2. 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

3. 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

4. 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

5. MICROBIAL INVASIONS OF NATURAL ECOSYSTEMS: –Cannot be eradicated –Problematic because not noticeable for decades –Can cause limited problems –Can cause major alterations: Because of lack of coevolution between host and pathogen Because they are where similar organisms were not before

6. Introduced organisms Have a smaller genetic variation than original population Strong founder effects Each founder can create a significantly different population if not in equilibrium Mating will homogenize variation Mating barriers will increase difference

7. How does DNA help Identify microbe Determine whether equally named organism from elsewhere is the same or not Determine how it is reproducing Quantify organism Determine whether it is hybridizing or not

8. Definitions Phylogeny Phylogeography Gene geneaology

9. DISEASES AND TREES What exactly is a disease? It is the outcome of an interaction between a plant and the environment, resulting in an altered physiology of the host Sustained interaction=biotic Single event= abiotic

16. What is a pathogen? Strictly speaking a pathogen is the causal agent of disease Bacteria Viruses Nematodes Stramenopiles Algae Phytoplasmas Higher plants

17. Nematodes

19. And of course… fungi Fungi: saprophytic, symbionts, and pathogens Polyphyletic group in evolutionary terms –Basidiomycetes Ascomycetes Zygomycets Animals Plants Red algae Brown algae Myxomycetes

20. Diversity of fungi, but all have ideal structure for plant infection: –hypha/cord/rhizomorph/infection peg/appressorium –Sexual vs. asexual reproduction: can do both –Do not photosinthesize –Chitin in cell wall –Exogenous digestion –Indefinite growth –Phenotypic plasticity and pleomorphisms

21. Septa Pores CELLS

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

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

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

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

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

30. Ploidy is mostly n

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

32. Toadstools and huitacochle are both basidiomycetes

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

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

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

38. Oomycetes are not fungi Cellulose in cell wall Ploidy is 2n Result of sexual activity is oospore (2n) Meiosis, somatogamy, caryogamy all occur at the same time Water adapted biology, flagellate phase No septa, holocoenocytic hyphae Chitin in cell wall Ploidy is n, or n+n Result of sexual activity is a spore n Meiosis, somatogamy,caryogamy are usually interupted by vegetative (somatic phase) Better adapted for aerial transmission Septate hyphae

39. Phytophthora Some important plant pathogens, with very well known history –Phytophthora infestans and the Irish potato famine –Phytopthora cinnamomi and the Jarrah dieback in Australia

40. The Irish Potato Famine From 1845 to 1850 Phytophthora infestans Resulted in the death of 750,000 Emigration of over 2 million, mainly to the United States.

41. Phytophthora: “plant destructor” Best known pathogen whose long-distance transport linked to agriculture. –Infected root-stocks –Infested soil –Infected plants

42. 70 species of Phytophthora 60 until a few years ago, research accelerated, especially by molecular analyses Differentiated on basis of: –Type of sexual intercourse –Type of sexual activity –Number of hosts –Ideal temperature –Type of biology –Evolutionary history (Waterhouse-Cooke)

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

44. Zoospore

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

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

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

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

51. 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

52. 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

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

54. 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

55. Chlamydospores of P. ramorum

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

58. Colony diameter (mm) at 13 days

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

60. 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

61. 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.

63. Effects of fire exclusion

64. DISEASE: plant microbe interaction Basic compatibility need to be present Chemotaxis, thighmotropy Avirulence in pathogen matched by resistance in host according to the gene for gene model Pathogenicity factors such as toxins and enzymes important in the infection process

65. Effects of diseases on host mortality, growth and reproduction Young plants killed before reaching reproductive age Affect reproductive output Directly affect flowers and fruits

66. WGR

67. Complexity of forest diseases At the individual tree level: 3 dimensional At the landscape level” host diversity, microclimates, etc. At the temporal level

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

69. 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

70. 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!!)

71. 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)

72. 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.

73. 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

74. Blonde Blue-eyed

75. Blonde Blue-eyed Hairy

76. Blonde Blue-eyed Hairy 6 feet tall

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

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

79. Complexity of forest diseases Primary vs. secondary Introduced vs. native Air-dispersed vs. splash-dispersed, vs. animal vectored Root disease vs. stem. vs. wilt, foliar Systemic or localized

80. Progression of cankers Older canker with dry seep Hypoxylon, a secondary sapwood decayer will appear

81. Stem canker on coast live oak

82. Root disease center in true fir caused by H. annosum

85. 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

86. Seed diseases Up to 88% mortality in tropical Uganda More significant when seed production is episodic

87. Stress cone cropBS on DF

88. Seedling diseases Specific diseases, but also diseases of adult trees can affect seedlings Pythium, Phytophthora, Rhizoctonia, Fusarium are the three most important ones Pre- vs. post-emergence Impact: up to 65% mortality in black cherry. These diseases build up in litter Shady and moist environment is very conducive to these diseases

89. Foliar diseases In general they reduce photosynthetic ability by reducing leaf area. At times this reduction is actually beneficial Problem is accentuated in the case of small plants and in the case other health issues are superimposed Often, e.g. with anthracnose,needle cast and rust diseases leaves are point of entry for twig and branch infection with permanent damage inflicted

92. Systemic infections Viral? Phytoplasmas Peronospora and smuts can lead to over 50% mortality Endophytism: usually considered beneficial

93. Grass endophytes Clavicipetaceae and grasses, e.g. tall fescue Mutualism: antiherbivory, protection from drought, increased productivity Classic example of coevolutionary development: Epichloe infects “flowers” of sexually reproducing fescue, Neotyphodium is vertically transmitted in species whose sexual reproductive ability has been aborted

94. Parasitic plants True (Phoradendron) and dwarf mistletoe (Arceuthobium) Effects: –Up to 65% reduction in growth (Douglas-fir) –3-4 fold mortality rate increase –Reduced seed and cone production Problem accentuated in multistoried uneven aged forests

99. Cankers, wilts, and die-backs Includes extremely aggressive, often easy to import tree diseases: pine pitch canker, Dutch elm disease, Chestnut blight, White pine blister rust Lethal in most cases, generally narrow host range with the exception of Sudden Oak Death

100. Root diseases Extremely common, probably represent the most economically damaging type of diseases Effects: tree mortality (direct and indirect), cull, effect on forest structure, effect on composition, stand density, growth rate Heterobasidion, Armillaria, Phellinus weirii, Phytophthora cinnamomi

102. Removing food base causes infection of roots of other trees Hyphae in plant tissue or soil (short- lived) Melanin-covered rhizomorphs will allow for fungus to move to new food Sources (Armillaria mellea)

111. Floral diseases Pollinator vectored smut on silene offers an example of well known dynamic interaction in which pathogen drives genetic variability of hosts and is affected by environmental condition Puccinia monoica produces pseudoflowers that mimic real flowers. Effects: reduction in seed production, reduction in pollinators visits

112. POPULATION DYNAMICS Species interactions and diversity

113. Density-dependence Most diseases show positive density dependence Negative dependence likely to be linked to limited inoculum: e.g. vectors limited If pathogen is host-specific overall density may not be best parameter, but density of susceptible host/race In some cases opposite may be true especially if alternate hosts are taken into account

114. Counterweights to numerical effects Compensatory response of survival can exceed negative effect of pathogen “carry over” effects? –NEGATIVE: progeny of infected individuals less fit; –POSITIVE; progeny more resistant (shown with herbivory)

115. Disease and competition Competition normally is conducive to increased rates of disease: limited resources weaken hosts, contagion is easier Pathogens can actually cryptically drive competition, by disproportionally affecting one species and favoring another

116. Diseases and succession Soil feedbacks; normally it’s negative. Plants growing in their own soil repeatedly have higher mortality rate. This is the main reason for agricultural rotations and in natural systems ensures a trajectory towards maintaining diversity Phellinus weirii takes out Douglas fir and hemlock leaving room for alder

117. Janzen-Connol Regeneration near parents more at riak of becoming infected by disease because of proximity to mother (Botryosphaeria, Phytophthora spp.). Maintains spatial heterogeneity in tropical forests Effects are difficult to measure if there is little host diversity, not enough host-specificity on the pathogen side, and if periodic disturbances play an important role in the life of the ecosystem

118. The red queen hypothesis Coevolutionary arm race Dependent on: –Generation time has a direct effect on rates of evolutionary change –Genetic variability available –Rates of outcrossing (Hardy-weinberg equilibrium) –Metapopulation structure

119. Frequency-, or density dependent, or balancing selection New alleles, if beneficial because linked to a trait linked to fitness will be positively selected for. –Example: two races of pathogen are present, but only one resistant host variety, suggests second pathogen race has arrived recently

120. Diseases as strong forces in plant evolution Selection pressure Co-evolutionary processes –Conceptual: processes potentially leading to a balance between different ecosystem components –How to measure it: parallel evolution of host and pathogen

121. Rapid generation time of pathogens. Reticulated evolution very likely. Pathogens will be selected for INCREASED virulence In the short/medium term with long lived trees a pathogen is likely to increase its virulence In long term, selection pressure should result in widespread resistance among the host