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

3. Alternatively fixed alleles: Two flower species (species 1 and species 2) can have one of two features: –Long (L) or short (s) leaves –Red ( R) or white (w) flowers Ten individuals from species 1 have the following traits: –LR; LR ;LR ;LR; LR; LR ;LR; sR; sR; sR Ten individuals from species 2 have the following traits: –sw; sw ;sw ;sw; sw; sw ;sw; Lw; Lw; Lw

4. Which one is the alternatively fixed allele? Both alleles will differentiate the groups (frequencies are significantly different) Only one will be diagnostic because alternatively fixed It is the color of the flower: all flowers in species 1 are R, all flowers in species 2 are w (“all” implies your sampling size is adequate!!)

5. Dominant vs. co-dominant markers Flowers are red or white or yellow, DNA sequence is agg, agt, agc; DNA fragment is 10, 12 0r 14 bp long (CO-DOMINANT, we know what alternative alleles are) Flowers are red or non-red, DNA is agg or not, size is 10bp or not. We only see the dominant allele and we express it in binary code 1(present), 0(absent)

6. Limitations of co-dominant markers Not all non-red flowers are the same, but we assume they are (non red flowers can be orange or yellow) If at one locus we have a dominant A allele and a recessive a allele, using a codominant marker we would say AA=Aa but not aa. We know in reality AA and Aa are quite different.

7. Genotype A unique individual as defined by an array of genetic markers. (the more markers you have the less mistaken identity you will have. blonde

8. Blonde Blue-eyed

9. Blonde Blue-eyed Hairy

10. Blonde Blue-eyed Hairy 6 feet tall

11. Blonde Blue-eyed Hairy 6 feet tall Missing two molars

12. In the case of microbes it will probably be something like Genotype A= 01010101 Genotype B= 00110101 Genotype C= 00010101

13. 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

16. Fungi… again! ASCOASCOMYCETES BASIDIOBASIDIOMYCETES OOMYCETES (fungus-like, water molds)

17. ASCO ASCOMYCETES Yeasts (fermentation, human mycoses)Yeasts (fermentation, human mycoses) Truffles, morelsTruffles, morels Penicillia (penicillin), Fusaria (potent toxins, damping off of seedlings), molds

18. Ascus is the sack in which the spores are contained

19. Asci can be placed on a disk (apothecium), many apothecia can be together in a fruitbody Morel fruitbody

21. Asci can be carried inside a flask (perithecium) Nectria

22. Ploidy is mostly n

23. BASIDIO BASIDIOMYCETES Mushrooms. mycorrhizalMushrooms. mycorrhizal Wood decay organismsWood decay organisms Rusts, Smuts Yeasts and damping off

24. Toadstools and huitacochle are both basidiomycetes

25. Basidium means “club”, it carries the basidiospores (dispersion propagules) naked

28. Most of their life, they are n+n (dikaryons), some rare ones are diploid

29. Oomycetes Belong to the kingdom Stramenopila, used to be called Chromista Phytophthora, Pythium, Saprolegnia H20H20

30. Hyphae, sporangia, and zoospores of P. ramorum

31. Most of their lifecycle they are 2n Have cellulose in cell wall Not fungi!!, but look like them because of convergent evolution

32. Fungi do not photosynthesize Biotrophic: mycorrhyzae, rusts Endophites: clavicipetaceae, Necrotrophic; most pathogens Saprobes: primary (involved in litter decomposition)

33. DISEASE!! Symptoms vs. signs; e.g. chlorosis vs. fruit- body The disease triangle

34. host-pathogen-environment Susceptibility of individuals or of portions of individuals Genetic variability Basic compatibility (susceptibility) between host and pathogen Ability to withstand physiological alterations

35. Genetic resistance in host Length of lesion (mm) Proportion of stem girdled (%) Nicasio\42.5 a 0.71 a China Camp40.5 a 0.74 a San Diego27.8 b 0.41 b Ojai25.0 b 0.47 b Interior live oak (Maricopa) 14.1 b 0.33 b

36. Cankers by P. ramorum at 3 months from time of inoculation on two coast live oaks

37. host-pathogen-environment Basic compatibility with host (virulence) Ability to maintain diversity: sex vs. no sex Size of genetic pool Agressiveness (pathogenicity) towards hosts Ability to survive without host

38. Chlamydospores of P. ramorum

40. host-pathogen-environment Temperatures Shading Relative humidity Free standing water pH and any potentially predisposing factors Nutrient status

41. Colony diameter (mm) at 13 days

42. Presence of free water Between 6 and 12 hours required for infection of bay leaves

43. Some pathogen roles in natural plant communities Selection of individuals best suited for the site Maintenance of genetic diversity and stability in host plant populations Establishment or maintenance of host geographic ranges Natural succession Regulation of stand density, structure, and composition

44. Human activities affecting disease incidence in forests Introduction of exotic pathogens Planting trees in inappropriate sites Changing stand density, age structure, composition, fire frequency Wound creation Pollution, etc.

46. Effects of fire exclusion