1. Molecular Markers • DNA & PROTEINS • mtDNA = often used in systematics; in general, no recombination = uniparental inheritance • cpDNA = often used in systematics; in general, no recombination = uniparental inheritance • Microsatellites = tandem repeats; genotyping & population structure • Allozymes = variations of proteins; population structure • RAPDs = short segments of arbitrary sequences; genotyping • RFLPs = variants in DNA exposed by cutting with restriction enzymes; genotyping, population structure • AFLPs = after digest with restriction enzymes, a subset of DNA fragments are selected for PCR amplification; genotyping

2. Genetic analysis requires variation at loci, variation of markers (polymorphisms) • How the variation is structured will tell us • Does the microbe reproduce sexually or clonally • Is infection primary or secondary • Is contagion caused by local infectious spreaders or by a long-disance moving spreaders • How far can individuals move: how large are populations • Is there inbreeding or are individuals freely outcrossing

3. CASE STUDY • A grou A stand of adjacent trees is infected by a disease: How can we determine the way trees are infected?

4. CASE STUDY • A grou A stand of adjacent trees is infected by a disease: How can we determine the way trees are infected? BY ANALYSING THE GENOTYPE OF THE MICROBES: if the genotype is the same then we have local secondary tree-to-tree contagion. If all genotypes are different then primary infection caused by airborne spores is the likely cause of Contagion.

5. CASE STUDY • A grou WE HAVE DETERMINED AIRBORNE SPORES (PRIMARY INFECTION ) IS THE MOST COMMON FORM OF INFECTION QUESTION: Are the infectious spores produced by a local spreader, or is there a general airborne population of spores that may come from far away ? HOW CAN WE ANSWER THIS QUESTION?

6. If spores are produced by a local spreader.. • Even if each tree is infected by different genotypes (each representing the result of meiosis like us here in this class)….these genotypes will be related • HOW CAN WE DETERMINE IF THEY ARE RELATED?

7. HOW CAN WE DETERMINE IF THEY ARE RELATED? • By using random genetic markers we find out the genetic similarity among these genotypes infecting adjacent trees is high • If all spores are generated by one individual • They should have the same mitochondrial genome • They should have one of two mating alleles

8. WE DETERMINE INFECTIOUS SPORES ARE NOT RELATED • QUESTION: HOW FAR ARE THEY COMING FROM? ….or…… • HOW LARGE IS A POPULATION? Very important question: if we decide we want to wipe out an infectious disease we need to wipe out at least the areas corresponding to the population size, otherwise we will achieve no result.

9. HOW TO DETERMINE WHETHER DIFFERENT SITES BELONG TO THE SAME POP OR NOT? • Sample the sites and run the genetic markers • If sites are very different: • All individuals from each site will be in their own exclusive clade, if two sites are in the same clade maybe those two populations actually are linked (within reach) • In AMOVA analysis, amount of genetic variance among populations will be significant (if organism is sexual portion of variance among individuals will also be significant) • F statistics: Fst will be over ) 0.10 (suggesting stongt structuring) • There will be isolation by distance