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Quantitative Genetics

inheritance of quantitative traits

Polygenic traits

traits with multiple genes

Monogenic traits

traits with just one gene

Quantitative traits

traits that are best described with a numeric measurement on a continuum

Discreet traits

traits that have a finite number of phenotypes

multifactorial traits

traits with genetic and environmental influence

discontinuous variation

discreet distinguished categories

continuous variation

long range of uninterrupted continuum

Major genes vs minor/modifier genes

Major genes determines most of the effect (eg general eye color) and minor genes determine the differences within the general major phenotype (eg. what shade of brown)

Additive genes

when there are no major genes, just increments of equal effect

how to calculate number of possible gene dosages

2N + 1 with N genes and 2 alleles per gene

genetic liability model

within a population, the propensity of a genotype to develop a disease above a certain threshold of expression

this is because there are many genes but only two phenotypes: diseased and not diseased

Calculate how many genes underlie a trait

n = D²/(8(s2² - s1²))

n = lower bound for number of genes influencing trait

D = difference in phenotypes between parents

s1² = variance in F1 (lower, because averaged)

s2² = variance in F2 (higher, because independent assortment)

mean, median, mode, variance

mean = average

median = middle value

mode = most common value

variance = how variable values are in a frequency distribution

calculate phenotypic variance between genotype and environment

Phenotype variance is additive since genes and environment are independent of each other

Vp = Vg + VE

Vp = phenotypic variance

Vg = variance due to genotype, will be 0 in inbred or clonal populations, allowing VE to be measured

VE = variance due to environment, will be 0 in tightly controlled lab experiments, allowing Vg to be measured

Calculating Vg

Vg = VA + VD + VI

VA = additive genetic variance - heterozygotes exactly intermediate

VD = Dominance variance - heterozygotes not exactly intermediate

VI = interactive variance, from epistatic interactions with other alleles on other genes

Heritability

Genetic component of phenotypic variation, which varies from trait to trait

traits with high heritability have most of the difference caused by genotypic variation; traits with low heritability have most difference caused by environment

heritability does not say what the mechanism by which the phenotype arises, nor does it say how much a trait relies on the action of genes

calculate broad/narrow sense heritability

Broad sense heritability:

H² = Vg/Vp

measure broad sense heritability using twin studies

Falconer’s formula for broad sense heritability:

H = 2(MZ phenotypic correlation - DZ phenotypic correlation)

Narrow sense heritability

h² = VA/Vp

(allelic variance over phenotypic variance)

or:

R = h²S

R = response to selection (= population mean - offspring mean)

S = selection differential (= mating population mean - population mean)

why do twin studies overestimate heritability

1. Because stronger shared maternal effect for MZ than DZ since embryonic environment is also shared

2. VE is less in MZ twins because social treatment is more similar

Overall MZ have more similar environments

Quantitative trait loci

genes that contribute to variation of quantitative traits

QTL mapping process

1. Have inbred parental lines that differ in phenotype of interest and known genetic markers

2. Cross to generate F1 heterozygotes for all markers

3. Cross F1s to get F2 to make the QTL mapping population

4. Massive phenotype of F2s were generated, so look at the alleles associated with a specific phenotype

Hardy-weinberg population assumptions

1. Infinite population (no genetic drift)

2. Population is hermaphrodidic with random mating

3. No natural selection

4. No mutation

5. No migration/no gene flow

Hardy-weinberg allele frequency equations

Allele frequency: p + q = 1

genotypic frequency: p² + 2pq + q² = 1

p = dominant allele

q = recessive allele

directional selection

environmental advantage of one phenotype is selected for, leads to fixaton

heterozygote advantage

it is more advantageous to be a heterozygote for a trait than to be either homozygote

effects of inbreediing

genotypic frequencies change but not allele frequencies, eliminates heterozygotes after long enough, leads to inbreeding depression

inbreeding depression

too much inbreeding leads to loss of fitness due to recessive deleterious alleles that are revealed

effects of genetic drift

1. Allele frequencies change in population

2. Variance in allele frequencies increases in population over time

3. Genetic variability decreases in population over time (allele fixation)

gene flow

migration into or out of population, which changes allele frequencies

bateson-dobzhansky-muller model

genetic basis of reproductive isolation

after populations diverge and different alleles fixate in the population, fixated alleles may not be compatible when the two species recombine

orr’s snowball

when allelic incompatibilities accumulate

each new allele that fixates may be incompatible with any other new alleles in other populations, and since the new alleles evolved in an environment without the original alleles, they are also incompatible with those

muller’s ratchet

explains the advantages of sex

least loaded class of asexual populations may fail to reproduce, and if that happens, the least loaded class is lost forever. asexual populations accumulate deleterious mutations over time

kondrashov’s hatchet

sexual reproduction sequesters and deletes the most deleterious genotypes so that it can create more advantageous ones because there is more variance in genotypes

allele fixation

smallest unit of adaptation

stochastic loss

when a beneficial mutation is lost by chance since it is initially rare

calculate probability of fixation vs stochastic loss

2s, where s is the selection coefficient, which is the % advantage over the wild type

haldane’s sieve

dominant adaptive mutations are much much more likely to survive and fixate than recessive adaptive mutations because natural selection cannot see the recessive ones

Fisher’s genetic model

describes mutations as vectors towards or away from the population mean on a coordinate plane

beneficial mutations go towards the origin, but it is much more likely that you go away from the origin

larger mutations are much more likely to go away from the origin so smaller mutations are more likely to be beneficial

opinions on fisher genetic model and best size of mutations

Fisher = small mutations are best mutations

Kimura = medium mutations are best mutations because small mutations have a too small probability of fixation

Orr = as optimum is approached, smaller and smaller effect mutations are fixed

Model for human expansion

RAO (recent african origin)

SNP

single nucleotide polymorphism - base pair that is variable within a species

Fst

fixation index - measure how genetically different two populations are

if Fst = 0, alleles are exactly the same and it’s just one population

admixture

when two different populations interbreed

evidence of african origin

• all human mitochondria trace back to mitochondrial eve in africa

• great apes in africa are trichromatic like us but bichromatic in south america

adaptive integration

when genes from different populations confer a benefit

FOXP2

gene important for understanding and producing speech - denisovans and neanderthals had very similar changes in FOXP2

why are humans have different skin

when we lost all our fur for better cooling, our skin became dark to protect us from the sun, then when we went north we got paler skin to get vitamin D (or possibly just loss of function mutations because we didn’t need all that protection anymore)

CODIS markers

markers used in forensic genetics to identify individuals

criteria:

1. must have multiple alleles, none of which are above 25% frequency

2. must be at a known chromosome location and assort independently to other CODIS markers

3. At least 4 bp must distinguish alleles from each other

most people are heterozygous for CODIS markers making it

Probability of CODIS genotype

hardy-weinberg = 2(prob first allele)(prob second allele) if heterozygote

Squared if homozygote

conservation genetics

subset of population genetics focused on preserving genetic diversity

Extinction vortex

link between pop size, genetic diversity, and fitness - leads to inbreeding depression over time

census size vs effective population size

census size = number of individuals

effective population size = minimum size of the ideal population with the same drift as the real population - basically, how small can a population be while still having the same amount of genetic diversity. caused by variation in reproductive success or variation in past census size

founder effect

type of bottleneck where a small group of individuals forms a new population that has less genetic diversity

habitat fragmentation

breaking larger habitats into smaller ones which prevents gene flow. fix with corridors or assisted gene flow, which reincrease genetic diversity

outbreeding depression

when fitness declines when two individuals of different populations reproduce

genetic swamping

when local genotypes disappear as the population recovers with assisted gene flow

Demographic rescue

can be used if population just needs more individuals - this is breeding programs

evolutionary rescue

when natural selection in a large and varied enough population allows population to adapt

admixture plots

assigns genome regions to different genetic ancestries

cryptic species

species that are morphologically similar and accidentally described as a different species