Transcript What is Population Genetics?

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