2. CLASS REVIEW 2008 Lectures

3. 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

4. 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

5. 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

6. 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

7. 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

8. 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

9. Definitions Alternatively fixed alleles Dominant vs. co-dominant markers Genotype

10. 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

11. 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

12. 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

13. 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

15. OUR ABILITY TO: Differentiate among different individuals (genotypes) Determine gene flow among different areas Determine allelic distribution in an area

16. 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

17. Important fungal genetic systems: Intersterility genes Somatic (vegetative) compatibility Mating system

18. Summary 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

19. Summary From raw data to genetic distance Distance distribution AMOVA Distance based trees Number of polymorphic alleles

20. 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)---

21. 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

24. 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

25. 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

26. CLASS REVIEW 2008 Research papers

28. Key points Organism is exotic, why? How does it kill oaks? How does it spread? What ecological conditions are necessary? What can be done?

30. 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

32. 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

34. 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

36. 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

38. 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