pmb 220 - week 11 species concepts in microbesn. sitophila (7) n. tetrasperma (4) ... neurospora:...

PMB 220 - Week 11Species concepts in microbes

Why are species important?

Geographic range and phenotype canbe misleading

Intraspecific variation can be high

Methods of species recognition caninfluence concepts about dispersaland adaptation

N. crassa (48)N.intermedia (71)

N. sitophila (7)N. tetrasperma (4)N. discreta (8)Putative hybrids (9)

Neurospora: Tropical and Subtropical

Perkins Lab - Fungal Genetics Stock Center

Jacobson et al. 2004 Mycologia

Neurosporadiscreta

in westernNorth America

Jacobson et al. 2004Mycologia

Jacobson et al. 2004 Mycologia

Neurospora discreta in western North America

Dettman,Jacobson &

TaylorMycologia

(in revision)

OutbreedingNeurospora

15 phylogeneticspecies

N.crassaclade

N.discretaclade

Dave Jacobson’s European Trip

Fall 2003

131 6

9

320

411

12938

52

DJJ

Neurospora sp.In Europe

FloridaItaly

Spain

Florida

Dettman,Jacobson &

TaylorMycologia

(in revision)

OutbreedingNeurospora


N.crassaclade

N.discretaclade

Dettman, Jacobson & Taylorunpublished

N. discretaclade:


Dettman,Jacobson &

Taylorunpublished

IndiaAsia

Asia

North America

Europe

Europe

Africa

Africa

North America

Neurospora discreta clade 4bEquator to 63˚ north latitude

N. crassa (48)N.intermedia (71)

N. sitophila (7)N. tetrasperma (4)N. discreta (8)Putative hybrids (9)

Neurospora: Tropical and Subtropical

Perkins Lab - Fungal Genetics Stock Center

Brubaker et al. 2005J Biogeography

Brubaker et al.2005

J Bio-geography

PopulusPollen


?

Distributionof

Coccidioidesspecies

Hector and Laniado-Laborin2005. PLoSMedicine

Coccidioides immitis dimorphic life cycle

Diagram courtesy of Theo Kirkland, UC San Diego

Arthroconidia

Coccidioides immitis dimorphic life cycle

Diagram courtesy of Theo Kirkland, UC San Diego

Spherules in an Endosporevfce.arl.arizona.edu

California- Coccidioides immitis Rixford and Gilchrist 1896

non-California- Coccidioides posadasii Fisher et al. 2002

Two phylogenetic species in Coccidioides

Fisher et al. 2002, Mycologia 94:73-84

At least fivepopulations

OfCoccidioides Fisher et al. 2001. PNAS 98:4558-4562

Fisher et al. 2002. PNAS 99:9067-9071

Phase-specific Transcription

Garry Cole and Ruth Schaller, Medical College of Ohio

Hypha Spherule S/Endospores

Arizona

Two individualsfrom one

C. posadasiipopulation

C. posadasii Texas C735

Hyphae Spherules Spherulesreleasing

endospores

RNAs

C. posadasii Arizona SilveiraRNAs

Silveira

C735

RNA Transcripts

RNA Transcripts

9 competitive hybridizations


S

H

S/E

S

H

S/E

C. posadasii Arizona Silveira

C735

Silveira

Up to 15 competitive hybridizations


S

H

S/E

S

H

S/E

C. posadasii Arizona Silveira

C735

Silveira

11 competitive hybridizations

Saprobic > ParasiticHyphae > Spherule

173

Johannesson et al. FGB in press

C735


173 182

C735 Silveira


173 182

92

Fay et al.2004

Genome Biol.5:R26 DNA sequence divergence

S. cerevisiae633 genes

Publication Year OrganismLeQuéré et al. 2005 PaxillusDrnevich et al. 2004 DrosophilaWhitehead & Crawford 2005 FundulusStranger et al. 2005 Homo

Intraspecific variation in other organisms

LeQuéré et al. 2004

Paxillus mycorrhizae

LeQuéré et al. 2004

Paxillus mycorrhizae66/1075

Low MCRSup

High MCRSup

Drnevich et al. 2004

Male competitive reproductive successDrosophila

Low MCRSup

High MCRSup

Drnevich et al. 2004

Male competitive reproductive successDrosophila

27 genes

Three populations, three individuals each, three tissues.

Whitehead andCrawford 2005

Fundulus192 genes

BlandFinley2002

Science296:1061

1 mm

100 µm 10 µm

Size of fungal spores

Figure 1a

Dettman et al.2003 Evolution

NcC

71/1.0

99/1.0

90/.94

97/1.0

100/1.0

80/1.0

100/1.0

76/.98

87/.60

100/1.0100/1.0

98/1.0

100/1.0

-/1.0

NcA

NiA

PSR BSR

-/.90

61/.96

D92 Yucatan

D86 Yucatan

D87 Yucatan

D58 Haiti

D23 FloridaD27 Florida

D62 HaitiD90 Yucatan

D88 YucatanD85 Yucatan

D59 HaitiD116 Louisiana

D143 LouisianaD60 HaitiD144 Panama

D115 LouisianaD68 Ivory Coast

D91 YucatanD140 Ivory Coast

D69 Ivory CoastD42 Tamil Nadu

D107 Tamil NaduD99 Tamil Nadu

D103 Tamil NaduD104 Tamil NaduD105 Tamil Nadu

D98 Tamil NaduD100 Tamil NaduD106 Tamil Nadu

D75 CongoD78 Congo

D77 CongoD55 Haiti

D57 Haiti

D1 TaiwanD2 Taiwan

D3 PhilippinesD8 Java

D7 JavaD16 Texas

D141 LiberiaD142 FijiD79 CongoD81 Congo

D51 MalaysiaD52 Thailand

D83 GabonD22 Florida

D25 FloridaD26 FloridaD64 Haiti

D122 HondurasD65 Ivory Coast

D66 Ivory CoastD73 Ivory Coast

D43 Tamil NaduD130 Karnataka

D127 KarnatakaD44 Tamil NaduD47 Tamil NaduD48 Tamil Nadu

D101 Tamil NaduD128 KarnatakaD129 KarnatakaD108 Tamil Nadu

D109 Tamil NaduD32 Anhiu

D35 Papua New GuineaD36 Tahiti

ND89 YucatanD93 Yucatan

D120 MadagascarD121 Madagascar

D17 Texas (N.discreta,outgroup)5 changes

67/.99

Neurospora

N.discretaclade

Dettman et al. 2006

N.crassaclade

Figure 1bN.crassa

PS3

N.intermedia

PS2

PS1

N.tetrasperma

N.sitophila

PS4 subgroup A

PS4 subgroup B

PS5

PS6

PS7

PS8

N.discreta sensu stricto

PS9

PS10

0.005 substitutions/site

Aa et al. 2006

Figure 2

Penn

CA & Italy

CA & Italy

ItalySaccharomyces cerevisiae

Liti et al. 2006Genetics 174:839-850

Six gene phylogeny

Sexual & Asexual Reproduction

Morphological SpeciesRecognition

Phylogenetic SpeciesRecognition

Sexual Reproduction Only

Biological Species Recognition

Evolutionary SpeciesConcept

Mayden 1997

Evolutionary Species Concept

"A phyletic lineage (ancestral-descendent sequenceof interbreeding populations) evolving independently ofothers, with its own separate and unitary evolutionary

role and tendencies." - G. G. Simpson 1950

"A species is a lineage of ancestral descendantpopulations which maintains its identity from othersuch lineages and which has its own evolutionarytendencies and historical fate." - E. O. Wiley 1978

Morphological Species Recognition


"Species are the smallest groups that areconsistently and persistently distinct and

distinguishable by ordinary means."- A. Cronquist 1978


"Actually or potentially interbreedingnatural populations which are reproductively

isolated from other such groups."- E. Mayr 1942

Phylogenetic Species Recognition

Phylogenetic Species Recognition

"... the smallest diagnosable clusterof individual organisms [forming amonophyletic group] within which

there is a parental pattern ofancestry and descent."

- Cracraft 1983, McKitrick & Zink 1988

A B C D W X Y ZRecombination

Species Species

.

CONCORDANCE

CONSENSUS

A B C D W X Y ZRECOMBINING

CLONAL

Meiosporic MeiosporicMitosporic

Consensus of gene genealogies

Genealogical Concordance

Phylogenetic Species Concept

Coccidioides immitis

Burt et al. 1996, 1997Koufopanou et al. 1997

Distributionof

Coccidioidesspecies

Hector and Laniado-Laborin2005. PLoSMedicine

Coccidioides immitis: Polymorphisms in five protein coding genes

Locus Dioxygenases Orotidine decarboxy. Serine proteinase Chitinase 396 bp 529 bp 396 bp 647 bp 443 bpSite 1 2 2 3 8 10 10 11 12 2 2 4 4 5 6 6 6 4 5 6 7 8 8 8 8 7 8 9 10 10 10 10 11

9 1 8 3 7 0 2 7 7 9 9 7 7 0 0 2 4 7 1 3 4 1 8 8 9 3 1 1 2 4 6 7 12 9 8 9 2 5 0 9 2 2 4 3 6 6 6 3 7 7 7 2 4 2 5 7 1 0 1 0 4 1 9 2 1

Nucleic acids ConsensusA G T G C C G C T C A A G C C A A G C C G G A C A C T T C T C C G

StrainS . . . . . . . . . . . . . . . . . . . . . . . . G A . . . . . . .AZ1 . . . . . . . . . . . . . . . . . . . . . C . . . . . . . . . . CAZ2 . . . A . . . . . . . . . . . . . . . . . . . . . A . . . . . . .TX1 . . . . . . . . . . . . . . . . . . . . . . G . . . . . . . . . .TX2 . . . . . . . . . . . . A . . . . . . . . . G . . . C . A C . . CMX1 . . . . . . . . . . . . . . . C . . . . . . G . . . . . . . . . .MX2 . . . . . . . . . . . . A . . . . . . . . . G . . . . . . . . . .AG1-5 . . . . . . . . . . . . . . . . . . . . . . G . . . . . . . . . .CA1 G A C A T T A T C . G G . T T . G C G T T . . T . . . C . . . . CCA2 G . C A T T A T C . G G . T T . G C G T T . . T . . . C . . T . CCA3 G A C A T T A T C G G G . T T . G C G T T . . T . . . C . . . . CCA4 G . C A T T A T C . . G . T T . G C G T T . . T . . . C . . . T CCA5 G . C A T T A T C . . G . T T . G C G T T . . T . . . C . . T . C

Amino acids ConsensusG K L E D I K D N T I L A H Y L L A T R A R N N I S * T N I N N T

Substit/s . . . . . . . . . S V . . . . . . P S . S S D . V Y * . K T . . .

Chitin syn.

CHITIN SYNTHASE

S, AZ1, TX1,2 MX1,2, AG1-5

2 1CA1,3 CA2,4,5 AZ21

SERINE PROTEINASE

51

1

1

S

AZ1AZ2

TX1,2, MX1,2 AG1-5

CA1-5

OROTIDINE DECARBOXYLASE

4

1

11 CA4,5CA3 CA1,2 MX1

TX2, MX2

S, AZ1,2 AG1-5, TX1 1

CHITINASE

3 1 1

11

1

S, AZ2AZ1

CA2,5CA1,3

CA4

TX2 TX1, MX1,2 AG1-5

DIOXYGENASE

5CA1- 5

S, TX1,2, MX1,2, AG1-5

Coccidioides immitis: Five gene genealogies

S

AZ1

AZ2

TX1

MX2

MX1, AG1-5

TX2

CA1

CA2

CA3

CA4

CA5

17 fixed sitesCA nonCA

Phylogenetic Species in C. immitis

Coccidioides immitis: Polymorphisms in five protein coding genes

Locus Dioxygenases Orotidine decarboxy. Serine proteinase Chitinase 396 bp 529 bp 396 bp 647 bp 443 bpSite 1 2 2 3 8 10 10 11 12 2 2 4 4 5 6 6 6 4 5 6 7 8 8 8 8 7 8 9 10 10 10 10 11

9 1 8 3 7 0 2 7 7 9 9 7 7 0 0 2 4 7 1 3 4 1 8 8 9 3 1 1 2 4 6 7 12 9 8 9 2 5 0 9 2 2 4 3 6 6 6 3 7 7 7 2 4 2 5 7 1 0 1 0 4 1 9 2 1

Nucleic acids ConsensusA G T G C C G C T C A A G C C A A G C C G G A C A C T T C T C C G

StrainS . . . . . . . . . . . . . . . . . . . . . . . . G A . . . . . . .AZ1 . . . . . . . . . . . . . . . . . . . . . C . . . . . . . . . . CAZ2 . . . A . . . . . . . . . . . . . . . . . . . . . A . . . . . . .TX1 . . . . . . . . . . . . . . . . . . . . . . G . . . . . . . . . .TX2 . . . . . . . . . . . . A . . . . . . . . . G . . . C . A C . . CMX1 . . . . . . . . . . . . . . . C . . . . . . G . . . . . . . . . .MX2 . . . . . . . . . . . . A . . . . . . . . . G . . . . . . . . . .AG1-5 . . . . . . . . . . . . . . . . . . . . . . G . . . . . . . . . .CA1 G A C A T T A T C . G G . T T . G C G T T . . T . . . C . . . . CCA2 G . C A T T A T C . G G . T T . G C G T T . . T . . . C . . T . CCA3 G A C A T T A T C G G G . T T . G C G T T . . T . . . C . . . . CCA4 G . C A T T A T C . . G . T T . G C G T T . . T . . . C . . . T CCA5 G . C A T T A T C . . G . T T . G C G T T . . T . . . C . . T . C

Amino acids ConsensusG K L E D I K D N T I L A H Y L L A T R A R N N I S * T N I N N T

Substit/s . . . . . . . . . S V . . . . . . P S . S S D . V Y * . K T . . .

Chitin syn.

Aspergillus flavus

Geiser et al. 1998

Aspergillus flavus -- Dave GeiserWiley Schell

A55, S, G-, B+++, CPA+++, CaliforniaA120, S, G-, B+++, CPA++, CaliforniaA399, S, G-, B+++, CPA+, CaliforniaTX18-11S, S, G-, B+, CPA++, TexasTX19-21S, S, G-, B++, CPA++, TexasTX20-32S, S, G-, B+++, CPA++, TexasTX21-1S, S, G-, B+, CPA++, Texas1-26, L, G-, B+++, CPA+++, Australia7-2, L, G-, B+, CPA+++, Australia7-4, S, G-, B-, CPA+++, AustraliaA111, L, G-, B-, CPA-, CaliforniaA130, L, G-, B-, CPA+, CaliforniaA150, L, G-, B-, CPA+, CaliforniaA. oryzae NRRL 448A. oryzae NRRL 449A. oryzae NRRL 469 , ?, G-, B-, CPA-F14, L, G-, B++, CPA+++, GeorgiaF60, L, G-, B+++, CPA+++, Georgia1-9, L, G-, B+, CPA++, Australia1-29, L, G-, B++, CPA++, Australia5-1, L, G-, B+, CPA++, Australia11-4, L, G-, B+, CPA++, Australia17-4, L, G-, B++, CPA+++, AustraliaF15, L, G-, B+, CPA++, GeorgiaF35, L, G-, B+, CPA++, Georgia3-2, L, G-, B+++, CPA-, Australia7-3, L, G-, B+, CPA++, Australia14-1, L, G-, B++, CPA++, Australia14-2, L, G-, B+++, CPA++, AustraliaTX12-10-2S, S, G-, B+, CPA-, Texas4-2, S, G+, B+, CPA+++, Australia12-4, S, G+, B+, CPA+++, Australia13-4, S, G+, B+, CPA+++, AustraliaNRRL A-11612, S, G++, B+, CPA+++, Nigeria1-22, S, G-, B+++, CPA+++, AustraliaA. parasiticus CA1-05, ?, G+, B+, CPA-, CaliforniaA. parasiticus CA3-01, ?, G+++, B+, CPA-, California

64

65

99

93

9285

62

95

82

99

63 72

100

Group I

Group II

IA

IB

IC96

Small SclerotiaAflatoxin BCyclopiazonic Acid

Large SclerotiaCyclopiazonic Acid

Large SclerotiaAflatoxin BCyclopiazonic Acid

Small SclerotiaAflatoxin B and GCyclopiazonic Acid

Geiser, Dorner,Horn, Taylor, 2001

Aspergillus flavus

0

5

10

15

20

25

30

35

40

45

0 4 8 10 15 18Day

= P < 0.05

California and non-California are phenotypically differentFive isolates from each species grown for 18 days on HIGH SA !LT PLATES ! ! ! !

CAnon-CA

0

5

10

15

20

25

30

35

40

45

50

0 4 8 10 15 18Day

2010200620072009200810381046103710391036

ISOLATE

Do the two species have differences in immunogenicity / pathogenicity?

….California grows faster

PhylogeneticSpeciesRecognition

Genetic isolationUncultivatedAsexual

Gevers et al. 2005

Doolittle et al. 1999

Daubin et al.2003

Daubin et al. 2003

Daubin et al.2003

A-J: Whitaker et Al. 2003,Martiny et al. 2006

K-W: Dettman et al. 2003,Taylor et al. 2006

Didn’t use the rest in 2006, but it could fit in the species lecture

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

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

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

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**

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…

• 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

pmb 220 - week 11 species concepts in microbesn. sitophila (7) n. tetrasperma (4) ... neurospora:...

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