w3 L1 positive selection and gene duplication: dN/dS

Question 1

What is dN and dS

Answer 1

dN is changes in non-synonymous site
dS is changes per synonymous site (silent mutation)
The number non-synonymous sites does not equal # synonymous Due to different in fold mutation

Question 2

Why is dN/dS interspersed (spread out )

Answer 2

-control for lineage (taxa) effects
-control for regional mutation biases

Question 3

Why is there more dS than dN

Answer 3

Synonymous sites are evolving faster
Synonymous sites rates show less variance because less heterogeneity in selective constraint

Question 4

dN<dS purifying selection

Answer 4

-changes that affect the amino acid sequences

Question 5

When does dN=dS

Answer 5

In pseudogene

Question 6

Circumstances which dN>dS

Answer 6

Complex in our immune system that is infamously variable. Arm race against pathogen

Question 7

dN/dS calculation

Answer 7

Question 8

Paralogs and Orthologs

Answer 8

Paralogs-genes whose lineages diverged at a gene duplication event
Orthologs-genes whose lineages diverged at a speciation event

Question 9

Gene Duplication by Retrotransposition

Answer 9

A mRNA can be reverse transcripted and inserted back to the genome
-the reinserted gene in know as retrocopy, usually considered a processed pseudogene. Contain a poly a tail, does not have intron and it’s found in an odd location

Question 10

Ohno’s Model of Gene Duplication

Answer 10

-when we have 2 copy of a gene, the second gene is free to accumulate mutation
-these mutation can be inactivation mutation, turning it into a pseudo-gene
-they can also be beneficial mutation which lead to new fuction

Question 11

How do you tell whether the extra copy is a pseudogene?

Answer 11

-After a certain level of divergence we expect inactivating mutations to arise as Frameshifts or nonsense mutations
- the expected dN=dS, exon=intron

Question 12

jingwei example

Answer 12

-working on Adh-like gene in D.teissieri and D.yakuba not interrupted by introns
* Polymorphic and divergent sites are mainly at “synonymous sites”
-found 3 extra exon upstream
-this gene seams to be a chimeric gene arose 2mya

Question 13

example of gene getting new function : neofunctionalization: RNA1B

Answer 13

-in Douc langur (monkey) have 2 copy of the gene RNASE1
- one gene gain a new fuction for digestion, having a pH optima of 6.3, from 7.4. DS RNA digestion->RNA digest. Move from the pancreas to small intestine

Question 14

Fate of duplicated gene: specialisation

Answer 14

-both gene have degenerative mutation which are complementary to each other
-both gene needed to fuction
Degenerate mutations increase the maintenance of duplicates

Question 15

engrailed gene of zebra fish

Answer 15

-eng1 code for pectoral fin bud
-eng1b code for hindbrain
But ancestral strain En1 code for both

Question 16

Gene duplication and dN/dS value

Answer 16

Pseudo gene:1
Sub fuctional action: <1
New fuction: random >