Class review 2009
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CLASS REVIEW 2009. 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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Class review 2009



Summary of first class

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

Summary of second class

  • 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

  • DNA-based phylogeography allowed to discover pine pathogen in Italy was of North American origin

  • DNA based genealogies allowed to identify hybridization between native and exotic pathogen

  • DNA allows to identify new species and to determine whether they are exotic or not



  • 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:

    • 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

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



  • Alternatively fixed alleles

  • Dominant vs. co-dominant markers

  • Genotype

Summary of previous lesson

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

Categories of wild plant diseases

Seed decay

Seedling diseases

Foliage diseases

Systemic infections

Parasitic plants

Cankers, wilts , and diebacks

Root and butt rots

Floral diseases

Summary of previous lesson1

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

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)





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

Important fungal genetic systems:

  • Intersterility genes

  • Somatic (vegetative) compatibility

  • Mating system



  • 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



  • From raw data to genetic distance

  • Distance distribution


  • Distance based trees

  • Number of polymorphic alleles

The scale of disease

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 disease1

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

Using dna sequences

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

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

Key points

  • Organism is exotic, why?

  • How does it kill oaks?

  • How does it spread?

  • What ecological conditions are necessary?

  • What can be done?

Key points1

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 points2

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 points3

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 points4

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 points5

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

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