SUMMARY

• 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..

Phylogenetic relationships within the

Heterobasidion

complex

NJ 0.05 substitutions/site Het INSULARE

Fir-Spruce

True Fir EUROPE Spruce EUROPE True Fir NAMERICA

Pine Europe

Pine EUROPE

Pine N.Am.

Pine NAMERICA

NJ

Geneaology of “S” DNA insertion into P ISG confirms horizontal transfer.

Time 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 NA S 6.11 SISG CA 9.4 SISG CA AWR400 SPISG CA 9b4y SISG CA 15a1x M6 PISG CA NA P 1M PISG MEX 9b2x PISG CA 890 bp CI>0.9

A152R FISG EU A62R SISG EU A90R SISG EU A93R SISG EU J113 FISG EU EU S J14 SISG EU J27 SISG EU J29 SISG EU 0.0005 substitutions/site 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 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

• 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 0.05 substitutions/site Het INSULARE

Fir-Spruce

True Fir EUROPE Spruce EUROPE True Fir NAMERICA

Pine Europe

Pine EUROPE

Pine N.Am.

Pine NAMERICA

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 1 2

• 1010101010 • 1011101010 • 1010101010 • 1010101010 • 1010101010 • 1010000000 • 1010111010 • 1010001010 • 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

• 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: example of habitat tracking

Heterobasidion

in Western Alps, Matsutake mushrooms that offer • Scale of dispersal (implicitely correlated to metapopulation structure)---

S-P ratio in stumps is highly dependent on distance from true fir and hemlock stands

.

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 Manan ti Ponsok David Coco Solo 0 237 273 307 Manan ti 0 60 89 Ponsok 0 113 Distances between study sites David 0 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 plant parasitic fungi.

AFLP study on single spores

Coriolopsis caperata

on

Laguncularia racemosa

Site # of isolates # of loci % fixed alleles Coco Solo 11 113 2.6

Dav id 14 104 3.7

Bocas 18 92 15.04

Coco Solo Bocas David Coco Solo 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

• Testing alternative trees: kashino hasegawa • Molecular clock • Outgroup • Spatial correlation (Mantel) • Networks and coalescence approaches

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