Homoplasy

Character similarity that does not represent common ancestry

3 Properties of DNA (Molecular basis of Evolution)

1. DNA can replicate

2. DNA can mutate and recombine

3. DNA encodes RNAs/protein that interact with environmental conditions to influence phenotype

Coalescence

All copies of homologous DNA trace back to a common ancestral molecule

Genetic Evolution

Fate of alternative forms of genes or gene combinations over space and time in a reproducing population

Mutation

Any detectable and heritable change in the genetic material not caused by genetic recombination

• Ultimate source of all new genetic variation
• Destroys identity by descent

Haplotype

Set of identical haploid genomes for a specified unit of measurement

SNP

Single nucleotide polymorphism (2 alternative bases in population)

Deme

A local population of reproducing individuals that has physical continuity over space and time

Gene Pool

The population of gene copies that are collectively shared by the individuals of a deme

p²+2pq+q²=1

H-W equilibrium for 2 alleles

p²+2pq+q²+2pr+2qr+r²=1

H-W Equilibrium for 3 alleles

2 Factors of Genetic Traits

1. Complexity of genotype/phenotype relationship
2. Confoundment of frequency and causation

Cause of sickle-cell anemia

Substitution of valine for glutamic acid at protein position 6

Scurvy

• Vitamin C deficiency
• Humans are fixed for a null allele at gene for vitamin C synthesis.

Two ways discrete genotypes lead to continuous phenotypes

1. Polygenic inheritance
2. Environmental variation

Mean

Average/Expected value (Measures center of distribution)

Variance

Average squared deviation of x_i from mean (Amount of dispersion/width)

Standard deviation %

±σ : 68%

±2σ : 95%

±3σ : 99.7%

Quantative Genetics

Genetics of continously varying phenotypes

σ_p²

Phenotypic Variance - A measure of all the variability for a quantative trait in a population

σ_g²

Genetic Variance: Component of the phenotypic variance for a trait that is due to genetic differences among individuals in a population

σ_p² = σ_g² + σ_e²

Variance formula of genetics (σ_e² is environmental variance)

Broad-sense heritability

The proportion of the phenotypic variance within a population that results from genetic differences among individuals (measured within a generation)

Narrow-sense heritability

The proportion of phenotypic variance that results from the additive effects of different alleles on the phenotype.

Average excess of a gamete type

The average genotypic deviation caused to a gamete bearing allele i after fertilization with a second allele drawn from the gene pool (assuming random mating).

Process to calculate variance

1. Determine H-W frequency and mean phenotype for each genotype. Then, calculate mean phenotype of population. 
2. Calculate genotypic deviations for each genotype (g_i=x_i - μ)
3. Calculate genetic variance (σ_g²=Σ(freq._i)(g_i)²)
4. Partition phenotypic variance into genetic and environmental variance.

Process to calculate Average Excess

1. Pick one allele i.
2. Average excess of allele i = Σ(Frequency of i/j deme)(genotypic deviation of i/j phenotype) - Probability of i deme is ASSUMED to be 100%!
3. Repeat to calculate average excess of all alleles.

Breeding Value

Additive genotypic deviation (measured influence of a diploid genotypic or phenotypic variation in the next generation)

Process to calculate Breeding Value

1. Pick genetype i/j.
2. Breeding value of i/j = Average excess of i + average excess of j
3. Repeat for all genotypes.

σ_a²

Additive genetic variance - average of the squared breeding values of all individuals in the population

To calculate: Σ(freq._i)(breeding value_i)²

σ_a²/σ_p²

Narrow sense heritability (Will never be larger than broad-sense heritability)

σ_g² = σ_a² + σ_d²

Genetic variance for single-locus model (σ_p² is dominance variance)

Dominance Variance

Nonadditive genetic variance at the population level

3 consequences of rare dominant allele

1. All dominant allele copies in heterozygous form.
2. All dominant allele copies contribute equally to phenotypic variation.
3. Variance is additive.

3 consequences of common dominant allele

1. Dominant allele copies in heterozygous and homozygous form.
2. Copies in heterozygotes contribute twice as much to phenotypic variation.
3. Produces some nonadditive variance.

Covariance

A measure of how much variance is shared by two individuals for certain traits.

Covariance formulas

x and y are traits of interest

1. cov_xy=(Σ(x_i-μ_x)(y_i-μ_y))/(n-1)
2. Fisher formula: cov_xy=.5σ_a²

Correlation coefficient

Statistic that meaures the strength of the assocation between two variables in the same experimental unit (ranges from -1 to 1).

Correlation Coefficient Formula

r=(cov_xy)/(σ_x²σ_y²)^1/2

(1/2)h²

Correlation between parental generation and offspring

(1/2)h²+(1/4)(σ_d²/σ_p²)

Correlation between two siblings for a quantitative trait

Quantitative Trait Locus

Locus where variation contributes to populational variation of a phenotype (can be used to help map regions of the genome that contain genes involved in specifying the trait in question) 

Linkage disequilibrium

Non-random association of alleles at two or more loci (some combination of alleles occur more or less frequently than expected if solely based random formation of haplotypes)

Origins of linkage disequilibrium

1. Mutational origin of variation
2. Changes in frequency of 2 complementary pairs of haplotypes

Histories that produce linkage disequilibrium

1. Hybridization of 2 populations
2. Founder events

Epistatic variance

Nonadditive, genetic variance at population level arising from interactions among genotypes at different level

Evolution (Population genetics)

Change in allele or gamete frequency in the gene pool

Evolutionary forces (Definition and list 2)

Factors that can change the frequency of an allele in the gene pool

1. Mutation
2. Genetic drift

"Ideal" population qualities

1. Constant size
2. Even sex ratio
3. Non-overlapping generations
4. Random mating
5. Poisson distributed fecundity (mean=variance)
6. No selection

Coalescence

Merging of genetic lineages back in time to a MRCA (loss of alleles)

Rates of Coalescence

Rate of loss = 1/2N

Average time for 2 genes = 2N generations

Average time for all genes = 4N generations

Effective population size (N_e)

The number of individuals in a population that would show the same amount of dispersion of allele frequencies under random genetic drift or the same amount of inbreeding.

Bottleneck Effect

Population had 1 or more generations of small size in the past.

Founder Effect

The loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population. It alters allelic frequency and decreases epistatic variance specifically.

Genetic Architecture

Number of variable loci affecting a phenotype/amount of additive and nonadditive variance

Neutral Allele

Allele that does not affect an organism's ability to reproduce or survive. They evolve by mutation and genetic drift.

2Nμ

Rate of origin of alleles by mutation (autosomal)

Unit Evolutionary Period

Time needed for 1% amino-acid sequence change between homologous proteins

Functional Density of Proteins

Proportion of amino-acid sites that perform specific functions

Gene Flow

Exchange of alleles between demes

Genetic drift

Random changes in allelic frequencies within a population over time; observed most often in small populations due to sampling error.

Synonymous Substitution

Evolutionary substitution of one base for another in a protein-coding are of the genome, but does not alter the amino-acid sequence of the resulting protein. Evolves more rapidly over time than nonsynonymous substitution.

Norm of Reaction

Range of phenotypes produced by a particular genotype in different environments.

Penetrance

The frequency with which a dominant or homozygously recessive trait is phenotypically expressed in a population.

Expressivity

The degree to which a particular gene is expressed in the genotype.

Pleiotropy

The ability of a single gene to have multiple phenotypic effects.

Multifactorial Trait

A characteristic determined by mutiple genes and environmental factors.

Natural Selection

Differential reproduction of individuals in a population resulting from differences in their genotypes.

Artificial Selection

Process for deliberating changing the phenotypic traits of a population by determining which individuals will survive and reproduce.