Microbial
Reproductive
Modes
Fungal Reproduction
Week 12, PMB 220
J. Taylor
The cost of sex is two-fold.
Clonal progeny have twice
as many parental genes.
The Value of Sex? The Red Queen Hypothesis.
"Now, here, you see, it takes all the running
you can do, to keep in the same place."
Lewis Carroll
John Tenniel (illus)
1872.
The Value of Sex?
Muller’s Ratchet
H. Muller, 1964
Goddard,
Godfray
Burt. 2005
Nature
434:636-640
Goddard,
Godfray
Burt
Nature
434:636-40
2005
Harsh
environment
Goddard,
Godfray
Burt
Nature
434:636-40
2005
Benign
environment
Sex is nearly ubiquitous.
Only the bdelloid rotifers have been
claimed to be an old asexual group.
Aydin Örstan
http://users.unimi.it/ricci/html/bdelloid.htm
Numbers of Species of Fungi
Ascomycota
Lichenized fungi
Basidiomycota
Chytridiomycota
Zygomycota
32,267
13,500
22,244
793
1,056
46.0%
18.7%
32.0%
1.0%
1.5%
Mitosporic fungi
14,104
19.6%
Dictionary of the Fungi, Hawksworth et al. 1996
What is a
species?
How do they
reproduce?
Determining the
reproductive mode
of Microbes:
Recombination v. clonality
Clonal:
Association
of Alleles.
Recombining: Lack of Association
Testing for reproductive mode.
Tree Length Test
Compter sex: Resampling
without replacement.
b
OBSERVED
SCRAMBLING
SCRAMBLED
Loci
Loci
1 2 3 4 5 6 7 8 9 10 11
1 2 3 4 5 6 7 8 9 10 11
0
1
0
1
0
1
0
1
0
1
0
0
0
1
1
0
0
1
1
0
0
1
1
0
1
0
1
0
1
0
1
0
1
1
1
1
0
0
1
0
0
0
1
0
1
0
1
1
0
1
0
0
1
0
1
0
0
1
1
1
0
1
0
0
0
1
1
0
1
1
0
1
0
0
1
0
1
1
1
1
0
0
1
0
0
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
0
1
1
0
0
1
1
0
0
1
0
1
1
1
0
1
0
1
1
1
0
Individuals
Individuals
Loci
1 2 3 4 5 6 7 8 9 10 11
0
0
0
1
1
0
0
1
1
0
0
1
1
0
1
0
1
0
1
0
1
0
1
0
1
1
0 1 0
1 0
1
0
1
1
1
0
0
1
0
0
0
1
0
1
0
1
1
0
1
0
0
1
0
1
0
0
1
1
1
0
1
0
0
0
1
c
1
0
1
1
0
1
0
0
1
0
1
1
1
1
0
0
1
0
0
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
0
1
1
0
0
1
1
0
0
1
0
1
1
1
0
1
0
1
1
1
0
Individuals
a
1
1
0
1
0
0
1
1
0
0
0
0
0
1
1
0
0
1
1
0
0
1
1
0
1
0
1
0
1
0
1
0
1
1
1
1
0
0
1
0
0
0
1
0
1
0
1
1
0
1
0
0
1
0
1
0
0
1
1
1
0
1
0
0
0
1
1
0
1
1
0
1
0
0
1
0
1
1
1
1
0
0
1
0
0
0
1
0
1
0
1
0
1
0
1
0
1
0
1
0
0
1
1
0
0
1
1
0
0
1
0
1
1
1
0
1
0
1
1
1
0
Tree
Length
Test
Index of Association
Clonal Reproduction
Distance
matrix
Distance
1
2
3
4
5
6
7
A
B
C
D
E
F
G
Matrix
1
2
3
4
5
6
7
- 0.14286 0.14286 0.57143 0.71429 0.85714 0.28571
1
- 0.28571 0.71429 0.85714 1.00000 0.42857
1
2
- 0.42857 0.57143 0.71429 0.14286
4
5
3
- 0.14286 0.28571 0.28571
5
6
4
1
- 0.14286 0.42857
6
7
5
2
1
- 0.57143
2
3
1
2
3
4
-
Recombining Reproduction
Distance
1
2
3
4
5
6
7
A
B
C
D
E
F
G
Matrix
1
2
3
4
5
6
7
- 0.28571 0.57143 0.57143 0.42857 0.71429 0.42857
2
- 0.57143 0.28571 0.14286 0.71429 0.42857
4
4
- 0.28571 0.42857 0.71429 0.42857
4
2
2
- 0.14286 0.42857 0.42857
3
1
3
1
- 0.57143 0.57143
5
5
5
3
4
- 0.57143
3
3
3
3
4
4
-
IA
CONCORDANCE
C
LO
AL
N
A
B C
D
W X Y
Z
EC
R
O
Gene
Genealogy
Concordance
G
IN
N
BI
M
CONSENSUS
.
Computer sex:
Shuffling variable nucleotides
among genes.
Aspergillus flavus
You have to know
the species before
you can study
reproductive mode.
Example:
Coccidioides immitis
Vasso Koufopanou
Austin Burt
Mat Fisher
Distribution
of
Coccidioides
immitis
Rippon, 1988
Phylogenetic Species in C. immitis
S
CA1
CA2
AZ1
17 fixed sites
AZ2
CA3
TX1
CA4
TX2
CA5
MX1, AG1-5
MX2
C. immitis
C. posadasii
Finding Single Nucleotide Polymorphisms
Agarose and SSCP gels of PCR products
Coccidioides immitis: multilocus genotypes
as single nucleotide polymorphisms (SNPs)
Locus
Isolate
abcdefghijklmnopqrstuvwxy
a1
a2
e2
k
q2
z
aa
am
bg
bk
bl
bq
af
cs
0000111000010100011100101
0000001000010000000000000
0000000000100010000000000
0010100001000111010010001
0000001000000000010000000
0111101110111101111100011
0111111110111101111100000
0000100000001010000000000
0101000000000001110000000
0000000000000000100100000
0001000010000000000111000
0011000000000100100001000
0000100010000101110101001
0000000011000000010101011
Primers
NS1
NS1
NS23
NS2
CNS19
NS24
NS24
NS23
ITS2
ITS4
NS26
ML5.1
ITS4
CS2
ITS5
ITS5
ITS5
NS22
ITS4
CNS19
CNS25
ML5.1
ML3.5
ML5.1
MS1
MS1
ITS1
CS4A
Size(bp)
286
154
183
590
163
260
207
309
165
369
822
433
630
260
Polymorphism
144C/T
40T/C
108TT/C189G/A
20C/T
13A/T
11A/G
66G/A;97C/T
34CTC/--146C/A
233T/C;733A/170A7/A8,9;235A/G;260T/C;293A/G
46T/A
53G/A
Parsimony analysis:
Consensus of 62 most parsimonious trees.
Test of association of alleles: Index of Association
Phylogenetic Species in C. immitis
S
CA1
CA2
AZ1
17 fixed sites
AZ2
CA3
TX1
CA4
TX2
CA5
MX1, AG1-5
MX2
C. immitis
C. posadasii
Isolate
2002
2007
IA, P = 0.28
2279
2271
2273
PTLPT, P = 0.09
2274
2276
2277
2006
2004
2008
2009
2010
2014
2015
91
2017
2649
2268
2269
2005
2267
Epidemic
CA
California
Coccidioides
2275
2012
2013
2281
Fisher et al. 2000
2270
98
2278
2280
3255
3257
3258
3262
3264
2808
2610
435
2011
1036
3272
NCA
Likelihood ratio tests
Kishino-Hasegawa
Two different topologies
Shimodaira-Hasagawa
Multiple topologies
Lichens
Scott Kroken
Trebouxia and Letharia
Letharia columbiana
Question: Are there two
species of Letharia, one
sexual and the other not?
Letharia vulpina
Letharia vulpina
• always produces soredia
• apothecia are rare
Letharia columbiana
• always produces apothecia
• sometimes produces isidia
Are they a “species pair” and how do they reproduce?
Distribution of Letharia species
Xerox
PARC
map
Sexual
Asexual
www.lichen.com
Thomas Nash
Apothecia, filled
with meiotic
ascospores
Soredia, algal
cells wrapped
in hyphae
Letharia 6 loci
51 individuals
6 species
suggested
Kroken and Taylor. 2000. Mycologia 93:38-53
Question: does the lichen
outbreed or inbreed?
Fertilization
Spermagonium-produces spermatia
Trichogyne-fuses with spermatium
Paternity analysis of lichen apothecia
Parent and progeny
Letharia “lupina” paternity analysis
‘lupina’ locus CS EarI
Mom1 and 7 kids
‘lupina’ ITS 1F/ 2 SacI
Mom2 and 6 kids
Mom1 and 7 kids
Mom2 and 6 kids
All 36 apothecia in both species
are the result of outcrossing
Kroken and Taylor 2001 Fungal Genetics & Biology 34:83-92
Outbreeding and
separate fertilizations
Dispersal of Letharia vulpina with its alga
Xerox
PARC
map
Högberg et al. 2002. Molecular Ecology 11:1191-1196
Recombining and Clonal in Letharia
Recombining:
North American
sorediate
Clonal: European and North African
sorediate Letharia species
Recombining:
North American
apotheciate
Daubin et al. 2003. Science 301:829-832
More polymorphism?
Microsatellites or
Short Tandem Repeats
Molecular markers- Microsatellites
• Dinucleotide repeats randomly dispersed through the genome
ctgcgtgtgacatACACACACACACACActgtatgtgatc
• Highly polymorphic and multialleleic due to polymerase
slippage during strand replication
Cocci_1
Cocci_2
Cocci_3
Cocci_4
ctgcgtgtgacatACACACACACACACA--------ctgtatgt
ctgcgtgtgacatACACACACACACACACA------ctgtatgt
ctgcgtgtgacatACACACACACACACACACA----ctgtatgt
ctgcgtgtgacatACACACACACACACACACACACActgtatgt
Allele size (bp)
0
0
220
226
228
229
237
238
239
240
241
243
249
252
253
255
257
258
259
227
212
210
209
208
207
206
204
208
209
210
211
212
213
214
215
216
217
218
219
220
227
228
229
231
232
233
235
240
241
247
248
249
250
426
424
422
420
419
418
416
414
621
ACJ
0.5
0.4
0.2
0.1
0.8
1
0.6
0.75
0.4
0.5
0.2
0.25
0
0
KO1
141
143
145
147
149
150
151
152
153
154
156
160
162
163
164
166
168
0.25
247
0.4
246
0.5
245
0.6
243
0.75
241
0.8
239
KO7
238
1
203
GA1
237
0
235
0
400
0
401
0.25
188
0.25
202
0.5
234
0.3
397
0.1
0.5
399
0.75
233
0.6
186
0.75
187
228
226
224
222
220
218
216
1
231
264
263
262
261
260
259
258
256
255
254
253
206
1
229
301
299
297
296
295
294
293
292
252
234
Microsatellites
262
GAC2
GA37
0.3
0.2
0
Allele size (bp)
KO3
Allele size (bp)
KO9
0.5
0.4
0.3
0.2
0.2
0.1
0
Microsatellite distance
58
Flanking-sequence distance
Central
Calif.
Southern
Calif.
CA
61
Arizona
99
59
100
70
69
Texas
64
68
non-CA
These trees have the same topology (Kishino-Hasegawa test non-significant)
THE MICROSATELLITE MARKERS ARE GOOD
(Fisher et al. Mol. Biol. Evol. 2000)
Renaming the species
California
- Coccidioides immitis Rixford and Gilchrist 1896
non-California
- Coccidioides posadasii after Alejandro Posadas
All populations
Arizona
Texas/
South America
North America/ Mexico C. immitis ( ) and C. posadasii ( )
show isolation by distance...
50
45
40
35
r = 0.694**
30
25
20
15
r = 0.905
10
5
0
0
200
400
600
Geographical
800
1000
distance
1200
1400
(miles)
1600
1800
...but NOT if South American isolates (all C. posadasii)
are included…
50
45
40
r = 0.694**
35
30
25
20
r = 0.023
15
10
5
0
0
1000
2000
3000
4000
5000
Geographical distance (miles)
6000
• S. American isolates contain 6% of the variation found in N. America
• 28% of loci are in linkage disequlibrium (7% in N. America)
• This is a bottlenecked population
…and is descended from
the TEXAS! population of
Coccidioides posadasii
Genetic dating show that South American
populations were founded from those in
North America between 9,000 - 140,000 BP
(the Pleistocene)
Migration of Homo sapiens into South America by
10,000 BC
Jared Diamond ‘Guns, Germs and Steel’, 1997
How did non-CA C. immitis arrive in South America?
Host-pathogen dispersal:
• 9,000 year old bones of Bison antiquus from Nebraska
contain C. immitis spherules. Demonstrates potential for
long-distance dispersal with a host
• Human infections are viable for more than 12 years
• Ancient Amerindian middens contain high concentrations of
C. immitis
• Documented invasion of South America by the Amerindians
12,500 yrs bp.
Does the present distribution of C. posadasii reflect the
co-dispersal of a host and its pathogen?
Recombining and Clonal in Coccidioides
Recombining
Recombining
Clonal (C. posadasii in Latin Amer?)
Daubin et al. 2003. Science 301:829-832 Fig 1
Daubin et al.
2003. Science
301:829-832
Fig 2
Daubin et al.
2003. Science
301:829-832
Fig 3