BIOL 3010 - Exam #4

If parents resemble their offspring, does that mean that variation in the trait is determined by genetic factors?

No, shared environmental effects can also play an effect since the environment tends to be similar (i.e., growing up in the same nest with the same amount of food)

Is heritability a fixed property of a species?

It is not a fixed property because it can vary depending on the specific population and environment being studied. It can also vary over time as genetic and environment factors change.

How does heritability change if the allele frequency of the causal SNPs change?

If a particular allele becomes more common, then the genetic variation associated with that allele will also become more common, and the heritability of any trait that is influenced by that allele will increase, and vice versa

Why is natural & artificial selection better able to act on additive compared to dominance variance?

Dominance can reduce effective NS via the masking of beneficial recessive alleles

What is linkage disequilibrium?

the tendency for certain alleles at 2 linked loci to occur together more often than expected by chance - varies in different populations; sources -- new mutations, genetic bottlenecks (founder effect), population divergence, natural selection

0 -- linkage equilibrium

1 -- perfect correlation

If you want more resolution in a QTL study, what do you need more of?

More generations (sample size) and more markers

Positive selection causes a beneficial allele to rise in frequency very quickly. Why does it generate linkage disequilibrium?

The frequency of the beneficial allele and the linked variants will increase together, and this pattern of co-inheritance can persist for many generations, creating linkage disequilibrium (close proximity due to low rates of recombination)

Does a F2 intercross have higher or lower linkage disequilibrium than a F5 cross?

It is higher because in later generational crosses they have undergone more rounds of recombination and segregation, leading to a greater breaking up of LD between loci

What is the relationship between the maximum allele frequency different and Fst (fixation index)?

As the maximum allele frequency increases, the fixation index increases as well. However, there are some other factors that may influence this, such as migration patterns, population size, and genetic drift

Do you need to know genotype frequencies to calculate fst?

No -- you only need allele frequencies -- assume HW in a subpopulation

How does the TMRCA relate to population size?

In general, TMRCA tends to be larger in larger populations and smaller in smaller populations, but this relationship is not always straightforward.

Are rare alleles or common alleles more likely to be lost during a bottleneck?

Rare alleles are present at low frequencies in a population. Therefore, they are more susceptible to being lost during a bottleneck due to the stochastic nature of genetic drift, which is the random fluctuation of allele frequencies in a population. In a small population undergoing a bottleneck, genetic drift can have a more pronounced effect, and rare alleles may have a higher likelihood of being lost as the population size decreases.

Are new, recessive deleterious mutations more or less likely to persist in populations if the population is expanding?

In general, recessive deleterious mutations are more likely to persist in populations during times of population expansion compared to times of population contraction. This is because during population expansion, there is an increase in the number of individuals carrying the mutation, which can potentially offset the negative effects of the mutation through heterozygote advantage or genetic drift.

Are P-elements used in genetic engineering autonomous or non-autonomous?

Non-autonomous -- require the helper plasmid to function

Would P-element transformation work in a P-background or an M-background or both?

M-background -- the p-element would get shut down in a p-background

Does methylation always shut down (reduce) expression of a protein coding gene?

No -- methylation at CpG sites can shut down the expression of non-coding RNA and subsequently leads to increased expression of a protein coding gene

What is the female P-type fly doing to the egg to protect the offspring from TE attack?

It employs a defense mechanism, known as piRNA-mediated silencing, in which their complexes bind to the TE transcripts to degrade or sequestrate the TE RNA molecules, preventing translation of the TE transcripts into functional proteins

What are the two other vocab words that could describe CpG islands?

SSR, micros

Which factors cam make allele fixation due to genetic drift more likely?

small population size, the allele's high starting frequency

When compared to an additive genetic relationship, what impact does dominant/recessive genetic relationship have on the effectiveness of natural selection?

Dominance can reduce effective natural selection via the masking of beneficial recessive alleles

What metric of FST can you use to make inferences about the demographic history?

The mean of the data

Side info:

Variance -- demography + selection

Extreme -- selection

fScientists argue that data shows a "serial bottleneck effect." What does this mean, demographically speaking?

Parts of the population formed a much smaller group several times over the years

What is the evidence for this?

The mean FST has several flat areas across distances, but jumps in average at certain distances

The population is experiencing sudden expansion; how old would you expect the MRCA to be compared to a population experiencing contraction? What about the FST?

younger, higher

Define epigenetics

Heritable modification to gene availability not coded for in the DNA

Small effect size requires what?

Larger population

Small populations affect genetic drift and FST in what ways?

They are increased

Inbred means what?

More homozygosity

Fundamental issues with GWAS

Signficant SNP may not be causal, only in high linkage

Human GWAS data can be disproportionate from European descent

Many traits are polygenetic with many SNPS contributing small amounts

Why does increase difference between alleles reduce linkage?

More distance means higher odds or recombination

QTL does what?

Helps you understand which alleles affect a phenotype -- chromosomal regions that are statistically associated with variation in phenotype

Which of the following genetic techniques is used to identify genes responsible for complex traits?

GWAS

What is the primary goal of GWAS?

To identify causative genes for a particular trait or disease -- linkage between marker SNPs and causal SNPs

What is population differentiation?

The differences in genetic composition between different populations

What is the main purpose of evolutionary inference of gene function?

To identify the function of a gene in a particular organism

What are transposable elements?

Repeating DNA sequences that can move to different locations in the genome

Define genetic drift

random (stochastic) force in evolution -- happens in small population

Define heritability

fraction of phenotypic variation that is caused by genetic variation

0 -- due to environmental effect

1 -- genetic variations

Situations where heritability estimates are truly equal to Va/Vp

Experiment controls environment and levels of relatedness and cross fosters

Situations where heritability are much more complicated

When the environment and genotype are both inherited, caused by maternal effects or by learned/social effects

QTL process

1. Cross two variables that are different in phenotype

2. Perform backcross

3. Phenotype the backers-1 generation

4. Gneotype the BC1 generation at multiple SNPs

5. Perform statistical test to identify which markers are associated with the phenotype

Define markers

Mutation (SNP, SSR) that you know is a fixed difference between your strains

LD gets smaller with physical distance. Why?

Extent of recombination varies across genome/chromsomes

Regions of the genome can experience high LD as a consequence of NS

How are SNP chips biased?

biased due to the fact that samples are primarily based towards Central Europeans

What does FST tell us about natural selection?

Extreme differentiation between populations at specific SNPs can indicate local adaptation due to differences in NS

0 -- no difference in allele frequency between populations

1 -- populations are fixed for alternate alleles

Why do TEs prefer to insert into genes?

They are trying to get copied through transcription

Consequences of TEs

1. Variation in genome size

2. Disrupt gene function

3. Induce ectopic recombination -- generates inversions, deletions

4. Add functionality

DNMT function

Replicates the pattern of CpG methylation

Mechanism of Action for Sex-Specific Imprinting

Maternal shuts down -- unmethylated CpG island recruits an insulator element that blocks enhancer

Paternal shuts down -- unmethylated CpG island allows expression of non-coding RNA that is complementary to the represor gene

Define muller's ratchet

in the absence of recombination (especially in an asexual population), an accumulation of irreversible deleterious mutations results.

Why is the complete loss of genes from the mtDNA a slow process, even if mtDNA is moved to the genome relatively quickly?

Most of the mtDNA that gets incorporated into the host genome is nonfunctional (to the mtDNA) and likely deleterious to the host

Why is a smaller genome beneficial to some mitochondria?

More efficient replication, protection from Muller's ratchet, unnecessary in new cellular environment

Why does recombination, and thus sex, required to alleviate the effects of Muller's Ratchet?

Recombination can break apart the linkage between mutations on different chromosomes, allowing NS to remove the deleterious mutations more efficiently.