BSCI222 Final

what is a quantitative trait?

trait influenced by many genes and often the environment which produces a range of continuous phenotypes

what are examples of quantitative traits?

height, skin color, or blood pressure

how are quantitative traits different from Mendelian traits?

mendelian traits are usually controlled by one gene and show discontinuous variation aka have distinct categories

what is an example of a mendelian trait?

red vs white flowers

what is monogenic inheritance?

when a single gene controls a trait and produces distinct phenotypic categories

what is polygenic inheritance?

when many genes contribute to a trait where each allele adds a small effect to the phenotype

what type of inheritance contributes to quantitative traits?

polygenic

what type of inheritance contributes to mendelian traits?

monogenic

what is discontinuous variation?

traits with distinct categories like blood types

what is continuous variation?

when traits can take any value between two extremes like height or weight

what are meristic traits?

polygenic traits that are measured in whole numbers but dont show continuous range

what is an example of a meristic trait?

number of pups in a litter or number of seeds produced by a plant

how to recognize a meristic trait?

it will involve counting discrete units

what is a threshold value trait?

traits that have a discontinuous aka on and off phenotype and only expressed if an individuals exeeds a specific threshold

do threshold value traits show continuous or discontinuous variation?

show a continuous distribution of susceptibility or risk

what is an example of a threshold value trait?

a person may have many or few alleles contributing to a disease but they only develop the disease if their total genetic and environmental risk crosses a certain point

how to recognize a threshold value trait?

description will mention a healthy versus diseased or present versus absent that depends on underlying measure of susceptibility

how do quantitative traits follow mendelian rules if they are continuous?

they are controlled by alleles at multiple loci and each locus follows segregation and independent assortment but their combine effect creates a continuous distribution

what do continuous quantitative traits often exhibit?

additive genetic variation

what is additive genetic variation?

where each allele at every locus adds a specific amount to the total phenotype

what is the (¼) ⁿ rule in a hybrid cross used for?

used to estimate the number of genes (n) involved in a polygenic trait

how does the (¼) ⁿ rule work?

in a F2 generation the expected proportion of offspring that expresses a parental phenotype is ¼ so u multiply that by number of genes (n)

what is an example of the (¼)ⁿ rule?

if 1/16 of offspring resemble each parent, then (1/4)² = 1/16 which means 2 loci are involved

in the (1/4)ⁿ rule, what happens when n is high/increases?

offspring show more continuous variation and fewer individuals resemble the original parents

how is variation affected in a F1 generation in a quantitative cross?

usually shows a phenotype that is the mid-parent value aka halfway btwn the two parentswith low variance similar to the parents

how is variation affected in a F2 generation in a quantitative cross?

the mean stays similar to the F1 gen but variance increases significantly

what causes increased variance in F2 generations in quantitative crosses?

the recombination of alleles at many loci which creates many new multi locus genotypes

true or false: different genotypes can result in the same phenotype in quantitative genetics?

true… multiple loci contribute to the same trait so different combinations of additive alleles can sum up to the same total phenotypic value

what is the role of the mean in quantitative genetics?

the average value for a specific trait within a population aka center of phenotypic distribution

how are standard deviation and variance used to describe a trait?

standard deviation is a measure of variance that describes how much individual phenotypes deviate from the mean

what happens in a normal distribution?

about 66% if populations falls within +-1 SD of the mean, 95% within +-2 SD of the mean, and 99% within +-3 SD of the mean

what is the correlation coefficient {r}?

measures the strengths of association between two traits

what does the correlation coefficient indicate?

the relationship between changes in one variable and changes in a second variable

what does a high correlation mean?

pleiotropy aka where one gene affects multiple traits

what is the purpose of regression analysis?

allows for prediction of one variable based on the value of another variable

what is phenotypic variance (V_p)?

total variation in a trait observed in a population

what is the formula for phenotypic variance?

Va + Vd + Vi + Ve + Vge

what is additive genetic variance (V_A)?

proportion of phenotypic variance explained by summing the effects of different alleles in a genotype

what does the additive genetic variance represent?

genetic component that is most directly responsible for the resemblance between parents and offspring

what is dominance genetic variance (V_D)?

proportion of genetic variance that is non additive due to the influence of dominant alleles

what is gene interaction variance (V_I)?

genetic variance resulting from one gene influencing the expression of another gene aka epistasis

what is environmental variance (V_E)?

proportion of phenotypic variance caused by differences in the environment among individuals

what is gene by environment interaction (V_GE)?

occurs when the effect of a genotype depends specifically on the environment in which it is expressed

what experimental design can be used to estimate genetic variance?

researchers can raise individuals in the same controlled environment so environmental differences are minimized aka V_E = 0

what experimental design can be used to estimate environmental variance?

genetically identical individuals can be raised in different environments so genetic differences are minimized aka V_G = 0

what is the formula for broad sense heritability (H²)?

V_G / V_P

how would you calculate V_G?

V_p - V_E

why use genetically identical individuals to estimate environmental variance?

it removes genetic differences so any remaining variation is caused by environmental factors

why use similar environments to estimate heritability?

it minimizes environmental variance so remaining phenotypic differences are due to genetic variance

how can heritability be estimated from parent offspring regression analysis?

when a proportion of phenotypic variance has a genetic component which will show show as a correlation between parent and offspring phenotypes

what does it mean when h² = 0?

offspring phenotype does not match mean parental phenotype at all

what does it mean when h² = 1?

offspring phenotype correlates perfectly with mean parental phenotype

what does a low heritability and weak relationship indicate?

greater environmental influence

what does a high heritability and strong relationship indicate?

greater genetic influence

what does the regression slope represent?

narrow sense heritability (h²) aka V_A/V_P

what are the limitations of using regression to estimate heritability?

it’s population specific, depends on the current environment, and does not provide info about the specific nature of genes

what is a genome wide association study (GWAS)?

method used to identify genetic variants associated with quantitative traits by comparing SNPs across many individuals in a population

what type of genetic markers are commonly used in GWAS?

SNPs aka single nucleotide polymorphisms

how does GWAS identify genes contributing to a quantitative trait?

looks for SNPs that consistently correlate with differences in a trait so if SNPs are associated with the trait, they may be located near genes influencing the phenotype

why are large sample sizes important in GWAS?

increase the ability to detect reliable statistical associations btwn SNPs and quantitative traits

what is the main limitation of GWAS?

identifies correlations btwn SNPs and traits but does not prove that a specific SNP directly causes the trait

how is GWAS different from QTL mapping?

QTL mapping tracks inheritance of markers through controlled crosses whereas GWAS studies natural variation in populations

what is response to selection (R)?

the change in the average value of a trait after selection occurs over one generation

what is the selection differential (S)?

the difference btwn the mean phenotype of selected parents and the original population mean

how is narrow-sense heritability (h²) related to selection?

narrow sense heritability determines how strongly a trait responds to selection

what do traits with higher h² indicate for selection?

traits with higher h2 respond more strongly

what equation is used to calculate response to selection?

R = h²S

how can narrow-sense heritability be calculated from selection experiments?

h² = R/S aka response to selection divided by selection differential

The average beak size in a bird population is 10 mm. After selection, the selected parents have an average beak size of 14 mm. In the next generation, offspring have an average beak size of 12 mm.

How to calculate the selection differential?

14 - 10 = 4 aka beak size after selection minus original beak size

The average beak size in a bird population is 10 mm. After selection, the selected parents have an average beak size of 14 mm. In the next generation, offspring have an average beak size of 12 mm.

How to calculate response to selection?

12 - 10 = 2 aka beak size in generation after selection minus orginal beak size

how to calculate narrow sense heritability in relation to selection?

R/S aka 2/4 = 0.5

how do you calculate genotype frequency?

number of individuals with genotype divided by total population like Aa divided by total population

how do you calculate allele frequencies?

total number each allele of interest and divide by total number of alleles in population

what is the formula for calculating allele frequency for p?

2(AA) + Aa / 2N

what is the formula for calculating allele frequency for p?

2(aa) + Aa / 2(N)

what does p represent in allele frequency calculations?

dominant allele

what does q represent in allele frequency calculations?

recessive allele

how to calculate expected allele frequencies for dominant allele aka p?

p²

how to calculate expected allele frequencies for dominant allele aka p?

p²

how to calculate expected allele frequencies for heterozygotes (Aa)?

2pq

what is hardy weinberg equilibrium?

describes a population in which allele and genotype frequencies remain constant aka no evolution

what are the assumptions required for hard weinberg equilibrium?

no natural selection, no mutation, no migration, random mating and no genetic drift

what happens if natural selection violates HW equilibrium?

alleles that increase survival or reproduction become more common which changes allele frequencies over time

what happens if mutation violates HW equilibrium?

new alleles are introduced into the population which changes allele frequencies

what happens if migration aka gene flow violates HW equilibrium?

individuals moving btwn population introduce or remove alleles which changes allele frequencies

what happens if mating is nonrandom?

changes genotype frequencies which increases homozygosity or certain phenotypes

why does HW require a large population?

they minimize genetic drift so theres no chance for random change in allele frequencies

what is genetic drift?

random fluctuation of allele frequencies which mostly occur in small populations

In a rabbit population, white rabbits are easier for predators to spot in snowy winters, while gray rabbits survive more often and reproduce more successfully. Over time, the gray fur allele increases in frequency. what assumption was violated?

no natural selection

A mutation occurs in a flower population that produces a new purple petal allele that was not previously present. what assumption was violated?

no mutation

Several fish from a nearby lake enter a pond population and introduce alleles for larger body size. what assumption was violated?

no migration/gene flow

Female birds only choose males with the brightest feathers as mates. what assumption was violated?

random mating

A wildfire randomly kills most of a beetle population, leaving only a few survivors whose allele frequencies differ from the original population. what assumption was violated?

large population size so genetic drift occured

what happens when the chi squared value is smaller than critical value?

fail to reject null hypothesis which means population is in HW

what happens when the chi squared value is larger than critical value?

we fail null hypothesis which means population is not in HW

how to calculate df?

allele categories - number of alleles

what is non random mating?

when individuals choose mates based on specific traits rather than mating randomly within a population

what is assortative mating?

when individuals mate with others that are phenotypically similar to themselves

what is a consequence of assortative mating?

increases homozygosity bc similar genotypes are more likely to mate together