growth and increases extinction risk