The biology of the organism drives an epidemic Autoinfection vs. alloinfection P

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The biology of the organism drives an epidemic Autoinfection vs. alloinfection P

Burns, Julie, News Director has reference to this Academic Journal, PHwiki organized this Journal 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 OUR ABILITY TO: Differentiate among different individuals (genotypes) Determine gene flow among different areas Determine allelic distribution in an area

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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 IN ORDER TO UNDERSTAND PATTERNS OF INFECTION If John gave directly Mary an infection, in addition to Mary gave it to Tom, they should all have the same strain, or GENOTYPE (comparison=secondary spread among as long as est trees) If the pathogen is airborne in addition to sexually reproducing, Mary John in addition to Tom will be infected by different genotypes. But if the source is the same, the genotypes will be sibs, thus related Recognition of self vs. non self Intersterility genes: maintain species gene pool. Homogenic system Mating genes: recognition of “other” to allow as long as recombination. Heterogenic system Somatic compatibility: protection of the individual.

Somatic incompatibility SOMATIC COMPATIBILITY Fungi are territorial as long as two reasons Selfish Do not want to become infected If haploids it is a benefit to mate with other, but then the n+n wants to keep all other genotypes out Only if all alleles are the same there will be fusion of hyphae If most alleles are the same, but not all, fusion only temporary SOMATIC COMPATIBILITY SC can be used to identify genotypes SC is regulated by multiple loci Individual that are compatible (recognize one another as self, are within the same SC group) SC group is used as a proxy as long as genotype, but in reality, you may have some different genotypes that by chance fall in the same SC group Happens often among sibs, but can happen by chance too among unrelated individuals

Recognition of self vs. non self What are the chances two different individuals will have the same set of VC alleles Probability calculation (multiply frequency of each allele) More powerful the larger the number of loci in addition to the larger the number of alleles per locus Recognition of self vs. non self: probability of identity (PID) 4 loci 3 biallelelic 1 penta-allelic P= 0.5×0.5×0.5×0.2=0.025 In humans 99.9%, 1000, 1 in one million INTERSTERILITY If a species has arisen, it must have some adaptive advantages that should not be watered down by mixing with other species Will allow mating to happen only if individuals recognized as belonging to the same species Plus alleles at one of 5 loci (S P V1 V2 V3)

INTERSTERILITY Basis as long as speciation These alleles are selected as long as more strongly in sympatry You can have different species in allopatry that have not been selected as long as different IS alleles MATING Two haploids need to fuse to as long as m n+n Sex needs to increase diversity: need different alleles as long as mating to occur Selection as long as equal representation of many different mating alleles MATING If one individuals is source of inoculum, then the same 2 mating alleles will be found in local population If inoculum is of broad provenance then multiple mating alleles should be found

MATING How do you test as long as mating Place two homokaryons in same plate in addition to check as long as as long as mation of dikaryon (microscopic clamp connections at septa) Clamp connections MATING ALLELES All heterokaryons will have two mating allelels, as long as instance a, b There is an advantage in having more mating alleles (easier mating, higher chances of finding a mate) Mating allele that is rare, may be of migrant just arrived If a parent is important source, genotypes should all be of one or two mating types

Two scenarios: A, A, B, C, D, D, E, H, I, L A, A, A,B, B, A, A Two scenarios: A, A, B, C, D, D, E, H, I, L Multiple source of infections (at least 4 genotypes) A, A, A,B, B, A, A Siblings as source of infection (1 genotype) SEX Ability to recombine in addition to adapt Definition of population in addition to metapopulation Different evolutionary model Why sex Clonal reproductive approach can be very effective among pathogens

Long branches in between groups suggests no sex is occurring in between groups Fir-Spruce Pine Europe Pine N.Am. Small branches within a clade indicate sexual reproduction is ongoing within that group of individuals 890 bp CI>0.9 NA S NA P EU S EU F Index of association Ia= if same alleles are associated too much as opposed to r in addition to om, it means sex is not occurring Association among alleles calculated in addition to compared to simulated r in addition to om distribution

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If SEX is not happening Number of genotypes less than that theorethically expected E.G. Three biallelic loci should give 8 genotypes Basic definitions again Locus Allele Dominant vs. codominant marker RAPDS AFLPs How to get multiple loci R in addition to om genomic markers: RAPDS Total genome RFLPS (mostly dominant) AFLPS Microsatellites SNPs Multiple specific loci SSCP RFLP Sequence in as long as mation Watch out as long as linked alleles (basically you are looking at the same thing!)

RAPDS use short primers but not too short Need to scan the genome Need to be “readable” 10mers do the job (un as long as tunately annealing temperature is pretty low in addition to a lot of priming errors cause variability in data) RAPDS use short primers but not too short Need to scan the genome Need to be “readable” 10mers do the job (un as long as tunately annealing temperature is pretty low in addition to a lot of priming errors cause variability in data) RAPDS can also be obtained with Arbitrary Primed PCR Use longer primers Use less stringent annealing conditions Less variability in results

From Garbelotto in addition to Chapela, Evolution in addition to biogeography of matsutakes Biodiversity within species as significant as between species Microsatellites or SSRs AGTTTCATGCGTAGGT CG CG CG CG CG AAAATTTTAGGTAAATTT Number of CG is variable Design primers on FLANKING region, amplify DNA Electrophoresis on gel, or capillary Size the allele (different by one or more repeats; if number does not match there may be polimorphisms in flanking region) Stepwise mutational process (2 to 3 to 4 to 3 to2 repeats)

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