Download Lecture Review - College of Natural Resources

CLASS REVIEW 2008
Lectures
Summary of first class
• Undertanding of nature, an essential
part of culture
• Forests essential for life on the planet
• Fungi essential for survival of forests
Summary of second class
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DNA mutates, evolves, and different DNA sequences can be assigned to
different individuals, populations from different provenances, closely related
species, different species, different microbial pathovars
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DNA-based phylogeography allowed to discover pine pathogen in Italy was
of North American origin
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DNA based genealogies allowed to identify hybridization between native
and exotic pathogen
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DNA allows to identify new species and to determine whether they are
exotic or not
Definitions
• Propagule= structure used by an
organism to spread or survive
• Locus= a physical portion of a
chromosome,a gene
• Intron= a portion of DNA , a locus that
does not code for a protein
• Exon= a coding gene
Definitions-2
• Alleles= different DNA sequences at the
same locus
• If a locus has variation in sequence it is
polymorphic (many forms)
• Polymorphisms are differences in DNA
among organisms, the more polymorphisms
the easier it is to differentiate organisms
• There are more polymorphisms in introns
Definitions-3
• Invasive organisms: exotic organism that reproduces
and occupies progressively a larger area:
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Fast reproductive cycle
Vectored
Hardy
Occupy unoccupied niches
Different drain on natural resources
Make environment favorable for itself and other invaders
Linked to disturbances
If pathogen , more changes because top of pyramid
May hybridize with native species: new taxon is created
Summary of third lesson
• DNA polymorphisms can be diagnostic
– Mutations/Sex/Barriers to mating
• Plant Diseases can be biotic (interaction between
host and causal agent ), or abiotic
• Many organisms can cause plant diseases, but fungi
are the No.1 cause
• Diversity of fungi, but all have ideal structure for plant
infection:
– hypha/cord/rhizomorph/infection peg/appressorium
– Sexual vs. asexual reproduction: can do both
Definitions
• Alternatively fixed alleles
• Dominant vs. co-dominant markers
• Genotype
Summary of previous lesson
• Dominant vs. codominant genetic markers
• Concept of “genotype”
• Alternatively fixed allele vs.difference in frequencies
• PLANT HOST INTERACTION: timing, physical/chemical
interaction, basic genetic compatibility leads to virulence, gene for
gene hypothesis, pathogenicity
Categories of wild plant
diseases
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Seed decay
Seedling diseases
Foliage diseases
Systemic infections
Parasitic plants
Cankers, wilts , and diebacks
Root and butt rots
Floral diseases
Summary of previous 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
• Density dependance
The biology of the organism
drives an epidemic
• Autoinfection vs. alloinfection
• Primary spread=by spores
• Secondary spread=vegetative, clonal spread, same
genotype . Completely different scales (from small to
gigantic)
Coriolus
Heterobasidion
Armillaria
Phellinus
OUR ABILITY TO:
• Differentiate among different individuals
(genotypes)
• Determine gene flow among different areas
• Determine allelic distribution in an area
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
Important fungal genetic
systems:
• Intersterility genes
• Somatic (vegetative) compatibility
• Mating system
Summary
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AFLP, RAPDs, RFLPs, microsatellites
Repeatability
Test for power (PID and test progeny)
Have we sampled enough? Rarefaction
curves, resampling, need to be ob flat
portion of curve
Summary
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From raw data to genetic distance
Distance distribution
AMOVA
Distance based trees
Number of polymorphic alleles
The “scale” of disease
• Dispersal gradients dependent on propagule size,
resilience, ability to dessicate, NOTE: not linear
• Important interaction with environment, habitat, and
niche availability. Examples: Heterobasidion in
Western Alps, Matsutake mushrooms that offer
example of habitat tracking
• Scale of dispersal (implicitely correlated to
metapopulation structure)---
The scale of disease
• Curves of spore dispersal (rapid dilution effect, e.g
most spores fall near source, but a long low tail, a
few spores will travel long distances
• Genetic structure of species: the more structure the
more fragmented the less dispersal
• Mantel tests, spatial autocorrelation: plot the genetic
distance against the geographic distance
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y = 0.2452x + 0.5655
r 2 = 0.0266
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Φ ST/(1-Φ ST)
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2
1
0
1.5
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2.5
3
3.5
4
4.5
Ln Geographic Distance (m)
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5.5
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6.5
1
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0.5
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Moran's I
0.3
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0.1
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-0.1
-0.2
1
10
100
1000
10000
Mean Geographical Distance (m)
2
100000
1000000
Using DNA sequences
• Obtain sequence
• Align sequences, number of parsimony informative
sites
• Gap handling
• Picking sequences (order)
• Analyze sequences
(similarity/parsimony/exhaustive/bayesian
• Analyze output; CI, HI Bootstrap/decay indices
Population genetics concepts
• Gene flow, migration
• Lack of gene flow, genetic
substructuring=differentiation
• Hardy Weinberg= for diploid or dikaryotic organims
predicts levels of heterozygosity
• Inbreeding coefficient
• Fst
CLASS REVIEW 2008
Research papers
Key points
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Organism is exotic, why?
How does it kill oaks?
How does it spread?
What ecological conditions are
necessary?
• What can be done?
Key points
• Native fungus, host specialized
• How does it infest stands? Does it need
stumps?
• How was research done? Sampling and
analysis
• What type of forests will enhance secondary
spread?
• Is source of inoculum local or not?
• How was it shown that nuclei can rearrange
themselves
Key points
• Wood decay fungus, generalist
• Sexually reproducing hence lots of local
diversity
• Easily airborne, easy to find hosts, no
genetic structure within Sweden
• Structure between Sweden and Finland
• Methods: RAPDS and AMOVA
Key points
Pathogen, very host-specific
• Infection is mostly primary by airborne
meiospores
• Method: AFLP analysis on haploid
meiospores
• AMOVA indicated significant genetic diversity
both within and among populations
• Lack of host= barrier to migration
Key points
• Mycorrhizal fungus, obligate symbiont
• Symbiont with most conifers, air dispersed
• Japanese market buys some species, rejects
others
• Species accepted by market are
monophyletic
• At least 3 species: circumboreal, mexican,
and west coast
• North America= center of diversity
• Oldest species is in North America
• Methods: DNA sequencing and AFLPs
• Isolation by distance: distant populations
more different genetically
Key points
• Specific mycorrhizal symbiont, underground
mushrooms, animal dispersed
• Islands in islands
• Compare genetics of fruitbodies and of seed
banks
• Genetic structure indicate low gene flow
among sites, but similar genetic structure
between two islands