What is a fungal species?

1. What is a fungal species?

2. 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?

3. 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)

4. 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.

5. Operational Species Concepts • Morphological Species Concept • Biological Species Concept • Phylogenetic Species Concept

6. 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.

7. Example • Ceuthosporalunata, 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

9. Light strain conidia 6-11 x 2-3.5 μm Dark strain conidia 7-15 x 2-3.5 μm Strasseriageniculata– another fruit rot pathogen

10. Conidia

12. Carris (1990) Can. J. Bot. 68:2283-2291 • Light strain = Allantophomopsiscytisporea, originally described by Fries (1893) on Vacciniumvitis-idaeain Sweden • Dark strain = Allantophomopsislycopodina, originally described by von Höhnel (1909) on Lycopodiumin Austria

13. 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)

14. Tilletia L.-R. & C. Tulasne 1847 • Type species: Tilletia caries (DC.) Tulasne based on 1815 specimen from Triticumaestivum (France) • T. laevis Kühn (1873) based on 1872 specimen from wheat (Germany)

15. 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

16. Dwarf bunt teliospores Common bunt teliospores

17. Tilletia contraversa Kühn (1874) • Based on smut in ovaries of Elymusrepens from Germany • Kühn compared quack grass smut with wheat bunt based on spore morphology and germination

18. 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

20. 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

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

22. Questions • 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? • Is additional evidence needed? If so, what type of evidence?

23. Germination at 5C 100 100 100 100 MP analysis-- EF1A, ITS, RPB2 T. caries 4 70 T. caries J19 T. laevis 98-194 T. laevis V766 Triticum spp. T. contraversa WSP 71280 87 94 T. contraversa V528 T. contraversa 94-10 T. laevis WSP 71278 100 T. trabutii V764 Hordeum spp. 100 T. trabutii VPRI 32106 Secale cereale T. secalis WSP 71279 99 T. brevifaciens HUV 20.802 Thinopyrum intermedium 83 100 T. brevifaciens V412 T. bromi ChInterc LC1328 Bromus spp. 100 T. bromi WSP 71271 100 T. bromi WSP 71272 86 87 T. bromi WSP 71273 T. vankyi WSP 71266 84 82 Lolium perenne T. vankyi ChInterc LC1326 100 T. vankyi ChInterc LC1325 90 Festuca rubra T. vankyi WSP 71270 99 100 T. vankyi FF7-8 Lagurus ovatus 93 T. laguri HUV 16.352 Lolium rigidum T. lolii V767 T. goloskokovii WSP 71281 Apera interrupta T. goloskokovii WSP 69687 T. goloskokovii WSP 69688 100 100 Agrostis stolonifera T. sphaerococca ChInterc LC1327 Loliolum subulatum T. lolioli V763 Vulpia microstachys T. fusca WSP 71275 Elymus glaucus T. elymi WSP 71274 T. togwateei WSP 71277 Poa reflexa T. togwateei WSP 71276 5 changes

24. 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

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

28. Questions • What can you conclude from the Pimentel et al study regarding reproductive compatibility of T. bromi, T. contraversa, and T. laevis? • Do the results of this study provide evidence for or against the conspecific status of the wheat bunt pathogens?

29. Phylogenetic Species Concept (PSC) • A species is the smallest (exclusive) monophyletic group of common ancestry (de Queiroz & Donoghue 1988)

30. Example: Morchella • Morchella–true morels • Black morels—M. elatagroup • Common morels—M. esculenta • Half-free morels—M. semilibera

31. Morchellaelatagroup--Black Morel Morchella esculenta—Common or Yellow Morel Morchellaesculenta courtesy of George Barron Morchellasemilibera—Half-free morel

32. Mountain Blonde Morel—undescribed species Verpa conica Verpa bohemica

36. 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

37. 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

38. 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

39. 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

40. 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?

41. Fig. 3 from Taylor et al. 2000

42. 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)

43. de Queiroz K PNAS 2005;102:6600-6607

44. 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)

45. 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)

46. Consolidated Species Concept • Extension of the “polyphasic” approach to fungal identification that weights MSC, ESC and PSC characteristics (Quaedvlieg et al 2014. Persooniain press)