Unit 2 Evolution and Systematics

Population genetics

The study of genetic variation within populations and how it changes over time through processes like selection, mutation, and migration.

Population thinking vs Individual thinking

Focuses on allele frequencies and how they change over time, rather than predicting individual traits using Mendelian ratios.

Hardy-Weinberg Model

A null model that predicts genotype frequencies when no evolutionary forces are acting on a population.

Five assumptions of the Hardy-Weinberg Model

1) No natural selection 2) Random mating (no assortative mating) 3) No mutations 4) No migration (gene flow) 5) Infinitely large population size.

Natural selection effect on allele frequencies

Beneficial alleles increase in frequency over time, while deleterious alleles decrease.

Selection coefficient (s)

A measure of how much a particular allele reduces an individual's fitness.

Selection coefficient (s) effect on allele fixation

A higher selection coefficient against an allele leads to faster elimination of that allele from the population.

Two broad categories of selection

Frequency-independent selection and Frequency-dependent selection.

Frequency-independent selection

Fitness of a phenotype does not depend on its frequency.

Frequency-dependent selection

Fitness of a phenotype depends on its frequency in the population.

Directional selection

When one allele is consistently favored, leading to its eventual fixation.

Overdominance

When heterozygotes have higher fitness than either homozygote, leading to maintenance of genetic diversity. Example: Sickle cell trait provides resistance to malaria.

Underdominance

When heterozygotes have lower fitness than either homozygote, leading to fixation of one allele and loss of genetic variation.

Incomplete dominance effect on allele fixation

Incomplete dominance leads to faster fixation of an advantageous allele because heterozygotes have slightly reduced fitness compared to homozygous dominant individuals.

Coat coloration in rock pocket mice and natural selection

Dark-colored mice are favored on lava fields, while light-colored mice are favored on sand. The Mc1R gene controls this trait, and selection acts against mismatched coat colors.

Deviations from Hardy-Weinberg Equilibrium in studying evolution

Differences between observed and expected genotype frequencies indicate that evolutionary forces (e.g., selection, mutation, migration) are acting on the population.

Causes of evolution

+Selection (natural or artificial)

+emigration/migration

+genetic drift

Directional selection

Selection that favors a shift in a trait toward a single new phenotype.

Effect of directional selection on alleles

It leads to the replacement of one allele with another.

Purifying selection

Selection that favors the current phenotype/ allele state and selects against deviations.

Another name for purifying selection

Stabilizing selection.

Disruptive selection

Selection that favors two distinct phenotypes and selects against intermediates.

Genetic drift

Evolution due to chance events in small populations; changes in allele frequencies due to sampling error, with no external force acting.

The effect of Genetic Drift on alleles in small populations

Some lineages may lose an allele entirely, becoming fixed for the other allele.

Anagenesis

Evolutionary change within a single lineage over time (descent with modification).

Cladogenesis

The formation of two or more species from a common ancestral species (speciation).

Coalescence

The process where a lineage converges on a single genotype over time.

Coalescent theory

All alleles in a population trace back to a single common ancestor.

Population size and coalescence

+Smaller populations → Faster coalescence

+Declining populations → Faster coalescence

+Growing populations → Slower coalescence

Selection and coalescence

It strongly influences the rate and pattern of allele convergence.

Hardy-Weinberg Model Assumptions

1. No natural selection 2. Random mating (no assortative mating) 3. No mutation 4. No migration 5. Infinite population size

Genetic Drift Effect on Small Populations

Random changes in allele frequencies are more pronounced, leading to loss of alleles and fixation of others.

Wright-Fisher Model

It accounts for genetic drift in small populations where offspring do not overlap with parents, and survival/reproduction is stochastic.

Population Bottleneck

A drastic reduction in population size leading to a loss of genetic diversity due to accelerated genetic drift.

Founder Effect

A form of genetic drift where a new population is established by a small number of individuals, leading to reduced genetic diversity.

Coalescence Theory

All alleles in a population trace back to a single common ancestor.

Population Size and Coalescence

Smaller populations experience coalescence faster, while larger populations have coalescence deeper in time.

Effective Population Size (Ne) Reduction Factors

Skewed sex ratios, mortality rates, mating systems, and fluctuations in population size.

Genetic Drift and Mutation Interaction

Drift leads to allele loss, while mutation introduces new alleles.

Haldane's Rule

A beneficial mutation may not be fixed if the effective population size (Ne) is small, as drift can eliminate it.

Selection Coefficient (s)

The relative reduction in fitness of a genotype compared to another.

Selection vs Drift Dominance

If s >> ½ Ne, selection dominates. If s << ½ Ne, drift dominates. If s ≈ ½ Ne, both are important.

polygenic traits

Traits influenced by multiple genes, where the phenotype results from the sum of effects of each allele.

Nilsson-Ehle's discovery (1908)

Kernel color is determined by additive genetic effects of three genes.

latent variation

The presence of many potential genotypes, where some allele combinations are rare or not observed unless selected for.

epistasis

Interaction where alleles at multiple loci influence phenotype in non-additive ways, with effects depending on the genetic context.

example of epistasis in animals

The MC1R gene affects pigmentation only in certain Agouti locus contexts, as seen in Labrador retrievers.

pleiotropy

A single gene influences multiple phenotypic traits.

antagonistic pleiotropy

When a gene is beneficial in one context but harmful in another, e.g., beneficial in youth, detrimental in adulthood.

physical linkage

When loci are close on a chromosome and tend to be inherited together.

linkage disequilibrium (LD)

The non-random association of alleles at different loci.

factors causing and breaking down LD

LD arises from mutation, selection, migration, non-random mating, and drift. Recombination reduces LD.

how LD is measured

Using the coefficient D, where D = hAB - fAfB, ranging from -0.25 to 0.25.

selective sweep

When a beneficial mutation spreads rapidly through a population, reducing genetic variation and creating strong LD.

haplotype

A set of closely linked genetic markers inherited together.

recombination effect on linked genes

It can separate linked genes, generating new allele combinations and reducing LD.

importance of understanding LD

It helps explain how allele frequencies evolve and how genetic associations impact traits.

linkage disequilibrium (LD)

the non-random association of alleles at different loci, meaning certain allele combinations occur more or less frequently than expected by chance.

causes of linkage disequilibrium

Mutation, selection, non-random mating, migration, and genetic drift.

breaks down linkage disequilibrium

Recombination.

selective sweep

A process where a beneficial mutation rapidly increases in frequency, reducing genetic variation at nearby loci due to strong positive selection.

genetic hitchhiking

When neutral or mildly deleterious alleles increase in frequency because they are linked to a beneficial allele undergoing positive selection.

broad-sense heritability (H)

The proportion of total phenotypic variance in a trait that is due to genetic variance (including additive, dominance, and epistatic effects).

narrow-sense heritability (h²)

The proportion of phenotypic variance due to additive genetic effects alone.

C-value paradox

The observation that genome size does not correlate with organismal complexity.

contributes to the C-value paradox

The amount of non-coding DNA, including transposable elements and other 'selfish' genetic elements.

genome size effect on cellular processes

Larger genomes can influence cell size, division rate, metabolic rate, and molecular transport, although these relationships are not always consistent.

genetic hitchhiking over time

It diminishes as recombination breaks the association between neutral and beneficial alleles.