Microbial Reproductive Modes Fungal Reproduction Week 12, PMB 220 J. Taylor
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Transcript of Microbial Reproductive Modes Fungal Reproduction Week 12, PMB 220 J. Taylor
MicrobialReproductive
ModesFungal
ReproductionWeek 12, PMB 220
J. Taylor
The cost of sex is two-fold.Clonal progeny have twiceas many parental genes.
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."
The Value of Sex?
Muller’s Ratchet
H. Muller, 1964
Goddard,GodfrayBurt. 2005Nature434:636-640
Goddard,GodfrayBurtNature434:636-402005
Goddard,GodfrayBurtNature434:636-402005
Benignenvironment
Harshenvironment
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.
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
What is aspecies?
How do they reproduce?
Determining thereproductive mode
of Microbes:
Recombination v. clonality
Clonal:Associationof Alleles.
Recombining: Lack of Association
.
Clonal 1234567----------A 0101111B 0101011C 0111111D 1011110E 1010110F 1010100G 1111111
LOCI 1234567---------A 0001110B 0011111C 1111010D 1111111E 1011111F 1100101G 0110110
RecombiningLOCI
Testing for reproductive mode.
Tree Length Test
A 0101111B 0101011C 0111111D 1011110E 1010110F 1010100G 1111111
13 5
2, 746
Clonal
Trees: 1Length: 7 stepsConsistency Index: 1.0Homoplasy Index: 0.0
Recombining A 0001110B 0011111C 1111010D 1111111E 1011111F 1100101G 0110110Trees: 9Length: 11 stepsConsistency Index: 0.63Homoplasy Index: 0.36
a b
00110011001
10110100101
01010101010
10101010101
11100100010
10110100101
00111010001
11100100010
10101010101
00110011001
01110101110
OBSERVED
00110011001
10110100101
10101010101
11100100010
10110100101
00111010001
11100100010
10101010101
00110011001
01110101110
SCRAMBLING
0
0
1101
0 10
10
00110011001
10110100101
110100110
10101010101
11100100010
10110100101
00111010001
11100100010
10101010101
00110011001
01110101110
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 11
Loci Loci Loci
Compter sex: Resampling without replacement.
. .
0
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600
Observed
Recombining p< 0.996
0
100
200
300
400
500
600
Observed
Clonal p< 0.002
A 0101111B 0101011C 0111111D 1011110E 1010110F 1010100G 1111111
13 5
2, 746
Clonal
Trees: 1Length: 7 stepsConsistency Index: 1.0Homoplasy Index: 0.0
Recombining A 0001110B 0011111C 1111010D 1111111E 1011111F 1100101G 0110110Trees: 9Length: 11 stepsConsistency Index: 0.63Homoplasy Index: 0.36
a b
c d
TreeLengthTest
.
Clonal 1234567----------A 0101111B 0101011C 0111111D 1011110E 1010110F 1010100G 1111111
LOCI 1234567---------A 0001110B 0011111C 1111010D 1111111E 1011111F 1100101G 0110110
RecombiningLOCI
Index of Association
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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0
1
2
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9
10
.1 .2 .3 .4 .5 .6 .7 .8 .9 1 1.1
Distance
Variance = 7.3 x 10-2
0
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.1 .2 .3 .4 .5 .6 .7 .8
Distance
Variance = 2.7 x 10-2
MeanMean
Dist ribut ion of Dist ances Dist ribut ion of Dist ances
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-.8 -.6 -.4 -.2 0 .2 .4 .6 .8 1 1.2 1.4
Index of Association
Observed1.187
p = 0.003
0
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120
-.8 -.6 -.4 -.2 0 .2 .4 .6 .8 1 1.2 1.4
Index of Association
Observed-0.153 p = 0.785
IA
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CONCORDANCE
CONSENSUS
ABCDWXYZGeneGenealogyConcordance
00110011001
10110100101
01010101010
10101010101
11100100010
10110100101
00111010001
11100100010
10101010101
00110011001
01110101110
LociOBSERVED
10110100101
11100100010
LociSCRAMBLING
00111010001
11100100010
01010101010
00110011001
10110100101
01010101010
10101010101
11100100010
10110100101
00111010001
11100100010
10101010101
00110011001
01110101110
LociSCRAMBLED
1 2 43 51 2 431 2 43Gene A Gene B Gene C
1 2 43 51 2 431 2 43Gene A Gene B Gene C
1 2 43 51 2 431 2 43Gene A Gene B Gene C
Computer sex:Shuffling variable nucleotidesamong genes.
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0
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40 45 50 55 60
actual summedtree lengths = 42
summed tree lengths
Aspergillus flavus
You have to know the
species before you can study reproductive
mode.
Example:Coccidioides immitis
Vasso KoufopanouAustin BurtMat Fisher
Distributionof
Coccidioidesimmitis
Rippon, 1988
Phylogenetic Species in C. immitis
S
AZ1
AZ2
TX1
MX2
MX1, AG1-5
TX2
CA1
CA2
CA3
CA4
CA5
17 fixed sites
C. immitis C. posadasii
Finding Single Nucleotide PolymorphismsAgarose and SSCP gels of PCR products
Coccidioides immitis: multilocus genotypesas single nucleotide polymorphisms (SNPs)
Locus Isolate Size(bp) Polymorphismabcdefghijklmnopqrstuvwxy
a1 0000111000010100011100101 NS1 ITS5 286 144C/T
a2 0000001000010000000000000 NS1 ITS5 154 40T/C
e2 0000000000100010000000000 NS23 ITS5 183 108TT/C-
k 0010100001000111010010001 NS2 NS22 590 189G/A
q2 0000001000000000010000000 CNS19 ITS4 163 20C/T
z 0111101110111101111100011 NS24 CNS19 260 13A/T
aa 0111111110111101111100000 NS24 CNS25 207 11A/G
am 0000100000001010000000000 NS23 ML5.1 309 66G/A;97C/T
bg 0101000000000001110000000 ITS2 ML3.5 165 34CTC/---
bk 0000000000000000100100000 ITS4 ML5.1 369 146C/A
bl 0001000010000000000111000 NS26 MS1 822 233T/C;733A/-
bq 0011000000000100100001000 ML5.1 MS1 433 170A7/A8,9;235A/G;260T/C;293A/G
af 0000100010000101110101001 ITS4 ITS1 630 46T/A
cs 0000000011000000010101011 CS2 CS4A 260 53G/A
Primers
a b c d e f g i h j k l m n o p q r s t u v w x y
Parsimony analysis:Consensus of 62 most parsimonious trees.
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10 15 20 25 30 35 40 45
MinimumPossible
14
Observed38
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300
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Tree Length
Test of association of alleles: Index of Association
Phylogenetic Species in C. immitis
S
AZ1
AZ2
TX1
MX2
MX1, AG1-5
TX2
CA1
CA2
CA3
CA4
CA5
17 fixed sites
C. immitis C. posadasii
91
98
I s o l a t e
20052267
20122013
2275
2281
2270
22712273227422762277
2002
20042006
2007
20082009201020142015
2017264922682269
2278
2279
22803255325732583262326428082610
435201110363272
E p i d e m i c
C A
N C A
IA, P = 0.28
PTLPT, P = 0.09
CaliforniaCoccidioides
Fisher et al. 2000
Likelihood ratio tests
Kishino-HasegawaTwo different topologies
Shimodaira-HasagawaMultiple topologies
Lichens
Trebouxia and Letharia
Scott Kroken
Question: Are there two species of
Letharia, one sexual and the other not?
Letharia columbiana
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
XeroxPARCmap
Thomas Nash
Apothecia, filled with
meiotic ascospores
www.lichen.com
Soredia, algal cells wrapped
in hyphae
SexualAsexual
sorediate
apotheciate
apotheciate
apotheciate
apotheciate
sorediate
77
95
83
10064
80
601 of 4608 treesCIre=.57202 steps 1 step
Letharia 6 loci51 individuals
6 species suggested
Kroken and Taylor. 2000. Mycologia 93:38-53
Question: does the lichen outbreed or
inbreed?
Paternity analysis of lichen apothecia
Fertilization
Spermagonium--produces spermatia
Trichogyne--fuses with spermatium
Parent and progeny
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
Outbreeding and separate fertilizations
Dispersal of Letharia vulpina with its alga
XeroxPARCmap
Högberg et al. 2002. Molecular Ecology 11:1191-1196
Recombining:North Americansorediate
Recombining:North Americanapotheciate
Clonal: European and North African sorediate Letharia species
Recombining and Clonal in Letharia
Daubin et al. 2003. Science 301:829-832
More polymorphism?
Microsatellites orShort 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 ctgcgtgtgacatACACACACACACACA--------ctgtatgtCocci_2 ctgcgtgtgacatACACACACACACACACA------ctgtatgtCocci_3 ctgcgtgtgacatACACACACACACACACACA----ctgtatgtCocci_4 ctgcgtgtgacatACACACACACACACACACACACActgtatgt
Microsatellites
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
California- Coccidioides immitis Rixford and Gilchrist 1896
non-California- Coccidioides posadasii after Alejandro Posadas
Renaming the species
All populations
Arizona
Texas/ South America
North America/ Mexico C. immitis ( ) and C. posadasii ( )show isolation by distance...
0
5
10
15
20
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Geographical distance (miles)
r = 0.905
r = 0.694**
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Geographical distance (miles)
r = 0.023
r = 0.694**
...but NOT if South American isolates (all C. posadasii) are included…
• 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 Recombining
Clonal (C. posadasii in Latin Amer?)
Recombining and Clonal in Coccidioides
Daubin et al. 2003. Science 301:829-832 Fig 1
Daubin et al.2003. Science301:829-832Fig 2
Daubin et al.2003. Science301:829-832Fig 3