259 research outputs found
AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa
Background
Current tools for Co-phylogenetic analyses are not able to cope with the continuous accumulation of phylogenetic data. The sophisticated statistical test for host-parasite co-phylogenetic analyses implemented in Parafit does not allow it to handle large datasets in reasonable times. The Parafit and DistPCoA programs are the by far most compute-intensive components of the Parafit analysis pipeline. We present AxParafit and AxPcoords (Ax stands for Accelerated) which are highly optimized versions of Parafit and DistPCoA respectively.
Results
Both programs have been entirely re-written in C. Via optimization of the algorithm and the C code as well as integration of highly tuned BLAS and LAPACK methods AxParafit runs 5–61 times faster than Parafit with a lower memory footprint (up to 35% reduction) while the performance benefit increases with growing dataset size. The MPI-based parallel implementation of AxParafit shows good scalability on up to 128 processors, even on medium-sized datasets. The parallel analysis with AxParafit on 128 CPUs for a medium-sized dataset with an 512 by 512 association matrix is more than 1,200/128 times faster per processor than the sequential Parafit run. AxPcoords is 8–26 times faster than DistPCoA and numerically stable on large datasets. We outline the substantial benefits of using parallel AxParafit by example of a large-scale empirical study on smut fungi and their host plants. To the best of our knowledge, this study represents the largest co-phylogenetic analysis to date.
Conclusion
The highly efficient AxPcoords and AxParafit programs allow for large-scale co-phylogenetic analyses on several thousands of taxa for the first time. In addition, AxParafit and AxPcoords have been integrated into the easy-to-use CopyCat tool
Phylogenetic classification of Cordyceps and the clavicipitaceous fungi
Cordyceps, comprising over 400 species, was historically
classified in the Clavicipitaceae, based on cylindrical asci,
thickened ascus apices and filiform ascospores, which often disarticulate into
part-spores. Cordyceps was characterized by the production of
well-developed often stipitate stromata and an ecology as a pathogen of
arthropods and Elaphomyces with infrageneric classifications
emphasizing arrangement of perithecia, ascospore morphology and host
affiliation. To refine the classification of Cordyceps and the
Clavicipitaceae, the phylogenetic relationships of 162 taxa were
estimated based on analyses consisting of five to seven loci, including the
nuclear ribosomal small and large subunits (nrSSU and
nrLSU), the elongation factor 1α (tef1), the largest
and the second largest subunits of RNA polymerase II (rpb1 and
rpb2), β-tubulin (tub), and mitochondrial ATP6
(atp6). Our results strongly support the existence of three
clavicipitaceous clades and reject the monophyly of both Cordyceps
and Clavicipitaceae. Most diagnostic characters used in current
classifications of Cordyceps (e.g., arrangement of perithecia,
ascospore fragmentation, etc.) were not supported as being phylogenetically
informative; the characters that were most consistent with the phylogeny were
texture, pigmentation and morphology of stromata. Therefore, we revise the
taxonomy of Cordyceps and the Clavicipitaceae to be
consistent with the multi-gene phylogeny. The family Cordycipitaceae
is validated based on the type of Cordyceps, C. militaris,
and includes most Cordyceps species that possess brightly coloured,
fleshy stromata. The new family Ophiocordycipitaceae is proposed
based on Ophiocordyceps Petch, which we emend. The majority of
species in this family produce darkly pigmented, tough to pliant stromata that
often possess aperithecial apices. The new genus Elaphocordyceps is
proposed for a subclade of the Ophiocordycipitaceae, which includes
all species of Cordyceps that parasitize the fungal genus
Elaphomyces and some closely related species that parasitize
arthropods. The family Clavicipitaceae s. s. is emended and
includes the core clade of grass symbionts (e.g., Balansia,
Claviceps, Epichloë, etc.), and the entomopathogenic
genus Hypocrella and relatives. In addition, the new genus
Metacordyceps is proposed for Cordyceps species that are
closely related to the grass symbionts in the Clavicipitaceae s.
s. Metacordyceps includes teleomorphs linked to
Metarhizium and other closely related anamorphs. Two new species are
described, and lists of accepted names for species in Cordyceps,
Elaphocordyceps, Metacordyceps and Ophiocordyceps
are provided
Phacidium and Ceuthospora (Phacidiaceae) are congeneric: taxonomic and nomenclatural implications
The morphologically diverse genus Ceuthospora has traditionally been linked to Phacidium sexual morphs via association, though molecular or cultural data to confirm this relationship have been lacking. The aim of this study was thus to resolve the relationship of these two genera by generating nucleotide sequence data for three loci, ITS, LSU and RPB2. Based on these results, Ceuthospora is reduced to synonymy under the older generic name Phacidium. Phacidiaceae (currently Helotiales) is suggested to constitute a separate order, Phacidiales (Leotiomycetes), as sister to Helotiales, which is clearly paraphyletic. Phacidiaceae includes Bulgaria, and consequently the family Bulgariaceae becomes a synonym of Phacidiaceae. Several new combinations are introduced in Phacidium, along with two new species, P. pseudophacidioides, which occurs on Ilex and Chamaespartium in Europe, and Phacidium trichophori, which occurs on Trichophorum cespitosum subsp. germanicum in The Netherlands. The generic name Allantophomopsiella is introduced to accommodate A. pseudotsugae, a pathogen of conifers, while Gremmenia is resurrected to accommodate the snow-blight pathogens of conifers, G. abietis, G. infestans, and G. pini-cembrae
The Botryosphaeriaceae: genera and species known from culture
In this paper we give an account of the genera and species in the Botryosphaeriaceae. We consider morphological characters alone as inadequate to define genera or identify species, given the confusion it has repeatedly introduced in the past, their variation during development, and inevitable overlap as representation grows. Thus it seems likely that all of the older taxa linked to the Botryosphaeriaceae, and for which cultures or DNA sequence data are not available, cannot be linked to the species in this family that are known from culture. Such older taxa will have to be disregarded for future use unless they are epitypified. We therefore focus this paper on the 17 genera that can now be recognised phylogenetically, which concentrates on the species that are presently known from culture. Included is a historical overview of the family, the morphological features that define the genera and species and detailed descriptions of the 17 genera and 110 species. Keys to the genera and species are also provided. Phylogenetic relationships of the genera are given in a multi-locus tree based on combined SSU, ITS, LSU, EF1-α and β-tubulin sequences. The morphological descriptions are supplemented by phylogenetic trees (ITS alone or ITS + EF1-α) for the species in each genus.We would like to thank the curators of the numerous fungaria and Biological Resource Centres cited in this paper, for making specimens and cultures available for examination over the past 15 yr, without which this study would not have been possible. Part of this work was supported by Fundação para a Ciência e a Tecnologia (Portugal) through grant PEst-OE/BIA/UI0457/2011. Artur Alves and Alan Phillips were supported by the programme Ciência 2008, co-funded by the Human Potential Operational Programme (National Strategic Reference Framework 2007–2013) and the European Social Fund (EU).publishe
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