SUMMARY

1
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

2
Evolution and Population genetics

• Positively selected genes
• Negatively selected genes
• Neutral genes normally population genetics
  demands loci used are neutral
• Loci under balancing selection..

3
Evolution and Population genetics

• Positively selected genes
• Negatively selected genes
• Neutral genes normally population genetics
  demands loci used are neutral
• Loci under balancing selection..

4
Evolutionary history

• Darwininan vertical evolutionray models
• Horizontal, reticulated models..

5
Phylogenetic relationships within the
Heterobasidion complex
Fir-Spruce
Pine Europe
Pine N.Am.
6
Geneaology of S DNA insertion into P ISG
confirms horizontal transfer.Time of
cross-over uncertain
NA S
NA P
EU S
890 bp CIgt0.9
EU F
7
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
  (Iaindex of association)

8
How to get multiple loci?

• Random genomic markers
• RAPDS
• Total genome RFLPS (mostly dominant)
• AFLPS
• Microsatellites
• SNPs
• Multiple specific loci
• SSCP
• RFLP
• Sequence informat5ion

9
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

10
Sequence information

• Multiple gene genealogiesdefinitive phylogeny
• Need to ensure gene histories are comparable
  partition of homogeneity test
• Need to use unlinked loci

11
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

12
(No Transcript)
13
Phylogenetic relationships within the
Heterobasidion complex
Fir-Spruce
Pine Europe
Pine N.Am.
14
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

15
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.

16
From the population level to the individual

• Autoinfection vs. alloinfection
• Primary spreadby spores
• Secondary spreadvegetative, clonal spread, same
  genotype . Completely different scales
• Coriolus
• Heterobasidion
• Armillaria
• Phellinus

17
Basic definitions again

• Locus
• Allele
• Dominant vs. codominant marker
• RAPDS
• AFLPs

18
(No Transcript)
19
Root disease center in true fir caused by H.
annosum
20
Ponderosa pine
Incense cedar
21
Yosemite Lodge 1975 Root disease centers
outlined
22
Yosemite Lodge 1997 Root disease centers
outlined
23
(No Transcript)
24
(No Transcript)
25
(No Transcript)
26
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

27
RAPD combination1 2

• 1010101010
• 1010101010
• 1010101010
• 1010101010
• 1010000000

• 1011101010
• 1010111010
• 1010001010
• 1011001010
• 1011110101

28
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

29
Dealing with dominant anonymous multilocus markers

• Need to use large numbers
• Repeatability
• Graph distribution of distances
• Calculate distance using Jaccards similarity
  index

30
Jaccards

• Only 1-1 and 1-0 count, 0-0 do not count
• 1010011
• 1001011
• 1001000

31
Jaccards

• Only 1-1 and 1-0 count, 0-0 do not count
• A 1010011 AB 0.6 0.4 (1-AB)
• B 1001011 BC0.5 0.5
• C 1001000 AC0.2 0.8

32
Now that we have distances.

• Plot their distribution (clonal vs. sexual)

33
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

34
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

35
AMOVA groupings

• Individual
• Population
• Region
• AMOVA partitions molecular variance amongst a
  priori defined groupings

36
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

37
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 Wrights statistsis

38
(No Transcript)
39
(No Transcript)
40
(No Transcript)
41
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)---

42
S-P ratio in stumps is highly dependent on
distance from true fir and hemlock stands
.
.
San Diego
43
Have we sampled enough?

• Resampling approaches
• Saturation curves

44
(No Transcript)
45
(No Transcript)
46
If we have codominant markers how many do I need

• Probability calculation based on allele frequency.

47
White mangroves Corioloposis caperata
48
Distances between study sites
White mangroves Corioloposis caperata
49
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
50
(No Transcript)
51
From Garbelotto and Chapela, Evolution and
biogeography of matsutakes
Biodiversity within species as significant as
between species
52
(No Transcript)
53
(No Transcript)
54
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

55
Using DNA sequences

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

56
(No Transcript)