GENE30001 Lecture Notes - Lecture 5: Gene Duplication, Concerted Evolution, Sister Chromatids
14 Jun 2018
School
Department
Course
Professor
dN = changes per non-synonymous sites
dS= changes per synonymous site
THESE DON'T EQUAL EACH OTHER.
MET E N G W G V I I V L G
MET E V G E V G E
000 002 002 004 000 002 004 003 003 004 204 002
Q1
Synonymous sites = 2
Non-synonymous sites =5
[0] = 25
[1] = 0
[2]= 5
[3] = 2
[4]= 4
# S = [4]+2/3*[3]+ 1/3*[2]
= 4+((1/3)*5)+((2/3)*2)=7.0
# N = [0]+2/3[2]+1/3*[3]
= 25+(2/3)*5+(1/3)*2 = 29
dN = 5/29
dS= 2/7
dN/dS = (5/29)/(2/7) = 0.6034
Roughly 0.6
B) Jukes and Cantor Method
Total sites - 36
# of sites that changed = 7
D = 7/36=0.1944
-3/4* ln(1-0.1944*4/3) = 0.225018446737626
What if dN>dS?
Then it is the result of adapative evolution/positive election
Scenario: The MHC complex, viral coat proteins
Paralogs: genes whose lineages diverged at a gene duplication
event (para - duplication
Orthologs: genes who lineages diverged at a gene speciation
event (ortho -speciation)
Unequal Cross Over (exchange of genetic material b/w non-
sister chromatids during prophase 1 of meiosis ->
homogenisation of genes -> concerted evolution)
1.
Reverse transcription (where it is integrated into genome,
usually a processed pseudogene)
2.
Genome duplication
3.
Gene duplication:
When dN = dS
= inactivating mutation
When dN >>dS
= beneficial mutation = new function
Neofunctionalisation = when a new gene from
Lecture 5: dN/dS Positive Selection and Gene Duplication
Wednesday, 22 June 2016
1:50 PM
Lecture Notes 1- 12 Molecular Evolution and Population Genetics Page 1
Document Summary
Lecture 5: dn/ds positive selection and gene duplication. Met e n g w g v i i v l g. Met e v g e v g e. Then it is the result of adapative evolution/positive election. Scenario: the mhc complex, viral coat proteins dn = changes per non-synonymous sites ds= changes per synonymous site. = 25+(2/3)*5+(1/3)*2 = 29 dn = 5/29 ds= 2/7 dn/ds = (5/29)/(2/7) = 0. 6034. Paralogs: genes whose lineages diverged at a gene duplication event (para - duplication. Orthologs: genes who lineages diverged at a gene speciation event (ortho -speciation) Unequal cross over (exchange of genetic material b/w non- sister chromatids during prophase 1 of meiosis -> homogenisation of genes -> concerted evolution) Reverse transcription (where it is integrated into genome, usually a processed pseudogene) Lecture notes 1- 12 molecular evolution and population genetics page 1. Neofunctionalisation = when a new gene from a duplication is formed.
