Wolfgang Maier

Current state and perspectives of fungal DNA barcoding and rapid identification procedures

Fungal research is experiencing a new wave of methodological improvements that most probably will boost mycology as profoundly as molecular phylogeny has done during the last 15xa0years. Especially the next generation sequencing technologies can be expected to have a tremendous effect on fungal biodiversity and ecology research. In order to realise the full potential of these exciting techniques by accelerating biodiversity assessments, identification procedures of fungi need to be adapted to the emerging demands of modern large-scale ecological studies. But how should fungal species be identified in the near future? While the answer might seem trivial to most microbiologists, taxonomists working with fungi may have other views. In the present review, we will analyse the state of the art of the so-called barcoding initiatives in the light of fungi, and we will seek to evaluate emerging trends in the field. We will furthermore demonstrate that the usability of DNA barcoding as a major tool for identification of fungi largely depends on the development of high-quality sequence databases that are thoroughly curated by taxonomists and systematists.

Vestibular labyrinth diversity in diprotodontian marsupial mammals

ABSTRACT The bony labyrinth of specimens representing eight diprotodontian species were visualized by high-resolution computed tomography. Linear measurements of the labyrinth were taken, e.g., the height and width of the arc of each semicircular canal. The relative sizes and spatial arrangements of the semicircular canals were compared and some of the variation was atomized into 17 characters, which were then phylogenetically interpreted. There has been a change both in size and in relative arrangement of the semicircular canals that for some aspects maps onto the ecological change from arboreality to terrestriality. In particular, there are differences among diprotodontians in the height of the anterior semicircular canal in relation to the posterior one. In arboreal species, the lateral semicircular canal is relatively longer than the equivalent semicircular canals of terrestrial species. A rounder anterior semicircular canal is widespread for Diprotodontia with a shift in Pseudocheiridae, where it is more flattened. Dendrolagus shows features typical of terrestrial species in spite of its arboreal lifestyle. The fact that it shows the derived character state is congruent with the fact that it has secondarily and only recently evolved an arboreal lifestyle.

Paleontological and developmental evidence resolve the homology and dual embryonic origin of a mammalian skull bone, the interparietal

The homologies of mammalian skull elements are now fairly well established, except for the controversial interparietal bone. A previous experimental study reported an intriguing mixed origin of the interparietal: the medial portion being derived from the neural crest cells, whereas the lateral portion from the mesoderm. The evolutionary history of such mixed origin remains unresolved, and contradictory reports on the presence or absence and developmental patterns of the interparietal among mammals have complicated the question of its homology. Here we provide an alternative perspective on the evolutionary identity of the interparietal, based on a comprehensive study across more than 300 extinct and extant taxa, integrating embryological and paleontological data. Although the interparietal has been regarded as being lost in various lineages, our investigation on embryos demonstrates its presence in all extant mammalian “orders.” The generally accepted paradigm has regarded the interparietal as consisting of two elements that are homologized to the postparietals of basal amniotes. The tabular bones have been postulated as being lost during the rise of modern mammals. However, our results demonstrate that the interparietal consists not of two but of four elements. We propose that the tabulars of basal amniotes are conserved as the lateral interparietal elements, which quickly fuse to the medial elements at the embryonic stage, and that the postparietals are homologous to the medial elements. Hence, the dual developmental origin of the mammalian interparietal can be explained as the evolutionary consequence of the fusion between the crest-derived “postparietals” and the mesoderm-derived “tabulars.”

Is it Really that Difficult to Parse German

This paper presents a comparative study of probabilistic treebank parsing of German, using the Negra and TuBa-D/Z tree-banks. Experiments with the Stanford parser, which uses a factored PCFG and dependency model, show that, contrary to previous claims for other parsers, lexicalization of PCFG models boosts parsing performance for both treebanks. The experiments also show that there is a big difference in parsing performance, when trained on the Negra and on the TuBa-D/Z treebanks. Parser performance for the models trained on TuBa-D/Z are comparable to parsing results for English with the Stanford parser, when trained on the Penn treebank. This comparison at least suggests that German is not harder to parse than its West-Germanic neighbor language English.

Data-Driven Parsing with Probabilistic Linear Context-Free Rewriting Systems

This paper presents the first efficient implementation of a weighted deductive CYK parser for Probabilistic Linear Context-Free Rewriting Systems (PLCFRSs). LCFRS, an extension of CFG, can describe discontinuities in a straightforward way and is therefore a natural candidate to be used for data-driven parsing. To speed up parsing, we use different context-summary estimates of parse items, some of them allowing for A* parsing. We evaluate our parser with grammars extracted from the German NeGra treebank. Our experiments show that data-driven LCFRS parsing is feasible and yields output of competitive quality.

Characterizing discontinuity in constituent treebanks

Measures for the degree of non-projectivity of dependency grammar have received attention both on the formal and on the empirical side. The empirical characterization of discontinuity in constituent treebanks annotated with crossing branches has nevertheless been neglected so far. In this paper, we present two measures for the characterization of both the discontinuity of constituent structures and the nonprojectivity of dependency structures. An empirical evaluation on German data as well as an investigation of the relation between the measures and grammars extracted from treebanks shows their relevance.

Nasal anatomy of the non-mammaliaform cynodont Brasilitherium riograndensis (Eucynodontia, Therapsida) reveals new insight into mammalian evolution.

The mammalian nasal cavity is characterized by a unique anatomy with complex internal features. The evolution of turbinals was correlated with endothermic and macrosmatic adaptations in therapsids and in early mammals, which is still apparent in their twofold function (warming and moistening of air, olfaction). Fossil evidence for the transformation from the nonmammalian to the mammalian nasal cavity pattern has been poor and inadequate. Ossification of the cartilaginous nasal capsule and turbinals seems to be a feature that occurred only very late in synapsid evolution but delicate ethmoidal bones are rarely preserved. Here we provide the first µCT investigation of the nasal cavity of the advanced non‐mammaliaform cynodont Brasilitherium riograndensis from the Late Triassic of Southern Brazil, a member of the sister‐group of mammaliaforms, in order to elucidate a critical anatomical transition in early mammalian evolution. Brasilitherium riograndensis already had at least partially ossified turbinals as remnants of the nasoturbinal and the first ethmoturbinal are preserved. The posterior nasal septum is partly ossified and contributes to a mesethmoid. The nasal cavity is posteriorly expanded and forms a distinctive pars posterior (ethmoidal recess) that is ventrally separated from the nasopharyngeal duct by a distinct lamina terminalis. Thus, our observations clearly demonstrate that principal features of the mammalian nasal cavity were already present in the sister‐group of mammaliaforms. Anat Rec, 297:2018–2030, 2014.

Evolution of the mammalian middle ear: a historical review.

Here we present a brief, historical review of research into the mammalian middle ear structures. Most of their essential homologies were established by embryologists, notably including Reichert, during the 19th century. The evolutionary dimension was confirmed by finds of fossil synapsids, mainly from the Karroo of South Africa. In 1913, Ernst Gaupp was the first to present a synthesis of the available embryological and paleontological data, but a number of morphological details remained to be solved, such as the origin of the tympanic membrane. Gaupp favoured an independent origin of the eardrum in anurans, sauropsids, and mammals; we support most of his ideas. The present review emphasizes the problem of how the mammalian middle ear structures that developed at the angle of the lower jaw were transferred to the basicranium; the ontogenesis of extant marsupials provides important information on this question.

Annotation Schemes and their Influence on Parsing Results

Most of the work on treebank-based statistical parsing exclusively uses the Wall-Street-Journal part of the Penn treebank for evaluation purposes. Due to the presence of this quasi-standard, the question of to which degree parsing results depend on the properties of treebanks was often ignored. In this paper, we use two similar German treebanks, TuBa-D/Z and NeGra, and investigate the role that different annotation decisions play for parsing. For these purposes, we approximate the two treebanks by gradually taking out or inserting the corresponding annotation components and test the performance of a standard PCFG parser on all treebank versions. Our results give an indication of which structures are favorable for parsing and which ones are not.

DNA barcoding in the rust genus Chrysomyxa and its implications for the phylogeny of the genus.

Chrysomyxa rusts are fungal pathogens widely present in the boreal forest. Taxonomic delimitation and precise species identification are difficult within this genus because several species display similar morphological features. We applied a DNA barcode system based on the ribosomal internal transcribed spacer region (ITS), large subunit (28S) ribosomal RNA gene, mitochondrial cytochrome oxidase 1 (CO1) and mitochondrial NADH dehydrogenase subunit 6 (NAD6) in 86 strains from 16 different Chrysomyxa species, including members of the Chrysomyxa ledi species complex. The nuclear ITS and 28S loci revealed higher resolving power than the mitochondrial genes. Amplification of the full CO1 barcode region failed due to the presence of introns limiting the dataset obtained with this barcode. In most cases the ITS barcodes were in agreement with taxonomic species based on phenotypic characters. Nevertheless we observed genetically distinct (different DNA barcodes) lineages within Chrysomyxa pyrolae and Chrysomyxa rhododendri, providing some evidence for allopatric speciation within these morphologically defined species. This finding, together with the observed pattern of host specificities of the studied rust fungi, suggest that species diversification within the C. ledi species complex might be governed by a set of factors such as specialisation to certain Ericaceae species as telial hosts and to a lesser extent specialization to different spruce species as aecial hosts. Moreover allopatric speciation by geographic disruption of species also seems to take place. When our data were integrated into a broader phylogenetic framework the Chrysomyxa genus unexpectedly was not resolved as a monophyletic group. Indeed the spruce cone rusts C. pyrolae and C. monesis coalesced with the pine needle rusts belonging to the genus Coleosporium, whereas the microcyclic species Chrysomyxa weirii was embedded within a clade comprising the genus Melampsora.