Genomes-L15-Evolutionary Genomics

what are the 4 evolutionary forces that change allele frequencies over time?

1. mutation- source of all variation

2. NS- survival of the fittest- organisms with the most offspring

3. gene flow/migration- one population has the opportunity to introduce new alleles into another population

4. genetic drift- change of relative frequency of different genotypes in a population due to chance

how does sequencing help detect mutations?

• by sequencing different individuals and comparing their sequences

• you can see deletions, and single base pair variants and polymorphims

issues with sequencing mutations

• errors can happen when reading DNA

• you can sequence the same DNA region multiple times to increase confidence that a mutation is REAL

explain coverage in terms of sequencing

• coverage: the amount of times a specific DNA spot is read

• low coverage means- DNA spot is read a few times- less confidence

• high coverage- DNA spot read many times- more confidence mutations are reliable

detecting mutations with sequencing- what are the issues when it comes it?

• need to know what the mutations do?

• how do we distinguish beneficial from neutral?

• how do we distinguish frequency

how does sequencing tell us NS has occurred?

• comparing genome of individuals species and use maths aphorisms to find areas of the genome where we can see less diversity as expected

• mutations here- beneficial mutation- NS happened

how would we detect selection using synonyms vs non synonymous mutations?

• mutations in the 1st or 2nd position usually changes the protein itself- mutations under selection

• 3rd position is usually a silent mutation- neutral mutation

if we see changes in the 1st and 2nd place more than the 3rd- the suggests selection

how do we detect selection by phylogenetic trees

• balances tree suggested no selection

• unbalanced tree- things go extinct and 1 survive suggests it is evolving

why is using sequencing to detect mutation biased?

1. there is only one copy of a new mutatiion- only can detect this by sequencing a population

2. if a mutation is deleterious- it will be selected against

how do we prevent selection removing deleterious mutations? what is it used for?

using mutation accumulation- isolate mutations by minimising natural selection in the lab

• chasing organisms randomly regardless of fitness- chosen by humans

• water fleas- after 40 generations- sequence the genomes- identify what mutations accumulated

• looking at mutations- look at fitness and correlate to the mutations

• increased fitness- good mutation etc

how do you detect and indeitfy genes and their effects?

1. quantitative trait loci- crosses individuals- Mendel studies basically

   • lose variation though

2. genome wide association study- GWAS- phenotyping and genotyping entire population- correlate genotype to phenotype

   • sensitive to pop structure BUT get all population variation!

what is the evolution experiment? what was it done for?

• 40k generations of e.coli grown

• the medium it grew in had citrate- which isn’t available to e.coli

• after 31k generations- e.coli grew on the citrate- sequences found to show this

how did e.coli learn to grow on citrate? what experiment is this? 3 steps

evolution experiement

1. potentiation- before it could grow on citrate- it needed to have accumulated the right mutations

2. the actual mutation that allowed it to grow on citrate- in e.coli it was a duplication and fusion citrate transporter and kinase- expressed in aerobic now

3. further mutations refined this- more mutations increase the benefit

when do evolution experiments determine if the right gene was detected? what methods are used to do this? 4 ways

by knocking out the gene and checking the effect

• in e.coli- disrupt the presumed citrate gene

• using Zinc fingers, TALE nucleases

• homing endonucleases

• CRISPR

• RNAi

how do we use RNAi

• using small interfering RNA to silence the geneby degrading mRNA and preventing translation.

how do we use zinc fingers and tale nucleases

• they recognise specific DNA strands

• they and go cleave the DNA- to insert new genes or delete it

what are homing nucleases?

• selfish genetic elements- insert themselves at specific location in the genome

• have a selective advantage- leave more copies of themselves

• they can also cut specific DNA at specific sites

what is CRISPR used for?

• originally a way bacteria protect themselves from viruses

• cas-9 cuts the target DNA and disable the virus

• using CRISPR to cut DNA- if there’s a match of DNA

• used to edit target genes

if evolution were to start from square 1- would we see the same plants and animals?

• it can- if evolutionary pressure are the same- sugar glider and flying squirrel

examples of repeated experimental evolution

• done in dolphins and bats as they use Prestin protein for echolocation

• they have similar mutations in the hearing gene Preston

• lenski e.coli experiement- did it again

  • 8 duplications that were similar to the one foumd

  • one large deletion

  • but allowed the same phenotype- but not same outcome

can evolution be predictable?

Yes, under certain conditions, it can be predictable if the same environmental pressures lead to similar adaptations in species.

• such as influenza phylogenetic tree- shows selection

• influenza strains with hemagglutin mutations- usually are dominant strain- aid vaccine development

how do we detect gene flow?

1. using mitochondrial markers- looking at jay species as they’re seperated by mountain ranges

   • sequencing 20 individuals showed there’s still gene exchange