Please enable JavaScript.

Coggle requires JavaScript to display documents.

topic 5: experimental evolution - Coggle Diagram

- - - - MA experiments can be used to estimate the distribution of fitness effects (DFE)
        
        eg. adaptive evolution has a low relative frequency of mutations with extreme fitness effects, but a higher relative rate of beneficial compared to deleterious that remain substituted
        
        neutral mutations remain unchanged
        
        lethal mutations are never substituted
  - - - engineering an e coli strain In which the tufa gene which encodes elongation factor Tu was replaced by a 700 myo inferred ancestor
      - the hybrid had a two fold drop in fitness which was restored after 2000 generations of experimental evolution
      - sequencing revealed that the restoration of fitness was primarily due to mutations in the promoter region that increased gene expression, rather than mutations in the structural proteins
    - - additional stress factors are often applied to gradually improve the response of specie sot these stresses
        
        these include
        
        extreme pH
        
        osmotic pressre
        
        oxygenation
        
        extreme temperature
        
        UV radiation
        
        antibiotics
        
        microgravity
        
        biotic stressors
        
        presence of phage
      - complex in vivo environments
        
        more closely mimic the real world: multiple biotic and/or abiotic stressors
        
        in situ evolution in plant and animal hosts
        
        eg. a lactococcus lactic strain from a plant was adapted to growth in milk
    - - what is the role of standing genetic variaition vs newly arising mutations in contributing to selection response? how reproducible is evolution at the molecular level?
        
        population genetics can be predictive for the early stage of adaptation, provided we know the distribution of fitness effects, the mutation rate and the recombination rate
        
        what is the role of protein coding vs regulatory variation in adaptation?
- - - - 6.6 generations per day
      - cultures frozen every 100 generations
      - 6 populations of ara- (unable to grow on arabinose)
      - 6 populations of Ara+ (isogenic mutant)
      - the marker differences permit strains to be differentiated on tetrazolium arabinose plates, on which Ara- colonies appear red, while Ara+ colonies appear white to pink
      - adaptation to growth medium determined by competing evolved culture with ancestral stock
    - - has now run for >76,000 generations - corresponds with humans to 1.2my+
      - 12 populations vary in whether or not they contain stable co-existing variants (polymorphisms)
        
        one population has two lineages that have coexisted for over 40,000 generations. their coexistence depends on cross feeding, in which one lineage is the superior competitor for the exogenously supplied glucose, and the other is better at using acetate excreted into the medium
        
        diversity might arise even in homogenous environments in time, due to the adaptation for the utilisation of waste metabolites from other members of the populations
        
        hence strictly homogenous envvironemntats are difficult to achieve because the presence of the bacteria provides opportunities for other abctera
        
        this is an example of negative frequency dependent selection (NFDS) which is an important mechanism for maintaining diveristy
        
        other LTEE populations have had transiently stable polymorphisms and still others appear to have remained more homogenous
    - - after 10,000 generations 40% increase in fitness
        
        hypermutators emerged in half of the twelve populations
        
        20,000 generations is sufficient time for essentially all possible mutations to have arisen in at least one cell in one of the 12 lines
        
        only ~100 mutations were fixed after this time: 10-20 of which were beneficial
      - most rapid increase in fitness over the first 2000 generations (rate of adaptation slows down as the population gets fitter, due to negative returns epistasis)
      - cell size almost doubled over 10,000 generations (again with most rapid increase early on)
      - growth rate increased
      - lag times became shorter
      - cell shape became more spherical and less rod like
      - cell volume increased
      - genome size decreased
      - broad adaptive trends are the same in each of the 12 flasks and there are similar changes in gene expression
        
        however subtle differences reveal the role of chance and contingency in evolution
        
        contingency means the consequence of subsequent mutations are contingent on prior mutations (epistasis)
        
        in 2008 around generation 33127, one of the lines evolved the ability to utilise citrate as a carbon source, something which has not been described for wt e coli
        
        the ability to use citrate could spontaneously revolve in populations from earlier time points int eh populations history, but not from clones before generation 20,000
        
        the evolution of citrate utilisation thus dependent on an earlier, perhaps non adaptive potentiating mutation which only arose in one of the 12 lines
        
        altered gene regulation shown to be a crucial component of the ability to utilise citrate
        
        tandem copy amplification and fussion proteins of citrate-succinate anti porter - promoter capture in cit+ strains
  - - - parallels can occur at different scales
        
        parallel changes in phenotype - but these may be brought about by very different types of genetic changes in different populations ('convergence)
        
        115 lines of e coli for 2000 generations - 1331 total mutations affecting 600+ sites
        
        few mutations were shared among replicates but a strong pattern of convergence emerged at the level of genes, operons and functional complexes
        
        adaptation occurred through many different genetic paths, showing parallelism at the level of genes and interacting protein complexes, but only rarely at the nucleotide level
        
        parallel changes may affect the same locus in different populations but the site in the gene may be different
        
        for example in the LTEE over 50% of non synonymous mutations that arose in non-hypermutable lineages concentrated in just 2% of the protein coding genes
        
        parallel changes affecting exactly the same nucleotide independently in different populations ('homoplasy')
      - an interesting observation - among the first large-effect adaptive steps, selection seems to recruit mutations in global regulators
        
        eg. RNA polymerase is a major mutational target in many different adaptations, ranging from high temperature to glycerol minimal media
        
        surprising given that this operon is generally highly conceived among bacterial species
        
        it is unclear why changes in this operon are so often favoured in experimental evolution settings despite the function of these genes being highly conserved in nature
      - the genomic precision of reproducibility depends on the selective regime used, including the media used for selection as well as the mode of culture (chemostats vs batch culture)
        
        eg. antibiotic treatments select almost exclusively for mutations in the active sit of specific target genes, whereas for less specific environmental stressors in highly replicated experiments many genes and alternative mutations among genes are recovered
        
        the particular mutations used depends in part on the mutations that occur early on in the experiment, the genetic backgrounds they occur on and the action of clonal interference
- - - - in a large population mutations with the highest fitness or the combination of mutations with the highest fitness will eventually reach fixation, and other beneficial mutations will be lost
        
        by outcompeting other lineages in the population, the overall diversity is greatly reduced
        
        selective sweep - recurrent selective sweeps referred to as periodic selection
      - however in the presence of high levels of recombination, mutations can switch backgrounds and many mutations can simultaneously increase in frequency in a population
      - intermediate levels of recombination can result in genetic 'hitchhiking'. if neutral (or deleterious) passenger mutations are linked to a beneficial allele then they will also rise in frequency during a selective sweep
  - - - phenotypic evolution ina. population may involve gradual optimisation, discontinuous innovation or perhaps some mixture of the two
      - a discontinuous change such as the ability to survive a previously lethal stress or to grow on a new resource, might be followed by a period of gradual refinement of that new ability
      - the benefit of adaptive mutations are higher in bacteria with low intial fitness
        
        as the fitness of the bacteria increases, the benefit conferred by subsequent beneficial mutations decreases - referred to a s diminishing returns epistasis
  - - - occasionally increasing mutation rates will be advantageoud
      - occurs when the chance of a strongly adaptive mutation arising outweighs the cost of many deleterious mutations (such as in a highly stressful environment)
    - - these may have ~100x increase in mutation rate
      - often arise by disruption of mismatch repair genes eg. mut, rec
      - mutator phenotype is more likely to confer an advantage in small populations than large ones because under normal circumstances adaptive mutations are more likely to arise in large populations even at normal rates of mutation
    - - possibly an example of a trait under second order selection - that is there is selection on modifiers of mutation rate that act indirectly on the consequences of elevated mutation rate
      - hypermutation in a natural population: an outbreak of MRSA
        
        selection for the Lac+ phenotype which is greatly stimulated in mismatch repair-deficient strains, results in an increase in the percentage of mutators in the selected population from less than 1 per 100,000 cells to 1 per 200 cells.
        
        all the mutators detected were deficient in the mismatch repair systme
        
        mutagenesis combined with two or more successive selection can generate a population that is 100% mutator
      - cos and benefits of high mutation rates: adaptive evolution of bacteria in the mouse gut
        
        shown that bacterial mutation rates change during the experimental colonisation of the mouse gut
        
        a high mutation rate was initially beneficial because It allowed faster adaptation, but this benefit disappeared once adaptation was achieved
        
        mutator bacteria accumulated mutations that, although neutral in the mouse gut, are often deleterious in secondary environemnts
        
        consistently, the competitiveness of mutator bacteria is reduced during transmission to and recolonisation of similar hosts
        
        the short term advantages and long term disadvantages of mutator bacteria could account for their frequency in nature
- - - - experimental evolution can also be used to understand the emergence of social behaviour and conditions under which cheating should be adaptive
      - bacteria produce a number of common goods - molecules which are synthesised by the cell but then secreted for use by the whole population
        
        one example is siderophores which are secreted, bind iron and can then be picked ip by other cells
        
        although the production of siderophores is advantageous for the population, it is also costly for the individual cells
        
        any cell which doesnt produce siderophores can still reap the benefit from other cells (ie. cheat)
        
        in the case of diffusible molecules like siderophores, the viscosity of the medium also plays a role (as they are more likely to be used by the same related cluster of cells)
        
        high siderophore production can be maintained only when populations are exposed to strong genetic bottlenecks, ensuring that relatedness is high
      - there is evidence that cheating is less common in populations that are highly related
        
        this is consistent with the operation of kin selection - whereby it pays to be altruistic to close relatives
    - - this soil dwelling predator "swarms" across soft surfaces by a process called s motility - involving type 4 pili encoded by the pilA gene
        
        mechanism of swarming is dependent upon cooperation between cells, and requres cell-cell proximity, pili and an extracellular matrix of cohesive fibril composed of carbs and protiens
        
        mutants with the pilA gene knocked out cannot swarm
      - experimental evolution to regain swarming ability in these mutants
        
        imposed strong selection pressure by picking cells that made it to the edge of a growing colony on a plate
        
        after 32 rounds of selection, motility was restored in 8 independent popualtions
        
        in two strains this motility was evolved through the production of fibril, which increased the motility of other cells also - a cooperative act, but also increased cohesion between producers
        
        results show that fundamental transitions to primitive cooperation can readily occur in bacteria
  - - - this can be studied experimentally using bacteria and phage. the resistance of bacteria, or virulence of the phage, can be measured against contemporary or past populations to understand the dynamics and consequences of these oscillations
      - studies shown theat coevolution can radically alter host genetic diversity and impose selection for evolvability (increased mutation rates)
      - early experimental coevolution studies between bacteria and phage suggested that the potential for long term coevolution is constrained because of mutational asymmetry
        
        this means that it is easier for the bacteria to evolve sesitance than it is for the phage to regain infectivity, hence the bacteria always win
        
        later work on other phage/bacterial combinations demonstrated sustained coevolution up to c. 250 generations
        
        after this point, the associated costs with increased resistance in the bacteria and increased virulence in the phage became too high and the system reverted to oscillating frequencies of variants within the populations (through frequency dependent selection) rather than continued evolution of new variants
    - - bacterial communties can be very diverse, so it should pay for phage to be generalists (ie infect as many different hosts as possible)
      - there exists a trade off between overall fitness and host range - generalist phage ar like the jack of all trades but master of none
        
        can result from two mechanisms
        
        antagonistic pleiotropy: a mutation which leads to increased infectivity on one host but lower infectivity on a different host
        
        selection for a less efficient but more general mechanism of infection
  - - - the environment in which adaptation takes place affects the dynamics and outcomes of evolution
        
        in heterogeneous, structured environments, specialist diversity can emerge and be maintained due to the availability of multiple different niches
      - in static environments like chemostats, specialists evolve, but these tend to be less fit in other environments due to the "cost of adaptation"
        
        eg. a highly specialised mutant emerged in the LTEE which was optimally able to grow on glucose but only in the presence of citrate (as an iron chelator) at a specific temperature. if these conditions were not met, the mutant was poorly competitive
      - in changing environments, the trade-off costs of specialism competes with the cost of generalist leading to a mix of generalists and specialists
        
        trade offs can result from
        
        the accumulation of neutral mutations in the selective environment that become deleterious in newly encountered situations
        
        antagonistic pleiotropy, where adaptive mutations under one condition are maladaptive under another
  - - - pseudomonas aeruginosa also swarms over surfaces in search of food
        
        phenotype requires coordination of several pathways
        
        flagellar motility
        
        cell-cell signaling/quorum sensing
        
        biosurfactant secretion
        
        colonies that each the edge of the plate first were flushed off and added to a new swarming plate
        
        after a few days a hyper swarming phenotype repeatedly evolved (25% faster swarming than the ancestors). this happened 25/25 populations
        
        hyper swarming is caused single point mutations in the flagellar synthesis regulator FleN, which cause the bacteria to assemble multiple polar flagella and gain a strong growth rate-independent advantage in swarming competitions
        
        hyper swarmers become poor biofilm formers and are outcompeted by the ancestral strain in biofilm competitions
        
        experimental evolution in swarming thus provides a unique example of parallel evolution and suggests an evolutionary trade-off between motility and biofilm formation
    - - immotile strains of the bacterium pseudomonas fluorescent lack flagella due to deletion of the regulatory gene fleQ
      - regained flagella within 96hours via a two step evolutionary pathway
        
        step 1 - mutations increase intracellular levels of phosphorylated NtrC, a distant homolog of FleQ, which takes control of the fleQ regulon at the cost of disrupting nitrogen uptake andassimilation
        
        step 2 mutation in NtrC away from nitrogen uptake and towards a flagellar regulator
      - study demonstrates that natural selection can rapidly rewire regulatory networks in a very few repeatable mutational steps
    - - rhizobia induce nodule formation in leguminous plants and are able to enter a mutualistic relationship by fixing nitrogen
        
        represent diverse genera and have originated through independent acquisition of plasmids and gene islands that contain genes encoding key symbiotic functions
      - this study used an experimental evolution approach to examine the changes associated with the evolution of mutualism in rhizobia
        
        evolved a plant pathogen into a nodulating symbiont of mimosa by addition of a symbiosis plasmid followed by a selection in the plant enviornment
        
        in addition to the acquisition of the plasmid, two types of adaptive mutations are required for the transition from pathogenicity to mutualism
        
        inactivation of the hrcV structural gene of the type III secretion allows nodulation to occur
        
        inactivation of the virulence regulator hrpG allowed intracellular infection of nodule cells
        
        result in nodule formation and colonisation but not nitrogen fixation, other changes are required for this
  - - - when grown in heterogenous environments, 3 colony morphologies evolve, each adapted to different "niches" in the tube
      - however this does occur if the cultures are mixed, which homogenises the environment
      - evolution of cooperation and conflict in experimental bacterial populations
        
        wrinkly spreader occupies air.broth interface. doesnt suffer from oxygen depletion
        
        evolves due to the over production of an adhesive polymer causing the cells to stick to each other and to surfaces, thus forming a floating mat
        
        all cells in this mat benefit regardless of whether they produce polymer or not, thus individual cells can "cheat". if too many cells join the mat, it will sink
        
        smooth ancestral type occupies planktonic niche
        
        fuzzy spreader sticks to side and bottom of the flask
        
        in a homogenous environment you only seethe planktonic form
        
        cooperation occurs at many levels - genes within cells, cells within a body and groups of individuals
        
        for cooperating communities there is a problem - the investment in a common good can benefit other individuals regardless of whether they contribute or not