Experimental Evolution Flashcards
what are the three methods of studying evolution?
- fossil data
- genome sequencing
- experimental evolution
how can we study evolution through fossil data?
- traditionally at macroevolution level use fossil records
- if evolution is slow and steady we’d expect to see the entire transition from ancestor to descendent in the fossil record
- can see the evolution of organisms
what are the limitations of fossil data?
- fossil records are often incomplete and not all organisms form fossils
- they only form in specific conditions
- eg if they dont have a skeleton wont get a fossil
how can we study evolution through genome sequence data?
- genomics is a rapidly expanding field
- good at showing genetic relatedness between organisms
- can build phylogenetic trees to show relatedness
what are the limitations of genome sequence data?
- cant be used to establish causality
how can we study evolution through experimental evolution?
- replaying tape of life real-time
- use of labatory or controlled field manipulations to investigate evolutionary processes
- usually makes use of an organims with rapid generation times and small physical size (eg microbes)
what are the limitations of experimental evolution?
it would take to long to observe evolution in large multicellular organisms - occurs too slowly
what are the stages of phase 1 of experimental evolution: selection experiment?
- start with a single bacterial clone and replicate to get a genetically uniform base
- expose to certain selection pressures
- need a control population
- grow in a test tube and every 24hrs transfer a small subset of the population to a new medium
- new mutations will be introduce
- could be fitter than the ancestral bacteria
- selection acts on mutations
- can store some bacteria from each stage -80degrees
what are the stages of experimental evolution phase 2: compare changes in fitness?
- measure adpatation, done first at phenotypic level
- compare the evolved population to the ancestral or controlled population
- use direct competition to assess fitness
- 1:1 mix and compare
- see which increases in frequncy
- can then sequence genes and find mutations underlying the changes
what does experimental evolution combine?
the fossil record and sequence genomes together in a controlled lab experiment
what is the LTEE?
- long term evolution experiment
- 12 replicate populations adapting to glucose
- 1% transferred to fresh media every day and samples stored at around -80 degrees
- experiment has lasted around 30 years
- fitness measured bin direct competition against ancestral bacterial strain
- followed by genome sequencing
what are some key factors affect the rate and trajectory of evolution?
- genetic variation
- mutations
what does genetic variation provide?
raw material for selection
what are the key factors in generating mutations in bacteria?
- de novo mutations (new mutations)
- recombination (eg HGT)
how is antibiotic resistance an example of genetic variation?
- initial population, only a couple are resistant
- initiate selection process (most are killed but the resistant survive)
- resistance increase in frequency
what are the sources of mutations?
- HGT, resistant plasmids can move between bacteria
- mutations as bacterial replication can have a lot of errors
what are the 3 key factors in the emergence of potentially benefecial de novo mutations?
- mutation rate
- mutation supply rate
- generation time
what is mutation rate?
the frequency of new mutations in a single gene or organism over time
why do viruses have higher mutation rates than eukaryotes?
RNA is less stable than DNA
what is mutation supply rate?
rate of adaptation as a function of the relative mutation supply rate (ie population size * mutation rate)
what is the mutation supply rate in larger populations?
- larger population has more mutations appearing as there is more cell division which means there is more chances for error
what does an increase in mutation rate speed up?
evolution
what does the increase in the mutation rate for a small population do?
increases evolution
what effect does mutation rate have on large populations?
none
why does mutation rate not have an effecto on large populations?
- in large populations all mutants experience lots of competition between each other
- takes a long time to reach fixation
what is the impact of clonal interference on mutation supply rate?
- no way of incorporating some of the mutations in as theres no recombination, so can get competition and a combination of alleles could become extinct
what is the impact of sexual reproduction on mutation supply rate?
recombination can combine mutants between different genotypes
what is generation time?
mutation rates differ between species are measured in substitutions per base pair per generation
- faster adapting organisms are likely to evolve faster
how does bacteria evolve in response to increased concentrations of antibiotics?
- the bacteria will spread and then get killed off leaving the mutants to spread
- they accumulate successive mutations
- can evolve resistance to high concentrations of antibiotics in a short space of time
what is meant by lethal concentrations ?
- strong selection pressure, 100% reduction in growth rate
- will leave one single genotype that has a much higher relative fitness
what is meant by sub-lethal concentrations?
-weak selection pressure, 3% reduction in growth rate
what happened to the bacteria as a result of lethal concentrations?
- strong antibiotic selection
- leads to evolution of one highly resistant genotype consistently across replicates
- strong parallel evolution
where was the mutation for strong antibiotic selection in bacteria?
changed the structure of rpsL which was the target of streptomycin
what happened to the bacteria as a result of sub-lethal concentrations?
- weak antibiotic resistance leads to evolution of multiple genotypes that vary in their level of resistance
- highly resistant ones carry multiple mecahnisms linked with different resistant mechanisms
- weak parallel evolution
what were the mutations as a result of weak antibiotic selection in bacteria?
- alteration of the ribosomal RNA target of streptomycin
- reduction in streptomycin uptake
- induction of the streptomycin modifying enzyme AadA
what experiments did they carry out following the sub-lethal concentrations?
- addition experiments - introduced the different mutations individually or in different combinations
- 1 mutant a small change
- 2 mutants a bigger `change etc
why is the discovery of small resistance mutations leading to high-level antibiotic resistance worrying?
antibiotic resistance could be selected under low antibiotic exposure in natural environments
how were mice used to study evolution?
- mouse with 2 phenotypes, light and dark to match their environment
- mice that dont match the environment though to be more vulnerable
- starting pop: 75-100 mice half dark and half light in different envirnoments
- capture and measured
- surviving phenotypes genotyped to identify underlying mutations
what were the results of the mice evolution experiment?
- non-local mice had higher mortality compared to camouflaged
- camouflage increased the chance of survival
- found the mutation by sequencing the ‘camouflage’ gene
- found a single amino acid deletion at position 48 in exon 2
what are the key differences between experimental evolution using mice v bacteria?
- source of genetic variation
- naturality
- evolution time scale
- strength of selection
how does the source of genetic variation differ between mice v bacteria evolutionary experiments?
- de nove mutations
- standing genetic variation (mix the genotypes and let selection act on the standard variation)
how does the naturality differ between mice v bacteria evolutionary experiments?
- bacterial experiments in labs
- mice experiment in semi-natural experiments
how does the evolutionary time scale differ between mice v bacteria evolutionary experiments?
- bacterial experiments are multi-generational
- mouse experiments within one generation
how does the strength of selection differ between mice v bacteria evolutionary experiments?
- bacterial experiments harsher
- predation pressure not quantified in mice experiments
