VL3 Allel frequencies Flashcards
What is discontinuous variation, and what did Mendel discover about it?
Discontinuous variation is a trait that shows a limited number of distinct categories, such as the presence or absence of stripes in Cepaea or flower color in peas. No intermediates exist between the categories and often controlled by a single gene.
Gregor Mendel discovered that traits are inherited according to specific laws, including the law of segregation (first law), which states that each individual has two alleles for each gene, which segregate during gamete formation so that each gamete receives only one allele.
How does the Punnett square illustrate Mendel’s first law?
The Punnett square shows the segregation of alleles and predicts the genotype and phenotype ratios of offspring from a cross between individuals.
What is the Hardy-Weinberg principle, and what are its assumptions?
The Hardy-Weinberg principle states that allele frequencies in a population remain constant over time, provided the following assumptions are met:
- infinite population size,
- diploid organisms,
- random mating,
- no population structure,
- no mutations,
- no selection, and
- no migration.
It serves as a null hypothesis for detecting evolutionary forces acting on a population.
It describes the behaviour of alleles in “ideal” populations
-> Many populations ARE in Hardy-Weinberg equilibrium (at least for most of their loci)
HW principle results from a generalization of Mendels first law to allel frequencies different from 0,5 : 0,5
How do you calculate whether a population is in Hardy-Weinberg equilibrium?
To calculate Hardy-Weinberg equilibrium:
1. estimate allele frequencies from genotypes,
2. calculate expected phenotype frequencies
3. Test whether observed and expected phenotype frequencies match (chi-square test to compare observed and expected frequencies)
Significant deviations suggest non-random mating, selection, or hidden population structure.
What are the effects of inbreeding and assortative mating on allele frequencies?
Inbreeding ( mating of closely related individuals) increases the frequency of homozygous individuals, leading to inbreeding depression by making deleterious recessive alleles homozygous.
Assortative mating (mating between similar phenotypes) -> increased homozygosity.
And disassortative mating (mating between different phenotypes) -> increased hetrozygosity.
all lead to deviations from Hardy-Weinberg equilibrium.
What is the fixation index (FST), and how is it calculated?
The fixation index (FST) quantifies genetic differentiation among subpopulations and is calculated as
𝐹𝑆𝑇 = (𝐻𝑇−𝐻𝑆) /𝐻𝑇
*𝐻𝑇 is the overall expected heterozygosity of the metapopulation,
*𝐻𝑆 is the average expected heterozygosity of all subpopulations.
FST values range from 0 to 1, with higher values indicating greater genetic differentiation.
FST = 0: Populations genetically identical. No divergence
FST = 1: Populations completely seperated. No gene flow
FST-values increase with distance = Isolation by distance.
Natural populations are normally only prtially isolated from each other.
We can quantify the extend of genetic islatio using the fixation index.
How does genetic drift affect allele frequencies, and why is it more significant in small populations?
What is the average time to fixation of a new mutation?
- Genetic drift causes random fluctuations in allele frequencies, which are more pronounced in small populations. This leads to faster fixation or loss of alleles and lower genetic diversity.
- The average time to fixation of a new mutation is shorter in smaller populations, making genetic drift more significant.
-> Deleterious muatations have a greater chance to become fixed before the are removed by selection .
Mathematically, the average time to fixation of a new mutation (with a frequency of 1/2N) is 4 N generations
What is effective population size (Ne), and how does it differ from actual population size (N)?
Effective population size (Ne) is the number of breeding individuals in an idealized population that would show the same amount of genetic diversity as the observed population.
It is usually smaller than the census size (N) and can vary across different sections of the genome due to factors like uneven sex ratios or variance in reproductive success.
How do genetic drift and gene flow interact in metapopulations, and what is isolation by distance?
In metapopulations (a group of more or less connected populations), genetic drift leads to allele fixation within subpopulations, according to the initial allele frequencies, while gene flow introduces new alleles, counteracting drift and increasing genetic diversity.
The overall allel frequencies will not change.
Isolation by distance occurs when populations diverge over space and time, showing greater genetic differentiation (higher FST) with increasing geographic distance.
What was the genetic consequence of the typhoon on Pingelap island in 1775, and what does it illustrate about genetic drift?
The typhoon reduced the population to about 20 survivors, leading to a high frequency of complete color-blindness (Achromatopsia) due to genetic drift in the small population. This illustrates how genetic drift can lead to significant changes in allele frequencies and increase the prevalence of deleterious traits in small populations.
How does the probability of fixation of a new mutation depend on initial allele frequency?
The probability of fixation is equal to the initial allele frequency; for a new mutation in a diploid population, the probability is 1/(2N), where N is the population size.
Neutral Mutation: The fixation probability equals the initial allele frequency 1/2𝑁.
Beneficial Mutation: The fixation probability is greater than 1/2𝑁 and is enhanced by the selection coefficient 𝑠.
Deleterious Mutation: The fixation probability is less than 1/2𝑁 and deleterious mutations are unlikely to fix in the population.
Recapitulation Hardy-Weinberg
- The Hardy-Weinberg principle results from a generalization of Mendel’s first law to allele frequencies different from 0.5 : 0.5.
- The expected genotype (and thereby phenotype) numbers can be calculated from the observed allele frequencies and the total number of individuals.
- Whether observed and expected genotype numbers differ significantly can be tested using the chi-square test.
- A deviation from Hardy-Weinberg equilibrium usually implies that mating is non-random, that the genetic locus studied is under selection or that there is hidden population structure, which also leads to non-random mating.
FIS
Quantifying the effect relative to Hardy- Weinberg
to measure inbreeding/outbreeding (values from -1 to 1)
Fis = (Hs-HI)/HS
- Hs: expected frequencies of heterozygotes
- HI: observed ferquency of heterozygotes
FIS = 0 indicates random mating -> observed heterozyg. matches the expected frequencies under HWE
FIS > 0 positive values indicate a deficit of heterozygoutes, suggesting some levels of Inbreeding or non random mating
FIS < 0 neative values indicate an excess of heterzygoutes -> Disassortative mating or outbreeding.
Fis is 1 when there are no heterozygots.
