Introduction

Question 1

Histone proteins nucleotide substitution rates

Answer 1

• most changes have lethal consequences

- strong functional constraints again changing

Question 2

Immunoglobins substitution rates

Answer 2

high

- selection favors mutations in these regions

Question 3

Compare Different types of DNA evolution rates

Answer 3

non-synonymous
- lowest
- mutations change amino acid sequences
synonymous/silent
- codon usage bias
- doesn't change amino acid sequence but not high due to codon bias
Introns
- some splice sites can me mutated or selected against
Pseudogenes
- evolve neutrally

Question 4

molecular clocks

Answer 4

synonymous substitutions can be looked at over time to find when sequences diverged

• but not fool proof
• silent site but be neutral and silent substitution rate is not consistent

Question 5

codon usage bias

Answer 5

certain codon preferentially used to code for aa

• varies by organism
• can select against nucleotide changes at silent sites
• not all silent sites are neutral evolving

Question 6

origins of new genes

Answer 6

• gene duplication
• retro-position
• exon shuffling
• integration of transposable elements
• gene fusion
• gene fission
• de novo
• horizontal or lateral gene transfer
• change in subcellular localizations

Question 7

Human TPA gene

Answer 7

evolved from ancestral exon shuffling

Question 8

Mitochondrial ribosomal protein s8

Answer 8

gene duplication, divergence, and change of subcellular localization
- move cytosolic homolog to mito

Question 9

Mitochondrial ribosomal Protein s13

Answer 9

Chloroplast nuclear gene is duplicated and acquires mitochondrial signaling sequence so change in subcellular localization to mitochondria

Question 10

internal duplication

Answer 10

ex. AFGP protein (antifreeze) part of gene is duplicated many times

Question 11

Jingwei gene

Answer 11

gene duplication
duplicate copy 2 changes to yande gene
- retro position of another gene into yande
— know is retroposed due to no introns and it has a poly a signal

Question 12

selsctive sweep

Answer 12

one allele rises to fixation within a population due to positive selection

Question 13

how to tell if selective sweep occured

Answer 13

reduced nucleotide diversity in surrounding regions of gene of interest

Question 14

how to study function of gene

Answer 14

knockout in gene region

transcriptome comparisons

Question 15

Why to tell if something functions as a non-coding RNA

Answer 15

• dn/ds ratios between groups close to 1 so neutrally evolving
• antibody again ORF’s did not yield signal
• evaluate if feasible for translation initiation in possible start codons