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genes and genomes ii > Experimental Evolution > Flashcards

Experimental Evolution Flashcards

1
Q

what are the three methods of studying evolution?

A
  1. fossil data
  2. genome sequencing
  3. experimental evolution
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2
Q

how can we study evolution through fossil data?

A
  • 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
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3
Q

what are the limitations of fossil data?

A
  • 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
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4
Q

how can we study evolution through genome sequence data?

A
  • genomics is a rapidly expanding field
  • good at showing genetic relatedness between organisms
  • can build phylogenetic trees to show relatedness
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5
Q

what are the limitations of genome sequence data?

A
  • cant be used to establish causality
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6
Q

how can we study evolution through experimental evolution?

A
  • 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)
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7
Q

what are the limitations of experimental evolution?

A

it would take to long to observe evolution in large multicellular organisms - occurs too slowly

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8
Q

what are the stages of phase 1 of experimental evolution: selection experiment?

A
  • 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
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9
Q

what are the stages of experimental evolution phase 2: compare changes in fitness?

A
  • 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
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10
Q

what does experimental evolution combine?

A

the fossil record and sequence genomes together in a controlled lab experiment

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11
Q

what is the LTEE?

A
  • 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
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12
Q

what are some key factors affect the rate and trajectory of evolution?

A
  • genetic variation

- mutations

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13
Q

what does genetic variation provide?

A

raw material for selection

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14
Q

what are the key factors in generating mutations in bacteria?

A
  • de novo mutations (new mutations)

- recombination (eg HGT)

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15
Q

how is antibiotic resistance an example of genetic variation?

A
  • initial population, only a couple are resistant
  • initiate selection process (most are killed but the resistant survive)
  • resistance increase in frequency
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16
Q

what are the sources of mutations?

A
  • HGT, resistant plasmids can move between bacteria

- mutations as bacterial replication can have a lot of errors

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17
Q

what are the 3 key factors in the emergence of potentially benefecial de novo mutations?

A
  1. mutation rate
  2. mutation supply rate
  3. generation time
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18
Q

what is mutation rate?

A

the frequency of new mutations in a single gene or organism over time

19
Q

why do viruses have higher mutation rates than eukaryotes?

A

RNA is less stable than DNA

20
Q

what is mutation supply rate?

A

rate of adaptation as a function of the relative mutation supply rate (ie population size * mutation rate)

21
Q

what is the mutation supply rate in larger populations?

A
  • larger population has more mutations appearing as there is more cell division which means there is more chances for error
22
Q

what does an increase in mutation rate speed up?

A

evolution

23
Q

what does the increase in the mutation rate for a small population do?

A

increases evolution

24
Q

what effect does mutation rate have on large populations?

A

none

25
Q

why does mutation rate not have an effecto on large populations?

A
  • in large populations all mutants experience lots of competition between each other
  • takes a long time to reach fixation
26
Q

what is the impact of clonal interference on mutation supply rate?

A
  • 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
27
Q

what is the impact of sexual reproduction on mutation supply rate?

A

recombination can combine mutants between different genotypes

28
Q

what is generation time?

A

mutation rates differ between species are measured in substitutions per base pair per generation
- faster adapting organisms are likely to evolve faster

29
Q

how does bacteria evolve in response to increased concentrations of antibiotics?

A
  • 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
30
Q

what is meant by lethal concentrations ?

A
  • strong selection pressure, 100% reduction in growth rate

- will leave one single genotype that has a much higher relative fitness

31
Q

what is meant by sub-lethal concentrations?

A

-weak selection pressure, 3% reduction in growth rate

32
Q

what happened to the bacteria as a result of lethal concentrations?

A
  • strong antibiotic selection
  • leads to evolution of one highly resistant genotype consistently across replicates
  • strong parallel evolution
33
Q

where was the mutation for strong antibiotic selection in bacteria?

A

changed the structure of rpsL which was the target of streptomycin

34
Q

what happened to the bacteria as a result of sub-lethal concentrations?

A
  • 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
35
Q

what were the mutations as a result of weak antibiotic selection in bacteria?

A
  1. alteration of the ribosomal RNA target of streptomycin
  2. reduction in streptomycin uptake
  3. induction of the streptomycin modifying enzyme AadA
36
Q

what experiments did they carry out following the sub-lethal concentrations?

A
  • addition experiments - introduced the different mutations individually or in different combinations
  • 1 mutant a small change
  • 2 mutants a bigger `change etc
37
Q

why is the discovery of small resistance mutations leading to high-level antibiotic resistance worrying?

A

antibiotic resistance could be selected under low antibiotic exposure in natural environments

38
Q

how were mice used to study evolution?

A
  • 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
39
Q

what were the results of the mice evolution experiment?

A
  • 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
40
Q

what are the key differences between experimental evolution using mice v bacteria?

A
  • source of genetic variation
  • naturality
  • evolution time scale
  • strength of selection
41
Q

how does the source of genetic variation differ between mice v bacteria evolutionary experiments?

A
  • de nove mutations

- standing genetic variation (mix the genotypes and let selection act on the standard variation)

42
Q

how does the naturality differ between mice v bacteria evolutionary experiments?

A
  • bacterial experiments in labs

- mice experiment in semi-natural experiments

43
Q

how does the evolutionary time scale differ between mice v bacteria evolutionary experiments?

A
  • bacterial experiments are multi-generational

- mouse experiments within one generation

44
Q

how does the strength of selection differ between mice v bacteria evolutionary experiments?

A
  • bacterial experiments harsher

- predation pressure not quantified in mice experiments

genes and genomes ii (8 decks)

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