Module 5: Population Genetics

the classical hypothesis

populations contain very little variation, selection maintains a single best allele at any locus, and heterozygotes are rare. heterozygotes occur as a result of rare deleterious mutations that are quickly eliminated by selection

the balance hypothesis

individuals are heterozygous at many loci, and balancing selection maintains lots of genetic variability within populations

balance selection

any form of selection that results in the maintenance of genetic variation (allelic diversity) in natural populations

population genetics

the study of the way alleles and genes behave within populations

in the early days, evolutionary biologists needed to use phenotypic diversity

within populations as a surrogate for genetic diversity within populations p

prior to 1960s, two views concerning the magnitude of genetic variation in natural populations

1. classical hypothesis

2. balance hypothesis

one of the most frequently used measures of population genetic variation is

the population heterzygosity - the number of heterozygotes divided by the total number of individuals in a population

heterozygosity

number of heterozygotes/total number of individuals

one of the first methods that became available to enable evolutionary biologiets to assay individual’s genotypes within that population

protein electrophoresis

one of the first organisms to be looked at in protein electrophoresis

humans

humans displaed levels of genetic variation which

DID NOT support classical hypothesis

early studies showed classical hypothesis was clearly incorrect

substantial population genetic variation in all kinds of organisms including vertebrates, invertebrates, and plants

the selection hypothesis maintained the reason we see so much

variability at the genetic level in natural poopulations bc balancing selection results in the maintenance of very high genetic variability

neutral hypothesis maintained that

most of the alleles and the diversity that we see in natural populations are selectively natural and do not affect an organism’s fitness

genotype frequency

the number of individuals of a specific genotype divided by the total number of individuals in our sample

HW principle is a model of

random maitng in the absence of evolutionary mechanisms

HW principle allows us to predict

genotype frequencies from allele frequencies under certain conditions - it serves as a starting point or null hypothesis in a population genetic studies

panmictic

randomly mating

panmictic population

a sexually reproducing population where each male has an equal probability of mating with each female, and each female has an equal probability of mating with each male

assumptions for genotype frequencies in panmictic population

genotype frequencies are the same among males and females and the population is infinitely large

meiosis

reduction divisions that produces haploid (1 set of chromosomes) gametes (eggs/sperm) from diploid parent cells. gametes unite to form offspring (zygotes)

a random mating population can be thought of as a pool of gametes or a

pool of alleles

gametes carrying a specific allele are produced in the

same proportion as the frequency of the allele in the population

if a population is out of HW equilibrium,

it will take a single generation of random mating to restore HW equilibrium

if there are no violations of its assumptions,

the HW principle shows that genotype and allele frequencies will not change from one generation to the next

HW disequilibrium will always result as a consequence of a

heterozygote deficit or a heterozygote excess

evolutionary mechanism

anything capable of changing population allele frequencies on its own

FOUR big evolutionary mechanisms

1. selection

2. mutation

3. migration

4. genetic drift

fixed (or fixation)

when an evolutionary mechanism results in an allele moving to a frequency of 1, we say that the population has become fixed for that allele, or moved to fixation for that allele.

heterozygote superiority

when (in a two allele system, e.g. 3 possible genotypes), the heterozygote has the highest fitness. Heterozygote superiority is a form of balancing selection.

heterozygote inferiority

when (in a two allele system, e.g. 3 possible genotypes), the heterozygote has lowest fitness.

the magnitude of the impact that selection has on allele and genotype frequencies will depend on whether

alleles are common or rare, dominant or recessive, as well as te fitness of the different genotypes

deleterious recessive alleles will “escape” natural selection when they are in heterozygotes because

the deleterious condition will only be manifested when they are in homozygous form

selection happens when

individuals with particular phenotypes survive to sexual maturity at higher rates than those with other phenotypes, or when individuals with particular phenotypes produce more offspring during reproduction that those with other phenotypes

selection can lead to evolution - when the phenotypes that exhibit differences in reproductive sucess are heritable

when certain phenotypes are associated with certain genotypes

when we think of selection as if it acts directly on genotypes, its defining feature is

that some genotypes contribute more alleles to future generations than others - there are differences among genotypes in fitness

violation of the no selection assumption has resulted in

violation of conclusion 1 & 2 of the HW principle

Dawson’s beetle experiment, l allele was lethal

his theory predicted the + allele frequency would increase over time, and l allele would decrease- this was correct

the rate of evolution depends on both

dominance and allele frequency

natural selection acts faster when

the recessive allele is common: both phenotypes appear frequently, allowing natural selection to act efficiently

natural selection slows down when

the recessive allele is rare: most recessive alleles are hidden in heterozygotes, making them “invisible” to selection

dominant alleles are not inherently advantageous

many dominant mutations are harmful such as one causing fibrodysplasia ossificans progressiva

rare recessive alleles are often protected inside

heterozygotes and change very slowly in frequency

in nature there are not usually differences in survival rates large enough to make a big impact over a single genertion (but sometimes there can be)

smaller changes typically accumulate over numerous generations

selection and the HW principle

1. selection can change allele frequencies, therefore it is an evolutionary force or an evolutionary mechanism

2. it can also change population genotype frequencies

3. it can change genotype and allele frequencies in a way that causes HW disequilibrium, in the form of heterozygote excess and heterozygote deficit

if one allele is recessive and the other is dominant then the

fitness of the heterozygote is equal to that of one of the homozygotes

fitness can be between

that of the two homozygotes (codominant)

fitness can also be superior or

inferior to that of either homozygote

heterozygote inferiority (underdominance)

or superiority (overdominance) can produce interesting outcomes

quantitative traits

phenotypic characteristic that varies continuously, as opposed to discretely and involve multiple loci

directional selection will either increase or decrease the mean of a quantitative trait in the population.

it will also reduce the variance of that trait.

stabilizing selection results in little or no increase in the mean of the trait in our population

educes the variance of the trait because in this case, we've lost individuals at the extreme ends of the distribution.

directional selection increases or decreases the value of the mean in the population, and reduces the variance, stabilizing selection has little or no effect on the mean in the population

also reduces the variance, disruptive selection has little or no effect on the mean of a trait in the population, but it increases its variance.

if directional and stabilizing selection are really quite common and if they both reduce the amount of phenotypic variation in a population, why do natural populations exhibit so much phenotypic variation?

One reason for that is that many populations may not yet be in evolutionary equilibrium with respect to directional or stabilizing selection. A second reason is that within populations, there tends to be a balance between mutation and selection and we're going to say a little more about that in our next topic. And in addition, it may be that disruptive selection is quite a bit more common than we think it is.

Selective sweep

the rapid fixation of a new advantageous mutation by selection.

Mutation-selection balance

the equilibrium allele frequency established when the mutation rate of a deleterious allele into a population is equal to the rate of its removal by selection. This is another reason why deleterious alleles can persist in populations.

directional and stabilizing selection are common and

disruptive is believed to be more rare

directional and stabilizing selection

reduce phenotypic variation in a population

mutation will not result in HW disequilibrium in a randomly mating population even though

it chainges allel frequencies (albeit slightly)

Not all violations of hte assumptions of the HW principle result in HW disequilibrium however

mutation does change allele frequencies and when all of the assumptions of the HW principle are met, allele and genotype frequencies are stable from generation to generation

why doesn’t mutation cause HW principle

as long as our gametes unite randomly according to p squared, two times p times q, and q-squared, the zygotes will be in perfect Hardy-Weinberg equilibrium. But, they will be in perfect Hardy-Weinberg equilibrium on the basis of the new allele frequencies in the gametes, not on the basis of the old allele frequencies within the adults.

mutation is it is the ultimate source of all genetic variation and it does change allele frequencies and so it is an evolutionary force. But,

it only has a minor impact on allele frequencies over time

at some point the rate at which new copies of a deleterious allele appear through

mutation will equal the rate at which selection removes them

migration

refers to the movement of alleles into (or among) populations and is typically referred to as geneflow

the rate of geneflow among populations

will be in part dependent on the dispersal capabilities of the organism in question

migration is an evolutionary force that can potentially act against selection OR

work with selection and aid in the fiation of a beneficila allele

migration is a mechanism that homogenizes populations or

makes them more similar to each in terms of allele frequencies

allele frequency shift under migration

our allele frequencies have changed, our genotype frequencies have also changed, and the genotype frequencies have changed initially in a way which is inconsistent with Hard Weinberg equilibrium. In other words, we have Hardy-Weinberg disequilibrium with a heterozygote deficit.

although migration can result in heterozygote excesses and heterozygote deficits, that doesn't mean

that it will do so all of the time.

the ultimate effect is that migration will homogenize the populations in terms of their allele frequencies, and each population will

converge on an equilibrium allele frequency that will be equal to the average allele frequency among the initial allele frequencies in the starting populations.

FST is a measure of

genetic differentiation among populations. In other words, it's a measure of how much populations differ from each other in terms of their allele frequencies

if FST is equal to zero, it means all of our populations are identical to each other with respect to allele frequencies, and when FST is equal to one,

it means all of our populations are fixed for different alleles and that there are no shared alleles among our populations.

The impact then of migration, since it homogenizes populations and makes them all similar to each other,

is to reduce the magnitude of FST as measured between or among populations

evolutionary force is

anything that can change population allele frequencies

natural selection is a ______

non-random mechanism of evolution

mutation is a ______

random mechanism

migration can be either

random or non-random

genetic drift is a

purely random and stochastic mechanism of evolution

sampling theory: black and white balls

as long as our sampling method is unbiased, a larger sample size will better represent the frequencies in our initial population than will most likely be the case with a smaller sample size

genetic drift (definition)

random or chance fluctuations in allele frequencies as a result of randomly sampling gametes each generation

what drives genetic drift (topic 8)

random sampling of the gamete pool initially produced by the adults that drives genetic drift and results in allele freq changes

sampling error can result in

evolutionary change

(9) Over time, genetic drift reduces population and heterozygosity and allelic variability, causing alleles to randomly go to fixation. These effects will be strongest

and fastest when population is small

(9) although drift changes allele frequencies in a manner that does not cause HW disequilibrium

allele frequencies will be stable from one generation to the next when all of the HW principle’s assumptions are met

(9) when population size is small, genetic drift can overpower

natural selection and result in the random fixation of a deleterious allele

(9) because genetic drift is random and unpredictable, it could also work with

selection and aid selection with the fixation on an advantageous allele

(9) genetic drift is a mechanism that results in the divergence of

population in terms of allele frequencies and increases the values of Fst

(9) migration homogenizes populations in terms of allele frequencies and decreases the value of FST, hence,

migration and drift are evolutionary mechanisms that act in opposition to each other

founder effect

allelic sampling error that occurs when a group of individuals from a population colonize a new area, and start (or found) in a new population. the new population can differ in allele frequencies in comparison to the source population as a result of sampling error

(9) population bottleneck

a sharp reduction in population size that can alter allele frequencies as a result of sampling error

(9) genetic drift can cause allele frequencies to “wander” over generations which has two effects

1. alleles drift fixation (the population has a frequency of one for a spcific allele) or loss (allele gains a frequency of 0)

2. the frequency of heterozygotes or heterozygosity decreases over time

(9) at any given time the probability that an allele will be fixed by drift is

equal to the frequency of that allele

(9) the founder effect is based on sampling error when we

found a new population from a parental population

(9) bottle neck effect is absed on sampling error during a

reduction in population size within a single population

(9) both founder effects and population bottlenecks can result in HW disequilibrium

cause either heterozygote deficit or excess.

(10) outbreeding is the opposite of inbreeding

a higher incidence of mating among distantly related individuals than expected in a randomly mating population.

(10) outbreeding causes HW disequilibrium with heterozygote excesses but

does not change allelel frequencies and on its own is not a mechanism of evolution

(10) Positive assortative mating

individuals with similar phenotypes mate, e.g large individuals only mate with other large individuals

(10) negative assortative mating

when individuals with dissimilar phenotypes mate e.g (small individuals only mate with large individuals) at a higher frequency than ccurs in a random mating panmictic population

(10) Inbreeding and outbreeding affect ALL loci, but hw disequilibrium only occurs at

those loci involved in the traits for which assortative making is taking place