Nikolaus U. Szucsich

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.

Decisive Data Sets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects

Phylogenetic relationships of the primarily wingless insects are still considered unresolved. Even the most comprehensive phylogenomic studies that addressed this question did not yield congruent results. To get a grip on these problems, we here analyzed the sources of incongruence in these phylogenomic studies by using an extended transcriptome data set. Our analyses showed that unevenly distributed missing data can be severely misleading by inflating node support despite the absence of phylogenetic signal. In consequence, only decisive data sets should be used which exclusively comprise data blocks containing all taxa whose relationships are addressed. Additionally, we used Four-cluster Likelihood Mapping (FcLM) to measure the degree of congruence among genes of a data set, as a measure of support alternative to bootstrap. FcLM showed incongruent signal among genes, which in our case is correlated neither with functional class assignment of these genes nor with model misspecification due to unpartitioned analyses. The herein analyzed data set is the currently largest data set covering primarily wingless insects, but failed to elucidate their interordinal phylogenetic relationships. Although this is unsatisfying from a phylogenetic perspective, we try to show that the analyses of structure and signal within phylogenomic data can protect us from biased phylogenetic inferences due to analytical artifacts.

Testing for misleading effects in the phylogenetic reconstruction of ancient lineages of hexapods: influence of character dependence and character choice in analyses of 28S rRNA sequences

The present analyses employ the almost complete sequence of the 28S rRNA gene to investigate phylogenetic relationships among Pancrustacea, placing special emphasis on the position of basal hexapod lineages. This study utilizes a greater number of characters and taxa of Protura, Collembola and Diplura than previous analyses to focus on conflicts in the reconstruction of the early steps in hexapod evolution. Phylogenetic trees are mainly based on Bayesian approaches, but likewise include analyses with Maximum Likelihood and Maximum Parsimony. Different analyses, including the application of a mixed DNA/RNA substitution model, were performed to narrow possible misleading effects of non‐stationarity of nucleotide frequencies, saturation and character independence down to a minimum. This is the first time that a mixed DNA/RNA model is applied to analyse 28S rRNA sequences of basal hexapods. All methods yielded strong support for the monophyly of Collembola, Diplura, Dicondylia and Insecta s.str., as well as for a cluster composed of Diplura and Protura (‘Nonoculata‐hypothesis’). However, the last cluster may be an artifact caused by a shared GC bias of the 28S sequences between these orders, in combination with a long branch effect. The instability of the position of the ‘Nonoculata’ within Pancrustacea further bears out the misleading effect of non‐stationarity of nucleotide frequencies. Protura and Diplura either form the sister‐group to Collembola (Entognatha) or cluster with branchiopod crustaceans. Overall, the phylogenetic signal of the complete sequences of the 28S rRNA gene favours monophyly of Hexapoda over paraphyly. However, further corroboration from independent data is needed to rule out the competing hypothesis of mutually paraphyletic Crustacea and Hexapoda.

Morphology and function of the proboscis in Bombyliidae (Diptera, Brachycera) and implications for proboscis evolution in Brachycera.

Abstract Based on serial semithin sections and SEM photographs of representatives of European Bombyliinae and Anthracinae, the mouthparts of Bombyliidae are studied and compared with the relevant data from literature on other families of Diptera Brachycera. The three moving units of the proboscis (clypeo-cibarial region, haustellum-maxillary base region, and labella) and their structures and muscles are described. Functions and possible movements are inferred from the structures observed. Articulations both between the parts of the organ and to the head capsule enable the fly to retract its proboscis into a resting position. Proboscis movement from a resting to a feeding position encompasses the following submovements: rotating of the basal clypeo-cibarial region (= fulcrum) against the head capsule, folding of the haustellum-maxillary base region against the fulcrum, evagination and invagination of the labial base, and the labella movements. This is a novelty as compared to the rigid proboscis of Tabanidae and agrees largely with the conditions in the Cyclorrhapha. The evolution of these novelties and their functional significance are discussed. The fulcrum, as well as the haustellum-maxillary base, as the new moving units are deduced from the plesiomorphic state as present in Tabanidae by fusions of sclerites, shifts of musculature and formation of new articulations.

Homology: a synthetic concept of evolutionary robustness of patterns

The history of the homology concept is a history of attempts to conceive the basis of sameness in biology. Since it was formulated in the middle of the 19th century, the concept has had to fit an ever growing number of scientific fields and purposes. These different demands have resulted in diverging, sometimes, incompatible definitions. The inconsistencies are mostly due to the lack of a clear separation of hypotheses of maintenance from hypotheses of transformation.

Mandibles with two joints evolved much earlier in the history of insects: dicondyly is a synapomorphy of bristletails, silverfish and winged insects

The evolution of two‐jointed mandibles is considered to be a major step during the evolution of early insects enabling the exploration of new types of food. Two‐jointed – or dicondylic – mandibles are believed to be a groundplan characteristic for winged insects and silverfish. Jumping bristletails are thought to possess mandibles with one joint and are the sistergroup of winged insects + silverfish. However, our knowledge of the cephalic morphology of bristletails is limited to data from a few species and thus fragmentary. We investigated the cephalic morphology of both families of bristletails, Meinertellidae and Machilidae. We focused on skeletal elements and the musculature and compared them with the corresponding structures found in silverfish and winged insects. Bristletails show a previously unknown coupling structure between the maxillary palps and the mandibles and an additional anterior articulation of the mandibles in the region of the anterior tentorial pits. The articulation can be homologised with the anterior articulation in silverfish and winged insects. Together with a description of the functional morphology of the mandible system of bristletails and a discussion of the homology of mandibular articulations and related characters, we provide conclusive evidence that bristletails are, in fact, dicondylic insects.

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.

The Arthropod Head

The anterior region of arthropods is profoundly influenced by effects of condensation and integration that has taken place in various character complexes. Prominent examples are the cerebralization of the central nervous system, the integration of anterior appendages to encompass sensory function and food uptake, the integration of anterior segments covered by a continuous dorsal shield, and a condensation of the endoskeleton which has resulted in the partial obscuring of the segmental organization. The borders between these different complexes, however, do not necessarily correspond. The exact composition and origin of the ‘arthropod head’ is an enduring problem in arthropod evolution.

Brain anatomy in Diplura (Hexapoda).

BackgroundIn the past decade neuroanatomy has proved to be a valuable source of character systems that provide insights into arthropod relationships. Since the most detailed description of dipluran brain anatomy dates back to Hanström (1940) we re-investigated the brains of Campodea augens and Catajapyx aquilonaris with modern neuroanatomical techniques. The analyses are based on antibody staining and 3D reconstruction of the major neuropils and tracts from semi-thin section series.ResultsRemarkable features of the investigated dipluran brains are a large central body, which is organized in nine columns and three layers, and well developed mushroom bodies with calyces receiving input from spheroidal olfactory glomeruli in the deutocerebrum. Antibody staining against a catalytic subunit of protein kinase A (DC0) was used to further characterize the mushroom bodies. The japygid Catajapyx aquilonaris possesses mushroom bodies which are connected across the midline, a unique condition within hexapods.ConclusionsMushroom body and central body structure shows a high correspondence between japygids and campodeids. Some unique features indicate that neuroanatomy further supports the monophyly of Diplura. In a broader phylogenetic context, however, the polarization of brain characters becomes ambiguous. The mushroom bodies and the central body of Diplura in several aspects resemble those of Dicondylia, suggesting homology. In contrast, Archaeognatha completely lack mushroom bodies and exhibit a central body organization reminiscent of certain malacostracan crustaceans. Several hypotheses of brain evolution at the base of the hexapod tree are discussed.

The mouthparts of Scutigerella immaculata: Correspondences and variation among serially homologous head appendages.

Descriptions of the skeletomuscular system of the symphylan head are characterized by a high number of incongruencies among authors. The increased accuracy and transparency of 3D-reconstruction methods allows for an allocation of some of the incongruencies to (i) misinterpretations of literature descriptions, or (ii) different views of what constitutes a separate muscle. A structural comparison allows to homologize muscles among the serially arranged mouthparts of Symphyla.