Population Genetics Final

Genes that are in random association are said to be in a state of …

linkage equilibrium

Mutation and Recombination introduce changes necessary for evolution. True or False

True

… can limit the amount of genetic variability available in small isolated populations. This can be especially bad if there are genetic abnormality alleles present.

Founder effects

Under the Wright-Fisher model, the fixation probability is based on memory and therefore reflects an average of the allele frequencies over teh last several generations. True or False

False

Genetic Drift affects … in terms of loss or fixation

alleles

Genetic drift is less severe is large populations. True or False

True

The infinite alleles model says

Mutation creates a new allele every time

A randomly evolving DNA sequence that contains mutations with no effect on the fitness and survival of an organism is called a

Neutral allele

Which of teh following is one of the patterns of natural selection?

Directional selection

Which of the following statements best describes the theory of natural selection?

Organisms better adapted to their environment have greater reproductive success

Pick out the statement that is false:

IBS is IBD

IBD is IBS

IBS is IBD

Allozygous genotypes can be heterozygous. True or False

True

Name the 4 evolutionary processes that affect Hardy Weinberg Equilibrium as stated in the definition of population genetics.

Natural Selection, Genetic Drift, Gene Flow, and Mutation

Name 4 assimptions of the Hardy-Weinberg Principle

1. Organisms are diploid

2. Reproduction is Sexual

3. Generations are non-overlapping

4. Mating is random

Few, if any, populations in nature meet all the assumptions of the Hardy-Weinberg law. If this is the case, how can the Hardy-Weinberg law be of any use in population genetics? Explain!

HWE is a check for data to see if it was generated correctly, it also could indicate other forces impacting the data.

What is the Bonferronic Correction (give description of how it is calculated) and why is it important?

The Bonferronic Correction accounts for the false positives that occur in calculations for larger populations. This test is more stringent.

It is calculated by taking the original correction value (0.05) and dividing it by m, the total number of tests in the population.

Bonferroni Correction = 0.05/m

What is recombination rate ( r ) and how is it calculated?

Recombination rate is the random shuffling of genes and is calculated by adding up all of the recombinant allele frequencies in the population

What can r (from question 5) tell us about location, what are the units of measure?

It can tell us how close together (less recombination) or far apart (more recombination) two alleles are. Units of measure are centimorgans

Explain the difference between the terms Linkage, and Linkage Disequilibrium

Linkage is the physical proximity between loci on a chromosome and Lnikage Disequilibrium is the non-random association of genes

What is genetic drift? Give a simple idea of it or analogy

Genetic drift is the random change in allele frequencies over time, like the toss of a coin

Explain how genetic drift can affect populations. What are its main features? Include information on within and between populations

Genetic drift has a high impact on smaller populations since there is less variance in genotypes present.

The main features are that it leads to the fixation of alleles or sometimes loss of heterozygotes.

Within populations there is less diversity since a smaller varaince of individuals is present.

Between populations there is high diversity. Breeding between the two populations would increase diversity.

What does the Wright-Fisher model say about allele frequencies in drift?

The Wright-Fisher model states that the allele frequencies can be used to determien if they will be fixed in future generations

What is the bottle-neck effect? Give a general example

A bottle-neck event is when a population and its allele frequencies drastically reduces in size over a short period of time due to a natural disaster such as a population after a tsunami

Explain population effect size and at least 2 of its parameters

Population effect size (Ne) is the measure of how a population compares to the theoretical population value. Two of its parameters are unequal sex ratios and lower amount of offspring

What is the Neutral Theory of Molecular Evolution? Explain it. Why is it useful?

The Neutral Theory of Molecular Evolution states that genetic drift and mutation are working together to randomly change allele frequencies over time. This is useful since it shows how the forces are correlating in terms of evolution and how traits are gained/lost over time

What is the purpose of Tajimas test?

Tajima’s D test is a test for neutrality to see if alleles are working with or against the neutral theory or molecular evolution (genetic drift & mutation)

What is the term Coalescence? What are we trying to do and what are we interested in finding out as we investigate it?

Coalescence is the history of genes and how they are connected to a most recent common ancestor. We are trying to find an ancestor where a common gene between individuals has a merging point to understand how that gene came about

Explain the difference between Coalescence and Phylogeny?

Coalescence is the evolutionary history of alleles. Phylogeny is the evolutionary history of species

What does IBS stand for? Describe what is means

IBD stands for Identical by Descent. IBD means that two or more individuals share a gene and it can be linked back to a merging point (ancestor) that is shared between the two

Name two types of natural selection in diploid organisms

Two types of natural selection are viability and sexual selection

Explain and name the 3 patterns of natural selection, give an example of each?

In diploid organisms there is disruptive selection, directional selection, and stabilizing selection.

Disruptive selection is when the population will be monomorphic for the homozygous genotype with the highest fitness creating an extreme phenotype.

Directional selection is when the population will be monomorphic for a homozygous genotype but which one depends on the initial allele freuquencies present in the population.

Stabilizing selection is when viability pushes for a stable polymorphism where all three alleles will be present but at different frequencies.

Explain overdominance and give an example of it, what will happed to the alleles and their frequency after multiple generations?

Overdominance is when a new allele is introduced into a population and can alter/override the current phenotypes. An example of this would be sickle-cell disease where alleles A and S are in the population: AA being resistant, AS being carrier, and SS being susceptible to sickle-cell. A new allele C is introduced into the population and has a higher fitness towards resistance. This new allele (C) is overdominant of the other alleles.

Both allele frequencies will be high

Albinism is a rare, genetically inherited trait that is only expressed in the phenotype of homozygous recessive individuals. The most characteristic symptom is a marked deficiency in the skin and hair pigment melanin. This condition can occur among any human group as well as among other animal species. The average human frequency of the albinism phenotype in North America is only about 1 in 17,000.

Please calculate the following:

1. The frequency of the phenotype Albinism in the population

2. The frequency of the dominant non-Albinism allele in the population

3. The percentage of carriers in the population

1. 0.00005929 or 0.0059%

2. q = 0.00775 p = 0.99225

3. 0.01538 or 1.54%

Selection is the transfer of genetic variation from one population to another. True or False

False

Two-way migration leads to homogenization of allele frequencies in sub populations

True

All types of migration lead to genetic differences between populations

False

Which of the following processes does not contribute to changing allele frequencies in populations?

Inbreeding

Which of the following is true about monozygotic twins

They have a genetic relatedness of 1

Inbreeding causes an increase in the probability that individuals carry alleles that are identical by descent. True or False

True

A FST value of 0 could indicate…

Random mating between the populations

The calculation of the inbreeding coefficient is influenced by alleles that Identical by State and Identical by Descent. True or False

True

The minimum allele frequency formula, used in Forensics if an allele has not been observed at least 5 times is …

5/2N

A selective sweep is a type of process that is evident when looking for genetic signatures of adaptation, there can be hard and soft sweeps. True or False

True

A super sweep is a type of signature of natural selection to look for in genetic data. True or False

False

Hard sweeps are from …

Selection from novel adaptive variants

Currently, the ‘Out of Africa theory’ suggests our ancestors moved around but still within Africa about 100k years ago. True or False

False

As hard sweep happens slowly over time, surrounding regions are all the same genotype/sequence within all individuals. True or False

False

You can measure the amount of genetic differentiation between sub populations by utilizing R calculations. True or False

False

Sliding windows are used in scans for genetic signatures. True or False

True

Name for a SNP that is indirectly involved/responsible for disease/phenotype

Tagging

Linkage studies are performed using unrelated individuals. True or False

False

You can understand what chromosome a variant is on and therefore find out its haplotype using a method called phasing. True or False

True

When working with data with large numbers of missing genotypes, what is the best options to do from the list below to get the best from your search?

Impute the missing genotypes

A QQ plot will quickly tell you if your GWAS has hits as the snps will skew upwards at the tail-end. True or False

True

Performing prior statistical power calculations on your dataset will not help you desing a good GWAS. True or False

False

When doing a GWAS study with cases and controls, the phenotype can be coded as 1 and 0. True or False

True

A heat map can be a useful figure to explain blocks of inheritance. True or False

True

Migration makes sub populations look genetically more …

Similar

In order to find out what your Y and Mito specific Haplogroup is for biogeography ancestry, you must genotype certain sites that are indicative of the tree root as well as the variants that can resolve the tree further into …

Branches

What specifically does Fst measure in theory? Also give the formula

Fst = 1 - (Hs/Ht)

Fst measures the degree of differentiation between subpopulations

What is the definition of the Inbreeding Coefficient?

The inbreeding coefficient (F) is the amount of inbreeding an individual has. Probability alleles are IBD and can be a result of ancestry or environment

What is the difference between IBD and IBS?

Identical by Descent has a most recent common ancestor linkge shared traits between individuals.

Identical by State does not have a common ancestor linking shared traits between individuals.

What is the formula for genotype frequencies if inbreeding is present? Give all 3 (hint HWE with F)

AA = p² + pqF

Aa = 2pq - 2pqF

aa = q² + 2pqF

(Bottom Diagram) Calculate the F of an Individual O (no prior inbreeding)

The F of the individual would be 0.0625 or 1/16 inbreeding

Explain the Wahlund effect fully?

The Wahlund effect overestimates heterozygosity as it assumes HWE, but there are subpopulations present which decrease heterozygosity

Explain the connection between inbreeding and recessive disorders within a population, give an example

As a population is inbreeding it is increasing in homozygosity and decreasing in heterozygosity. If a recessive disorder (q) is increasing in homozygosity with this population the prevelance and effects of this disorder will increase in the population. This could cause a decline in the population if the disorder is fatal or a higher abundance of individuals within the population to have and trasmit the disorder. An example of this would be sickle-cell anemia

In genetic signatures of adaptation, why do we do it, what do the patterns contain, give 1 example of a type of pattern and how you would find it?

We do it to understand why genes have changes over time either as a result of environment, mutations, disease, or a natural disaster. Essentially we are trying to put a reason behind the change. The types of patterns are disruptive, directional, and selective. You would find it by viewing allele frequency changes throughout the population and seeing if certain alleles are dominant, increasing in frequency, or are fixed. A classic selective sweep (hard sweep) is when a beneficial mutation rapidly spreads within a population and it can be viewed by a rapid increase in allele frequency until fixation

Who though of population F statistics? Name the three hierarchy levels

Wright throught of population F statistics and the three hierarchy levels are individual (I), subpopulation (S), and population (T)

Give an example of genetic adaptation over acclimatization and compare the two fully?

Genetic adaptation is when a trait is when a trait increases in frequency as it is preferrable to an environment or region. Adaptations could also occur over time as you move into a new environment and circumstances lead to other traits being preferred. This is long-term effect resulting in a change in genes, an example woul deb skin color in humans.

Genetic acclimatization is a short-term change and does not alter your genes. An example of this would be runners training at higher altitude to prepare for a race.

Genetic adaptation is a long-term premament change to your genes whereas genetic acclimation is a short-term change that does not alter your genes.

What is convergent evolution, give an example and explain fully

Convergent evolution is when a similar phenotype has emerged by two separate means. An example of this would be European and Asian skin color since over time they have developed similar skin tones while having developed in different environments and circumstances

What is a linkage analysis study? Explain 2 pro’s and 2 con’s

Linkage analysis is using families to find variants responsible for a trait/phenotype

Pros: can be used when you don't have pedigrees, they can identify rare alleles or mutations such as BRCA1

Cons: need to identify a large number of family with several affected generations, this is less helpful for complex traits such as Diabetes since multiple genes can be involved

Explain 2 types of association study, how are they different from each other?

Fine Mapping and Genome wide are two types of association studies along with Candidate SNPs and Candidate Genes.

Fine Mapping involves looking at several hundred SNPs to view the possible location of the causal variant. As opposed to Genome wide, where you are looking into the entire genome to view impacts of the causal variant.

What is population stratification? Explain fully, give a scenario

Population stratification is when you do not correct for ancestry in a dataset and are therefore getting false positives. For examples, if you are trying to get genotypic information specific to a few regions and you do not take into account the ancestry of individuals who may have recently migrated to a new area in the past 4-5 generations, you will get false positives from the regions they migrated from. This would ultimately skew the dataset

What are Haplogroups? What can they be used for? Mention the different kinds you learned about, and explain how they are different in general

Haplogroups are groups of mutations that combine to form the haplogroups (subclade) of an individual. Haplogroups can be usde to find patterns of influence of these mutations and they differ according to the environment and ancestry of the individual