Download DISEASES AND TREES - UC Berkeley College of Natural Resources

SUMMARY
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Disease and disease triangle
Pathogen
Native vs. exotic diseases
Type of diseases
Long term effect of disease
Density dependence- Janzen Connol
Gene for gene- Red queen hypothesis
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..
NJ
Phylogenetic relationships
within the Heterobasidion
complex
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)
How to get multiple loci?
• Random genomic markers:
– RAPDS
– Total genome RFLPS (mostly dominant)
– AFLPS
• Microsatellites
• SNPs
• Multiple specific loci
– SSCP
– RFLP
– Sequence informat5ion
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
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
NJ
Phylogenetic relationships
within the Heterobasidion
complex
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
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
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.
From the population level to the
individual
• Autoinfection vs. alloinfection
• Primary spread=by spores
• Secondary spread=vegetative, clonal spread,
same genotype . Completely different scales
Coriolus
Heterobasidion
Armillaria
Phellinus
Basic definitions again
• Locus
• Allele
• Dominant vs. codominant marker
– RAPDS
– AFLPs
Root disease center in true fir caused by H. annosum
Ponderosa pine
Incense cedar
Yosemite Lodge 1975 Root disease centers outlined
Yosemite Lodge 1997 Root disease centers outlined
Are my haplotypes sensitive
enough?
• To validate power of tool used, one needs to
be able to differentiate among closely
related individual
• Generate progeny
• Make sure each meiospore has different
haplotype
RAPD combination
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2
• 1010101010
• 1011101010
• 1010101010
• 1010111010
• 1010101010
• 1010001010
• 1010101010
• 1010000000
• 1011001010
• 1011110101
Conclusions
• Only one RAPD combo is sensitive enough
to differentiate 4 half-sibs (in white)
• Mendelian inheritance?
• By analysis of all haplotypes it is apparent
that two markers are always cosegregating,
one of the two should be removed
Dealing with dominant
anonymous multilocus markers
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Need to use large numbers
Repeatability
Graph distribution of distances
Calculate distance using Jaccard’s similarity
index
Jaccard’s
• Only 1-1 and 1-0 count, 0-0 do not count
1010011
1001011
1001000
Jaccard’s
• Only 1-1 and 1-0 count, 0-0 do not count
A: 1010011 AB= 0.6
B: 1001011 BC=0.5
C: 1001000 AC=0.2
0.4 (1-AB)
0.5
0.8
Now that we have distances….
• Plot their distribution (clonal vs. sexual)
Now that we have distances….
• Plot their distribution (clonal vs. sexual)
• Analysis:
– Similarity (cluster analysis); a variety of
algorithms. Most common are NJ and UPGMA
Now that we have distances….
• Plot their distribution (clonal vs. sexual)
• Analysis:
– Similarity (cluster analysis); a variety of
algorithms. Most common are NJ and UPGMA
– AMOVA; requires a priori grouping
AMOVA groupings
• Individual
• Population
• Region
AMOVA: partitions molecular variance
amongst a priori defined groupings
Now that we have distances….
• Plot their distribution (clonal vs. sexual)
• Analysis:
– Similarity (cluster analysis); a variety of
algorithms. Most common are NJ and UPGMA
– AMOVA; requires a priori grouping
– Discriminant, canonical analysis
Now that we have distances….
• Plot their distribution (clonal vs. sexual)
• Analysis:
– Similarity (cluster analysis); a variety of algorithms.
Most common are NJ and UPGMA
– AMOVA; requires a priori grouping
– Discriminant, canonical analysis
– Frequency: does allele frequency match expected
(hardy weinberg), F or Wright’s statistsis
The “scale” of disease
• Dispersal gradients dependent on propagule size,
resilience, ability to dessicate, NOTE: not linear
• Important interaction with environment, habitat,
and niche availability. Examples: Heterobasidion
in Western Alps, Matsutake mushrooms that offer
example of habitat tracking
• Scale of dispersal (implicitely correlated to
metapopulation structure)---
S-P ratio in stumps is highly dependent
on distance from true fir and hemlock stands
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San Diego
Have we sampled enough?
• Resampling approaches
• Saturation curves
If we have codominant markers
how many do I need
• Probability calculation based on allele
frequency.
White mangroves:
Corioloposis caperata
Coco Solo
Mananti
Ponsok
David
Coco Solo
0
237
273
307
Mananti
Ponsok
David
0
60
89
0
113
0
Distances between study sites
White mangroves:
Corioloposis caperata
Forest fragmentation can lead to loss of gene flow among
previously contiguous populations. The negative
repercussions of such genetic isolation should most severely
affect highly specialized organisms such as some plantparasitic fungi.
AFLP study on single spores
Coriolopsis caperata on
Laguncularia racemosa
Site
# of isolates
# of loci
% fixed alleles
Coco Solo
11
113
2.6
David
14
104
3.7
Bocas
18
92
15.04
Coco Solo
Coco Solo
Bocas
David
0.000
0.000
0.000
Bocas
0.2083
0.000
0.000
David
0.1109
0.2533
0.000
Distances =PhiST between pairs of
populations. Above diagonal is the Probability
Random d istance > Observed distance (1000
iterations).
From Garbelotto and Chapela,
Evolution and biogeography of matsutakes
Biodiversity within species
as significant as between
species
Using DNA sequences
• Obtain sequence
• Align sequences, number of parsimony
informative sites
• Gap handling
• Picking sequences (order)
• Analyze sequences
(similarity/parsimony/exhaustive/bayesian
• Analyze output; CI, HI Bootstrap/decay indices
Using DNA sequences
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Testing alternative trees: kashino hasegawa
Molecular clock
Outgroup
Spatial correlation (Mantel)
• Networks and coalescence approaches
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.