Population Genetics

Question 1

Approaches to analyse the genome at the molecular level

Answer 1

• Chromossomal analysis : kariotype
• RFLP: Restriction Fragment Length Polymorphisms
• Southern Blotting
• PCR: Polymerase Chain Reaction
• DNA sequencing

Question 2

What are probes? And what types?

Answer 2

single strand sequences of DNA or RNA that hybridize through complementary pairing with SSDNA or RNA to identify specific sequences within a mixture of fragments

• Single locus probe
• Multi locus probe

Question 3

Examples of probes

Answer 3

• cDNA Probes: obtained through reverse transcription of RNA, complementary to RNA
• DNA probes: complementary to genomic DNA
• Oligonucleotide Probes: synthetically produced short DNA probes (14-25 nucleotides)

Question 4

Explain RFLP

Answer 4

Restriction fragment lenght polymorphisms: sees variation between homologous DNA sequences- polymorphisms. Identifies specific sequences of different lengths with the loss or gain of specific sites - very specific.
1 - DIGESTION : With a restriction endonuclease (enzyme that cleaves DNA) cut in the specific restriction site, obtaining 2 fragments (with sticky ends)
Even with just 1 nucleotide change the RE isn’t able to recognize the site and isn’t able to cut it

Question 5

Explain Southern Blotting

Answer 5

Detect specific DNA sequence in sample using restriction enzymes
1 - uses the RFLP method and then separates the fragments based on size trough electrophoresis.
2 - Denaturation into single strands and transfer to blotting membrane
3 - hybridization of probe to the specific DNA
4 - Detection with the bands where it was hybridized

Question 6

what can RFLP + Southern Blot identify

Answer 6

Point mutations (SNP, single base pair), deletions and insertions

Question 7

Diagnosis of Sickle cell anemia with RFLP / Southern blot

Answer 7

The restriction site is MstII, βA is the wild type and βS has the mutation that removes the restriction site. In the mutation the band is bigger because in the wild type the probe only hybridizes to the restriction site.
The band would be the bigger site in the SS genotype, the smallest on the AA and appear both in AS. EcoRI is the restriction enzyme that cuts the fragment

Question 8

What are DNA Polymorphisms

Answer 8

Differences in DNA sequence, 2 or more alleles at a locus with >1% frequency

Question 9

what are VNTR, STR and SNP

Answer 9

• VNTR: variable number of tandem repeats (minisatellite- 14 to 100 base pairs)
• STR: short tandem repeats (microsatellite)
• SNP: single nucleotide polymorphism
• Satalite DNA: non-coding DNA with short sequences repeated a number of times
• Tandem repeat: sequence of two or more DNA base pairs that is repeated, the repeats lie adjacent to each other on the chromosome

Question 10

What is PCR?

Answer 10

Polymerase Chain Reaction
1. Denaturation: (94–98°C) for 15–30 seconds, denatures your DNA and primers, which will allow them to anneal to each other in the next step.
2. Annealing: temperature is rapidly lowered (50–64°C), polymerase will bind to your primer/template DNA
3. Extension: rapidly heated (72–80°C), polymerase begins reading (in the 5´-3´ direction) and copying your template DNA (in the 3´-5´direction).
… REPEAT
Double the ammount of DNA per cycle

Question 11

Diagnosis of Sickle cell anemia with PCR

Answer 11

Amplify the region of interest with a specific primer and procede with gel electrophoresis. The only DNA present is of the interest region- saves time from southerblot and allows for replicas

Question 12

What is Hardy Winberg Equilibrium?

Answer 12

States that allele and genotype frequencies in a population will remain constant from generation to generation in the absence of other evolutionary influences - predict allele frequencies within a region

Is reached fast in autozygous and +/- 10 generations with X-linked alleles

Question 13

What are the Hardy Winberg Equilibrium assumptions?

Answer 13

• Organisms are diploid
• only sexual reproduction
• generations don’t overlap
• random mating
• infinitely large population
• equal allele frequency in the sexes
• no gene flow, admixtur, mutation or selection

Question 14

What is genetic drift?

Answer 14

Mechanism of evolution in which allele frequencies of a population change over generations due to chance, sampling error in selectiong alleles for the next generation. Stronger in small populations. Frequency between 0 (allele no longer present) or 1( only allele still present)
- Neutral mutations are not object to selection so they can only fixate trough genetic drift

Question 15

Bottleneck effect vs Founder effect

Answer 15

In the bottleneck effect there’s a catrastofic event that reduces the nº of individuals and thus of original alleles, while in the founder effect the original population still exists but the new one is isolated.
Highly affected by genetic drift due to the small population size

Question 16

Effective population size

Answer 16

the number of individuals in an idealised population (every indv. reproduces) in which the rate of genetic drift is equal to the value of that quantity in the population of interest.

Question 17

Heterozygote deficiency is caused by…

Answer 17

subdivisions of populations, inbreeding or self crossing and it leads to fixation

Question 18

Autozygous vs Allozygous

Answer 18

Autozygous - identical alleles due to inbreeding, same descent
Allozygous - copies not due to inbreeding

Question 19

Relative fitness

Answer 19

is the average number of progeny of a particular genotype which survives, with respect to the average number of progeny of the competing genotypes wich survives after a single generation

Question 20

Loss of heterozygosity trough inbreeding vs genetic drift

Answer 20

with inbreeding the probability of homozygosity is the same for each allele, in drift alleles with high frequencies have higher probability of homozygosity

Question 21

Linkage equilibrium vs disequilibrium

Answer 21

L.E. is when the genotype of a chromossome at one locus is independent from the the other locus on the same chromossome, while in L.D. there’s non-random association of alleles at different loci

Question 22

Conditions to have Linkage equilibrium

Answer 22

• Frequency of B on chromossomes that also have A is the same of B in chromossomes also having a
• Frequency of a chromossomal haplotype can be calculated by multiplying the frequencies of constituent alleles( f(AB)= f(A) x f(B)
• LD coeficient = 0
• D = f(AB)f(ab)-f(Ab)f(aB)

Question 23

Linkage disequilibrium coeficient

Answer 23

D = f(AB)f(ab)-f(Ab)f(aB)
can be between -0.25 / 0.25
D = 0.25 is when AB and ab are the only genotypes and both have f=0.5
D = - 0.25 is when aB and Ab are the only genotypes and both have f=0.5

Question 24

What can introduce Linkage disequilibrium?

Answer 24

• Selection acting on multilocus genotypes (many genes at the same time)
• Genetic Drift (new mutation)
• Mixing of populations

Question 25

How is Linkage disequilibrium eliminated from a population?

Answer 25

It can be eliminated because of genetic recombination - Sexual reproduction due to meioric crossing over that breakes linkage between alleles

Question 26

How could we use Linkage disequilibrium to detect strong positive selection?

Answer 26

When a new allele appears it’ll be in Linkage disequilibrium, if it’s not lost with drift it can increase frequency. LD is dissipated trough recombination. If an allele has high LD it’s recent and will stop being rare if favoured by selection

Question 27

When will dissipation of likage disequilibrium be arrested?

Answer 27

In the presence of heterozygosis for a chromosomal inversion - Paracentric (in the arm) and pericentric inversions (in the centromer). There’s splitting of the arm, occurs because the homologous chromossomes that are normally paired come appart - there’s a inversion on one of the arms so they don’t pair properly. These lead to defective recombination products.

Question 28

Forces that influence allele frequency

Answer 28

Mutation
Migration
Selection
Genetic Drift

Question 29

Types of Selection

Answer 29

Directional: for one extreme trait, against the other extreme
Stabilizing: for moderate traits, against both extremes (could lead to loss of genetic variability)
Disruptive: for both extreme traits, against moderate traits
Frequency Dependent: for one phenotype only when it’s rare or common
Heterozygote advantage: have a better fitness

Question 30

Effects of positive selection in Additive, Dominant and Recessive alleles

Answer 30

Positive selection leads to fixation in both recessive and additive (homozigous are subject to the stronggest selection) alleles, in Dominant alleles the frequency increases but never reaches fixation because selection is also operating in heterozygous

Question 31

Differences between a stable, semistable and unstable equilibrium

Answer 31

A stable equilibrium - selection in the presence of overdominance / heterozygous advantage, is always the same regardless of initial allele frequency.
When it’s unstable - underdominance / heterozygous disadvantage, the sistem will only remain in equilibrium if it starts exactly at that point.
Semistable if the allele shows no tendency to change regardless of initial frequency (HWE)

Question 32

How does genetic hitchhiking lead to slective sweep?

Answer 32

Genetic hitchhiking - when trough linkage the positive selection of an allele afects the neutral ones, leads to slective sweep because the near by genes will show lower polymorphisms than expected even when neutral. This resoults in reduced varability in the region surrounding the mutation site. The same happens with deleterious mutations - purifying selection.
In selective sweep, positive selection causes the new mutation to reach fixation so quickly that linked alleles can “hitchhike” and also become fixed.

Question 33

Why does average fitness always increases under selection?

Answer 33

In overdominance / heterozygote advantage it can only increase to reach the equilibrium
In underdominance / heterozygote disadvantage in both frequencies lower than equilibrium and higher fitness evolves - becomes higher, against the eq. value.

Question 34

Examples of neutral mutations

Answer 34

• Synonymous base / nucleotyde changes - the a.a. is still codded
• Base changes in non- coding and non-regulatory regions lik pseudogenes and introns (appart from the splycing regions)
• non-synonymous can be neutral if they don’t influence protein function

Question 35

Neutral theory vs Selectionist theory

Answer 35

Neutral: most mutations are neutral, some are deleterious (tend to be eliminated) and only a few have a positive selection effect - genetic drift dominates molecular evolution
Selectionist: advantageous mutations are more common than expected - high selection in molecular evolution

Question 36

Support and problems with the Neutral theory

Answer 36

Support:

• DNA substitutions occur constantly and are mostly synonymous
• pseudogenens should evolve more rapidly - true: divergence is one of the highest observed, the accumulate more mutations than the copies
• synonymous substitutions accumulate more rapidly - evolve faster
• non-degenerate sites (all changes are non-synonymous) have the lowest substitution rates, pseudogenes have the highest with fourfold degenerate (all synonymous)
• Vital genes show low substitution rate

Problem:
Mutation rate between species due to generation time can be the same in some lineages (mice vs men)

Question 37

Nearly Neutral theory

Answer 37

There’s a equilibrium with the chance of fixation between selection and drift, this means that some mutations that should have been deleterious are acting as neutral and are subject to drift rather than selection. Slightly deleterious mutations are eliminated only when (fixation for a new mutation under selection) s>1/Ne (fixation for a new neutral mutation). In larger populations genetic drift canno overpower selection so there’s fewer fixation events and slower mulecular evolution.
Favorable mutations are more likelly to fix in a growing population - more offspring means that a rare allele is less likelly to get lost
Deleterious alleles are more likelly to fix in a declining population - higher effects of genetic drift

Question 38

Efective population size vs selection/drift

Answer 38

Species with shorter generation time will have a larger Efective population size (Ne) and selection is more effective in large populations with shorter generation time. In small populations drift is more effective thus small Ne can lead to fixation of slightly deletorious mutations rather than being removed trough selection, and more slightly advantageous mutations are likelly to be lost.

Question 39

Genetic schools of tought - hypothesis

Answer 39

Mutationist = evolution due to mutation
Neutralist = mutation + genetic drift + purifying selection
Selectionist = mutation + positive selection + balancing selection

Question 40

How can we tell if a region was subject to selection?

Answer 40

Compare the non-synonimous/synonimous rate in polymorphic sites (within species) with fixed differences (between species), under HWE it would be = 0
If fixed substitutions are neutral the rate is comparable to synonymous substitution.
There’s a fixed difference if there’s no intraspecific differences between species.If fixed&raquo_space;> polymorphic there was positive selection

Question 41

What is Codon Bias?

Answer 41

Different organisms have differences in the frequency of occurrence of synonymous codons (encode a.a.) in their coding DNA, meaning that some codons are rarely used while other codons are frequently used in a particular organism. So it’s stronger in highly expressed genes

The genetic codes of different organisms are often biased towards using one of the several codons that encode the same amino acid over the others—that is, a greater frequency of one will be found than expected by chance.