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SUMMARY

SUMMARY. Disease and disease triangle Pathogen Native vs. exotic diseases Type of diseases Long term effect of disease Density dependence- Janzen Connol Gene for gene- Red queen hypothesis. Evolution and Population genetics. Positively selected genes:…… Negatively selected genes……

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SUMMARY

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  1. SUMMARY • Disease and disease triangle • Pathogen • Native vs. exotic diseases • Type of diseases • Long term effect of disease • Density dependence- Janzen Connol • Gene for gene- Red queen hypothesis

  2. Evolution and Population genetics • Positively selected genes:…… • Negatively selected genes…… • Neutral genes: normally population genetics demands loci used are neutral • Loci under balancing selection…..

  3. Evolution and Population genetics • Positively selected genes:…… • Negatively selected genes…… • Neutral genes: normally population genetics demands loci used are neutral • Loci under balancing selection…..

  4. Evolutionary history • Darwininan vertical evolutionray models • Horizontal, reticulated models..

  5. Phylogenetic relationships within the Heterobasidioncomplex Fir-Spruce Pine Europe Pine N.Am.

  6. Geneaology of “S” DNA insertion into P ISG confirms horizontal transfer.Time of “cross-over” uncertain NA S NA P EU S 890 bp CI>0.9 EU F

  7. Because of complications such as: • Reticulation • Gene homogeneization…(Gene duplication) • Need to make inferences based on multiple genes • Multilocus analysis also makes it possible to differentiate between sex and lack of sex (Ia=index of association)

  8. How to get multiple loci? • Random genomic markers: • RAPDS • Total genome RFLPS (mostly dominant) • AFLPS • Microsatellites • SNPs • Multiple specific loci • SSCP • RFLP • Sequence informat5ion

  9. Sequence information • Codominant • Molecules have different rates of mutation, different molecules may be more appropriate for different questions • 3rd base mutation • Intron vs. exon • Secondary tertiary structure limits • Homoplasy

  10. Sequence information • Multiple gene genealogies=definitive phylogeny • Need to ensure gene histories are comparable” partition of homogeneity test • Need to use unlinked loci

  11. HOST-SPECIFICITY • Biological species • Reproductively isolated • Measurable differential: size of structures • Gene-for-gene defense model • Sympatric speciation: Heterobasidion, Armillaria, Sphaeropsis, Phellinus, Fusarium forma speciales

  12. Phylogenetic relationships within the Heterobasidioncomplex Fir-Spruce Pine Europe Pine N.Am.

  13. SEX • Ability to recombine and adapt • Definition of population and metapopulation • Different evolutionary model • Why sex? Clonal reproductive approach can be very effective among pathogens

  14. Recognition of self vs. non self • Intersterility genes: maintain species gene pool. Homogenic system • Mating genes: recognition of “other” to allow for recombination. Heterogenic system • Somatic compatibility: protection of the individual.

  15. From the population level to the individual • Autoinfection vs. alloinfection • Primary spread=by spores • Secondary spread=vegetative, clonal spread, same genotype . Completely different scales Coriolus Heterobasidion Armillaria Phellinus

  16. Basic definitions again • Locus • Allele • Dominant vs. codominant marker • RAPDS • AFLPs

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

  18. Ponderosa pine Incense cedar

  19. Yosemite Lodge 1975 Root disease centers outlined

  20. Yosemite Lodge 1997 Root disease centers outlined

  21. Are my haplotypes sensitive enough? • To validate power of tool used, one needs to be able to differentiate among closely related individual • Generate progeny • Make sure each meiospore has different haplotype

  22. 1010101010 1010101010 1010101010 1010101010 1010000000 1011101010 1010111010 1010001010 1011001010 1011110101 RAPD combination1 2

  23. Conclusions • Only one RAPD combo is sensitive enough to differentiate 4 half-sibs (in white) • Mendelian inheritance? • By analysis of all haplotypes it is apparent that two markers are always cosegregating, one of the two should be removed

  24. Dealing with dominant anonymous multilocus markers • Need to use large numbers • Repeatability • Graph distribution of distances • Calculate distance using Jaccard’s similarity index

  25. Jaccard’s • Only 1-1 and 1-0 count, 0-0 do not count 1010011 1001011 1001000

  26. Jaccard’s • Only 1-1 and 1-0 count, 0-0 do not count A: 1010011 AB= 0.6 0.4 (1-AB) B: 1001011 BC=0.5 0.5 C: 1001000 AC=0.2 0.8

  27. Now that we have distances…. • Plot their distribution (clonal vs. sexual)

  28. Now that we have distances…. • Plot their distribution (clonal vs. sexual) • Analysis: • Similarity (cluster analysis); a variety of algorithms. Most common are NJ and UPGMA

  29. Now that we have distances…. • Plot their distribution (clonal vs. sexual) • Analysis: • Similarity (cluster analysis); a variety of algorithms. Most common are NJ and UPGMA • AMOVA; requires a priori grouping

  30. AMOVA groupings • Individual • Population • Region AMOVA: partitions molecular variance amongst a priori defined groupings

  31. Now that we have distances…. • Plot their distribution (clonal vs. sexual) • Analysis: • Similarity (cluster analysis); a variety of algorithms. Most common are NJ and UPGMA • AMOVA; requires a priori grouping • Discriminant, canonical analysis

  32. Now that we have distances…. • Plot their distribution (clonal vs. sexual) • Analysis: • Similarity (cluster analysis); a variety of algorithms. Most common are NJ and UPGMA • AMOVA; requires a priori grouping • Discriminant, canonical analysis • Frequency: does allele frequency match expected (hardy weinberg), F or Wright’s statistsis

  33. 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)---

  34. S-P ratio in stumps is highly dependent on distance from true fir and hemlock stands . . San Diego

  35. Have we sampled enough? • Resampling approaches • Saturation curves

  36. If we have codominant markers how many do I need • Probability calculation based on allele frequency.

  37. White mangroves: Corioloposis caperata

  38. Distances between study sites White mangroves: Corioloposis caperata

  39. Forest fragmentation can lead to loss of gene flow among previously contiguous populations. The negative repercussions of such genetic isolation should most severely affect highly specialized organisms such as some plant-parasitic fungi. AFLP study on single spores Coriolopsis caperata on Laguncularia racemosa

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