Population & Quantitative Genetics

Population

Any group of members of the same species in a given geographical area
capable of mating and producing fertile offspring

Mendelian population

A group of interbreeding, sexually reproducing individuals that have a common set of genes

Gene Pool

A collection of alleles present in a population; A population evolves through changes in its gene pool

Determining Probability of Inheriting Each Allele

Probability of any given allele is based on how abundant or rare it is in the population (or gene pool) (its frequency)

Calculating Allelic Frequency

Add up number of a given allele and divide by the total number of alleles (each person has two) ; f(A) = Number of A alleles/N; f(a) = Number of a alleles/N

Evolution

Change in allele frequency in a population over time; Tracking allele frequency changes from one generation to the next can reveal evolution in action (populations evolve, individuals do not)

HW Assumptions

1. Large

2. Random mating

3. No mutation

4. No migration

5. No natural selection

When HW Assumptions are met:

Reproduction alone does not alter allelic or genotypic frequencies; Allelic frequencies determine genotypic frequencies

If assumptions for HW are true…

1. The allelic frequencies of a population do not change

2. The genotypic frequencies stabilize after one generation in the proportions p² (f(AA)), 2pq (f(Aa)), and q² (f(aa))

HW Equilibrium vs. Disequilibrium

HW Equilibrium is when genotypes are in the expected proportions of p², 2pq, and q²; When the genotypic proportions are not what is expected, the population is in disequilibrium

Sickle Cell Anemia

Mutation in hemoglobin with a reduced capacity to carry oxygen; HBS Homozygous alleles have sub-optimal fitness and increased mortality; Because the deleterious allele is maintained rather than being lost each generation, it may have an advantage in heterozygous state (reduces ability of malaria parasite to live in blood cells)

How to find if a population is in Hardy-Weinberg Equilibrium

See if the genotypic frequencies calculated using the observed allelic frequencies in the HW equation equal the observed genotypic frequencies in the actual population

HW Equilibrium is rare for ____

Protein-coding genes because they are subject to natural selection

Genetic Drift

Allele frequency changes resulting from chance events; Produces changes in allele frequencies and reduces genetic variation

Founder Effect

Small groups migrating to a new location

Genetic Bottleneck

Population of an animal reduced to almost extinction

Discontinuous Characteristic

Allows predictions about genotypes and genetic cross outcomes; Qualitative; Few distinct phenotypes (Mendel’s traits); Controlled by one or few genes; Produce, clear, separate categories

Continuous Characteristic

Polygenic and influenced by the environment; Multifactorial; Quantitative; Many overlapping phenotypes; Show a range of values with many intermediates; Frequently produced by combined effects of many genes and environmental effects

Polygenic Trait

Many genotypes are possible; Several genotypes may produce the same phenotype; Often environmental factors influence phenotype

Quantitative Genetics

Genetic analysis of complex characteristics

Quantitative Trait Loci (QTL)

Chromosomal regions (loci) containing genes that influence a quantitative trait (ex. height, weight, etc.)

Continuous Characteristics

Exhibit a wide range of phenotypes; Frequently produced by the combined effects of many genes and environmental effects

Multifactorial

Polygenic and under environmental influence

Additive Genetics

Each + allele contributes a small, fixed amount to the trait (no single trait dominates);

How many possible phenotypes (additive genetics)?

2n + 1 where n = loci (or # alleles + 1)

Phenotypic Distribution Shape

Can help estimate number of genes contributing to a trait

Frequency Distribution

Represents the phenotypic variation in a group

Distribution Shapes

Normal (one peak), Skewed, and Bimodal (multiple peaks)

Variance

Variability of a group of measurement; Sum squared deviations/# minus 1

Standard Deviation

Only 1% of a normally distributed population lies outside the range of 3sds from the mean

Regression

Using correlations to make predictions; Line = b = best fit line

Polygenic Inheritance (with tobacco flowers)

P generation: Short flower x Long flower; F1 generation: Mean length about halfway between parents, similar variance to parents; F2 generation: Mean length similar to F1, greater variance than F1

Heritability

Used to estimate the proportion of total phenotypic variation (Vp) in a population that is due to genetic variation (Vg); H² = Vg/Vp (broad sense heritability)

Phenotypic Variance

Vp = Vg + Ve + Vge

Genetic Variance (Vg)

Phenotype variance due to differences in genotypes among individuals in a population

Environmental Variance (Ve)

Phenotype variance due to environmental differences between individuals

Genetic-Environmental Interaction (Vge)

Phenotype variance from when the effect of a gene depends on the specific environment in which it is found

Components of Genetic Variance

Vg = Va + Vd + Vi

Additive Genetic Variance (Va)

Additive effects of genes on the phenotype (can be summed to determine overall effect); Primarily determines the resemblance between parents and offspring

Dominance Genetic Variance (Vd)

When some genes have a dominance component; The effect of an allele depends on the identity of the other allele at the locus

Genic Interaction Variance (Vi)

When genes at different loci interact in the same way that alleles at the same locus interact (ex. color in dogs or epistasis)

Broad-Sense Heritability (H²)

Heritability takes into account genetic variation due to all genetic causes (Vg); H² = Vg/Vp; Ranges from 0-1 where 0 = all differences in phenotype due to differences in environment and 1 = all differences in phenotype due to differences in genotype

Narrow-Sense Heritability (h²)

Heritability only takes into account the variation due to additive effects caused by the alleles (Va); h² = Va/Vp; Ranges from 0-1; Used to identify the proportion of phenotypic variance resulting from additive genetic variance; 0 = no relation between parental and offspring haplotype; 1 = offspring phenotype same as parents; 0.5 = both genes and environment contribute to the difference sin phenotype

How can we measure heritability?

1. Eliminate all environmental variance (infer genetic variance - keep environment the same)

2. Eliminate all genetic variance (infer environmental variance - inbreed and vary the environment)

3. Compare parent and offspring phenotypes (parent-offspring regression)

4. Compare individuals of varying degrees of relatedness (ex. monozygotic twins compared to dizygotic twins)

Response to Selection (R)

R = h² x S; S = Selection Differential (difference between the mean phenotype of the selected parents and the mean phenotype of the starting population)