Microbial Evolution

1
Microbial Evolution

• Ecology and Evolution are inextricably connected

2

• Ecology the study of interactions between
  organisms and their environment (physical,
  chemical and biological conditions)
•  
• Evolution changes in the genetic composition of
  a population with the passage of each generation
• change in allelic frequency in populations over
  time (alleles are different versions of the same
  gene)

3
Consider how the amount of genetic divergence
(change) forms a continuum

• Microevolution Macroevolution small
  changes large changes

Microevolution adaptation Macroevolution
speciation
4
Four distinct mechanisms generate evolution
(change in allelic frequency in populations over
time)

• 1. mutation
• 2. gene flow
• 3. genetic drift
• 4. selection (natural and artificial)

5

• 1. Mutation a heritable change in the
  nucleotide sequence of the genetic nucleic acid,
  resulting in an alteration in the products coded
  for by the gene
•  

6

• 2. Gene flow introduction or loss of new
  alleles into the population through immigration
  or emigration.
•  
•  

Wilson Bossert, 1971
7

• 3. Genetic drift stochastic shifts in allele
  frequencies in small populations
•  
•  

Wilson Bossert, 1971
8

• 4. Selection change in allele frequencies over
  generations due to differential survival and
  reproductive success of genotypes
•  

Darwinian evolution is evolution by natural
selection
9
Natural selection leads to adaptive radiation and
speciation
10
What is the mechanism of natural selection?

• 1. Genotypes within populations vary and this
  variability is heritable.
•  
• 2. Biotic and abiotic components of an organisms
  environment act as selection pressures.
•  
• 3. Genotypes that are best adapted to these
  selection pressures leave the most offspring.
•  

11
Closely examine these three premises

• What introduces variability among genotypes?

12
Closely examine these three premises

• What introduces variability among genotypes?
• Mutations
• introduce new genetic variation

13
Closely examine these three premises

• What introduces variability among genotypes?
• Mutations
• Plasmids
• Transformation
• Transduction
• Conjugation
• can all introduce genetic variability to
  bacterial populations

Horizontal gene transfer
14
(No Transcript)
15
Closely examine these three premises

• What introduces variability among genotypes?
• Mutations
• Anastomosis
• can introduce genetic variability to fungal
  populations

16

•  Populations with diverse gene pools have a lot
  of variation in alleles.
• How is this variability passed on (heritable)?

17
genotypes pass on this variability through
reproduction
18
genotypes pass on this variability through
reproduction

• In sexually reproducing organisms (eg. many
  species of algae, zooplankton, fungi, and
  protozoa), recombination occurs with reproduction
  (the genetic deck of cards gets shuffled every
  generation). That means that novel alleles that
  arise through mutations are immediately placed in
  a diversity of genetic environments.

19
genotypes pass on this variability through
reproduction

• In contrast, recombination is not tied to
  reproduction in asexual organisms (e.g. bacteria,
  archaea, many species of algae, fungi ....).
  Recombination happens in asexual organisms, but
  it is not necessarily tied with reproduction.

20
genotypes pass on this variability through
reproduction

• Recombination has major ramifications on how
  natural selection acts on variance in the
  populations.
• Although sexual recombination is rare in bacteria
  (Cohen, 1996), horizontal gene transfer appears
  to be more common than previously thought
  (Pennisi 2004)

21
2. What are selection pressures in an organisms
environment?
22
2. What are selection pressures in an organisms
environment?

• Examples of biotic factors
• predators
• competitors
• mutualists

• Examples of abiotic factors
• resource availability
• physical conditions
• chemical conditions

23
(No Transcript)
24
Selection can be

• natural or anthropogenic

25
3. Genotypes that are best adapted to these
selection pressures leave the most offspring

• Premise 3 leads to the concept of adaptation and
  fitness

26
3. Genotypes that are best adapted to these
selection pressures leave the most offspring

• Premise 3 leads to the concept of adaptation and
  fitness
• Adaptation a genetically determined
  characteristic that improves an organisms
  ability to survive and reproduce in a particular
  environment.

27
Premise 3 leads to the concept of adaptation and
fitness

• Adaptation a genetically determined
  characteristic that improves an organisms
  ability to survive and reproduce in a particular
  environment.
• Adapt the evolutionary process by which
  organisms become better suited to their
  environments

28

• Fitness

29

• Fitness
• the relative contribution by an individuals
  descendants to future generations.

30
Some important properties of fitness

• Fitness is specific to a particular
  environment.(Consider both the biotic and abiotic
  environment).
• As the environment changes, so do the fitness
  values of the genotypes
• Notice the connection between ecology and
  evolution.

31
Some important properties of fitness

• Fitness is a property of a genotype, not of an
  individual or a population.
• Individuals with the same genotype share the
  same fitness within the same environment.
• Fitness is measured over one generation or more.

32

• New genotypes and alleles enter the population
  through mutation, immigration (horizontal gene
  transfer) etc. A new genotype that is fitter
  than the current one will gradually replace it.
  If the current genotype cannot be replaced by an
  invading one, it is said to represent the
  evolutionarily stable strategy or ESS (Maynard
  Smith and Price, 1973).

33

• The concepts of fitness and adaptation are
  relevant ONLY in a particular ecological context.
  There is no such thing as fitness in an absolute
  sense.

34
Which of the 4 evolutionary mechanisms generates
adaptation?1. mutation2. gene flow3. genetic
drift4. selection
35
Which of the 4 evolutionary mechanisms generates
adaptation?1. mutation2. gene flow3. genetic
drift4. selection

• Only natural selection, the other mechanisms
  generate change, but the change has no linkage to
  improved survival in the environment

36

• There can be multiple paths to higher fitness in
  response to many but not all types of natural
  selection

(e.g. Contrast the results of Lenskis
experiments of glucose starvation in E. coli with
Bulls experiments with high-temperature stress
in a bacteriophage
37
(No Transcript)
38
The role of genetic exchange (recombination of
alleles) in evolution.

• The paradigm of geographic speciation was
  developed from studies of sexually reproducing
  populations
• This paradigm assumes
• Allelic combinations are reshuffled every
  generation.
• Successful mating only occurs between individuals
  that are closely related.

39
geographic speciation allopatric speciation
40
This paradigm falls apart with bacteria and other
asexual organisms because

• 1. Allelic combinations are NOT reshuffled every
  generation. Only a small amount of genetic
  material is exchanged (via conjugation,
  transformation, transduction, plasmid transfer).
  
• Cohan suggests this exchange happens at a low
  frequency (10-8 to 10-7 exchanges per gene
  segment per genome per generation). But Pennisi
  suggests this exchange rate is MUCH higher,
  particularly in stressful environments.

41
This paradigm falls apart with bacteria and other
asexual organisms because

• 2. Successful genetic exchange occurs between
  individuals that are NOT closely related
  ("promiscuous genetic exchange").

42

• The process of periodic selection in bacteria
  purges diversity in populations gene pools.
  (Figure 3 in Cohan, 1996)

43

• Even with relatively low levels of recombination,
  there is enough genetic exchange, so that diverse
  allelic combinations can arise.
• (Figure 4 in Cohan, 1996)  

44
Cohan (1996) concluded that

• Recombination does NOT preserve genetic
  diversity in bacteria.
• Genetic exchange does NOT threaten the
  integrity of population adaptations.
• Genetic exchange can transfer adaptations
  across bacterial taxa.

45
Implications of this

• Adaptive mutations in bacteria have the potential
  to purge diversity from the populations.
• In contrast, in sexually reproducing organisms,
  adaptive mutation is transferred into many
  genetic backgrounds and does not follow the
  entire genome of the individual carrying the
  original mutation.

46
Implications of this

• 2. At recombination rates gt 10-5 exchanges per
  gene segment per genome per generation,
  ecologically distinct populations may be
  indistinguishable (variance within populations is
  as great as variance between populations )
  because of sufficient neutral sequence variance.

47
Implications of this

• 3. Adaptive gene sequences can go ANYWHERE