Population Genetics Flashcards
Define population genetics.
Evolutionary processes within populations over smaller time scales; study of distribution of alleles within populations and the mechanisms that cause allele frequencies to change over time
Genetic definition of evolution
Evolution is any change in allele frequency in a population over time
What is an allele?
Variant (mutant) version of a gene or other genetic locus
Define a gene pool.
All alleles in a population exist in a single, completely mixing gene pool
Define genotype
Particular combination of alleles an individual carried
What is a dominant allele?
Produce the same phenotype whether they are paired with an identical allele or a different allele
What is a recessive allele?
Produce their characteristic phenotypes only when paired with an identical allele
Define phenotype
An observable, measurable characteristic of an organism; often determined by genotype (but not always) and can be determined by environmental conditions; not inheritable, only genes are inheritable
What is population genetics?
The study of the distribution of alleles within populations and the mechanisms that can cause allele frequencies to change over time
The Hardy Weinberg Equilibrium definition
In the absence of outside forces, the allele frequencies of a population will not change from one generation to the next
What is the HWE equation?
p2 + 2pq + q2 = 1
Name the 5 assumptions underlying HWE.
- No selection 2. No mutation 3. No migration 4. Infinite population size (no genetic drift this way) 5. Random mating
Is HWE possible in a real environment?
NO! It provides mathematical proof that evolution will not occur in the absence of selection, drift, migration, or mutation, and serves as a theoretical null model.
What is the difference between a gene and a locus?
A gene is a genetic locus coding for a functional RNA transcript. A locus is any defined segment of DNA.
What is a mutation?
Any change in the genomic sequence of an organism.
What is point mutation?
A single base changes from one nucleotide to another (AKA substitution)
What is insertion?
a segment of DNA is inserted into the middle of an existing sequence
What is deletion?
a segment of DNA may be deleted accidentally
What is duplication?
a segment of DNA is copied a second time
What is inversion?
a segment of DNA is flipped around and inserted backward into its original position
What is chromosome fusion?
two chromosomes are joined as one
What is a polymorphism?
a mutation that is segregating in a population; a discontinuous genetic variation resulting in the occurrence of several different forms or types of individuals among the members of a single species; divides the individuals of a population into two or more sharply distinct forms
What are somatic mutations?
Affect cells in the body, genetic alteration acquired by a cell that are not passed to the progeny of the mutated cell; end with death
What are germline mutations?
They affect the gametes of an individual and can be transmitted from parents to offspring; heritable variation within populations arises; is any detectable and heritable variation in the lineage of germ cells. Mutations in these cells are transmitted to offspring, while, on the other hand, those in somatic cells are not
What does it mean when the positively selected allele is co-dominant and advantageous?
A1 allele fixes and A2 allele disappears. In the beginning, heterozygotes have some advantage over A2A2 individuals, but it is small so evolution proceeds somewhat slowly.
The rate of adaptation depends on whether the selected allele is dominant or recessive and advantageous.
How does evolution occur when the positively selected allele is overdominant, and the heterozygote has advantage?
A1A1 don’t arise until heterozygotes are common enough that A1A2 x A1A2 matings begin to occur
What are examples of heterozygote advantage?
Malaria
What is purifying selection?
Mode of natural selection which removes extreme phenotypes
What is directional selection?
Type of natural selection that favors an extreme phenotype
What is disruptive selection?
It is a type of natural selection that disfavors phenotypic intermediates.
Do alleles with dominant advantage reach fixation?
They can increase in frequency rapidly. However, they have difficulty in reaching complete fixation.
What is fixation?
Fixation only occurs when the deleterious alternative (recessive) allele is eliminated from the population, and once the deleterious allele becomes sufficiently rare, it is found mostly or only in heterozygotes which do not suffer the selective cost.
Do alleles with recessive selective advantage ever reach fixation?
Alleles with recessive selective advantage are not favored by selection when they are so rare that they are always found in heterozygotes, so their frequency tends not to increase (even though they would be adaptive if homozygous). However, if an allele with a recessive benefit becomes common enough to show up in homozygous form, natural selection can drive the allele to fixation.
How do allele frequencies change?
- Real populations are finite in size.
- Catastrophes can change allele frequencies
- Population bottlenecks or founder events can change allele frequencies
- Random sampling of gametes and/or adults can change allele frequncies
What changes the amount of genetic drift that occurs?
Depends on population size.
Smaller populations have:
- higher probability of large frequency jumps in any given generation
- shorter expected time to fixation or loss
The probability that an allele will ultimately become fixed is ____ to its current frequency in the population
exactly equal
Ex. Two alleles with equal frequencies (p = q = 0.5), have an equal chance of becoming fixed (50%)
Does the probability of ultimate fixation stay stable every generation?
No, it updates every generation, since it has no memory of the frequency in previous generations.
Genetic drift is a force that ____ genetic variation in populations.
Mutation is a force that ___ genetic variation in populations.
decreases, increases
What is one of the dangers of small populations in regards to traits in populations?
Small populations could cause an increase in the levels of negative traits in populations.
What is “inbreeding depression”?
In this case, inbreeding does not necessarily mating between very close relatives. But close enough so there is still a loss of genetic variation in the population (drift) and increased exposure of recessive traits (increased homozygosity)
What is the equation that depicts the idea that negative traits can increase in frequency by drift?
N x S < 1
Selection is fairly weak and population size is small
How is migration considered an evolutionary force?
It can introduce new alleles to populations and change the frequency of existing alleles.
What is gene flow?
Migration = gene flow, the movement and incorporation of genes from one population into the gene pool of another population; migrants must have reproductive sucess to be part of gene flow
In order for migration to be genetically meaningful, populations need to be subdivided. How do populations become subdivided?
- Individuals may migrate to new locations and found new subpopulations.
- Existing populations may become fragmented by newly arising barriers.
- Distant points in a species range may be isolated from each other by virtue of physical (geographic) distance
How do isolated subpopulations become genetically differentiated?
By genetic drift, which happens independently in each subpopulation. Independent drift causes populations to diverge in allele frequencies.
What is FST (what does it show) and what do its ranges mean?
It is commonly used as a statistic to quantify the divergence of subpopulations. It shows variance in allele frequency among subpopulations.
FST = 0, then have identical allele frequencies (populations not different)
FST = 1 then the populations are fixed for different alleles and are very different
Usually between 0 and 1
What is the relationship between FST , genetic drift, and migration rate? (Equation)
FST = 1/ (4Nm + 1)
N = size of population being considered
m = migration rate
Genetic drift causes subpopulations to ___ from each other.
Migration causes subpopulations to become more ___ to each other.
diverge, become more similar
What is the equation for VP (total phenotypic variance)?
VP = VA + VD + VI + VE
A = additive genetic variance
D = dominance variance
I = interaction variance
E = environmntal variance
What is the equation for VG?
VG = VA + VI + VD
A = additive genetic variance
I = interaction variance
D = dominance variance
What is narrow sense heritability?
the proportion of phenotypic variance in a trait that has an additive (simple) genetic basis; is the heritability that selection can efficiently act upon; causes offpsring to ressemble parents and population to evolve in response to selection
What is the equation for narrow sense hertiability?
h2 = VA / VP
is the proportion of phenotypic variance in a trait that has a simple genetic basis; only uses the ratio of additive genetic variation to the total phenotypic variation observed
0 = none of the phenotypic variation in a trait is explained by genetic polymorphism
1 = the phenotypic variation in a trait is explained by genetic polymorphism
What is the equation for broad sense heritability?
H2 = VG / VP
refers to the inclusion of all potential sources of genetic variation (additive, dominance, epistatic, maternal and paternal effects)
What is covariance in parents/offspring?
Degree of similarity between parents and offspring.
In a graph showing covariance, what does the slope of the line represent?
Heritability
Important Fact:
Narrow sense heritability can be estimated from the relationship between offspring phenotypes and the average phenotype of the two parents (the “midparent” value).
Look at graph
The environment can have very large effects on heritability. Therefore, heritability estimates are only meaningful…
…in the population and environment from which they were obtained.
Heritability predicts how well our population will respond to directional selection. What is the equation showing this?
R = h2S
R = response to selection
h2 = narrow sense heritability
S = selection differential
What is the selection differential defined as?
The difference between the mean phenotype of the breeding individuals (selected) and the mean phenotype of the whole population
mean phenotype of pop. - mean phenotype of breeding indiv.
Large S = strong selection
What is response to selection defined as?
The difference between the trait mean in the progeny and the trait mean of the (pre-selection) parents.
What are some uses of heritability?
Animal/Plant breeding
How is a heritability estimate changed in humans?
It can be overestimated, especially if environment is correlated within families. Interpret estimates of heritability with extreme caution, especially when they are applied to slippery phenotypes like social measures in humans.
What are transacting elements?
Sequences of DNA lcoated far from the focal gene (the gene code for protein, microRNA, etc.)
What is aneuploidy?
A type of mutation where a chromosome is duplicated or lost
What are cisacting elements?
They are stretches of DNA located near genes that influence the expression of genes
What is genetic polymorphism?
It is the simultaneous occurrence of 2+ discrete phenotypes in a population.
What is polyphenism?
It occurs when multiple, discrete phenotypes can arise from a single genotype, depending on environmental conditions
As long as parents mated with each other randomly, their gametes would mix in unpredictable/predictable ways.
Predictable
Do populations change their allele frequencies?
No, once alleles were in genotypes, populations would retain the alle and genotype frequencies indefinitely.
Name the 5 possible mechanisms of evolution.
- drift
- selection
- migration
- mutation
What is a null hypothesis?
It is the default hypothesis that there is no relationship between two measured phenomena.
What is an additive allele?
It is an allele that yields 2x phenotypic effect when 2 copies are present at a given locus than the effect that occurs when only 1 copy is present; Additive genes are those genes that code for the same trait and their effects work together on the phenotype.
Ex. eye color
Are additive alleles vulnerable to selection?
Yes, they are vulnerable; favorable alleles remain and become common
Are dominant and recessive alleles additive?
No, they are not; dominant allele overshadows the recessive, and the recessive only affects the phenoype when paired with another recessive
When does natural selection occur?
- Individuals vary in expression of their phenotypes.
- Variation causes some individuals to perform better than others.
Is natural selection more common in larger populations or smaller ones?
Large populations
In a small population, which is stronger: effects of drift, or selection?
effects of drift
What is pleiotropy?
mutation of 1 gene affects expression of more than 1 different phenotypic trait
What is antagonistic pleiotrophy?
Mutation with beneficial effects for one trait causes detrimental effects on other traits
What is a genetic bottleneck?
Event in which the number of individuals in a population decrease drastically; changes in genetic variation in population
Why do certain alleles make it through before a bottleneck and others don’t?
The probability of an allele being lost during each generation of a bottleneck is based on the severity of the bottleneck and the frequency of the allele. The rarer the allele before the bottleneck, the less likely it is to make it through.
What is the founder effect?
A type of genetic drift, or genetic bottleneck; describes the loss of allelic variation that accompanies founding a new population from a very small number of individuals
Does inbreeding change allele frequency?
No, it only rearranges alleles such that homozygotes for rare recessive alleles are more common.
Why do the detrimental effects of inbreeding recession occur?
Because rare recessive alleles become expressed in homozygous state where they can detrimentally affect the performance of an individual.
What is broad sense heritability?
It is the proportion of total phenotypic variance of a trait that is attributable to genetic variance where genetic variance is a single value.
