Summary of sixth lesson

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Summary of sixth lesson

• Janzen-Connol hypothesis explanation of why
  diseases lead to spatial heterogeneity
• Diseases also lead to heterogeneity or changes
  through time
• Driving succession
• The Red Queen Hypothesis selection pressure will
  increase number of resistant plant genotypes
• Co-evolution pathogen increase virulence in
  short term, but in long term balance between host
  and pathogen
• Complexity of forest diseases primary vs.
  secondaruy, modes of dispersal etc

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HOST-SPECIFICITY

• Biological species
• Reproductively isolated
• Measurable differential size of structures
• Gene-for-gene defense model
• Sympatric speciation Heterobasidion, Armillaria,
  Sphaeropsis, Phellinus, Fusarium forma speciales

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Phylogenetic relationships within the
Heterobasidion complex
Fir-Spruce
Pine Europe
Pine N.Am.
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Recognition of self vs. non self

• Intersterility genes maintain species gene pool.
  Homogenic system
• Mating genes recognition of other to allow for
  recombination. Heterogenic system
• Somatic compatibility protection of the
  individual.

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INTERSTERILITY

• If a species has arisen, it must have some
  adaptive advantages that should not be watered
  down by mixing with other species
• Will allow mating to happen only if individuals
  recognized as belonging to the same species
• Plus alleles at one of 5 loci (S P V1 V2 V3)

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MATING

• Two haploids need to fuse to form nn
• Sex needs to increase diversity need different
  alleles for mating to occur
• Selection for equal representation of many
  different mating alleles

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SEX

• Ability to recombine and adapt
• Definition of population and metapopulation
• Different evolutionary model
• Why sex? Clonal reproductive approach can be very
  effective among pathogens

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Long branches in between groups suggests no sex
is occurring in between groups
Fir-Spruce
Pine Europe
Pine N.Am.
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Small branches within a clade indicate sexual
reproduction is ongoing within that group of
individuals
NA S
NA P
EU S
890 bp CIgt0.9
EU F
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SOMATIC COMPATIBILITY

• Fungi are territorial for two reasons
• Selfish
• Do not want to become infected
• If haploids it is a benefit to mate with other,
  but then the nn wants to keep all other
  genotypes out
• Only if all alleles are the same there will be
  fusion of hyphae
• If most alleles are the same, but not all, fusion
  only temporary

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The biology of the organism drives an epidemic

• Autoinfection vs. alloinfection
• Primary spreadby spores
• Secondary spreadvegetative, clonal spread, same
  genotype . Completely different scales (from
  small to gigantic)
• Coriolus
• Heterobasidion
• Armillaria
• Phellinus

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OUR ABILITY TO

• Differentiate among different individuals
  (genotypes)
• Determine gene flow among different areas
• Determine allelic distribution in an area

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WILL ALLOW US TO DETERMINE

• How often primary infection occurs or is disease
  mostly chronic
• How far can the pathogen move on its own
• Is the organism reproducing sexually? is the
  source of infection local or does it need input
  from the outside

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Evolution and Population genetics

• Positively selected genes
• Negatively selected genes
• Neutral genes normally population genetics
  demands loci used are neutral
• Loci under balancing selection..

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Evolution and Population genetics

• Positively selected genes
• Negatively selected genes
• Neutral genes normally population genetics
  demands loci used are neutral
• Loci under balancing selection..

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Evolutionary history

• Darwininan vertical evolutionray models
• Horizontal, reticulated models..

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Phylogenetic relationships within the
Heterobasidion complex
Fir-Spruce
Pine Europe
Pine N.Am.
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Geneaology of S DNA insertion into P ISG
confirms horizontal transfer.Time of
cross-over uncertain
NA S
NA P
EU S
890 bp CIgt0.9
EU F
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Because of complications such as

• Reticulation
• Gene homogeneization(Gene duplication)
• Need to make inferences based on multiple genes
• Multilocus analysis also makes it possible to
  differentiate between sex and lack of sex
  (Iaindex of association)

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Basic definitions again

• Locus
• Allele
• Dominant vs. codominant marker
• RAPDS
• AFLPs

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How to get multiple loci?

• Random genomic markers
• RAPDS
• Total genome RFLPS (mostly dominant)
• AFLPS
• Microsatellites
• SNPs
• Multiple specific loci
• SSCP
• RFLP
• Sequence information
• Watch out for linked alleles (basically you are
  looking at the same thing!)

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Sequence information

• Codominant
• Molecules have different rates of mutation,
  different molecules may be more appropriate for
  different questions
• 3rd base mutation
• Intron vs. exon
• Secondary tertiary structure limits
• Homoplasy

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Sequence information

• Multiple gene genealogiesdefinitive phylogeny
• Need to ensure gene histories are comparable
  partition of homogeneity test
• Need to use unlinked loci

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DNA template
Reverse primer
Forward primer
Thermalcycler
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Gel electrophoresis to visualize PCR product
Ladder (to size DNA product)
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From DNA to genetic information (alleles are
distinct DNA sequences)

• Presence or absence of a specific PCR amplicon
  (size based/ specificity of primers)
• Differerentiate through
• Sequencing
• Restriction endonuclease
• Single strand conformation polymorphism

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Presence absence of amplicon

• AAAGGGTTTCCCNNNNNNNNN
• CCCGGGTTTAAANNNNNNNNN

AAAGGGTTTCCC (primer)
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Presence absence of amplicon

• AAAGGGTTTCCCNNNNNNNNN
• CCCGGGTTTAAANNNNNNNNN

AAAGGGTTTCCC (primer)
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RAPDS use short primers but not too short

• Need to scan the genome
• Need to be readable
• 10mers do the job (unfortunately annealing
  temperature is pretty low and a lot of priming
  errors cause variability in data)

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RAPDS use short primers but not too short

• Need to scan the genome
• Need to be readable
• 10mers do the job (unfortunately annealing
  temperature is pretty low and a lot of priming
  errors cause variability in data)

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RAPDS can also be obtained with Arbitrary Primed
PCR

• Use longer primers
• Use less stringent annealing conditions
• Less variability in results

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Result series of bands that are present or
absent (1/0)