microbial reproductive modes fungal reproduction week 12,...
TRANSCRIPT
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MicrobialReproductive
ModesFungal Reproduction
Week 12, PMB 220
J. Taylor
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The cost of sex is two-fold.Clonal progeny have twiceas many parental genes.
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Lewis CarrollJohn Tenniel (illus)1872.
The Value of Sex? The Red Queen Hypothesis."Now, here, you see, it takes all the runningyou can do, to keep in the same place."
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The Value of Sex?
Muller’s Ratchet
H. Muller, 1964
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Goddard,GodfrayBurt. 2005Nature434:636-640
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Goddard,GodfrayBurtNature434:636-402005
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Goddard,GodfrayBurtNature434:636-402005
Benignenvironment
Harshenvironment
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Aydin Örstan
http://users.unimi.it/ricci/html/bdelloid.htm
Sex is nearly ubiquitous.Only the bdelloid rotifers have beenclaimed to be an old asexual group.
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Numbers of Species of Fungi
Ascomycota 32,267 46.0%Lichenized fungi 13,500 18.7%Basidiomycota 22,244 32.0%Chytridiomycota 793 1.0%Zygomycota 1,056 1.5%
Mitosporic fungi 14,104 19.6%
Dictionary of the Fungi, Hawksworth et al. 1996
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What is aspecies?
How do they reproduce?
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Determining thereproductive mode
of Microbes:Recombination v. clonality
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Clonal:Associationof Alleles.
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Recombining: Lack of Association
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Testing for reproductive mode.
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Tree Length Test
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00110011001
10110100101
01010101010
10101010101
11100100010
10110100101
00111010001
11100100010
10101010101
00110011001
01110101110
Individuals
OBSERVED
00110011001
10110100101
10101010101
11100100010
10110100101
00111010001
11100100010
10101010101
00110011001
01110101110
Individuals
SCRAMBLING
0
0
1101
0 101
0
00110011001
10110100101
110100110
10101010101
11100100010
10110100101
00111010001
11100100010
10101010101
00110011001
01110101110
Individuals
SCRAMBLED
0
0
a b c
1 2 3 4 5 6 7 8 9 10 11 1 2 3 4 5 6 7 8 9 10 11 1 2 3 4 5 6 7 8 9 10 11Loci Loci Loci
Compter sex: Resampling without replacement.
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TreeLengthTest
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Index of Association
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Clonal Reproduction
1 2 3 4 5 6 71 A - 0.14286 0.14286 0.57143 0.71429 0.85714 0.285712 B 1 - 0.28571 0.71429 0.85714 1.00000 0.428573 C 1 2 - 0.42857 0.57143 0.71429 0.142864 D 4 5 3 - 0.14286 0.28571 0.285715 E 5 6 4 1 - 0.14286 0.428576 F 6 7 5 2 1 - 0.571437 G 2 3 1 2 3 4 -
Distance Matrix
Recombining Reproduction
1 2 3 4 5 6 71 A - 0.28571 0.57143 0.57143 0.42857 0.71429 0.428572 B 2 - 0.57143 0.28571 0.14286 0.71429 0.428573 C 4 4 - 0.28571 0.42857 0.71429 0.428574 D 4 2 2 - 0.14286 0.42857 0.428575 E 3 1 3 1 - 0.57143 0.571436 F 5 5 5 3 4 - 0.571437 G 3 3 3 3 4 4 -
Distance Matrix
Distancematrix
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IA
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.
CONCORDANCE
CONSENSUS
A B C D W X Y ZRECOMBINING
CLONAL
GeneGenealogyConcordance
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Computer sex:Shuffling variable nucleotidesamong genes.
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Aspergillus flavus
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You have to knowthe species before
you can studyreproductive mode.
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Example:Coccidioides immitisVasso KoufopanouAustin BurtMat Fisher
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Distributionof
Coccidioidesimmitis
Rippon, 1988
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Phylogenetic Species in C. immitisS
AZ1
AZ2
TX1
MX2
MX1, AG1-5
TX2
CA1
CA2
CA3
CA4
CA5
17 fixed sites
C. immitis C. posadasii
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Finding Single Nucleotide PolymorphismsAgarose and SSCP gels of PCR products
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Coccidioides immitis: multilocus genotypesas single nucleotide polymorphisms (SNPs)
Locus Isolate Size(bp) Polymorphismabcdefghijklmnopqrstuvwxy
a1 0000111000010100011100101 NS1 ITS5 286 144C/Ta2 0000001000010000000000000 NS1 ITS5 154 40T/Ce2 0000000000100010000000000 NS23 ITS5 183 108TT/C-k 0010100001000111010010001 NS2 NS22 590 189G/A
q2 0000001000000000010000000 CNS19 ITS4 163 20C/Tz 0111101110111101111100011 NS24 CNS19 260 13A/T
aa 0111111110111101111100000 NS24 CNS25 207 11A/Gam 0000100000001010000000000 NS23 ML5.1 309 66G/A;97C/Tbg 0101000000000001110000000 ITS2 ML3.5 165 34CTC/---bk 0000000000000000100100000 ITS4 ML5.1 369 146C/Abl 0001000010000000000111000 NS26 MS1 822 233T/C;733A/-bq 0011000000000100100001000 ML5.1 MS1 433 170A7/A8,9;235A/G;260T/C;293A/Gaf 0000100010000101110101001 ITS4 ITS1 630 46T/Acs 0000000011000000010101011 CS2 CS4A 260 53G/A
Primers
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Parsimony analysis:Consensus of 62 most parsimonious trees.
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Test of association of alleles: Index of Association
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Phylogenetic Species in C. immitisS
AZ1
AZ2
TX1
MX2
MX1, AG1-5
TX2
CA1
CA2
CA3
CA4
CA5
17 fixed sites
C. immitis C. posadasii
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91
98
Isolate
20052267
20122013
2275
22812270
22712273227422762277
2002
20042006
2007
200820092010201420152017264922682269
2278
2279
22803255325732583262326428082610435201110363272
EpidemicCA
NCA
IA, P = 0.28
PTLPT, P = 0.09
CaliforniaCoccidioides
Fisher et al. 2000
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Likelihood ratio tests
Kishino-HasegawaTwo different topologies
Shimodaira-HasagawaMultiple topologies
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Lichens
Trebouxia and Letharia
Scott Kroken
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Question: Are there twospecies of Letharia, one
sexual and the other not?
Letharia columbiana
Letharia vulpina
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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?
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Distribution of Letharia species
XeroxPARCmap
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Thomas Nash
Apothecia, filledwith meioticascospores
www.lichen.com
Soredia, algalcells wrapped
in hyphae
Sexual Asexual
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Letharia 6 loci51 individuals
6 species suggested
Kroken and Taylor. 2000. Mycologia 93:38-53
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Question: does the lichenoutbreed or inbreed?
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Paternity analysis of lichen apothecia
Fertilization
Spermagonium--produces spermatia
Trichogyne--fuses with spermatium
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Parent and progeny
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Letharia “lupina” paternity analysis
All 36 apothecia in both speciesare the result of outcrossing
‘lupina’ locus CS EarI ‘lupina’ ITS 1F/ 2 SacI
Mom1 and 7 kids Mom2 and 6 kids
Mom2 and 6 kidsMom1 and 7 kids
Kroken and Taylor 2001 Fungal Genetics & Biology 34:83-92
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Outbreeding andseparate fertilizations
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Dispersal of Letharia vulpina with its alga
XeroxPARCmap
Högberg et al. 2002. Molecular Ecology 11:1191-1196
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Recombining:North Americansorediate
Recombining:North Americanapotheciate
Clonal: European and North African sorediate Letharia species
Recombining and Clonal in Letharia
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Daubin et al. 2003. Science 301:829-832
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More polymorphism?
Microsatellites orShort Tandem Repeats
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Molecular markers- Microsatellites
• Dinucleotide repeats randomly dispersed through the genome
ctgcgtgtgacatACACACACACACACActgtatgtgatc
• Highly polymorphic and multialleleic due to polymerase slippage during strand replication
Cocci_1 ctgcgtgtgacatACACACACACACACA--------ctgtatgtCocci_2 ctgcgtgtgacatACACACACACACACACA------ctgtatgtCocci_3 ctgcgtgtgacatACACACACACACACACACA----ctgtatgtCocci_4 ctgcgtgtgacatACACACACACACACACACACACActgtatgt
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0
0.1
0.2
0.3
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
GA37
0
0.25
0.5
0.75
1
397
399
400
401
414
416
418
419
420
422
424
426
621
0
0.25
0.5
0.75
1
206
216
218
220
222
224
226
228
Allele size (bp)
GAC2
0
0.1
0.2
0.3
0.4
0.5
0.6234
252
253
254
255
256
258
259
260
261
262
263
264
Allele size (bp)
GA1
0
0.2
0.4
0.6
0.8
186
187
188
202
203
204
206
207
208
209
210
212
227
ACJ
0
0.25
0.5
0.75
1
220
226
228
229
237
238
239
240
241
243
249
252
253
255
257
258
259
KO3
0
0.25
0.5
0.75
1
262
292
293
294
295
296
297
299
301
Allele size (bp)
KO7
0
0.2
0.4
0.6
0.8229
231
233
234
235
237
238
239
241
243
245
246
247
KO1
0
0.1
0.2
0.3
0.4
0.5
141
143
145
147
149
150
151
152
153
154
156
160
162
163
164
166
168
KO9
Microsatellites
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Microsatellite distance Flanking-sequence distance
These trees have the same topology (Kishino-Hasegawa test non-significant)THE MICROSATELLITE MARKERS ARE GOOD
(Fisher et al. Mol. Biol. Evol. 2000)
100
64
70
61
69
5999
68
58
CA
non-CA
CentralCalif.
SouthernCalif.
Arizona
Texas
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California- Coccidioides immitis Rixford and Gilchrist 1896
non-California- Coccidioides posadasii after Alejandro Posadas
Renaming the species
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All populations
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Arizona
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Texas/ South America
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North America/ Mexico C. immitis ( ) and C. posadasii ( )show isolation by distance...
0
5
10
15
20
25
30
35
40
45
50
0 200 400 600 800 1000 1200 1400 1600 1800
Geographical distance (miles)
r = 0.905
r = 0.694**
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05
101520253035404550
0 1000 2000 3000 4000 5000 6000Geographical distance (miles)
r = 0.023
r = 0.694**
...but NOT if South American isolates (all C. posadasii) are included…
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• 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
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Genetic dating show that South American populations were founded from those in North America between 9,000 - 140,000 BP (the Pleistocene)
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Migration of Homo sapiens into South America by 10,000 BC
Jared Diamond ‘Guns, Germs and Steel’, 1997
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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.
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Does the present distribution of C. posadasii reflect the co-dispersal of a host and its pathogen?
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Recombining Recombining
Clonal (C. posadasii in Latin Amer?)
Recombining and Clonal in Coccidioides
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Daubin et al. 2003. Science 301:829-832 Fig 1
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Daubin et al.2003. Science301:829-832Fig 2
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Daubin et al.2003. Science301:829-832Fig 3