The phylogenetic positions of three Basal-hexapod groups (protura, diplura, and collembola) based on ribosomal RNA gene sequences

A new genus of japygids (Diplura: Japygidae) in mid-Cretaceous amber from northern Myanmar

Diplura is a cryptic and edaphic group of hexapod animals characterized by the presence of filiform or pincer-like cerci located at the end of the abdomen. As one of the early diverging lineages of Hexapoda, diplurans play a crucial role in unraveling the origin of the hyperdiverse insects. The fossil record of diplurans, however, is exceptionally limited due to their delicate bodies and habitat requirements. Here we report the discovery of a new japygid, Cretojapyx huangi gen. et sp. nov., entombed in mid-Cretaceous Kachin amber (northern Myanmar). This specimen exhibits distinctive features, including the well-developed carinae on abdominal segment X and cerci, left cercus lacking a prominent tooth and denticles, and right cercus with a postmedian tooth followed by uniseriate round denticles. Our finding provides a unique opportunity to gain valuable insights into the evolutionary history of this ancient lineage and deepen our understanding of terrestrial ecosystems during the Mesozoic.

First records of penicillate millipedes (Diplopoda, Polyxenidae) from Thailand, with descriptions of two new species

Two new species are described from the family Polyxenidae. Monographis panhai sp. nov. and Unixenus thailandicus sp. nov. represent the first records of their respective genera in Thailand. Monographis panhai sp. nov. shows distinct morphological differences in the arrangement of sensilla in the antennomere VI, as well as in the structures of the labrum and the claw. Collections from different areas of Thailand showed that not only is it widespread but also exhibits geographic variation in morphology. Unixenus thailandicus sp. nov. exhibits sexual dimorphism in the number of conical sensilla on the lateral palp, with 24 in males and 22 in females, differing from the typical count of 13 within the genus.

A New Genus of Sminthurididae (Collembola, Symphypleona) from Brazil, with Notes on the Systematics of the Family

The Sminthurididae family includes Symphypleona species highly adapted to courtship, with males exhibiting remarkable modifications on their antennae. Here we describe a new Neotropical genus and species of Sminthurididae from a Cerrado-Caatinga ecotonal zone in Brazil. Males of Parasminthurides spinosus gen. nov. sp. nov. have highly dimorphic antennal claspers similar to those of Sminthurides, but its females have unique strong spiniform chaetae on antennal segments II and III as well, which are possibly accessories for the courtship. The new genus can also be diagnosed by its elongated maxillae, males having large dorsal vesicles between abdomen II and III, ungues I–III with similar morphology and sizes, and interno-apical dental chaetae modified into large spiniform chaetae. We also present the main diagnostic features of all Sminthurididae genera, providing a comparative table and an updated identification key for them. Finally, we discuss the previous and current knowledge on the family’s systematics, suggesting some perspectives for future studies in this field.

Homoplasy and morphological stasis revealed through multilocus phylogeny of new myrmecophilous species in Armadillidiidae (Isopoda: Oniscidea)

The terrestrial isopod family Armadillidiidae presents higher diversity in karstic areas, with fewer species present in areas with reduced suitable subterranean habitats, such as siliceous sandy soils. Myrmecophily, although not widespread in the family Armadillidiidae, can help these animals to colonize sandy substrates, as is observed in several populations of myrmecophilous Armadillidiidae species in central and southern Spain. Morphological examination and multilocus phylogenetic analyses, including mitochondrial DNA (Cox1) and nuclear DNA (18S, 28S and H3) markers, indicate that these myrmecophilous populations represent four new taxa: Iberiarmadillidium pinicola gen. & sp. nov., Iberiarmadillidium psammophilum sp. nov., Iberiarmadillidium sakura sp. nov. and Cristarmadillidium myrmecophilum sp. nov. Some of the main diagnostic characters used in the taxonomy of Armadillidiidae are not clearly apomorphic. Among head morphologies, Eluma type seems to be the ancestral state, being typical of several unrelated lineages; duplocarinate and Armadillidium types are derived states observed in unrelated lineages. The presence of a schisma is a convergent character state, because it has been identified in several taxa nested in unrelated clades. The newly described taxa present patterns of morphological stasis and homoplasy, likely to be associated with their shared myrmecophilous habits. The generic taxonomy of the family needs a deep revision including phylogenetic approaches and thorough taxon sampling.

A review of the hexapod tracheal system with a focus on the apterygote groups

Respiratory systems are key innovations for the radiation of terrestrial arthropods. It is therefore surprising that there is still a considerable lack of knowledge. In this review of the available information on tracheal systems of hexapods (with a focus on the apterygote lineages Protura, Collembola, Diplura, Archaeognatha and Zygentoma), we summarize available data on the spiracles (number, position and morphology), the shape and variability of tracheal branching patterns including anastomoses, the tracheal fine structure and the respiratory proteins. The available data are strongly fragmented, and information for most subgroups is missing. In various cases, individual observations for one species account for the knowledge of the entire order. The available data show that there are strong differences between but also within apterygote orders. We conclude that the available data are insufficient to derive detailed conclusions on the hexapod ground plan and outline the possible evolutionary scenarios for the tracheal system in this group.

Two New Species of the Genus Eucorydia (Blattodea: Corydiidae) from the Nansei Islands in Southwest Japan

Two new species of the cockroach genus Eucorydia Hebard, 1929 from the Nansei Islands in Southwest Japan were compared to two closely related congeners, Eucorydia yasumatsui Asahina, 1971 and Eucorydia dasytoides (Walker, 1868). Eucorydia donanensis Yanagisawa, Sakamaki, and Shimano sp. nov. from Yonaguni-jima Island was characterized by an overall length of 12.5-14.5 mm in males. The dorsal side of the male abdomen was entirely dark purple and there was an obscure orange band running down the middle of the tegmen. Eucorydia tokaraensis Yanagisawa, Sakamaki, and Shimano sp. nov. was characterized by an overall length of 12.0-13.0 mm in males and a distinct orange band running down the middle of the tegmen. Eucorydia yasumatsui, E. donanensis, E. tokaraensis and the zonata population of E. dasytoides were divided into four lineages in a maximum-likelihood tree generated from a dataset concatenated from five (two nuclear, 28S rRNA, histone H3, and three mitochondrial, COII, 12S rRNA, 16S rRNA) genes. We recognized the three Japanese lineages E. yasumatsui, E. donanensis, and E. tokaraensis as distinct species, which were also supported by the pairwise genetic distances (5.4-7.8%, K2P) of the COI sequences. Morphometric analysis was performed on the genitalia. A principal component analysis plot revealed that the sizes of the genitalia in the three Japanese species were similar to each other and smaller than that of the zonata population of E. dasytoides. The analysis also revealed that the three Japanese species were distinguished from each other by combinations of the sizes of L3 and L7 sclerites and the shape of R2 sclerite, with some overlapping exceptions.

Re-Evaluating the Internal Phylogenetic Relationships of Collembola by Means of Mitogenome Data

Collembola are an ancient and early diverging lineage of basal hexapods that occur in virtually all terrestrial habitats on Earth. Phylogenetic relationships between the different orders of Collembola are fiercely debated. Despite a range of studies and the application of both morphological and genetic approaches (singly or in combination) to assess the evolutionary relationships of major lineages in the group, no consensus has been reached. Several mitogenome sequences have been published for key taxa of the class (and their number is increasing rapidly). Here, we describe two new Antarctic Collembola mitogenomes and compare all complete or semi-complete springtail mitogenome sequences available on GenBank in terms of both gene order and DNA sequence analyses in a genome evolution and molecular phylogenetic framework. With minor exceptions, we confirm the monophyly of Poduromorpha and Symphypleona sensu stricto (the latter placed at the most basal position in the springtail phylogenetic tree), whereas monophyly of Neelipleona and Entomobryomorpha is only supported when a handful of critical taxa in these two lineages are excluded. Finally, we review gene order models observed in the class, as well as the overall mitochondrial nucleotide composition.

Are there any risks of the disposal of pesticide effluents in soils? Biobed system meets ecotoxicology ensuring safety to soil fauna

The biobed is a purification system, which reduces soil pollution for receiving pesticide residues from handling and washing machinery in agricultural areas. The aims of this study were (1) to assess ecotoxicity effects over time to soil fauna, posed by Lorsban^® 480 BR (Chlorpyrifos) and Dithane^® NT (Mancozeb) residues when disposed of in a biobed system compared with two subtropical soils, and (2) to assess ecotoxicity effects over time to soil fauna simulating an accidental spillage with Lorsban^® 480 BR at the biobed. A semi-field experiment was conducted for 420 days in southern Brazil, testing continuous disposal of washing pulverization tanks in biobeds, Typic Haploperox or Typic Hapludults. In addition, different biobeds received a single dose (1 L) of Lorsban^® 480 BR to simulate an accidental spillage. Chronic ecotoxicity tests were performed using Folsomia candida, Eisenia andrei, and Enchytraeus crypticus in different sampling times for both experiments. F. candida was the most sensitive species. The biobed system was able to eliminate effects from residues of both pesticides over time in all species, which did not happen in both natural soils. In accidental spillage simulation, even 420 days after contamination, F. candida did not show reproduction. The biobeds can be a feasible alternative for the disposal and treatment residues of pesticides, also for handling and washing pesticides activities. The system was efficient in promoting degradation and reducing ecotoxicity effects posed by Lorsban^® 480 BR and Dithane^® NT for soil fauna. It is a safe alternative to avoid soil contamination.

Phylomitogenomic analyses on collembolan higher taxa with enhanced taxon sampling and discussion on method selection

Collembola are a basal group of Hexapoda renowned for both unique morphological characters and significant ecological roles. However, a robust and plausible phylogenetic relationship between its deeply divergent lineages has yet to be achieved. We carried out a mitophylogenomic study based on a so far the most comprehensive mitochondrial genome dataset. Our data matrix contained mitogenomes of 31 species from almost all major families of all four orders, with 16 mitogenomes newly sequenced and annotated. We compared the linear arrangements of genes along mitochondria across species. Then we conducted 13 analyses each under a different combination of character coding, partitioning scheme and heterotachy models, and assessed their performance in phylogenetic inference. Several hypothetical tree topologies were also tested. Mitogenomic structure comparison revealed that most species share the same gene order of putative ancestral pancrustacean pattern, while seven species from Onychiuridae, Poduridae and Symphypleona bear different levels of gene rearrangements, indicating phylogenetic signals. Tomoceroidea was robustly recovered for the first time in the presence of all its families and subfamilies. Monophyly of Onychiuroidea was supported using unpartitioned models alleviating LBA. Paronellidae was revealed polyphyletic with two subfamilies inserted independently into Entomobryidae. Although Entomobryomorpha has not been well supported, more than half of the analyses obtained convincing topologies by placing Tomoceroidea within or near remaining Entomobryomorpha. The relationship between elongate-shaped and spherical-shaped collembolans still remained ambiguous, but Neelipleona tend to occupy the basal position in most trees. This study showed that mitochondrial genomes could provide important information for reconstructing the relationships among Collembola when suitable analytical approaches are implemented. Of all the data refining and model selecting schemes used in this study, the combination of nucleotide sequences, partitioning model and exclusion of third codon positions performed better in generating more reliable tree topology and higher node supports than others.

The Genome of the Blind Soil-Dwelling and Ancestrally Wingless Dipluran Campodea augens: A Key Reference Hexapod for Studying the Emergence of Insect Innovations

The dipluran two-pronged bristletail Campodea augens is a blind ancestrally wingless hexapod with the remarkable capacity to regenerate lost body appendages such as its long antennae. As sister group to Insecta (sensu stricto), Diplura are key to understanding the early evolution of hexapods and the origin and evolution of insects. Here we report the 1.2-Gb draft genome of C. augens and results from comparative genomic analyses with other arthropods. In C. augens, we uncovered the largest chemosensory gene repertoire of ionotropic receptors in the animal kingdom, a massive expansion that might compensate for the loss of vision. We found a paucity of photoreceptor genes mirroring at the genomic level the secondary loss of an ancestral external photoreceptor organ. Expansions of detoxification and carbohydrate metabolism gene families might reflect adaptations for foraging behavior, and duplicated apoptotic genes might underlie its high regenerative potential. The C. augens genome represents one of the key references for studying the emergence of genomic innovations in insects, the most diverse animal group, and opens up novel opportunities to study the under-explored biology of diplurans.

Mitochondrial Genome Diversity in Collembola: Phylogeny, Dating and Gene Order

Collembola (springtails) are an early diverging class of apterygotes, and mark the first substantial radiation of hexapods on land. Despite extensive work, the relationships between major collembolan lineages are still debated and, apart from the Early Devonian fossil Rhyniella praecursor, which demonstrates their antiquity, the time frame of springtail evolution is unknown. In this study, we sequence two new mitochondrial genomes and reanalyze all known Collembola mt-genomes, including selected metagenomic data, to produce an improved phylogenetic hypothesis for the group, develop a tentative time frame for their differentiation, and provide a comprehensive overview of gene order diversity. Our analyses support most taxonomically recognized entities. We find support for an Entomobryomorpha + Symphypleona clade, while the position of Neelipleona could not be assessed with confidence. A Silurian time frame for their basal diversification is recovered, with an indication that divergence times may be fairly old overall. The distribution of mitochondrial gene order indicates the pancrustacean arrangement as plesiomorphic and dominant in the group, with the exception of the family Onychiuridae. We distinguished multiple instances of different arrangements in individual genomes or small clusters. We further discuss the opportunities and drawbacks associated with the inclusion of metagenomic data in a classic study on mitochondrial genome diversity.

The Complete Mitochondrial Genome of Platysternon megacephalum peguense and Molecular Phylogenetic Analysis

Platysternon megacephalum is the only living representative species of Platysternidae and only three subspecies remain: P. m. megalorcephalum, P. m. shiui, and P. m. peguense. However, previous reports implied that P. m. peguense has distinct morphological and molecular features. The characterization of the mitogenome has been accepted as an efficient means of phylogenetic and evolutionary analysis. Hence, this study first determined the complete mitogenome of P. m. peguense with the aim to identify the structure and variability of the P. m. peguense mitogenome through comparative analysis. Furthermore, the phylogenetic relationship of the three subspecies was tested. Based on different tRNA gene loss and degeneration of these three subspecies, their rearrangement pathways have been inferred. Phylogenetic analysis showed that P. m. peguense is a sister group to (P. m. megalorcephalum and P. m. shiui). Furthermore, the divergence time estimation of these three subspecies coincided with the uplift of the Tibetan Plateau. This study shows that the genetic distances between P. m. peguense and the other two subspecies are comparable to interspecific genetic distances, for example within Mauremys. In general, this study provides new and meaningful insights into the evolution of the three Platysternidae subspecies.

Diurodrilus kunii sp. nov. (Annelida: Diurodrilidae) and a Molecular Phylogeny of the Genus

A new species of stygobiontic interstitial annelid, Diurodrilus kunii sp. nov., is described based on material collected from medium sand sediment (ϕ = 1.2-1.7) at groundwater level (40-100 cm in depth; 5-15 m inland from splash zone) in the intertidal beach slope on Ishikari Beach, facing the Sea of Japan, Hokkaido, Japan. The new species differs from six known congeners in the arrangement of the anterior-head ventral ciliophores, the degree of development in the primary and secondary toes, and the shape of the spermatozoa. We inferred the phylogenetic position of the new species among other congeners for which 18S rRNA, 28S rRNA, and COI gene sequences were available in public databases. This is the first representative of the genus from the Northwest Pacific.

Going Deeper into High and Low Phylogenetic Relationships of Protura

Proturans are small, wingless, soil-dwelling arthropods, generally associated with the early diversification of Hexapoda. Their bizarre morphology, together with conflicting results of molecular studies, has nevertheless made their classification ambiguous. Furthermore, their limited dispersal capability (due to the primarily absence of wings) and their euedaphic lifestyle have greatly complicated species-level identification. Mitochondrial and nuclear markers have been applied herein to investigate and summarize proturan systematics at different hierarchical levels. Two new mitochondrial genomes are described and included in a phylum-level phylogenetic analysis, but the position of Protura could not be resolved with confidence due to an accelerated rate of substitution and extensive gene rearrangements. Mitochondrial and nuclear loci were also applied in order to revise the intra-class systematics, recovering three proturan orders and most of the families/subfamilies included as monophyletic, with the exception of the subfamily Acerentominae. At the species level, most morphologically described species were confirmed using molecular markers, with some exceptions, and the advantages of including nuclear, as well as mitochondrial, markers and morphology are discussed. At all levels, an enlarged taxon sampling and the integration of data from different sources may be of significant help in solving open questions that still persist on the evolutionary history of Protura.

Two new Lophoturus species (Diplopoda, Polyxenida, Lophoproctidae) from Queensland, Australia

Lophoturusqueenslandicus Verhoeff, 1924 was the first penicillate millipede in the family Lophoproctidae collected from Cairns, a tropical region in Queensland, Australia, to be formally described. Specimens collected from this region in a recent study had the morphological characters known to define this genus. However, their body form and length, as well as dorsal colouration proved to be different, suggesting the possibility of more than one Lophoturus species. This assertion was supported by the results of a phylogenetic analysis of DNA extracted and sequenced using 18S and COI regions from L.queenslandicus and two undescribed species from this genus. Specimens preserved in ethanol can prove difficult to confidently identify to species level because their colour gradually fades. Examination of live specimens with their body colour visible, together with morphological characters and DNA analysis is the most reliable way of correctly distinguishing between these three species. Two new species, L.boondallussp. n. and L.molloyensissp. n. collected in Queensland, Australia are described.

Two new species of Phryssonotus (Diplopoda : Synxenidae) from southern and western Australia

For many years Phryssonotus novaehollandiae Silvestri, 1923 was thought to be the only species of this genus present in Australia. Specimens collected from three geographically separated populations had similar taxonomically important morphological characters and body lengths. However, their body scale trichomes exhibited three distinctive patterns: a trapezoid, T-shape, or dark banding, and the length-to-width ratios of their trichomes also differed. These differences, as well as results of phylogenetic analysis using 18S and COI gene regions from representatives of the three populations, suggested that more than one Phryssonotus species were present. Specimens of Phryssonotus preserved in ethanol can prove difficult to distinguish because the colour patterning gradually fades. Examination of the colour patterns of live specimens, other morphological characters and DNA analysis together, were found to be the most reliable method of correctly distinguishing between these three species. P. novaehollandiae Silvestri, 1923, the first described species collected from South Australia, remains, with its range extended to inland Victoria, and two new species (P. australis, sp. nov. and P. occidentalis, sp. nov.) are described.

Morphology disentangles the systematics of a ubiquitous but elusive meiofaunal group (Kinorhyncha: Pycnophyidae)

Kinorhyncha is a group of benthic, microscopic animals distributed worldwide in marine sediments. The phylum is divided into two classes, Cyclorhagida and Allomalorhagida, congruent with the two major clades recovered in recent phylogenetic analyses. Allomalorhagida accommodates more than one-third of the described species, most of them assigned to the family Pycnophyidae. All previous phylogenetic analyses of the phylum recovered the two genera within Pycnophyidae, Pycnophyes and Kinorhynchus, as paraphyletic and polyphyletic. A major problem in these studies was the lack of molecular data of most pycnophyids, due to the limited and highly localized distribution of most species, often in the Arctic and the deep-sea. We here overcame the problem by adding a morphological partition with data for 79 Pycnophyidae species, 15 of them also represented by molecular data. Model-based analyses yielded seven clades, which each was supported by several morphological apomorphies. Accordingly, Kinorhynchus is synonymized with Pycnophyes and six new genera are described for the remaining recovered clades: Leiocanthus gen. nov., Cristaphyes gen. nov., Higginsium gen. nov., Krakenella gen. nov., Setaphyes gen. nov. and Fujuriphyes gen. nov.

Molecular Phylogeny of Cypridoid Freshwater Ostracods (Crustacea: Ostracoda), Inferred from 18S and 28S rDNA Sequences

With the aim of exploring phylogenetic relationships within Cypridoidea, the most species-rich superfamily among the podocopidan ostracods, we sequenced nearly the entire 18S rRNA gene (18S) and part of the 28S rRNA gene (28S) for 22 species in the order Podocopida, with representatives from all the major cypridoid families. We conducted phylogenetic analyses using the methods of maximum likelihood, minimum evolution, and Bayesian analysis. Our analyses showed monophyly for Cyprididae, one of the four families currently recognized in Cypridoidea. Candonidae turned out to be paraphyletic, and included three clades corresponding to the subfamilies Candoninae, Paracypridinae, and Cyclocypridinae. We propose restricting the name Candonidae s. str. to comprise what is now Candoninae, and raising Paracypridinae and Cyclocyprininae to family rank within the superfamily Cypridoidea.

Progress, pitfalls and parallel universes: a history of insect phylogenetics

The phylogeny of insects has been both extensively studied and vigorously debated for over a century. A relatively accurate deep phylogeny had been produced by 1904. It was not substantially improved in topology until recently when phylogenomics settled many long-standing controversies. Intervening advances came instead through methodological improvement. Early molecular phylogenetic studies (1985-2005), dominated by a few genes, provided datasets that were too small to resolve controversial phylogenetic problems. Adding to the lack of consensus, this period was characterized by a polarization of philosophies, with individuals belonging to either parsimony or maximum-likelihood camps; each largely ignoring the insights of the other. The result was an unfortunate detour in which the few perceived phylogenetic revolutions published by both sides of the philosophical divide were probably erroneous. The size of datasets has been growing exponentially since the mid-1980s accompanied by a wave of confidence that all relationships will soon be known. However, large datasets create new challenges, and a large number of genes does not guarantee reliable results. If history is a guide, then the quality of conclusions will be determined by an improved understanding of both molecular and morphological evolution, and not simply the number of genes analysed.

Trilobodrilus itoi sp. nov., with a Re-Description of T. nipponicus (Annelida: Dinophilidae) and a Molecular Phylogeny of the Genus

The marine interstitial annelid Trilobodrilus itoi sp. nov., the sixth member of the genus, is described on the basis of specimens collected intertidally at Ishikari Beach, Hokkaido, Japan; this is the second species in the genus described from the Pacific Rim. In addition, T. nipponicus Uchida and Okuda, 1943 is re-described based on fresh topotypic material from Akkeshi, Hokkaido, Japan. From both species, we determined sequences of the nuclear 18S and 28S rRNA genes, and the mitochondrial cytochrome c oxidase subunit I (COI) gene. Molecular phylogenetic trees based on concatenated sequences of the three genes showed that T. itoi and T. nipponicus form a clade, which was the sister group to a clade containing the two European congeners T. axi Westheide, 1967 and T. heideri Remane, 1925. The Kimura two-parameter distance for COI was 22.5-22.7% between T. itoi and T. nipponicus, comparable with interspecific values in other polychaete genera. We assessed the taxonomic utility of epidermal inclusions and found that the known six species can be classified into three groups.

Tubulanus tamias sp. nov. (Nemertea: Palaeonemertea) with Two Different Types of Epidermal Eyes

Based on specimens collected subtidally (∼10 m in depth) in Tomioka Bay, Japan, we describe the palaeonemertean Tubulanus tamias sp. nov., which differs from all its congeners in body coloration. In molecular phylogenetic analyses based on partial sequences of the nuclear 18S and 28S rRNA genes and histone H3, as well as the mitochondrial 16S rRNA and cytochrome c oxidase subunit I genes, among selected palaeonemerteans, T. tamias nested with part of the congeners in Tubulanus, while the genus as currently diagnosed appears to be non-monophyletic. Molecular cloning detected polymorphism in 28S rDNA sequences in a single individual of T. tamias, indicating incomplete concerted evolution of multiple copies. Tubulanus tamias is peculiar among tubulanids in having 9-10 pigment-cup eyes in the epidermis on either side of the head anterior to the cerebral sensory organs, and remarkably there are two types of eyes. The anterior 8-9 pairs of eyes, becoming larger from anterior to posterior, are completely embedded in the epidermis and proximally abutting the basement membrane; each pigment cup contains bundle of up to seven, rod-shaped structure that resemble a rhabdomeric photoreceptor cell. In contrast, the posterior-most pair of eyes, larger than most of the anterior ones, have an optical cavity filled with long cilia and opening to the exterior, thus appearing to have ciliary-type photoreceptor cells. The size and arrangement of the eyes indicate that the posterior-most pair of eyes are the remnant of the larval (or juvenile) eyes.

Phylogeny of Kinorhyncha Based on Morphology and Two Molecular Loci

The phylogeny of Kinorhyncha was analyzed using morphology and the molecular loci 18S rRNA and 28S rRNA. The different datasets were analyzed separately and in combination, using maximum likelihood and Bayesian Inference. Bayesian inference of molecular sequence data in combination with morphology supported the division of Kinorhyncha into two major clades: Cyclorhagida comb. nov. and Allomalorhagida nom. nov. The latter clade represents a new kinorhynch class, and accommodates Dracoderes, Franciscideres, a yet undescribed genus which is closely related with Franciscideres, and the traditional homalorhagid genera. Homalorhagid monophyly was not supported by any analyses with molecular sequence data included. Analysis of the combined molecular and morphological data furthermore supported a cyclorhagid clade which included all traditional cyclorhagid taxa, except Dracoderes that no longer should be considered a cyclorhagid genus. Accordingly, Cyclorhagida is divided into three main lineages: Echinoderidae, Campyloderidae, and a large clade, 'Kentrorhagata', which except for species of Campyloderes, includes all species with a midterminal spine present in adult individuals. Maximum likelihood analysis of the combined datasets produced a rather unresolved tree that was not regarded in the following discussion. Results of the analyses with only molecular sequence data included were incongruent at different points. However, common for all analyses was the support of several major clades, i.e., Campyloderidae, Kentrorhagata, Echinoderidae, Dracoderidae, Pycnophyidae, and a clade with Paracentrophyes + New Genus and Franciscideres (in those analyses where the latter was included). All molecular analyses including 18S rRNA sequence data furthermore supported monophyly of Allomalorhagida. Cyclorhagid monophyly was only supported in analyses of combined 18S rRNA and 28S rRNA (both ML and BI), and only in a restricted dataset where taxa with incomplete information from 28S rRNA had been omitted. Analysis of the morphological data produced results that were similar with those from the combined molecular and morphological analysis. E.g., the morphological data also supported exclusion of Dracoderes from Cyclorhagida. The main differences between the morphological analysis and analyses based on the combined datasets include: 1) Homalorhagida appears as monophyletic in the morphological tree only, 2) the morphological analyses position Franciscideres and the new genus within Cyclorhagida near Zelinkaderidae and Cateriidae, whereas analyses including molecular data place the two genera inside Allomalorhagida, and 3) species of Campyloderes appear in a basal trichotomy within Kentrorhagata in the morphological tree, whereas analysis of the combined datasets places species of Campyloderes as a sister clade to Echinoderidae and Kentrorhagata.

Embryonic development of a collembolan, Tomocerus cuspidatus Börner, 1909: with special reference to the development and developmental potential of serosa (Hexapoda: Collembola, Tomoceridae)

The embryogenesis of a collembolan, Tomocerus cuspidatus, was examined and described, with special reference to the development of serosa and its developmental potential. As a result of cleavage, which starts with holoblastic cleavage and changes to the superficial type, the blastoderm forms. At the center of the dorsal side of the egg, the primary dorsal organ develops. The mesoderm is segregated beneath the entire blastoderm, excluding the primary dorsal organ. The mesoderm then migrates to the presumptive embryonic area, and the embryonic and extra-embryonic areas differentiate. The area lined with mesoderm is the embryo, and that devoid of it is the serosa. Owing to blastokinesis completion, the extra-embryonic area or the serosa is highly stretched, and the serosal cells are often found to undergo mitosis. The serosa possesses the ability to differentiate into the body wall. It was confirmed, in contrast to the previous understanding, that the serosal cells do not degenerate, but participate in the formation of the body wall or definitive dorsal closure. Integrating this newly obtained information and other embryological evidence, the basal splitting of Hexapoda was phylogenetically discussed and reconstructed, and a phylogeny formulated as "Ellipura (=Protura+Collembola)+Cercophora (=Diplura and Ectognatha)" was proposed.

The complete mitochondrial genomes of three bristletails (Insecta: Archaeognatha): the paraphyly of Machilidae and insights into archaeognathan phylogeny

The order Archaeognatha was an ancient group of Hexapoda and was considered as the most primitive of living insects. Two extant families (Meinertellidae and Machilidae) consisted of approximately 500 species. This study determined 3 complete mitochondrial genomes and 2 nearly complete mitochondrial genome sequences of the bristletail. The size of the 5 mitochondrial genome sequences of bristletail were relatively modest, containing 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region. The gene orders were identical to that of Drosophila yakuba and most bristletail species suggesting a conserved genome evolution within the Archaeognatha. In order to estimate archaeognathan evolutionary relationships, phylogenetic analyses were conducted using concatenated nucleotide sequences of 13 protein-coding genes, with four different computational algorithms (NJ, MP, ML and BI). Based on the results, the monophyly of the family Machilidae was challenged by both datasets (W12 and G12 datasets). The relationships among archaeognathan subfamilies seemed to be tangled and the subfamily Machilinae was also believed to be a paraphyletic group in our study.

Systematic and biogeographical study of Protura (Hexapoda) in Russian Far East: new data on high endemism of the group

Proturan collections from Magadan Oblast, Khabarovsk Krai, Primorsky Krai, and Sakhalin Oblast are reported here. Twenty-five species are found of which 13 species are new records for Russian Far East which enrich the knowledge of Protura known for this area. Three new species Baculentulus krabbensissp. n., Fjellbergella lazovskiensissp. n. and Yichunentulus alpatovisp. n. are illustrated and described. The new materials of Imadateiella sharovi (Martynova, 1977) are studied and described in details. Two new combinations, Yichunentulus borealis (Nakamura, 2004), comb. n. and Fjellbergella jilinensis (Wu & Yin, 2007), comb. n. are proposed as a result of morphological examination. Keys to species of the genera Fjellbergella and Yichunentulus are given. An annotated list of all species of Protura from Russian Far East is provided and discussed. Widely distributed species were not recorded in this area. This may be because of the high sensitivity of Protura to anthropogenic impact and low dispersal ability of the group.

Overview on spermatogenesis and sperm structure of Hexapoda

The main characteristics of the sperm structure of Hexapoda are reported in the review. Data are dealing with the process of spermatogenesis, including the aberrant models giving rise to a reduced number of sperm cells. The sperm heteromorphism and the giant sperm exceeding the usual sperm size for length and width are considered. The characteristics of several components of a typical insect sperm are described: the plasma membrane and its glycocalyx, the nucleus, the centriole region and the centriole adjunct, the accessory bodies, the mitochondrial derivatives and the flagellar axoneme. Finally, a detailed description of the main sperm features of each hexapodan group is given with emphasis on the flagellar components considered to have great importance in phylogenetic considerations. This study may be also useful to those requiring an introduction to hexapod reproduction.

Two new species in the Echinoderes coulli group (Echinoderidae, Cyclorhagida, Kinorhyncha) from the Ryukyu Islands, Japan

Two new species belonging to the Echinoderes coulli group are described with their external morphologies and sequences of nuclear 18S rRNA and 28S rRNA genes, and mitochondrial COI gene. The first species, Echinoderes komatsuisp. n., is characterized by absence of acicular spines, and presence of lateroventral tubules on segments 5 and 8, laterodorsal tubules on segment 10, inverted triangle or wide oval shaped large sieve plates, lateral terminal accessory spines in female, and short tips of ventral pectinate fringe on segment 10. The second species, Echinoderes hwiizaasp. n., is characterized by absence of acicular spines, and presence of lateroventral tubules on segments 5 and 7–9, midlateral tubules on segment 8, laterodorsal tubules on segment 10, large narrow oval shaped sieve plates on segment 9, and thick, short and blunt lateral terminal spines about 10–15% of trunk length. The diagnostic characters and key to species of E. coulli group are provided as well.

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.

Evolutionary implications of dipluran hexamerins

Hexamerin, as a member of the highly conserved arthropod hemocyanin superfamily, has been shown to be a good marker for the phylogenetic study of insects. However, few studies have been conducted on hexamerins in basal hexapods. The first Diplura hexamerin CspHex1 was reported only recently (Pick and Burmester, 2009). Remarkably, CspHex1 was suggested to have evolved from hexapod hemocyanin subunit type 2, which is very different from all insect hexamerins originated from hexapod hemocyanin subunit type 1. Does this finding suggest double or even multiple origins of hexamerins in Hexapoda? To find more evidence on the evolution of dipluran hexamerins, eight putative hexamerin gene sequences were obtained from three dipluran species, as were three hemocyanin genes from two collembolan species. Unexpectedly, after adding the new sequences into the phylogenetic analyses, all dipluran hexamerins including CspHex1 grouped together and as sister to the insect hexamerins, with high likelihood and Bayesian support. Our analysis supports a single origin of the hexamerins in Hexapoda, and suggests the close relationship between Diplura and Insecta. In addition, our study indicates that a relatively comprehensive taxa sampling is essential to solve some problems in phylogenetic reconstruction.

Comparative analysis of mitochondrial genomes in Diplura (hexapoda, arthropoda): taxon sampling is crucial for phylogenetic inferences

Two-pronged bristletails (Diplura) are traditionally classified into three major superfamilies: Campodeoidea, Projapygoidea, and Japygoidea. The interrelationships of these three superfamilies and the monophyly of Diplura have been much debated. Few previous studies included Projapygoidea in their phylogenetic considerations, and its position within Diplura still is a puzzle from both morphological and molecular points of view. Until now, no mitochondrial genome has been sequenced for any projapygoid species. To fill in this gap, we determined and annotated the complete mitochondrial genome of Octostigma sinensis (Octostigmatidae, Projapygoidea), and of three more dipluran species, one each from the Campodeidae, Parajapygidae, and Japygidae. All four newly sequenced dipluran mtDNAs encode the same set of genes in the same gene order as shared by most crustaceans and hexapods. Secondary structure truncations have occurred in trnR, trnC, trnS1, and trnS2, and the reduction of transfer RNA D-arms was found to be taxonomically correlated, with Campodeoidea having experienced the most reduction. Partitioned phylogenetic analyses, based on both amino acids and nucleotides of the protein-coding genes plus the ribosomal RNA genes, retrieve significant support for a monophyletic Diplura within Pancrustacea, with Projapygoidea more closely related to Campodeoidea than to Japygoidea. Another key finding is that monophyly of Diplura cannot be recovered unless Projapygoidea is included in the phylogenetic analyses; this explains the dipluran polyphyly found by past mitogenomic studies. Including Projapygoidea increased the sampling density within Diplura and probably helped by breaking up a long-branch-attraction artifact. This finding provides an example of how proper sampling is significant for phylogenetic inference.

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.

Molecular phylogenetic analyses support the monophyly of Hexapoda and suggest the paraphyly of Entognatha

BACKGROUND

Molecular phylogenetic analyses have revealed that Hexapoda and Crustacea form a common clade (the Pancrustacea), which is now widely accepted among zoologists; however, the origin of Hexapoda remains unresolved. The main problems are the unclear relationships among the basal hexapod lineages, Protura (proturans), Collembola (springtails), Diplura (diplurans), and Ectognatha (bristletails, silverfishes, and all winged insects). Mitogenomic analyses have challenged hexapod monophyly and suggested the reciprocal paraphyly of Hexapoda and Crustacea, whereas studies based on nuclear molecular data support the monophyletic origin of hexapods. Additionally, there are significant discrepancies with respect to these issues between the results of morphological and molecular studies. To investigate these problems, we performed phylogenetic analyses of Pancrustacea based on the protein sequences of three orthologous nuclear genes encoding the catalytic subunit of DNA polymerase delta and the largest and second largest subunits of RNA polymerase II from 64 species of arthropods, including representatives of all hexapod orders.

RESULTS

Phylogenetic analyses were conducted based on the inferred amino acid (aa) sequences (~3400 aa in total) of the three genes using the maximum likelihood (ML) method and Bayesian inference. Analyses were also performed with additional datasets generated by excluding long-branch taxa or by using different outgroups. These analyses all yielded essentially the same results. All hexapods were clustered into a common clade, with Branchiopoda as its sister lineage, whereas Crustacea was paraphyletic. Within Hexapoda, the lineages Ectognatha, Palaeoptera, Neoptera, Polyneoptera, and Holometabola were each confirmed to be monophyletic with robust support, but monophyly was not supported for Entognatha (Protura + Collembola + Diplura), Ellipura (Protura + Collembola), or Nonoculata (Protura + Diplura). Instead, our results showed that Protura is the sister lineage to all other hexapods and that Diplura or Diplura + Collembola is closely related to Ectognatha.

CONCLUSION

This is the first study to include all hexapod orders in a phylogenetic analysis using multiple nuclear protein-coding genes to investigate the phylogeny of Hexapoda, with an emphasis on Entognatha. The results strongly support the monophyletic origin of hexapods but reject the monophyly of Entognatha, Ellipura, and Nonoculata. Our results provided the first molecular evidence in support of Protura as the sister group to other hexapods. These findings are expected to provide additional insights into the origin of hexapods and the processes involved in the adaptation of insects to life on land.

The spermatogenesis and oogenesis of the springtail Podura aquatica Linné, 1758 (Hexapoda: Collembola)

Podura aquatica is a springtail of uncertain systematic position. Our study dealing with the ultrastructure of the spermatogenesis and oogenesis of this species is a contribution to a better knowledge of both the reproduction and the systematics of the taxon. In the male, the spermatogenesis proceeds in a similar way to that of other Collembola. Primary spermatocytes do not show synaptonemal complexes which, instead, are found in primary oocytes. Thus a genomic recombination seems to be present only in females, as it occurs in other springtails. Degeneration of secondary spermatocytes, as reported in some families of the Symphypleona, was not observed in P. aquatica. At the end of spermiogenesis, a rolled up sperm cell provided with an anterior long appendage adhering to the acrosome is produced. In the female, the oogenesis also proceeds in a conventional way with the production of eggs rich in yolk. A branched spermatheca is present at the end of the common oviduct, close to the genital opening. It contains many sperm in its lumen. Contrary to the globular appearance of sperm cells in the male genital ducts, in the spermatheca they are straight, elongated, and lack the long anterior appendage. P. aquatica shows a spermatogenesis, sperm structure, and oogenesis similar to those of other Collembola. In agreement with the results of recent phylogenetic studies, we confirm that P. aquatica is a member of Poduridae, and it does not belong to a group close to the Symphypleona.

Molecular phylogeny of kinorhynchs

We reconstructed kinorhynch phylogeny using maximum-likelihood and Bayesian analyses of nuclear 18S and 28S rRNA gene sequences from 30 species in 13 genera (18S) and 23 species in 12 genera (28S), representing eight families and both orders (Cyclorhagida and Homalorhagida) currently recognized in the phylum. We analyzed the two genes individually (18S and 28S datasets) and in combination (18S+28S dataset). We detected four main clades (I-IV). Clade I consisted of family Echinoderidae. Clade II contained representatives of Zelinkaderidae, Antygomonidae, Semnoderidae, Centroderes, and Condyloderes, the latter two currently classified in Centroderidae; within Clade II, Zelinkaderidae, Antygomonidae, and Semnoderidae comprised a clade with strong nodal support. Clade III contained only two species in Campyloderes, also currently classified in the Centroderidae, indicating polyphyly for this family. Clades I-III, containing all representatives of Cyclorhagida included in the analysis except for Dracoderes abei, formed a clade with high nodal support in the 28S and 18S+28S trees. Clade IV, resolved in the 18S and 18S+28S trees with high nodal support, contained only species in order Homalorhagida, with the exception of the cyclorhagid Dracoderes abei. Order Cyclorhagida as it currently stands is thus polyphyletic, and order Homalorhagida paraphyletic. Our results indicate that Dracoderidae has been misplaced in Cyclorhagida based on homoplasious characters. Our analyses did not resolve the relationships among Clades I-III within Cyclorhagida. Neither gene alone nor the combined dataset resolved all nodes in trees, indicating that additional markers will be needed to reconstruct kinorhynch phylogeny.

Brain anatomy in Diplura (Hexapoda)

Background

In 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.

Results

Remarkable 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.

Conclusions

Mushroom 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.

Three species of Amphicorina (Annelida, Sabellida, Sabellidae) from Japan, with descriptions of two new species

We describe two new species and redescribe one in the polychaete genus Amphicorina Claparède, 1864 (Sabellidae) from Hokkaido, Japan. Amphicorina ascidicolasp. n. differs from its 38 congeners chiefly in the reduction of the collar, but also in having three pairs of radioles, one pair of ventral radiolar appendages, a bifurcate ventral lobe on the anterior peristomial ring, six abdominal chaetigers, and a large anterior tooth on the abdominal uncini. Amphicorina ezoensissp. n. has a crenulated collar, three pairs of radioles, and more than eight (12) abdominal chaetigers; Amphicorina ezoensis shares these character states with Amphicorina anneae (Rouse, 1994), Amphicorina eimeri (Langerhans, 1880), and Amphicorina persinosa (Ben-Eliahu, 1975), but differs from them in having two pairs of ventral radiolar appendages and a non-oblique collar. Amphicorina mobilis (Rouse, 1990) was previously known only from the type locality (New South Wales, Australia), but we identify our Japanese material as conspecific on the basis of morphological and molecular similarity.

Advances in insect phylogeny at the dawn of the postgenomic era

Most species on Earth are insects and thus, understanding their evolutionary relationships is key to understanding the evolution of life. Insect relationships are increasingly well supported, due largely to technological advances in molecular sequencing and phylogenetic computational analysis. In this postgenomic era, insect systematics will be furthered best by integrative methods aimed at hypothesis corroboration from molecular, morphological, and paleontological evidence. This review of the current consensus of insect relationships provides a foundation for comparative study and offers a framework to evaluate incoming genomic evidence. Notable recent phylogenetic successes include the resolution of Holometabola, including the identification of the enigmatic Strepsiptera as a beetle relative and the early divergence of Hymenoptera; the recognition of hexapods as a crustacean lineage within Pancrustacea; and the elucidation of Dictyoptera orders, with termites placed as social cockroaches. Regions of the tree that require further investigation include the earliest winged insects (Palaeoptera) and Polyneoptera (orthopteroid lineages).

The mitochondrial genome of Sinentomon erythranum (Arthropoda: Hexapoda: Protura): an example of highly divergent evolution

BACKGROUND

The phylogenetic position of the Protura, traditionally considered the most basal hexapod group, is disputed because it has many unique morphological characters compared with other hexapods. Although mitochondrial genome information has been used extensively in phylogenetic studies, such information is not available for the Protura. This has impeded phylogenetic studies on this taxon, as well as the evolution of the arthropod mitochondrial genome.

RESULTS

In this study, the mitochondrial genome of Sinentomon erythranum was sequenced, as the first proturan species to be reported. The genome contains a number of special features that differ from those of other hexapods and arthropods. As a very small arthropod mitochondrial genome, its 14,491 nucleotides encode 37 typical mitochondrial genes. Compared with other metazoan mtDNA, it has the most biased nucleotide composition with T = 52.4%, an extreme and reversed AT-skew of -0.351 and a GC-skew of 0.350. Two tandemly repeated regions occur in the A+T-rich region, and both could form stable stem-loop structures. Eighteen of the 22 tRNAs are greatly reduced in size with truncated secondary structures. The gene order is novel among available arthropod mitochondrial genomes. Rearrangements have involved in not only small tRNA genes, but also PCGs (protein-coding genes) and ribosome RNA genes. A large block of genes has experienced inversion and another nearby block has been reshuffled, which can be explained by the tandem duplication and random loss model. The most remarkable finding is that trnL2(UUR) is not located between cox1 and cox2 as observed in most hexapod and crustacean groups, but is between rrnL and nad1 as in the ancestral arthropod ground pattern. The "cox1-cox2" pattern was further confirmed in three more representative proturan species. The phylogenetic analyses based on the amino acid sequences of 13 mitochondrial PCGs suggest S. erythranum failed to group with other hexapod groups.

CONCLUSIONS

The mitochondrial genome of S. erythranum shows many different features from other hexapod and arthropod mitochondrial genomes. It underwent highly divergent evolution. The "cox1-cox2" pattern probably represents the ancestral state for all proturan mitogenomes, and suggests a long evolutionary history for the Protura.

Sperm accessory microtubules suggest the placement of Diplura as the sister-group of Insecta s.s

Sperm ultrastructure and spermiogenesis of the dipluran Japygidae (Japyx solifugus, Metajapyx braueri and Occasjapyx japonicus) and Campodeidae (Campodea sp.) were studied with the aim of looking for potential characters for the reconstruction of the phylogenetic relationships of basal hexapods. Both Japygidae and Campodeidae share a common sperm axonemal model 9+9+2, provided with nine accessory microtubules. These microtubules, however, after their formation lose the usual position around the 9+2 and migrate between the two mitochondria. In Japygidae, four of these microtubules are very short and were observed beneath the nucleus after negative staining and serial sections. Accessory microtubules have 13 protofilaments in their tubular wall. Diplura have a sperm morphology which is very different from that of the remaining Entognatha (Protura+Collembola). On the basis of the present results, the presence of accessory microtubules suggests that Diplura are the sister-group of the Insecta s.s.. Moreover, Japygidae and Campodeidae differ with regards to the relative position of the sperm components, the former having the axoneme starting from beneath the nucleus (above which sits the short acrosome), while the latter having a long apical acrosome and a nucleus running parallel with the proximal part of the axoneme. The present study also allowed to redescribe the male genital system of Japyx.

Phylogeny of the millipede order Spirobolida (Arthropoda: Diplopoda: Helminthomorpha)

This study examines relationships within the millipede order Spirobolida using an exemplar approach, sampling within families to maximize geographical and morphological diversity; due to lack of available material, Allopocockiidae and Hoffmanobolidae were not included in analyses. The focus of this study was to test monophyly of the order, the suborders, and the families of Spirobolida and to propose interfamilial relationships using morphological and molecular data in a total-evidence approach. Both maximum-parsimony analyses and Bayesian inference were employed to analyse two datasets consisting of combined morphological and molecular data, one aligned using progressive alignment methods and the second aligned by secondary structure models. Rhinocricidae was recovered sister to all remaining spirobolidan millipedes and is elevated to suborder status as suborder Rhinocricidea. Trigoniulidea was recovered as monophyletic as was Spirobolidea excluding Rhinocricidae; Spirobolidea is redefined to reflect this change. All previously recognized families were recovered, with the exception of Spirobolidae; in all instances, this family was paraphyletic or part of a polytomy that lacked sufficient resolution to assess its monophyly. The results reaffirm much of the existing taxonomic foundation within Spirobolida. This study provides the first phylogenetic test of higher-level relationships within Spirobolida and will serve as a foundation for future work in this group at finer levels. © The Willi Hennig Society 2010.

A phylogenomic approach to resolve the arthropod tree of life

Arthropods were the first animals to conquer land and air. They encompass more than three quarters of all described living species. This extraordinary evolutionary success is based on an astoundingly wide array of highly adaptive body organizations. A lack of robustly resolved phylogenetic relationships, however, currently impedes the reliable reconstruction of the underlying evolutionary processes. Here, we show that phylogenomic data can substantially advance our understanding of arthropod evolution and resolve several conflicts among existing hypotheses. We assembled a data set of 233 taxa and 775 genes from which an optimally informative data set of 117 taxa and 129 genes was finally selected using new heuristics and compared with the unreduced data set. We included novel expressed sequence tag (EST) data for 11 species and all published phylogenomic data augmented by recently published EST data on taxonomically important arthropod taxa. This thorough sampling reduces the chance of obtaining spurious results due to stochastic effects of undersampling taxa and genes. Orthology prediction of genes, alignment masking tools, and selection of most informative genes due to a balanced taxa-gene ratio using new heuristics were established. Our optimized data set robustly resolves major arthropod relationships. We received strong support for a sister group relationship of onychophorans and euarthropods and strong support for a close association of tardigrades and cycloneuralia. Within pancrustaceans, our analyses yielded paraphyletic crustaceans and monophyletic hexapods and robustly resolved monophyletic endopterygote insects. However, our analyses also showed for few deep splits that were recently thought to be resolved, for example, the position of myriapods, a remarkable sensitivity to methods of analyses.

Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees

Background

Methods of alignment masking, which refers to the technique of excluding alignment blocks prior to tree reconstructions, have been successful in improving the signal-to-noise ratio in sequence alignments. However, the lack of formally well defined methods to identify randomness in sequence alignments has prevented a routine application of alignment masking. In this study, we compared the effects on tree reconstructions of the most commonly used profiling method (GBLOCKS) which uses a predefined set of rules in combination with alignment masking, with a new profiling approach (ALISCORE) based on Monte Carlo resampling within a sliding window, using different data sets and alignment methods. While the GBLOCKS approach excludes variable sections above a certain threshold which choice is left arbitrary, the ALISCORE algorithm is free of a priori rating of parameter space and therefore more objective.

Results

ALISCORE was successfully extended to amino acids using a proportional model and empirical substitution matrices to score randomness in multiple sequence alignments. A complex bootstrap resampling leads to an even distribution of scores of randomly similar sequences to assess randomness of the observed sequence similarity. Testing performance on real data, both masking methods, GBLOCKS and ALISCORE, helped to improve tree resolution. The sliding window approach was less sensitive to different alignments of identical data sets and performed equally well on all data sets. Concurrently, ALISCORE is capable of dealing with different substitution patterns and heterogeneous base composition. ALISCORE and the most relaxed GBLOCKS gap parameter setting performed best on all data sets. Correspondingly, Neighbor-Net analyses showed the most decrease in conflict.

Conclusions

Alignment masking improves signal-to-noise ratio in multiple sequence alignments prior to phylogenetic reconstruction. Given the robust performance of alignment profiling, alignment masking should routinely be used to improve tree reconstructions. Parametric methods of alignment profiling can be easily extended to more complex likelihood based models of sequence evolution which opens the possibility of further improvements.