Genetic Variation Evolution Review

what are synonymous/nonsynonymous mutations?

• synonymous mutation: a mutation that does not cause an effect

• nonsynonymous mutation: a mutation that causes an effect

what are cis-regulatory elements?

non-coding DNA sequences that control the transcription of nearby genes → important for gene expression

what is incomplete dominance [additive inheritance]?

additive inheritance is used more than incomplete dominance because we focus on loci → the more red genes, the more red a flower will be

what are advantageous/beneficial mutations?

a genetic change that improves an organism’s fitness and helps it survive → rare

what are deleterious mutations?

a harmful change in the DNA sequence that can have negative consequences for the organism’s health and fitness via disease/disorder.

what are neutral mutations?

a change in the DNA sequence that has no significant effect on the organism’s fitness or ability to survive and reproduce

what is pleiotropy?

the amount of traits that are effected by mutations

• mutations that are more pleiotropic are more likely to decrease fitness

why are most mutations that affect fitness deleterious?

a random change in DNA is more likely to disrupt the normal function of a gene, leading to a protein that doesn’t work properly or isn’t produced at all

• machinery of life is so finely tuned that any random alteration is more likely to cause problems than provide an advantage

what is a point mutation and what does it do for evolution?

a base pair substitution in DNA sequences → creates new alleles

does the environment induce mutations?

the environment does not induce adaptive mutations; natural selection may act on mutations once they occur [by natural selection, an organism will live longer if it happens to develop a mutation that is beneficial]

polymorphism for alleles causes variation in what?

the genotype → polymorphism is the presence of two or more variants, and alleles are representative of the genotype

what are the 2 causes of phenotypic variation?

1. genetic → allelic differences

   1. white vs yellow flowers

2. environment → phenotypic plasticity [phenotype differs based on environment]

   1. sunny and moist environment → flowers grow closer, sunny and dry environment flowers grow further apart

what are the 5 causes of genetic variation?

1. mutation

2. migration

3. selection

4. drift

5. non-random mating

what is the hardy-weinberg equilibrium model?

a diploid population under random mating, in which genotypic frequencies attain HW values after one generation of random mating. model is represented by equation: p²+2pq+q²=1

• p is dominant allele

• q is recessive allele

• p² is genotypic frequency of dominant genotype

• q² is genotypic frequency of recessive genotype

• 2pq is genotypic frequency of heterozygous genotype

what are the assumptions of the hardy-weinberg equilibrium model?

• mating is random

• population is infinitely large [no genetic drift]

• genes do not move in/out of population [no gene flow]

• genes do not mutate from one allelic state to another

• all individuals have equal probabilities of survival and reproduction [no natural selection]

assumptions define conditions under which a population will NOT change, and thus implicitly defines the process that can cause a population to evolve

what are the 2 things that can occur when HWE is not met?

1. speciation

2. inbreeding

how do you detect if there are deviations from HWE?

1. if observed genotypic proportions differ significantly from expected values

2. chi-square test to evaluate goodness of fit between observed data and expected values based on HW model

3. using the following equation: x²=sum of (O-E)² / E

what is linkage disequilibrium?

non-random association of alleles at different loci in a given population

• frequency of association of different alleles is higher or lower than what would be expected if the loci were independent and associated randomly

• LESS random = HIGHER ld

• MORE random = LOWER ld

what are the 5 reasons why/how linkage disequilibrium happens?

THINK PIRFA

1. proximity on a chromosome → 2 close alleles travel together more through generations than alleles that are far

2. if some allelic combinations have high fitness → if you don’t have that allele combo, you die

3. random genetic drift → can cause certain alleles to be found together

4. founder effect → random sampling when a small group leaves and creates a new population, then expands [bunch of non-randomness]

5. admixture → when individuals from 2 or more populations mate and exchange genes

what is genetic diversity?

genetic variation, usually measured for a given population

• nucleotide diversity, allelic richness, hererozygosity

what is heterozygosity?

NOT THE SAME AS HETEROZYGOUS

• heterozygosity is the proportion of loci in a genome that are heterozygous

what is expected and observed heterozygosity, and how do they relate?

expected heterozygosity: expected frequency of heterozygotes in a population, represented by 2pq [for our class]

observed heterozygosity: observed frequency of heterozygotes

if they equal each other, then random mating is occuring

if not, then non-random mating is occuring

what 2 types of non-random mating is occurring if He =/= Ho?

1. inbreeding

2. population structure [aka genetic structure]→ non-random distribution of alleles across geographic space, maybe because of something like mountains or a road

how is gene flow estimated?

through F_ST = (H_T-H_S) / (H_T)

• exists in a range of 0-1

• 0 = high gene flow

• 1 = no gene flow, usually because of high population/genetic structure

what does it mean if the observed heterozygosity is higher than the expected heterozygosity?

may mean there are no homozygous individuals, maybe due to homozygosity being lethal at that locus

what influences the magnitude of gene flow?

migration

what effect does gene flow have on allele frequencies?

homogenizes allele frequencies [makes different populations more similar to each other through the sharing of alleles]

what does gene flow do to divergence among populations?

prevemts/decreases divergence

what does gene flow do to genetic diversity within populations?

either maintains genetic diversity, or increases genetic diversity

what populations does genetic drift occur in?

genetic drift occurs in ALL populations of NON-infinite size, because

• By chance, some individuals in a population have more offspring than others 

• By chance, more or fewer copies of an allele are passed on to the next generation 

why is genetic drift the driving force in smaller populations?

because there are less alleles to begin with, making the random change in allele frequency more noticeable each generation

• imagine death is due to RANDOM chance and not color in frogs, and brown frogs just so happen die while green frogs don’t, then the next generation will consist of more green frogs

what is the driving force in large populations?

in large populations, selection is the driving force

what is fixation?

the loss of polymorphism either by chance or selection

what doe genetic drift do to heterozygosity?

decreases it —> alleles become extinct, especially in small populations

What is N_e?

The effective population size → number of individuals that actually contribute alleles to the next generation

When does N_e differ from N [census population size]?

census population size: actual number of individuals

Ne is usually much lower than census population size

• Relationship between genetic diversity, mutation rate, and Ne

Ne is based on N when sex ratio is not 1:1

What does a bottleneck event do to Ne and heterozygosity?

Bottleneck event: an event in which a population experiences a drastic reduction in numbers [such as a volcanic eruption], where the surviving individual’s alleles are the only ones that persist to the next generation, likely contributing to low heterozygosity

What does a founder effect do to Ne and heterozygosity?

Founder effect: a small number of a population leaves and continues growing elsewhere, which also decreases heterozygosity

What is the Mutation - Genetic Drift Equilibrium?

Genetic Drift eliminates variation, pushing population towards increased homozygosity

Mutation pressure introduces variation, pushing population towards increased heterozygosity

However, genetic drift always removes more than mutation can create [as mutation is random, and most either do not do anything, or have negative effects that will not persist]