W4L2, continuation of molecular population genetic

Question 1

What is background selection

Answer 1

deleterious mutation removed. they are also linked to neutral variation which also lead to deletion
-it can also affect a neutral site, leading to high purifying selection of gene dense region

Question 2

Selective sweeps and tajimaD

Answer 2

• As a positive mutation occur, there will be a fixation of the variation
  -but the rare alleles can still remain on the shoulder of the adaptive variation. Leading to many rare mutation (negative tajimaD)

Question 3

Soft and hard selective sweep

Answer 3

-in hard sweep, advantageous only occur in one variant
-in soft sweep, advantageous occur in more than one variant, less rare allele
-it is believe that soft sweeps are the dominant mode of adaptation in human genome

Question 4

Vought et al.

Answer 4

• Determine if a gene is adaptive (unbiased): Create map of recent positive selection in human genome.
• Example: 800,000 SNPs, 209 unrelated individuals, 3 populations. Partial sweeps.
• Indicate focal SNP & classified state of variant between ancestral & derived allele by identifying an out group
• Consider haplotypes diff states, map length relative to each other: derived allele have longer haplotype
• Compares haplotype length of derived allele to ancestral allele (accounts for their freq.).
• Do the same for every single variant to observe parts of genome with the longest haplotypes with derived variants.

Question 5

A case study: CCR5D32

Answer 5

-expressed on the cell surface of immune cell
-HIV uses it as a receptor
* An allele with a 32 base pair deletion provides some protection against AIDS
-used hapotype to determine the gene of origin
- the gene in question have a higher frequency in Caucasian pop (possible adaptive selection) possible due to haemorrhagic fever

Question 6

Testing theory on CCR5D32 adaptation

Answer 6

• old human also have a high frequency of the variant
• data from analysis of old human indicate 13% present of the alleles

Question 7

Commonly agreed idea on neutral theory in modern day

Answer 7

-large fraction of the genome of organism are effectively neutral and is likely to evolve via drif
-many mutation that affect fitness are deleterious and is removed by purifying selection
-natural population are rarely in demographic equilibrium , shaping within species variation
-a combination of genetic drift with purifying selection shape the genome
-beneficial mutation can arise and reach fixation or high frequency