L7 Human vs Chimps, McDonald Kreitman Test

Question 1

dN/dS > 1

Answer 1

adaptive evolution

Question 2

dN/dS comparisons between humans and chimps

Answer 2

Individual genes may not have that much divergence between them, dN/dS may not have much power individually, hence, genes were grouped according to their biological process or their tissue abundance

Question 3

Organise genes by tissue they are most abundantly expressed in

Answer 3

• genes with maximal expression in the testis are enriched for genes with dN/dS > 1
• genes with maximal expression in the brain are depauperate for genes with dN/dS > 1

Question 4

As more genomes get sequence the more power there is to detect positive selection

Answer 4

see OneNote

Question 5

Red Queen Hypothesis

Answer 5

• dN/dS > 1
• co-evolutionary arms race e.g. pathogen evolves to avoid the immune system of the host and host immunes system evolves to identify the pathogen

Question 6

Do any of the CNS show human specific divergence?

Answer 6

Ultra conserved in other animals but have changed in humans

Human specific gain of function in HACNS1

Enhancer
Opposable Thumb

Question 7

McDonald Kreitman Test

Answer 7

See OneNote for calculations

Under the neutral model the patterns of nucleotide variation within species should match the patterns of nucleotide variation between species

dN/dS = pN/pS