Delimitation of cryptic species inside Claviceps purpurea

doi:10.1016/j.funbio.2014.10.003

Fungal Biology

Volume 119, Issue 1, January 2015, Pages 7-26

https://doi.org/10.1016/j.funbio.2014.10.003 Get rights and content

Highlights

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Data from 5 genes and 69 Claviceps purpurea specimens from various hosts and locations were used.
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Application of the genealogical sorting index and population genetic analysis showed presence of four cryptic species.
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The divergence time and the historical demography of the cryptic species were estimated.
•
We showed that both host and ecological speciation occurred in the evolution of C. purpurea species complex.
•
Formal taxonomic names are provided.

Abstract

Claviceps purpurea is an ovarian parasite infecting grasses (Poaceae) including cereals and forage plants. This fungus produces toxic alkaloids and consumption of contaminated grains can cause ergotism in humans and other mammals. Recent molecular genetics studies have indicated that it included three cryptic species (G1, G2, G3). In this study, reproductive isolation amongst these groups and among material from Phragmites and Molinia was tested using gene flow statistics for five polymorphic loci, and to support these data, phylogenetic affiliations based on gene trees and a multigene phylogeny were used. The four recognized species are characterized based on morphology and host spectrum and formal taxonomic names are proposed. Claviceps purpurea sensu stricto (G1 group) represents a typical rye ergot, but infects various other grasses. Typical hosts of Claviceps humidiphila (new name for G2 species), like Phalaris arundinacea, belong to grasses preferring humid locations. Claviceps spartinae (G3) is specific to chloridoid grasses from salt barches. The material from Phragmites and Molinia can be authenticated with the species Claviceps microcephala for which the new name Claviceps arundinis is proposed here. The divergence time between species was estimated and the tools for species identification are discussed.

Graphical abstract

Section snippets

Isolates and their characterization

In total 666 isolates were used in this study. The assignment to populations G1, G2, G3, and the newly defined G2a (Phragmites-Molinia) was based on DNA fingerprints obtained with ERIC 1R primer (Versalovic et al. 1991) (Table S1 in Supplement material). A subset of 69 specimens (G1 = 17 specimens, G2 = 16 specimens, G2a = 22 specimens, G3 = 14 specimens) was selected from the collection to cover the whole sampled area (Eurasia, North and South America, 17 countries) and habitats (Table 1).

Molecular data

Five loci were sequenced for this study across 69 isolates. All representative haplotypes of the five loci were submitted to public databases (Table 1, Table S2 in Supplement material). The concatenated aligned matrix contained 5109 characters and 186 parsimony-informative positions (Mcm7: 409, RPB2: 1119, EF-1α: 986, benA: 1470, ITS: 524, LSU: 597 positions). For *BEAST analysis, recombination-filtered datasets were used containing 64 isolates, 3362 characters and 135 parsimony-informative

Discussion

The introduction of DNA analysis has shown that four species differing to various extent in their habitat preferences exist within Claviceps purpurea, a taxon formerly considered a wide-ranging and morphologically variable single species. Phylogenetic analyses have been used to resolve the species together with population genetic approach, as recommended by Grünig et al. (2007). The multilocus phylogenetic analysis with concatenated data (GCPSR), which is sensitive to shared sequence haplotypes

Acknowledgements

Funding for this research has been provided through grants from Czech Science Foundation (GAČR, 13-00788S) and Texas AgriLife Research (Research Subcontract 470222). We thank to J. Marková, D. Stančík, and J. Malíček for the determination of the grass species.

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Citation Excerpt :
Biogeographical and host range data were derived from the literature listed in Fig. 2. DNA was isolated from young cultures using the ArchivePure DNA Yeast & Gram Kit (5 PRIME, Hamburg, Germany) following the procedure described in the study by Pažoutová et al. (2015). Five loci were chosen for analysis.
The ergot, genus Claviceps, comprises approximately 60 species of specialised ovarial grass parasites famous for the production of food toxins and pharmaceutics. Although the ergot has been known for centuries, its evolution have not been resolved yet. Our approach combining multilocus phylogeny, molecular dating and the study of ecological, morphological and metabolic features shows that Claviceps originated in South America in the Palaeocene on a common ancestor of BEP (subfamilies Bambusoideae, Ehrhartoideae, Pooideae) and PACMAD (subfamilies Panicoideae, Aristidoideae, Chloridoideae, Micrairoideae, Arundinoideae, Danthonioideae) grasses. Four clades described here as sections diverged during the Paleocene and Eocene. Since Claviceps are parasitic fungi with a close relationship with their host plants, their evolution is influenced by interactions with the new hosts, either by the spread to a new continent or the radiation of the host plants. Three of the sections possess very narrow host ranges and biogeographical distributions and have relatively low toxicity. On the contrary, the section Claviceps, comprising the rye ergot, C. purpurea, is unique in all aspects. Fungi in this section of North American origin have spread all over the world and infect grasses in all subfamilies as well as sedges, and it is the only section synthesising toxic ergopeptines and secalonic acids. The evolutionary success of the Claviceps section members can be explained by high toxin presence, serving as feeding deterrents and playing a role in their protective mutualism with host plants. Closely related taxa Neoclaviceps monostipa and Cepsiclava phalaridis were combined into the genus Aciculosporium.
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^†: This paper is dedicated to Dr. Sylvie Pažoutová, who died suddenly on 6th September 2013.

View full text

Delimitation of cryptic species inside Claviceps purpurea

Highlights

Abstract

Graphical abstract

Section snippets

Isolates and their characterization

Molecular data

Discussion

Acknowledgements

Molecular Phylogenetics and Evolution

Mycological Research

Fungal Genetics and Biology

Mycological Research

Trans Br Mycol Soc

Molecular Phylogenetics and Evolution

Molecular Phylogenetics and Evolution

Molecular Phylogenetics and Evolution

Fungal Genetics and Biology

Palaeogeography, Palaeoclimatology, Palaeoecology

Assessing the performance of single-copy genes for recovering robust phylogenies

Systematic Biology

Gene genealogies reveal cryptic species and host preferences for the pine fungal pathogen Grosmannia clavigera

Molecular Ecology

A reevaluation of the host range and geographical distribution of Claviceps species in the United States

Plant Disease

Origin and diversification of major clades in parmelioid lichens (Parmeliaceae, Ascomycota) during the Paleogene inferred by Bayesian analysis

PLoS ONE

Ergot of Grains and Grasses

Phylogeography: the history and formation of species

Ricerche sulla spezializzazione della Claviceps purpurea

Phytopathologische Zeitschrift

Ergot and Ergotism. Gurney and Jackson

Phylogenetic analysis reveals a cryptic species Blastomyces gilchristii, sp. nov. within the human pathogenic fungus Blastomyces dermatitidis

Plos One

Studies on ergot infection in gramineous hosts

Canadian Journal of Botany/Revue Canadienne de Botanique

Observations on Neobarya, including some new species and new combinations

Sydowia

A genealogical approach to quantifying lineage divergence

Evolution

Flore française

A congruence index for testing topological similarity between trees

Bioinformatics

Multigene analysis suggests ecological speciation in the fungal pathogen Claviceps purpurea

Molecular Ecology

Bayesian phylogenetics with BEAUti and the BEAST 1.7

Molecular Biology and Evolution

Claviceps purpurea var. spartinae var. nov.: An ergot adapted to the aquatic environment

Mycotaxon

The origins of C4 grasslands: integrating evolutionary and ecosystem science

Science

Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model

Molecular Ecology

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

Molecular Ecology Resources

Die pilzparasitären Krankheiten der Pflanzen

Systema Mycologicum

Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection

Genetics and Molecular Biology

Statistical tests of neutrality of mutations

Genetics and Molecular Biology

ITS primers with enhanced specificity for basidiomycetes — application to the identification of mycorrhizae and rusts

Molecular Ecology

Sur l'ergot du seigle

Journal de Pharmacie et de Chimie

Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution

Human Biology

The development of the annual population in Phragmites communis Trin

Annals of Botany

A new dawn for the naming of fungi: impacts of decisions made in Melbourne in July 2011 on the future publication and regulation of fungal names

MycoKeys

Early-Middle Pleistocene transitions: an overview and recommendation for the defining boundary

Bayesian inference of species trees from multilocus data

Molecular Biology and Evolution

Speciation despite globally overlapping distributions in Penicillium chrysogenum: the population genetics of Alexander Fleming's lucky fungus

Molecular Ecology

Estimation of levels of gene flow from DNA sequence data

Genetics

Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

BMC Bioinformatics