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Summary of sixth lesson
• Janzen-Connol hypothesis; explanation of why diseases lead to spatial heterogeneity
• Diseases also lead to heterogeneity or changes through time– Driving succession– The Red Queen Hypothesis: selection pressure will increase number of
resistant plant genotypes
• Co-evolution: pathogen increase virulence in short term, but in long term balance between host and pathogen
• Complexity of forest diseases: primary vs. secondaruy, modes of dispersal etc
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
Phylogenetic Phylogenetic relationships relationships within the within the HeterobasidionHeterobasidion complexcomplex
Het INSULARE
True Fir EUROPE
Spruce EUROPE
True Fir NAMERICA
Pine EUROPE
Pine NAMERICA
0.05 substitutions/site
NJ
Fir-SpruceFir-Spruce
Pine EuropePine Europe
Pine N.Am.Pine N.Am.
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.
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)
MATING
• Two haploids need to fuse to form n+n
• Sex needs to increase diversity: need different alleles for mating to occur
• Selection for equal representation of many different mating alleles
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
Long branches in Long branches in between groups between groups suggests no sex is suggests no sex is occurring in between occurring in between groupsgroups
Het INSULARE
True Fir EUROPE
Spruce EUROPE
True Fir NAMERICA
Pine EUROPE
Pine NAMERICA
0.05 substitutions/site
NJ
Fir-SpruceFir-Spruce
Pine EuropePine Europe
Pine N.Am.Pine N.Am.
Small branches within a clade Small branches within a clade indicate sexual reproduction is indicate sexual reproduction is
ongoing within that group of ongoing within that group of individualsindividuals
11.10 SISG CA
2.42 SISG CA
BBd SISG WA
F2 SISG MEX
BBg SISG WA
14a2y SISG CA
15a5y M6 SISG CA
6.11 SISG CA
9.4 SISG CA
AWR400 SPISG CA
9b4y SISG CA
15a1x M6 PISG CA
1M PISG MEX
9b2x PISG CA
A152R FISG EU
A62R SISG EU
A90R SISG EU
A93R SISG EU
J113 FISG EU
J14 SISG EU
J27 SISG EU
J29 SISG EU
0.0005 substitutions/site
NJ
890 bpCI>0.9
NA S
NA P
EU S
EU F
SOMATIC COMPATIBILITY
• Fungi are territorial for 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
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
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
Evolution and Population genetics
• Positively selected genes:……• Negatively selected genes……• Neutral genes: normally population genetics
demands loci used are neutral• Loci under balancing selection…..
Evolution and Population genetics
• Positively selected genes:……• Negatively selected genes……• Neutral genes: normally population genetics
demands loci used are neutral• Loci under balancing selection…..
Phylogenetic Phylogenetic relationships relationships within the within the HeterobasidionHeterobasidion complexcomplex
Het INSULARE
True Fir EUROPE
Spruce EUROPE
True Fir NAMERICA
Pine EUROPE
Pine NAMERICA
0.05 substitutions/site
NJ
Fir-SpruceFir-Spruce
Pine EuropePine Europe
Pine N.Am.Pine N.Am.
Geneaology of “S” DNA insertion into Geneaology of “S” DNA insertion into P ISG confirms horizontal transfer.P ISG confirms horizontal transfer.
Time of “cross-over” uncertainTime of “cross-over” uncertain
11.10 SISG CA
2.42 SISG CA
BBd SISG WA
F2 SISG MEX
BBg SISG WA
14a2y SISG CA
15a5y M6 SISG CA
6.11 SISG CA
9.4 SISG CA
AWR400 SPISG CA
9b4y SISG CA
15a1x M6 PISG CA
1M PISG MEX
9b2x PISG CA
A152R FISG EU
A62R SISG EU
A90R SISG EU
A93R SISG EU
J113 FISG EU
J14 SISG EU
J27 SISG EU
J29 SISG EU
0.0005 substitutions/site
NJ
890 bpCI>0.9
NA S
NA P
EU S
EU F
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)
How to get multiple loci?
• Random genomic markers:– RAPDS– Total genome RFLPS (mostly dominant)– AFLPS
• Microsatellites• SNPs• Multiple specific loci
– SSCP– RFLP– Sequence information
Watch out for linked alleles (basically you are looking at the same thing!)
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
Sequence information
• Multiple gene genealogies=definitive phylogeny
• Need to ensure gene histories are comparable” partition of homogeneity test
• Need to use unlinked loci
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
Thermalcycler
DNA template
Forward primer Reverse primer
From DNA to genetic information (alleles are distinct DNA sequences)
• Presence or absence of a specific PCR amplicon (size based/ specificity of primers)
• Differerentiate through:– Sequencing– Restriction endonuclease– Single strand conformation polymorphism
RAPDS use short primers but not too short
• Need to scan the genome
• Need to be “readable”
• 10mers do the job (unfortunately annealing temperature is pretty low and 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 (unfortunately annealing temperature is pretty low and 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