What is a fungal species?

Species

• Are species real?• How do we define a species?• Is there one “right” species concept that will

be applicable to all organisms? • What is the difference between a theoretical

species concept and a operational species concept?

Species—Latin, kind

• A species is the principal unit of evolution (Ernst Mayr 1980)

• The lowest principal rank in the nomenclatural hierarchy (Dictionary of the Fungi)

Theoretical species concept

• Evolutionary Species Concept (Simpson 1951, 1961; Wiley 1978)—A single lineage of ancestor-descendent populations which maintains its identity from other such lineages and which has its own evolutionary tendencies and historical fate.

Operational Species Concepts

• Morphological Species Concept• Biological Species Concept• Phylogenetic Species Concept

Morphological Species Concept (MSC)

• Traditional approach in mycology—species are units that can be delimited on the basis of morphological characters, ideally by discontinuities in several such characters.

Example

• Ceuthospora lunata, a coelomycete causing black rot disease of cultivated cranberry in eastern North America

• “light” and “dark” strains recognized based on colony morphology

• Cranberry fruit inoculated with dark strain developed a uniform black rot, fruit inoculated with light strain developed a pale brown discoloration

Light strain conidia 6-11 x 2-3.5 μm

Dark strain conidia7-15 x 2-3.5 μm

Strasseria geniculata – another fruit rot pathogen

Conidia

Carris (1990) Can. J. Bot. 68:2283-2291

• Light strain = Allantophomopsis cytisporea, originally described by Fries (1893) on Vaccinium vitis-idaea in Sweden

• Dark strain = Allantophomopsis lycopodina, originally described by von Höhnel (1909) on Lycopodium in Austria

Biological Species Concept (BSC)

• Species are groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups (Ernst Mayr 1942)

Tilletia L.-R. & C. Tulasne 1847

• Type species: Tilletia caries (DC.) Tulasne based on 1815 specimen from Triticum aestivum (France)

• T. laevis Kühn (1873) based on 1872 specimen from wheat (Germany)

Short or dwarf bunt of wheat

• First published report from Montana in 1935:– Stunted plants– Spore balls (sori) hard,

compact and round– Spores do not germinate

under same conditions as T. caries and T. laevis

– Soil infestation is the main source of infection; seed treatments ineffective

Common bunt teliospores Dwarf bunt teliospores

Tilletia contraversa Kühn (1874)

• Based on smut in ovaries of Elymus repens from Germany– Kühn compared quack grass

smut with wheat bunt based on spore morphology and germination

Dwarf Bunt or TCK Smut

– Reticulate teliospores with gelatinous sheath

– Germination in 3-6+ wk at 3-8 C; requires light (T. caries & T. laevis germinate in <7 da at 15C without light)

– Dwarf bunt infection occurs with deep, persistent snow cover

– Dwarf bunt pathogen considered to have a wide host range including 45 grass species in 17 different genera

Species Spores Germination # Sporidia

T. caries ReticulateExospore < 1 μm 14-25 μm diam

1-2 wk at 15Clight or dark

4-16

T. laevis Smooth14-22 μm diam

1-2 wk at 15CLight or dark

4-16

T. contraversa Reticulate with gelatinous sheath up to 5 μm thickExospore > 1 μm17-27 μm diam

3-10 wk at 5CLight required

14-30

The wheat bunt species are reproductively compatible

• Putative hybrids with spores exhibiting intermediate morphology found in natural populations

• Experimental hybrids generated by co-inoculation of wheat:– T. caries x T. contraversa– T. caries x T. laevis

Russell & Mills. 1993. Electrophoretic karyotypes of Tilletia caries, T. controversa, and their F1 progeny: further evidence for conspecific status. MPMI 6:66-74

Questions

1. If T. caries, T. contraversa and T. laevis are reproductively compatible and produce viable progeny, should they be recognized as one, two, or three species?

2. Is additional evidence needed? If so, what type of evidence?

T. caries 4

T. caries J19

T. laevis 98-194

T. laevis V766

T. contraversa WSP 71280

T. contraversa V528

T. contraversa 94-10

T. laevis WSP 71278

T. trabutii V764

T. trabutii VPRI 32106

T. secalis WSP 71279

T. brevifaciens HUV 20.802

T. brevifaciens V412

T. bromi ChInterc LC1328

T. bromi WSP 71271

T. bromi WSP 71272

T. bromi WSP 71273

T. vankyi WSP 71266

T. vankyi ChInterc LC1326

T. vankyi ChInterc LC1325

T. vankyi WSP 71270

T. vankyi FF7-8

T. laguri HUV 16.352

T. lolii V767

T. goloskokovii WSP 71281

T. goloskokovii WSP 69687

T. goloskokovii WSP 69688

T. sphaerococca ChInterc LC1327

T. lolioli V763

T. fusca WSP 71275

T. elymi WSP 71274

T. togwateei WSP 71277

T. togwateei WSP 712765 changes

Triticum spp.

Secale cereale

Thinopyrum intermedium

Hordeum spp.

Bromus spp.

Lolium perenne

Lolium rigidum

Lagurus ovatus

Apera interrupta

Agrostis stolonifera

Vulpia microstachys

Poa reflexa

Elymus glaucus

Festuca rubra

Loliolum subulatum

8794

100100

99100

100100

100100

10090

83

100

100100

100100

8482

99

93

70

8687

MP analysis-- EF1A, ITS, RPB2

Germination at 5C

Pimentel et al. 2000. Characterization of interspecific hybrids between Tilletia contraversa and T. bromi. Mycologia 92:411-420

• Has reproductive compatibility been retained among host specific species of Tilletia?– T. bromi and T. contraversa are closely related

species with overlapping host range; sympatric populations common in wheat fields in PNW

Pimentel et al. 2000. Characterization of interspecific hybrids between Tilletia contraversa and T. bromi. Mycologia 92:411-420

Questions1. What can you conclude from the Pimentel et

al study regarding reproductive compatibility of T. bromi, T. contraversa, and T. laevis?

2. Do the results of this study provide evidence for or against the conspecific status of the wheat bunt pathogens?

Phylogenetic Species Concept (PSC)

• A species is the smallest (exclusive) monophyletic group of common ancestry (de Queiroz & Donoghue 1988)

Example: Morchella

• Morchella –true morels– Black morels—M. elata group– Common morels—M. esculenta– Half-free morels—M. semilibera

Morchella elata group--Black Morel

Morchella esculenta—Common or Yellow Morel

Morchella esculenta courtesy of George Barron

Morchella semilibera—Half-free morel

Verpa conica Verpa bohemicaMountain Blonde Morel—undescribed species

Summary

• 3 major clades corresponding to black morels (24 species), yellow morels (16 species), and M. rufobrunnea

• 37/41 spp with Laurasian distribution with 33 spp represented by multiple specimens exhibiting continental endemism:– 16/18 North American– 13/15 Eurasian

Limitations to MSC

• Fungi have a limited number of morphological traits, these traits can be highly plastic– Pleomorphy, dimorphism– Intraspecific morphological variability

• Morphological traits may evolve slowly and recently diverged species may not differ morphologically

Limitations to BSC

• 20% of fungi are asexual, others are homothallic or can’t be grown or crossed in artificial culture

• Interbreeding may be retained as an ancestral trait

Limitations to PSC

• Distinguishing populations from species--where to draw the line

• Genealogies of different genes may give different species– Introgression, hybridization and horizontal gene

transfer• Recently diverged lineages may not show

reciprocal monophyly

Genealogical Concordance Phylogenetic Species Recognition (GCPSR; Taylor et al 2000)

• Based on concordance of multiple gene genealogies:– Is the clade present in the majority of single-locus

genealogies? – Is the clade well supported in at least one single-

locus genealogy? – Is there support for the clade in the combined

gene tree?

Fig. 3 from Taylor et al. 2000

Species concepts vs. speciation

• Species are separately evolving metapopulation lineages that acquire properties (reproductive isolation, ecological and phenotypic differences) at different time points during the course of divergence (de Queiroz 2007)

de Queiroz K PNAS 2005;102:6600-6607

A unified species concept?

• “Lineages do not have to be phenetically distinguishable, diagnosable, monophyletic, intrinsically reproductively isolated, ecologically divergent, or anything else to be considered species. They only have to be evolving separately from other lineages.” (de Queiroz 2007)

Another unified species concept

• “A species is the smallest aggregation of populations with a common lineage that share unique, diagnosable phenotypic characters.” (Harrington & Rizzo 1999)

Consolidated Species Concept

• Extension of the “polyphasic” approach to fungal identification that weights MSC, ESC and PSC characteristics (Quaedvlieg et al 2014. Persoonia in press)