Daniela Bartel

Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? A case study on major arthropod relationships

BackgroundWhenever different data sets arrive at conflicting phylogenetic hypotheses, only testable causal explanations of sources of errors in at least one of the data sets allow us to critically choose among the conflicting hypotheses of relationships. The large (28S) and small (18S) subunit rRNAs are among the most popular markers for studies of deep phylogenies. However, some nodes supported by this data are suspected of being artifacts caused by peculiarities of the evolution of these molecules. Arthropod phylogeny is an especially controversial subject dotted with conflicting hypotheses which are dependent on data set and method of reconstruction. We assume that phylogenetic analyses based on these genes can be improved further i) by enlarging the taxon sample and ii) employing more realistic models of sequence evolution incorporating non-stationary substitution processes and iii) considering covariation and pairing of sites in rRNA-genes.ResultsWe analyzed a large set of arthropod sequences, applied new tools for quality control of data prior to tree reconstruction, and increased the biological realism of substitution models. Although the split-decomposition network indicated a high noise content in the data set, our measures were able to both improve the analyses and give causal explanations for some incongruities mentioned from analyses of rRNA sequences. However, misleading effects did not completely disappear.ConclusionAnalyses of data sets that result in ambiguous phylogenetic hypotheses demand for methods, which do not only filter stochastic noise, but likewise allow to differentiate phylogenetic signal from systematic biases. Such methods can only rely on our findings regarding the evolution of the analyzed data. Analyses on independent data sets then are crucial to test the plausibility of the results. Our approach can easily be extended to genomic data, as well, whereby layers of quality assessment are set up applicable to phylogenetic reconstructions in general.

Genetic differentiation and shell morphology of Trochulus oreinos (Wagner, 1915) and T. hispidus (Linnaeus, 1758) (Pulmonata: Hygromiidae) in the northeastern Alps

Trochulus oreinos oreinos and T. oreinos scheerpeltzi are two land snail taxa endemic to the Northeastern Austrian Alps, which have been regarded as subspecies of the highly variable, widespread land snail T. hispidus. We analysed these three taxa morphologically and genetically to evaluate whether a delimitation between them is possible and, if so, to resolve their phylogenetic relationships. Shell morphological results revealed high similarity between the two T. oreinos taxa, and that they are clearly separated from T. hispidus. Additionally, the T. oreinos subspecies concur with respect to their habitat preferences, as they are both restricted to rocky high alpine areas, whereas the local form of T. hispidus is distributed over a wider altitudinal range in moist areas and scrubby perennial herb vegetation near water bodies. While the morphological and ecological results allow clear differentiation between T. hispidus and T. oreinos only, analyses of the mitochondrial cytochrome c oxidase subunit I and 16S rRNA genes revealed high sequence divergences between all three taxa, which indicates that they represent old lineages. The two T. oreinos taxa appear as distantly related sister groups, well separated from T. hispidus. Whether T. o. oreinos and T. o. scheerpeltzi should be considered as species cannot be decided at the current state of knowledge.

Paraphyly and budding speciation in the hairy snail (Pulmonata, Hygromiidae).

Delimitation of species is often complicated by discordance of morphological and genetic data. This may be caused by the existence of cryptic or polymorphic species. The latter case is particularly true for certain snail species showing an exceptionally high intraspecific genetic diversity. The present investigation deals with the Trochulus hispidus complex, which has a complicated taxonomy. Our analyses of the COI sequence revealed that individuals showing a T. hispidus phenotype are distributed in nine highly differentiated mitochondrial clades (showing p‐distances up to 19%). The results of a parallel morphometric investigation did not reveal any differentiation between these clades, although the overall variability is quite high. The phylogenetic analyses based on 12S, 16S and COI sequences show that the T. hispidus complex is paraphyletic with respect to several other morphologically well‐defined Trochulus species (T. clandestinus, T. villosus, T. villosulus and T. striolatus) which form well‐supported monophyletic groups. The nc marker sequence (5.8S–ITS2–28S) shows only a clear separation of T. o. oreinos and T. o. scheerpeltzi, and a weakly supported separation of T. clandestinus, whereas all other species and the clades of the T. hispidus complex appear within one homogeneous group. The paraphyly of the T. hispidus complex reflects its complicated history, which was probably driven by geographic isolation in different glacial refugia and budding speciation. At our present state of knowledge, it cannot be excluded that several cryptic species are embedded within the T. hispidus complex. However, the lack of morphological differentiation of the T. hispidus mitochondrial clades does not provide any hints in this direction. Thus, we currently do not recommend any taxonomic changes. The results of the current investigation exemplify the limitations of barcoding attempts in highly diverse species such as T. hispidus.

Molecular phylogeny of the Raphidiidae (Raphidioptera)

We present a molecular phylogeny of the family Raphidiidae including representatives of 21 of the 26 genera. Sequences from the nuclear gene for the large subunit ribosomal RNA (28S rRNA) and the mitochondrial cytochrome c oxidase subunit 3 gene (cox3) were used. For the phylogenetic reconstructions we applied automated and manual approaches for sequence alignment and different evolutionary models and tree building algorithms. The trees based on the two alignment approaches were rather similar in their overall topology. A combination of both marker sequences increased the resolution of the trees. The six clades within the raphidiid family that emerged represent either single genera or groups of genera, namely: (i) the Nearctic genus Agulla Navás, (ii) the Nearctic/Central American genus Alena Navás, (iii) the Central Asiatic and Eastern Palaearctic genus Mongoloraphidia H. Aspöck & U. Aspöck, (iv) the Palaearctic Puncha clade, (v) the western Mediterranean Ohmella clade, and (vi) the Palaearctic Phaeostigma clade. The New World taxa Agulla and Alena are placed as successive out‐groups to a monophyletic Palaearctic clade. The Mongoloraphidia clade is distributed in the eastern Palearctic while the remaining three clades are exclusively (Ohmella clade) or mainly distributed in the western Palaearctic. The early radiation of extant Raphidiidae is interpreted based on the phylogenetic tree obtained in the present study, and the geological and palaeobiological processes around the K–T boundary.

Where Taxonomy Based on Subtle Morphological Differences Is Perfectly Mirrored by Huge Genetic Distances: DNA Barcoding in Protura (Hexapoda)

Background Protura is a group of tiny, primarily wingless hexapods living in soil habitats. Presently about 800 valid species are known. Diagnostic characters are very inconspicuous and difficult to recognize. Therefore taxonomic work constitutes an extraordinary challenge which requires special skills and experience. Aim of the present pilot project was to examine if DNA barcoding can be a useful additional approach for delimiting and determining proturan species. Methodology and Principal Findings The study was performed on 103 proturan specimens, collected primarily in Austria, with additional samples from China and Japan. The animals were examined with two markers, the DNA barcoding region of the mitochondrial COI gene and a fragment of the nuclear 28S rDNA (Divergent Domain 2 and 3). Due to the minuteness of Protura a modified non-destructive DNA-extraction method was used which enables subsequent species determination. Both markers separated the examined proturans into highly congruent well supported clusters. Species determination was performed without knowledge of the results of the molecular analyses. The investigated specimens comprise a total of 16 species belonging to 8 genera. Remarkably, morphological determination in all species exactly mirrors molecular clusters. The investigation revealed unusually huge genetic COI distances among the investigated proturans, both maximal intraspecific distances (0–21.3%), as well as maximal congeneric interspecifical distances (up to 44.7%). Conclusions The study clearly demonstrates that the tricky morphological taxonomy in Protura has a solid biological background and that accurate species delimitation is possible using both markers, COI and 28S rDNA. The fact that both molecular and morphological analyses can be performed on the same individual will be of great importance for the description of new species and offers a valuable new tool for biological and ecological studies, in which proturans have generally remained undetermined at species level.

Morphological and Genetic Analysis of the Acerentomon doderoi Group (Protura: Acerentomidae) with Description of A. christiani sp. nov

Acerentomon christiani sp. nov. is described from Vienna, Austria. The new species is a member of the “doderoi” group, characterized by the presence of seta x on tergite VII. It is most similar to A. gallicum, A. brevisetosum and A. tenuisetosum, but differs from these species in the length of foretarsal sensillum c and certain other chaetotaxic measurements and indices. In addition to the morphological description, the DNA barcoding region of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) and the 28S ribosomal RNA of the new species are provided. The morphological characters and the barcode of the new species are discussed in comparison to those of other Acerentomon species. An identification key to all known Acerentomon spp. of the “doderoi” group is given.

Redescription and review of the most abundant conehead in Italy: Acerentomon italicum Nosek, 1969 (Protura: Acerentomidae)

Abstract Acerentomon italicum is the most abundant species of Protura in Italy. In this paper, A. italicum is redescribed according to the most recent revision of diagnostic characters (morphometry, porotaxy), examining the type material and 59 specimens from 11 different localities in our collection. For some characters, scanning electron microscope (SEM) pictures are presented. An updated detailed catalogue extracted from the authors’ database is provided: A. italicum is reported from 91 Italian localities (mainly from Northern Italian regions) in a total of 520 ♂♂, 669 ♀♀, 28 pre-imagines, 69 maturi junior, 25 larvae II, four larvae I and eight undetermined. Few specimens were collected in Switzerland (two, about 5 km away from the Italian border), Austria (three), Slovenia (one) and Corsica (eight). The entire data set is analysed for information on phenology (juveniles detectable every month in Liguria and Tuscany, but only during spring–summer in the remaining regions of Northern Italy) and sex ratio (M:F = 0.78) of this species. A. italicum was collected in localities from 0 to 2000 m above sea level in the soil and litter of pure and mixed forest. The geological substratum, when recorded, was limestone, quartz/mica schists and conglomerates. The DNA barcode is newly provided for 21 representatives from three Italian populations of A. italicum.