Title: Overview
1Overview
- Armillaria bulbosa (gallica)
- Known as the Humungous Fungus, or honey mushroom
- Form rhizomorphs, which make up much of the
humungous part - Basidiocarp cap 6 cm in diameter, stem is 5-10
cm tall - Facultative tree root pathogen
2Life cycle Reproduction
- Sexual
- Basidiocarps release spores (n) after karyogamy
and meiosis - 2 mating-type loci, each with multiple alleles in
the population - Isolates (n) must have different alleles at two
mating type loci to be sexually compatible - Asexual
- vegetative spreading of rhizomorph
- The large mass of rhizomorph that is genetically
isolated is called a clone
3Building up the question
- By extending the areas sampled in subsequent
years, we were finally able to delimit the large
area occupied by this genotype and then go on to
show that this genotype likely represents and
individual -
- - Myron Smith
4Researchers Question
- The clonal individual is especially difficult
to define because the network of hyphae is
underground - How do you unambiguously identify an individual
fungi within a local population?
5Approach
- 1. Collect samples
- 2. Check mating type
- - Somatic compatibility test
- - Distrubution of mating-type alleles
- 3. Molecular testing
- - RFLP
- - RAPD
- 4. Statistics
- 5. More testing
6Methods and Materials 1
- 1. Collecting samples
- Researcher collected samples over a 30 hectare
area by baiting Armillaria with poplar stakes and
taking tissues and spores - They then grew the successfully colonized stakes
in soil taken from the study site - Each fungal colony cultured was called an isolate.
7Methods and Materials 2
Example (not Armillaria)
- 2. Checking mating type
- - Somatic incompatibilityFor two fungal
isolates to fuse, all somatic compatibility loci
must be the same. - Fusion means theyre clones ?
8Methods and Materials 2
- 2. Checking mating type
- - Distrubution of mating alleles
- Mating occurs only when coupled isolates have
different alleles at two unlinked, multiallelic
loci A and B. (They have an incompatibility
system) - If fruit bodies had the same alleles at A and B,
and were collected from the same area, they were
assumed to be from the same clone
9Result 1
- Somatic compatilbilty
- isolates from vegetative mycelium from a large
sampling area fused - Mating alleles
- They had the same mating type
10Result 1
- Clone 1 was found to exceed 500 m in diameter
- Used previously collected mtDNA restriction
fragment patterns
11Sensitivity of Approach
- Problem These tests alone are not enough to
distinguish a clone from closely related
individuals
12Why?
- Q The first two tests were not sensitive enough
to tell a clone from a close relativeWhy? - A Spores from same point source have the same
mating-type alleles, but the offspring they
produce after inbreeding are genetically
distinct.
13Methods and Materials 3
- 3. Molecular Testing
-
- - RFLP analysis at 5 polymorphic, heterozyg. loci
of mtDNA from Clone 1 - - RAPD analysis at 11 loci
14RAPDS vs. RFLPs
- Use 1 short PCR primer
- When it finds match on template at a distance
that can be amplified (primer binds twice within
50 to 2000 bp) RAPD amplicon - Dominant, annoymous
- Total genomic, vs single locus
- Use endonuclease to digest DNA at specific
restriction site - Run digest and see how amplicon was cut
- Single locus is co-dominant
15Result 2
- RFLP
- All 5 loci from Clone 1 were heterozygous and
identical (both alleles present at loci
1,1) - RAPD
- All 11 RAPD products were present in all
vegetative isolates
16Statistical Analysis
- The probability of retaining heterozygosity at
each parental locus in an individual produced by
mating of sibling monospore isolates - 0.0013
- So they were pretty confident that cloning was
responsible for their results, not inbreeding
17More testing, just in case
- To be completely confident, they tested
- 1) that nearby Clone 2 was different and lacked 5
of the Clone 1 heterozyg. RAPD fragments, - 2) more loci, totaling
- 20 RAPD fragments
- 27 nuclear DNA RFLP fragments
- all were identical in Clone 1
18Sensitivity of RAPDs
- Tested on subset of spores from same basidiocarp
- RAPDs differentiated among full sibs
19Conclusions
- Somatic compatibility, mating allele loci, mtDNA,
RFLP, and RAPD tests all indicate that a single
organism could indeed occupy a 15 hectare area
20Conclusions
- The larger individual, Clone 1 was estimated to
weigh 9700 kg and be over 1500 years old
21Implications
- ?????
- Fungi are one of the oldest and largest organisms
on the planet - Recycle nutrientsvery important!
- Armillaria bulbosa also a pathogen its effects
on forest above may be huge as well.
22HOST-SPECIFICITY
- Biological species
- Reproductively isolated
- Measurable differential size of structures
- Gene-for-gene defense model
- Sympatric speciation Heterobasidion, Armillaria,
Sphaeropsis, Phellinus, Fusarium forma speciales
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24Phylogenetic relationships within the
Heterobasidion complex
Fir-Spruce
Pine Europe
Pine N.Am.
25The biology of the organism drives an epidemic
- Autoinfection vs. alloinfection
- Primary spreadby spores
- Secondary spreadvegetative, clonal spread, same
genotype . Completely different scales (from
small to gigantic) - Coriolus
- Heterobasidion
- Armillaria
- Phellinus
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27OUR ABILITY TO
- Differentiate among different individuals
(genotypes) - Determine gene flow among different areas
- Determine allelic distribution in an area
28WILL 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
29IN ORDER TO UNDERSTAND PATTERNS OF INFECTION
- If John gave directly Mary an infection, and Mary
gave it to Tom, they should all have the same
strain, or GENOTYPE (comparisonsecondary spread
among forest trees) - If the pathogen is airborne and sexually
reproducing, Mary John and Tom will be infected
by different genotypes. But if the source is the
same, the genotypes will be sibs, thus related
30Recognition 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.
31Recognition of self vs. non self
- What are the chances two different individuals
will have the same set of VC alleles? - Probability calculation (multiply frequency of
each allele) - More powerful the larger the number of loci
- and the larger the number of alleles per locus
32Recognition of self vs. non self
- It is possible to have different genotypes with
the same vc alleles - VC grouping and genotyping is not the same
- It allows for genotyping without genetic tests
- Reasons behing VC system protection of
resources/avoidance of viral contagion
33Somatic incompatibility
34More on somatic compatibility
- Perform calculation on power of approach
- Temporary compatibility allows for cytoplasmic
contact that then is interrupted this temporary
contact may be enough for viral contagion
35SOMATIC 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 nn 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
36SOMATIC COMPATIBILITY
- SC can be used to identify genotypes
- SC is regulated by multiple loci
- Individual that are compatible (recognize one
another as self, are within the same SC group) - SC group is used as a proxy for genotype, but in
reality, you may have some different genotypes
that by chance fall in the same SC group - Happens often among sibs, but can happen by
chance too among unrelated individuals
37Recognition of self vs. non self
- What are the chances two different individuals
will have the same set of VC alleles? - Probability calculation (multiply frequency of
each allele) - More powerful the larger the number of loci
- and the larger the number of alleles per locus
38Recognition of self vs. non selfprobability of
identity (PID)
- 4 loci
- 3 biallelelic
- 1 penta-allelic
- P 0.5x0.5x0.5x0.20.025
- In humans 99.9, 1000, 1 in one million
39INTERSTERILITY
- 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)
40INTERSTERILITY
- Basis for speciation
- These alleles are selected for more strongly in
sympatry - You can have different species in allopatry that
have not been selected for different IS alleles
41MATING
- Two haploids need to fuse to form nn
- Sex needs to increase diversity need different
alleles for mating to occur - Selection for equal representation of many
different mating alleles
42MATING
- If one individuals is source of inoculum, then
the same 2 mating alleles will be found in local
population -
- If inoculum is of broad provenance then multiple
mating alleles should be found
43MATING
- How do you test for mating?
-
- Place two homokaryons in same plate and check for
formation of dikaryon (microscopic clamp
connections at septa)
44Clamp connections
45MATING ALLELES
- All heterokaryons will have two mating allelels,
for instance a, b - There is an advantage in having more mating
alleles (easier mating, higher chances of finding
a mate) - Mating allele that is rare, may be of migrant
just arrived - If a parent is important source, genotypes should
all be of one or two mating types
46Two scenarios
- A, A, B, C, D, D, E, H, I, L
47Two scenarios
- A, A, B, C, D, D, E, H, I, L
- Multiple source of infections (at least 4
genotypes)
- A, A, A,B, B, A, A
- Siblings as source of infection (1 genotype)
48SEX
- Ability to recombine and adapt
- Definition of population and metapopulation
- Different evolutionary model
- Why sex? Clonal reproductive approach can be very
effective among pathogens
49Long branches in between groups suggests no sex
is occurring in between groups
Fir-Spruce
Pine Europe
Pine N.Am.
50Small branches within a clade indicate sexual
reproduction is ongoing within that group of
individuals
NA S
NA P
EU S
890 bp CIgt0.9
EU F
51Index of association
- Ia if same alleles are associated too much as
opposed to random, it means sex is not occurring - Association among alleles calculated and compared
to simulated random distribution
52Evolution and Population genetics
- Positively selected genes
- Negatively selected genes
- Neutral genes normally population genetics
demands loci used are neutral - Loci under balancing selection..
53Evolution and Population genetics
- Positively selected genes
- Negatively selected genes
- Neutral genes normally population genetics
demands loci used are neutral - Loci under balancing selection..
54Evolutionary history
- Darwininan vertical evolutionary models
- Horizontal, reticulated models..
55Phylogenetic relationships within the
Heterobasidion complex
Fir-Spruce
Pine Europe
Pine N.Am.
56Geneaology 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
57Because 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), and to identify
genotypes, and to study gene flow
58Basic definitions again
- Locus
- Allele
- Dominant vs. codominant marker
- RAPDS
- AFLPs
59How 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!)
60Example 2 Distinguishing taxa in the Pleurotus
eryngii (King Oyster Mushroom) complex using
AFLPs (Urbanelli et al., Appl. Microbiol.
Biotechnol. (2007) 74592-600)
Photo The New York Times
Photo Wikimedia Commons
60
61Distinguishing taxa in the Pleurotus eryngii
(King Oyster Mushroom) complex using AFLPs
- Goal to determine, using multilocus genotypes,
whether the distinction between Pleurotus
eryngii, P. ferulae, and P. eryngii var.
nebrodensis is supported by genetic data - 90 populations sampled
- 94 AFLP loci scored
61
P. ferulae (http//steinpilz.up.seesaa.net)
62Sample AFLP Gel
62
63AFLP Data Map from Urbanelli et al. (2007)
63
64AFLP Data Map with UPGMA dendogram from Urbanelli
et al. (2007)
64
65RAPDS 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)
66RAPDS 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)
67RAPDS can also be obtained with Arbitrary Primed
PCR
- Use longer primers
- Use less stringent annealing conditions
- Less variability in results
68Result series of bands that are present or
absent (1/0)
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70Root disease center in true fir caused by H.
annosum
71Ponderosa pine
Incense cedar
72Yosemite Lodge 1975 Root disease centers
outlined
73Yosemite Lodge 1997 Root disease centers
outlined
74WORK ON PINES HAD DEMONSTRATED INFECTIONS ARE
MOSTLY ON STUMPS
- Use meticulous field work and genetics
information to reconstruct disease from infection
to explosion - On firs/sequoia if the stump theory were also
correct we would find a stump within the outline
of each genotype
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81Are 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
- Calculate P
82RAPD combination1 2
- 1010101010
- 1010101010
- 1010101010
- 1010101010
- 1010000000
- 1011101010
- 1010111010
- 1010001010
- 1011001010
- 1011110101
83Conclusions
- 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
84If we have codominant markers how many do I need
- IDENTITY tests probability calculation based
on allele frequency Multiplication of
frequencies of alleles - 10 alleles at locus 1 P10.1
- 5 alleles at locus 2 P20,2
- Total P P1P20.02
85Have we sampled enough?
- Resampling approaches
- Saturation curves
- A total of 30 polymorphic alleles
- Our sample is either 10 or 20
- Calculate whether each new sample is
characterized by new alleles
86Saturation (rarefaction) curves
No Of New alleles
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
87Dealing with dominant anonymous multilocus markers
- Need to use large numbers (linkage)
- Repeatability
- Graph distribution of distances
- Calculate distance using Jaccards similarity
index
88Jaccards
- Only 1-1 and 1-0 count, 0-0 do not count
- 1010011
- 1001011
- 1001000
89Jaccards
- 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
90Now that we have distances.
- Plot their distribution (clonal vs. sexual)
91Now that we have distances.
- Plot their distribution (clonal vs. sexual)
- Analysis
- Similarity (cluster analysis) a variety of
algorithms. Most common are NJ and UPGMA
92Now 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
93AMOVA groupings
- Individual
- Population
- Region
- AMOVA partitions molecular variance amongst a
priori defined groupings
94Example
- SPECIES X 50blue, 50 yellow
95AMOVA example
Scenario 1
Scenario 2
v
POP 1
POP 2
v
96Expectations for fungi
- Sexually reproducing fungi characterized by high
percentage of variance explained by individual
populations - Amount of variance between populations and
regions will depend on ability of organism to
move, availability of host, and - NOTE if genotypes are not sensitive enough so
you are calling the same things that are
different you may get unreliable results like 100
variance within pops, none among pops
97Results Jaccard similarity coefficients
P. nemorosa
P. pseudosyringae U.S. and E.U.
98P. pseudosyringae genetic similarity patterns are
different in U.S. and E.U.
99Results P. nemorosa
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101The 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)---
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105RAPDSgt not used often now
106RAPD DATA W/O COSEGREGATING MARKERS
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108PCA
109AFLP
- Amplified Fragment Length Polymorphisms
- Dominant marker
- Scans the entire genome like RAPDs
- More reliable because it uses longer PCR primers
less likely to mismatch - Priming sites are a construct of the sequence in
the organism and a piece of synthesized DNA
110How are AFLPs generated?
- AGGTCGCTAAAATTTT (restriction site in red)
- AGGTCG CTAAATTT
- Synthetic DNA piece ligated
- NNNNNNNNNNNNNNCTAAATTTTT
- Created a new PCR priming site
- NNNNNNNNNNNNNNCTAAATTTTT
- Every time two PCR priming sitea are within
400-1600 bp you obtain amplification
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113Distances between study sites
White mangroves Corioloposis caperata
114Forest 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
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117Using 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
118Using DNA sequences
- Testing alternative trees kashino hasegawa
- Molecular clock
- Outgroup
- Spatial correlation (Mantel)
- Networks and coalescence approaches
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121From Garbelotto and Chapela, Evolution and
biogeography of matsutakes
Biodiversity within species as significant as
between species
122Microsatellites or SSRs
- AGTTTCATGCGTAGGT CG CG CG CG CG
AAAATTTTAGGTAAATTT - Number of CG is variable
- Design primers on FLANKING region, amplify DNA
- Electrophoresis on gel, or capillary
- Size the allele (different by one or more
repeats if number does not match there may be
polimorphisms in flanking region) - Stepwise mutational process (2 to 3 to 4 to 3 to2
repeats)
123ACACACACACACACACAC
- MS18 (AC)38 218 bp
- (AC)39 220 bp
- (AC)40 222 bp
- MS43a (CAGA)70 373 bp
- MS43a (CAGA)71 377 bp
- MS43a (CAGA)72 381 bp
- (220-218)2 22
- (222-218)2 42
- (377-373)2 42
- (381-373)2 82
- (39-38)2 12
- (40-38)2 22
-
- (71-70)2 12
- (72-70)2 22
AMOVA Analysis of Molecular Variance
123
124Example 1 Origins of the Sudden Oak Death
Epidemic in California(Mascheretti et al.,
Molecular Ecology (2008) 17 2755-2768)
Photo UC Davis
Photo www.membranetransport.org
124
Photo Northeast Plant Diagnostic Network
125Spatial autocorrelation
Within approx. 100 meters the genetic structure
correlates with the geographical distance
10 100 1000
Geographical distance (m)
125
126Spatial autocorrelation
Morans I (coefficient of departure from spatial
randomness) correlates with distance up to
Distribution of genotypes (6 microsatellite
markers) in different populations of P.ramorum
in California
126
127NJ tree of P. ramorum populations in California
HU-1
MA-1
HU-2
MA-2
SC-2 MO-1 MO-2
127
128Example microsatellites genotyping of P.
ramorum isolates
- Phytophthora ramorum (Oomycete)
- causal agent of Sudden Oak Death (SOD) first
reported in California in 1994 - SOD affects tanoak (Lithocarpus densiflora),
coast live oak (Quercus agrifolia), Californian
black oak (Quercus kelloggii), and Canyon live
oak (Quercus chrysolepis) - P.ramorum also cause a disease characterized
mostly by leaf blight and/or branch dieback in
over 100 species of both wild and ornamental
plants, including California bay laurel
(Umbellularia cailfornica), California redwood
(Sequoia sempervirens), Camellia and
Rhododrendron species
Collection of infected bay leaves from several
forests in Sonoma, Monterey, Marin, Napa,
Alameda, San Mateo
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129Microsatellites (I)mating type A1 (EU) and
mating type A2 (US)
- A2 (US) A1 (EU)
- Locus 29 325/ - 325/337
- -/337
-
- Locus 33 315/337 325/337
- Locus 65 234/252 236/244
- 220/222
129
130Microsatellites (II)mating type A2 (US)
- MS39a (GA)11 129 bp
- MS39b (GA)4(GATA)31 234, 242, 246, 250, 254 bp
- MS43a (CAGA)69 309, 329, 349, 353, 357, 361,
365, 369, 373, 377, 381 bp - MS43b (CAGA)75()(CAGA)16 416, 420, 466, 470,
474, 476, 478, 482, 486, 490, 494, 498 bp - MS45 (TCCG)11 167, 183, 187 bp
- MS18 (AC)39 218, 220, 222, 254, 264, 272, 274,
276, 278, 282 bp - MS64 (CT)16 342, 374, 376, 378 bp
130
131- Ind. MS39a MS39b MS43a MS43b MS45 MS18 MS64 Matin
g type - 1 129-129 246-246 369-369 486-486 167-187 220-278
342-374 A1 - 2 129-129 246-246 369-369 486-486 167-187 220-278
342-374 A1 - 3 129-129 246-246 373-373 486-486 167-187 220-274
342-374 A1 - 4 129-129 246-246 373-373 486-486 167-187 220-27
4 342-378 A1 - 5 129-129 246-246 373-373 486-486 167-187 220-27
4 342-378 A1 - 6 129-129 246-246 373-373 486-486 167-187 220-27
4 342-378 A1 - 7 129-129 246-246 373-373 486-486 167-187 220-27
8 342-378 A1 - 8 129-129 246-246 373-373 486-486 167-187 220-27
8 342-374 A1 - 9 129-129 250-250 369-369 486-486 167-187 220-278
342-374 A1 - 10 129-129 250-250 369-369 486-486 167-187 220-2
78 342-374 A1 - 11 129-129 250-250 369-369 486-486 167-187 220-27
8 342-374 A1 - 12 129-129 250-250 377-377 490-490 167-187 220-2
78 342-374 A1 - 13 129-129 250-250 377-377 490-490
167-187 220-278 342-381 A1 - 14 129-129 250-250 377-377 490-490
167-187 220-278 342-381 A1 - 15 129-129 250-250 377-377 490-490
167-187 220-278 342-381 A1 - 16 129-129 246-246 377-377 490-490
167-187 220-278 342-374 A1 - 17 129-129 246-246 377-377 486-486 167-187 220-2
78 342-374 A1
131
132 Ind. MS39a MS39b MS43a MS43b MS45 MS18 MS64 Matin
g type 1 11-11 32-32 69-69 17-17 11-16 39-68 18-
29 A1 2 11-11 32-32 69-69 17-17 11-16 39-68
18-29 A1 3 11-11 32-32 70-70 17-17 11-16
39-66 18-29 A1 4 11-11 32-32 70-70 17-17
11-16 39-66 18-30 A1 5 11-11 32-32 70-70
17-17 11-16 39-66 18-30 A1 6 11-11 32-32
70-70 17-17 11-16 39-66 18-30 A1 7 11-11
32-32 70-70 17-17 11-16 39-68 18-30
A1 8 11-11 32-32 70-70 17-17 11-16 39-68
18-29 A1 9 11-11 33-33 69-69 17-17 11-16
39-68 18-29 A1 10 11-11 33-33 69-69 17-17
11-16 39-68 18-29 A1 11 11-11 33-33 69-69
17-17 11-16 39-68 18-29 A1 12 11-11 33-33
71-71 18-18 11-16 39-68 18-29 A1 13 11-11
33-33 71-71 18-18 11-16 39-68
18-31 A1 14 11-11 33-33 71-71 18-18 11-16
39-68 18-31 A1 15 11-11 33-33 71-71 18-18
11-16 39-68 18-31 A1 16 11-11 32-32 71-71
18-18 11-16 39-68 18-29 A1 17 11-11
32-32 71-71 17-17 11-16 39-68 18-29
A1 18 11-11 32-32 69-69 17-17 11-16 39-68
18-29 A1 19 11-11 32-32 72-72 17-17 11-16
40-null 18-29 A2 20 11-11 9 32-32 72-72
19-19 11-16 40-null 18-29 A2
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133- China Camp State Park (Marin) n24
- Bean Creek Forest (Santa Cruz) n24
- Nurseries n14
133