Transcript Summary of sixth lesson - UC Berkeley College of Natural

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
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Biological species
Reproductively isolated
Measurable differential: size of structures
Gene-for-gene defense model
Sympatric speciation: Heterobasidion,
Armillaria, Sphaeropsis, Phellinus, Fusarium
forma speciales
Phylogenetic
relationships
within the
Heterobasidion
complex
NJ
Het INSULARE
Fir-Spruce
True Fir EUROPE
Spruce EUROPE
True Fir NAMERICA
Pine Europe
Pine EUROPE
Pine N.Am.
Pine NAMERICA
0.05 substitutions/site
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
between groups
suggests no sex is
occurring in between
groups
NJ
Het INSULARE
Fir-Spruce
True Fir EUROPE
Spruce EUROPE
True Fir NAMERICA
Pine Europe
Pine EUROPE
Pine N.Am.
Pine NAMERICA
0.05 substitutions/site
NJ
11.10 SISG CA
Small branches within a clade
indicate sexual reproduction is
ongoing within that group of
individuals
2.42 SISG CA
BBd SISG WA
F2 SISG MEX
NA S
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
890 bp
CI>0.9
EU S
A93R SISG EU
J113 FISG EU
J14 SISG EU
J27 SISG EU
J29 SISG EU
0.0005 substitutions/site
EU F
NA P
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…..
Evolutionary history
• Darwininan vertical evolutionray models
• Horizontal, reticulated models..
Phylogenetic
relationships
within the
Heterobasidion
complex
NJ
Het INSULARE
Fir-Spruce
True Fir EUROPE
Spruce EUROPE
True Fir NAMERICA
Pine Europe
Pine EUROPE
Pine N.Am.
Pine NAMERICA
0.05 substitutions/site
NJ
11.10 SISG CA
Geneaology of “S” DNA insertion into
P ISG confirms horizontal transfer.
2.42 SISG CA
BBd SISG WA
F2 SISG MEX
Time of “cross-over” uncertain
NA S
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
890 bp
CI>0.9
A90R SISG EU
EU S
A93R SISG EU
J113 FISG EU
J14 SISG EU
J27 SISG EU
J29 SISG EU
0.0005 substitutions/site
EU F
NA P
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)
Basic definitions again
• Locus
• Allele
• Dominant vs. codominant marker
– RAPDS
– AFLPs
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
DNA template
QuickTi me™ and a
T IFF (Uncompressed) decompressor
are needed to see thi s pi cture.
Forward primer
Thermalcycler
Reverse primer
Gel electrophoresis to
visualize PCR product
Ladder (to size
DNA product)
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
Presence absence of
amplicon
• AAAGGGTTTCCCNNNNNNNNN
• CCCGGGTTTAAANNNNNNNNN
AAAGGGTTTCCC (primer)
Presence absence of
amplicon
• AAAGGGTTTCCCNNNNNNNNN
• CCCGGGTTTAAANNNNNNNNN
AAAGGGTTTCCC (primer)
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
Result: series of bands that
are present or absent (1/0)