Wk3 : Fri : part 2 - Genetics and extinction

Genetic diversity

The variety of alleles within a population that enables adaptation and survival

Loss of genetic diversity

Reduction in allelic variation due to drift

Why genetic diversity is important

It increases adaptability

Effect of low genetic diversity

Increased extinction risk due to reduced fitness and adaptability

Inbreeding depression

Reduced survival and reproduction caused by mating between related individuals

Short-term effect of inbreeding

Lower survival and reproductive success

Long-term effect of inbreeding

Reduced ability to adapt to environmental changes

Population bottleneck

A sharp reduction in population size leading to loss of genetic variation

Why genetic variation recovers slowly

Because it depends on mutation and gene flow

Self-incompatibility system

A plant mechanism preventing fertilization when alleles are identical

Effect of reduced allelic diversity in plants

Lower fertilization success and increased extinction risk

Genetic diversity and disease resistance

High diversity reduces parasite success and disease spread

Microparasites

Small pathogens such as bacteria and viruses

Tasmanian devil example

Low genetic diversity contributed to susceptibility to transmissible cancer

Cheetah example

Very low genetic diversity due to ancient bottleneck leads to disease susceptibility

MHC genes

Highly polymorphic genes essential for immune response

Function of MHC diversity

Allows recognition of a wide range of pathogens

Small population size effect

Increases inbreeding and extinction risk

Effective population size (Ne)

Number of individuals contributing genes to the next generation

Census size

Total number of individuals in a population

Difference between Ne and census size

Ne is usually much smaller than census size

50/500 rule

Ne ≈ 50 for short-term survival and Ne ≈ 500 for long-term evolution

Updated rule (100/1000)

Ne ≈ 100 short-term and Ne ≈ 1000 long-term

Population Viability Analysis (PVA)

A model to estimate extinction risk and population dynamics

Purpose of PVA

Predict extinction probability and evaluate management strategies

Time horizon in PVA

Typically around 100 years

Key outputs of PVA

Extinction risk

Deterministic factors

Predictable pressures like habitat loss and pollution

Stochastic factors

Random variations affecting populations

Demographic stochasticity

Random variation in births

Environmental stochasticity

Random environmental variation such as rainfall

Genetic stochasticity

Random genetic changes such as drift and mutation accumulation

Catastrophes

Rare extreme events like fires or hurricanes

Extinction vortex

A reinforcing cycle where small population size leads to further decline

Cause of extinction vortex

Interaction of genetic

Effect of extinction vortex

Accelerating population decline toward extinction

Gene flow

Movement of alleles between populations

Carrying capacity (K)

Maximum population size an environment can sustain

Minimum viable population (MVP)

Smallest population size required for long-term survival

Drift inbreeding

Inbreeding caused by genetic drift in small populations

Probability allele loss

(1 - 1/(2N))^(2N) ≈ 1/e ≈ 0.37

Assortative mating

Individuals mate with genetically similar partners

Pedigree-based inbreeding (F_PED)

Expected probability that alleles are identical by descent

Limitation of pedigrees

Require complete and correct ancestry

Complete generation equivalent (CGE)

CGE = sum (1/2)^i

Base population assumption

Founders are unrelated and alleles are unique

Mendelian sampling

Random inheritance of alleles causing variation in relatedness

Effect of Mendelian sampling

Realized IBD differs from expected F_PED

IBD (identical by descent)

Alleles inherited from a common ancestor

IBS (identical by state)

Alleles identical in state but not necessarily from same ancestor

Relationship IBS vs IBD

All IBD alleles are IBS but not all IBS alleles are IBD

Homozygosity (HOM)

Proportion of homozygous markers in an individual

Range of HOM

Values between 0 and 1

What HOM measures

Identity by state (IBS) at markers

Inbreeding coefficient based on homozygosity (F_HOM)

Measure of excess homozygosity

F_HOM definition

Reduction in heterozygosity compared to expectation

F_HOM formula

F_HOM = 1 - Ho/He

Observed heterozygosity (Ho)

Proportion of heterozygous loci observed

Expected heterozygosity (He)

Expected proportion under Hardy-Weinberg equilibrium

Genotype frequencies without inbreeding

p^2

Genotype frequencies with inbreeding

p^2 + Fpq

Alternative F_HOM formula

F_HOM = (He - Ho)/He

Population-level inbreeding

F_t = 1 - H_t/H_0

Interpretation of F_HOM

Positive values indicate excess homozygosity (inbreeding)

Runs of Homozygosity (ROH)

Continuous stretches of homozygous genotypes

F_ROH definition

Proportion of genome covered by ROH

F_ROH formula

F_ROH = sum Li / Lgenome

Meaning of ROH

Indicates realized inbreeding

ROH length interpretation

Longer ROH indicates more recent inbreeding

ROH length expectation

Length ≈ 1/(2n)

Conversion Morgan to Mb

1 Morgan ≈ 100 Mb

Cumulative inbreeding formula

F_ROH

ROH detection criteria

Minimum length

Advantages of HOM

Simple and easy to calculate

Disadvantages of HOM

Measures IBS and includes ancient inbreeding

Advantages of F_HOM

Detects deviation from random mating

Disadvantages of F_HOM

May miss historical inbreeding

Advantages of F_ROH

Measures realized IBD and timing of inbreeding

Disadvantages of F_ROH

Requires genome map and parameter choices

Allele purging

Removal of deleterious alleles by selection

Historical demography via ROH

ROH number and length reflect past population size

Comparison of inbreeding measures

Choice depends on data availability and research goal

F_PED measures

Expected IBD from pedigree

HOM measures

Observed IBS at markers

F_HOM measures

Deviation from expected heterozygosity

F_ROH measures

Realized IBD from genomic data