Lecture 23

Question 1

Comparative genomics

Answer 1

• Purpose is to discover what is in common and what is different
• Things in common are called ‘conserved’ and may encode biology in common between species
• things that are different may encode organism specific biology
• so by comparing genomes you learn a little about which bits of genome do what

Question 2

How do you compare sequences

Answer 2

By lining them up next to each other and marking each point where sequences are the same

• aligning

Question 3

We can compare genomes within species

Answer 3

• by comparing genomes between individuals we can find out where differences occur
• differences might be associated with:
  
  • disease
  • characteristics of an individual
  • evolutionary history

Question 4

We can compare genomes between species

Answer 4

Can learn about an organism if we compare its genomes with others:
- what sort of genes they have
- how differences between species arise
- relationships between species

Question 5

DNA?

Answer 5

• DNA from dead things can remain in the environment
• DNA degrades and is masked by more modern DNA
• DNA bases are also modified as they degrade, sometimes changing the sequence
• Ancient DNA can be extracted and identified in very special circumstances
• it has been used to determine the relationships of extent animals

Question 6

What was discovered from sequencing Neanderthal genomes

Answer 6

• 4 billion Neanderthal nucleotides
• identify and discount modern contamination
• gathered sequence from 3 individuals
• enough sequence to compare with modern human genome sequences from around the world
• identified bits of dna that differ between Neanderthals and us

Question 7

Most amazing find

Answer 7

• some of us carry Neanderthal DNA
• modern humans from Europe and Asia carry Neanderthal alleles
• most parasimonious explanation for this is that where modern humans met Neanderthals, they interbred

Question 8

Diagram

Answer 8

Question 9

Some of us carry Neanderthal DNA

Answer 9

• this doesn’t mean that those of us with Neanderthal DNA have a different set of genes
  -it just means that our DNA holds variants that arose in Neanderthals
• 2- 4% of the genome of non-Africans is made up of variety’s that arose in neanderthals
• so Neanderthal DNA adds to the variation in our gene that might be related to our phenotype
• found in Denisovans was a finger bone, whose mitochondrial DNA doesn’t match Neanderthal or modern human DNA
• the genome from this species of archaic human was sequence from a teeth found in the same cave in 2010
• Denisovans variation is also found in human genome, where it makes up 4-6% of the genomes of present day melanesians

Question 10

Summary part 1

Answer 10

• the sequencing of genomes has helped us better understand who we are and where we came from
• the key technology here is being able to compare genomes
• by comparing whole genomes from multiple species we can start to understand where out charactersics come form
• this is the same approach used in modern disease genetics - data Rich and statistically intense analysis
• our extinct relatives are not just fossils in out museums, but live on as variants in our genomes which effect our biology

Question 11

Main summary

Answer 11

• having sequenced genomes we can compare them
• comparing genomes within a species can help us identify variants that might be related to phenotype
• comparing genomes with other species can help us identify variants related to the biology of an organism
• we are now able to compare the genomes of out closest living and extinct relatives
• our recent evolutionary history is complex
• we are still trying to discover the genes that make our species different