Image-based recognition of parasitoid wasps using advanced neural networks.

Hymenoptera has some of the highest diversity and number of individuals among insects. Many of these species potentially play key roles as food sources, pest controllers and pollinators. However, little is known about the diversity and biology and ~80% of the species have not yet been described. Classical taxonomy based on morphology is a rather slow process but DNA barcoding has already brought considerable progress in identification. Innovative methods such as image-based identification and automation can further speed up the process. We present a proof of concept for image data recognition of a parasitic wasp family, the Diapriidae (Hymenoptera), obtained as part of the GBOL III project. These tiny (1.2-4.5mm) wasps were photographed and identified using DNA barcoding to provide a solid ground truth for training a neural network. Taxonomic identification was used down to the genus level. Subsequently, three different neural network architectures were trained, evaluated and optimised. As a result, 11 different genera of diaprids and one mixed group of 'other Hymenoptera' can be classified with an average accuracy of 96%. Additionally, the sex of the specimen can be classified automatically with an accuracy of >97%.

Scratching the tip of the iceberg: integrative taxonomy reveals 30 new species records of Microgastrinae (Braconidae) parasitoid wasps for Germany, including new Holarctic distributions.

Substantial parts of the European and German insect fauna still remain largely unexplored, the so-called "dark taxa". In particular, midges (Diptera) and parasitoid wasps (Hymenoptera) are abundant and species-rich throughout Europe, yet are often neglected in biodiversity research. One such dark taxon is Microgastrinae wasps (Hymenoptera: Braconidae), a group of parasitoids of lepidopteran caterpillars with 252 species reported in Germany so far. As part of the German Barcode of Life Project GBOL III: Dark Taxa, reverse DNA barcoding and integrative taxonomic approaches were used to shed some light on the German Fauna of Microgastrinae wasps. In our workflow, DNA barcoding was used for molecular clustering of our specimens in a first step, morphological examination of the voucher specimens in a second step, and host data compared in a third step. Here, 30 species are reported for the first time in Germany, adding more than 10% to the known German fauna. Information for four species is provided in a new Holarctic context, reporting them for the Nearctic or, respectively, Palaearctic region, and 26 additional country records are added from sequenced material available in the collections accessible to us. Molecular clusters that show signs of discrepancies are discussed. Results show that we are just scratching the tip of the iceberg of the unexplored Microgastrinae diversity in Germany.

Discovery of the primary aphid (Hemiptera: Aphidomorpha) and scale insect (Hemiptera: Coccomorpha) type specimens from the collection of Theodor Hartig (18051880).

Theodor Hartigs aphid and scale insect type specimens have been presumed lost or destroyed for the last 140 years. Here we document their discovery at the Bavarian State Collection of Zoology (Zoologische Staatssammlung Mnchen, ZSM), in Munich, Germany. These specimens include primary types for 24 aphid, three adelgid, and two armored scale insect species named by Hartig between 1834 and 1851, as well as other specimens of unknown importance.

Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea).

DNA barcoding has become the most popular approach for species identification in recent years. As part of the German Barcode of Life project, the first DNA barcode library for terrestrial and freshwater isopods from Germany is presented. The analyzed barcode library included 38 terrestrial (78% of the documented species of Germany) and five freshwater (63%) species. A total of 513 new barcodes was generated and 518 DNA barcodes were analyzed. This analysis revealed surprisingly high intraspecific genetic distances for numerous species, with a maximum of 29.4% for Platyarthrushoffmannseggii Brandt, 1833. The number of BINs per species ranged from one (32 species, 68%) to a maximum of six for Trachelipusrathkii (Brandt, 1833). In spite of such high intraspecific variability, interspecific distances with values between 12.6% and 29.8% allowed a valid species assignment of all analyzed isopods. The observed high intraspecific distances presumably result from phylogeographic events, Wolbachia infections, atypical mitochondrial DNAs, heteroplasmy, or various combinations of these factors. Our study represents the first step in generating an extensive reference library of DNA barcodes for terrestrial and freshwater isopods for future molecular biodiversity assessment studies.

Peering into the Darkness: DNA Barcoding Reveals Surprisingly High Diversity of Unknown Species of Diptera (Insecta) in Germany.

Determining the size of the German insect fauna requires better knowledge of several megadiverse families of Diptera and Hymenoptera that are taxonomically challenging. This study takes the first step in assessing these "dark taxa" families and provides species estimates for four challenging groups of Diptera (Cecidomyiidae, Chironomidae, Phoridae, and Sciaridae). These estimates are based on more than 48,000 DNA barcodes (COI) from Diptera collected by Malaise traps that were deployed in southern Germany. We assessed the fraction of German species belonging to 11 fly families with well-studied taxonomy in these samples. The resultant ratios were then used to estimate the species richness of the four "dark taxa" families (DT families hereafter). Our results suggest a surprisingly high proportion of undetected biodiversity in a supposedly well-investigated country: at least 1800-2200 species await discovery in Germany in these four families. As this estimate is based on collections from one region of Germany, the species count will likely increase with expanded geographic sampling.

Out of taxonomic crypsis: A new trans-arctic cryptic species pair corroborated by phylogenetics and molecular evidence.

Cryptic species are a common phenomenon in cosmopolitan marine species. The use of molecular tools has often uncovered cryptic species occupying a fraction of the geographic range of the original morphospecies. Shipworms (Teredinidae) are marine bivalves, living in drift and fixed wood, many of which have a conserved morphology across cosmopolitan distributions. Herein novel and GenBank mitochondrial (cytochrome c oxidase subunit I) and nuclear (18S rRNA) DNA sequences are employed to produce a phylogeny of the Teredinidae and delimit a cryptic species pair in the Psiloteredo megotara complex. The anatomy, biogeography, and ecology of P. megotara, Psiloteredo sp. and Nototeredo edax are compared based on private and historic museum collections and a thorough literature review. Morphological and anatomical characters of P. megotara from the North Atlantic and Psiloteredo sp. from Japan were morphologically indistinguishable, and differ in pallet architecture and soft tissue anatomy from N. edax. The two Psiloteredo species were then delimited as genetically distinct species using four molecular-based methods. Consequently, the Northwest Pacific species, Psiloteredo pentagonalis, first synonymized with N. edax and then with P. megotara, is resurrected. Nototeredo edax, P. megotara and P. pentagonalis are redescribed based upon morphological and molecular characters. Phylogenetic analysis further revealed cryptic species complexes within the cosmopolitan species Bankia carinata and possibly additional cryptic lineages within the cosmopolitan Lyrodus pedicellatus.

Investigation into the Integration of Impregnated Glass and Carbon Textiles in a Laboratory Mortar Extruder (LabMorTex).

A promising process for the automatization of concrete structures is extrusion or extrusion molding. An innovative approach is the extrusion of concrete with imbedded technical textiles as reinforcement. For a successful extrusion, the rheological properties of the fresh concrete have to be optimized, as it must be extrudable and have sufficient early strength after leaving the mouthpiece. Within the scope of this paper, a process was developed which allows the integration of flexible as well as stiff impregnated textiles into the extrusion process. For this purpose, different textile-reinforced mortars (TRM) were extruded and their material characteristics were investigated. The results show that the mortar cross-section is considerably strengthened, especially when using carbon textiles, and that extrusion has considerable potential to produce high-performance TRM composites. In uniaxial tension tests with TRM, as well as in the pure roving tensile strength tests, textile stresses of approx. 1200 MPa were achieved for the glass textile and approx. 2250 MPa for the carbon textile. The position of the textile layer deviated a maximal 0.4 mm from its predesigned position, which shows its potential for producing tailor-made TRM elements. In addition, by adjusting the mortar mix design, it was possible to reduce the global warming potential (GWP) of the extrusion compound by up to 49.3% compared to the initial composition from preliminary studies.

Analytical and Numerical Investigation of an Electrochemical Chloride Barrier for Reinforced Concrete Structures.

During the development of a carbon-reinforced mortar interlayer for bridges, the idea of an electrochemical chloride barrier arose. An electrical field is generated between two carbon meshes, and the negatively charged chloride ions are held on the polarized upper carbon mesh to prevent chloride-induced corrosion in the reinforcement. Laboratory tests unexpectedly showed that higher voltages lead to an increase in chloride ions for certain depths of the reference probes. This paper discusses the implementation of analytical and numerical models that finally explain the effect only by the acting diffusion and migration with the help of a finite differences model and finite elements simulations. The effect of the local minimum is limited to positions above the depth of the first carbon layer of the test specimens. It is caused by the lines of the electrical field between the first and second carbon layer. According to the experimental and finite elements simulation results, higher voltages lead to lower chloride concentrations for all positions below the first carbon layer only after sufficient time duration. Therefore, the intended effect of an electrochemical chloride barrier can in general only be observed and confirmed after a certain time depending on position, conditions and parameters.

Influence of High Temperature Curing and Surface Humidity on the Tensile Strength of UHPC.

The objective of this study is an investigation of the different parameters that influence the tensile strength of ultra-high performance concrete (UHPC). Apart from the shrinkage and stiffness, the tensile strength is an important parameter for the design of crack-free concrete elements, e.g., in machine tool construction. One focus of our work is the influence of concrete curing and the great impact of the mechanical and physical characteristics of hydrated UHPC. For this reason, different curing regimes were investigated. The results show that even after heat treatment or autoclaving, the centric tensile strength of UHPC specimens is strongly influenced by the surrounding ambient humidity. Test specimens that were stored under water after a heat treatment or autoclaving and were still wet during the test had the highest tensile strengths. Storage at 20 °C and 65% relative humidity (rH), however, results in a 25% reduction in tensile strength. Alternating storage between water storage at 20 °C water and storage at 65% rH can also reduce the tensile strength dramatically by up to 70%. In particular, samples that were stored at 65% rH right before testing had very low tensile strengths. Surprisingly, the initially low tensile strength of previously dry stored UHPC can be restored by subsequent water storage. In the absence of any microstructural defects, e.g., microcracks, a possible explanation for this phenomenon can be the stress differences due to a humidity gradient between the core and surfaces and shrinkage combined with a continued reaction of the unhydrated binders of the UHPC.

Electrical Resistivity of Steel Fibre-Reinforced Concrete-Influencing Parameters.

This paper presents a systematic study of the electrical resistivity of different steel fibre-reinforced concretes with fibre contents from 0 kg/m3 to 80 kg/m3 in order to identify possible effects of interactions among concrete composition and fibre type and content regarding electrical resistivity. Based on a literature review, four parameters, w/c ratio, binder content, ground granulated blast-furnace slag (GGBS) and fineness of cement, which show a significant influence on the electrical resistivity of plain concrete, were identified, and their influence on the electrical resistivity as well as interaction effects were investigated. The results of the experiments highlight that the addition of fibres leads to a significant decrease in electrical resistivity, independent of all additional parameters of the concrete composition. Additionally, it was shown that a higher porosity of the concrete, e.g., due to a higher w/c ratio, also results in a lower electrical resistivity. These results are in agreement with the literature review on plain concrete, while the influence of the concrete composition on the electrical resistivity is weaker with the increase in fibre content. The influence of fibre reinforcement is thus not affected by changes in the concrete composition. In general, a higher fibre dosage leads to a decrease in electrical resistivity, but the impact on the electrical resistivity varies slightly with different types of steel fibres. Based on this study, the potential of determining the fibre content using electrical resistivity measurements could be clearly presented.

Relicts from Glacial Times: The Ground Beetle Pterostichus adstrictus Eschscholtz, 1823 (Coleoptera: Carabidae) in the Austrian Alps.

The last ice age considerably influenced distribution patterns of extant species of plants and animals, with some of them now inhabiting disjunct areas in the subarctic/arctic and alpine regions. This arctic-alpine distribution is characteristic for many cold-adapted species with a limited dispersal ability and can be found in many invertebrate taxa, including ground beetles. The ground beetle Pterostichus adstrictus Eschscholtz, 1823 of the subgenus Bothriopterus was previously known to have a holarctic-circumpolar distribution, in Europe reaching its southern borders in Wales and southern Scandinavia. Here, we report the first findings of this species from the Austrian Ötztal Alps, representing also the southernmost edge of its currently known distribution, confirmed by the comparison of morphological characters to other Bothriopterus species and DNA barcoding data. Molecular data revealed a separation of the Austrian and Finish specimens with limited to no gene flow at all. Furthermore, we present the first data on habitat preference and seasonality of P. adstrictus in the Austrian Alps.

A DNA barcode library for ground beetles of Germany: the genus Pterostichus Bonelli, 1810 and allied taxa (Insecta, Coleoptera, Carabidae).

Species of the ground beetle genus Pterostichus Bonelli, 1810 are some of the most common carabids in Europe. This publication provides a first comprehensive DNA barcode library for this genus and allied taxa including Abax Bonelli, 1810, Molops Bonelli, 1810, Poecilus Bonelli, 1810, and Stomis Clairville, 1806 for Germany and Central Europe in general. DNA barcodes were analyzed from 609 individuals that represent 51 species, including sequences from previous studies as well as more than 198 newly generated sequences. The results showed a 1:1 correspondence between BIN and traditionally recognized species for 44 species (86%), whereas two (4%) species were characterized by two BINs. Three BINs were found for one species (2%), while one BIN for two species was revealed for two species pairs (8%). Low interspecific distances with maximum pairwise K2P values below 2.2% were found for four species pairs. Haplotype sharing was found for two closely related species pairs: Pterostichus adstrictus Eschscholtz, 1823/Pterostichus oblongopunctatus (Fabricius, 1787) and Pterostichus nigrita Paykull, 1790/Pterostichus rhaeticus Heer, 1837. In contrast to this, high intraspecific sequence divergences with values above 2.2% were shown for three species (Molops piceus (Panzer, 1793), Pterostichus panzeri (Panzer, 1805), Pterostichus strenuus (Panzer, 1793)). Summarizing the results, the present DNA barcode library does not only allow the identification of most of the analyzed species, but also provides valuable information for alpha-taxonomy as well as for ecological and evolutionary research. This library represents another step in building a comprehensive DNA barcode library of ground beetles as part of modern biodiversity research.

A DNA barcode library for ground beetles of Germany: the genus Amara Bonelli, 1810 (Insecta, Coleoptera, Carabidae).

The genus Amara Bonelli, 1810 is a very speciose and taxonomically difficult genus of the Carabidae. The identification of many of the species is accomplished with considerable difficulty, in particular for females and immature stages. In this study the effectiveness of DNA barcoding, the most popular method for molecular species identification, was examined to discriminate various species of this genus from Central Europe. DNA barcodes from 690 individuals and 47 species were analysed, including sequences from previous studies and more than 350 newly generated DNA barcodes. Our analysis revealed unique BINs for 38 species (81%). Interspecific K2P distances below 2.2% were found for three species pairs and one species trio, including haplotype sharing between Amara alpina/Amara torrida and Amara communis/Amara convexior/Amara makolskii. This study represents another step in generating an extensive reference library of DNA barcodes for carabids, highly valuable bioindicators for characterizing disturbances in various habitats.

From water striders to water bugs: the molecular diversity of aquatic Heteroptera (Gerromorpha, Nepomorpha) of Germany based on DNA barcodes.

With about 5,000 species worldwide, the Heteroptera or true bugs are the most diverse taxon among the hemimetabolous insects in aquatic and semi-aquatic ecosystems. Species may be found in almost every freshwater environment and have very specific habitat requirements, making them excellent bioindicator organisms for water quality. However, a correct determination by morphology is challenging in many species groups due to high morphological variability and polymorphisms within, but low variability between species. Furthermore, it is very difficult or even impossible to identify the immature life stages or females of some species, e.g., of the corixid genus Sigara. In this study we tested the effectiveness of a DNA barcode library to discriminate species of the Gerromorpha and Nepomorpha of Germany. We analyzed about 700 specimens of 67 species, with 63 species sampled in Germany, covering more than 90% of all recorded species. Our library included various morphological similar taxa, e.g., species within the genera Sigara and Notonecta as well as water striders of the genus Gerris. Fifty-five species (82%) were unambiguously assigned to a single Barcode Index Number (BIN) by their barcode sequences, whereas BIN sharing was observed for 10 species. Furthermore, we found monophyletic lineages for 52 analyzed species. Our data revealed interspecific K2P distances with below 2.2% for 18 species. Intraspecific distances above 2.2% were shown for 11 species. We found evidence for hybridization between various corixid species (Sigara, Callicorixa), but our molecular data also revealed exceptionally high intraspecific distances as a consequence of distinct mitochondrial lineages for Cymatia coleoptrata and the pygmy backswimmer Plea minutissima. Our study clearly demonstrates the usefulness of DNA barcodes for the identification of the aquatic Heteroptera of Germany and adjacent regions. In this context, our data set represents an essential baseline for a reference library for bioassessment studies of freshwater habitats using modern high-throughput technologies in the near future. The existing data also opens new questions regarding the causes of observed low inter- and high intraspecific genetic variation and furthermore highlight the necessity of taxonomic revisions for various taxa, combining both molecular and morphological data.

Cryptic species in a well-known habitat: applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida).

Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of 'taxonomics'. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research.

Corrigendum: Recent pause in the growth rate of atmospheric CO2 due to enhanced terrestrial carbon uptake.

This corrects the article DOI: 10.1038/ncomms13428.

DNA barcoding and morphological studies confirm the occurrence of three Atarbolana (Crustacea: Isopoda: Cirolanidae) species along the coastal zone of the Persian Gulf and Gulf of Oman.

Two species of Atarbolana (Cirolanidae: Isopoda) from the intertidal zone of the Gulf of Oman and the Persian Gulf were studied and redescribed. The known distribution of this small genus is limited to the northern areas of the Indian Ocean, from the Pakistan coasts to the Persian Gulf. The analyses of DNA barcodes as well as detailed morphological studies clearly support the existence of three distinct Atarbolana species along the coastal zone of the Persian Gulf and northern Arabian Sea. Furthermore, A. dasycolus Yasmeen, 2004 is synonymized with A. setosa Javed and Yasmeen, 1989.

Recent pause in the growth rate of atmospheric CO2 due to enhanced terrestrial carbon uptake.

Terrestrial ecosystems play a significant role in the global carbon cycle and offset a large fraction of anthropogenic CO2 emissions. The terrestrial carbon sink is increasing, yet the mechanisms responsible for its enhancement, and implications for the growth rate of atmospheric CO2, remain unclear. Here using global carbon budget estimates, ground, atmospheric and satellite observations, and multiple global vegetation models, we report a recent pause in the growth rate of atmospheric CO2, and a decline in the fraction of anthropogenic emissions that remain in the atmosphere, despite increasing anthropogenic emissions. We attribute the observed decline to increases in the terrestrial sink during the past decade, associated with the effects of rising atmospheric CO2 on vegetation and the slowdown in the rate of warming on global respiration. The pause in the atmospheric CO2 growth rate provides further evidence of the roles of CO2 fertilization and warming-induced respiration, and highlights the need to protect both existing carbon stocks and regions, where the sink is growing rapidly.

A DNA barcode library for ground beetles (Insecta, Coleoptera, Carabidae) of Germany: The genus Bembidion Latreille, 1802 and allied taxa.

As molecular identification method, DNA barcoding based on partial cytochrome c oxidase subunit 1 (COI) sequences has been proven to be a useful tool for species determination in many insect taxa including ground beetles. In this study we tested the effectiveness of DNA barcodes to discriminate species of the ground beetle genus Bembidion and some closely related taxa of Germany. DNA barcodes were obtained from 819 individuals and 78 species, including sequences from previous studies as well as more than 300 new generated DNA barcodes. We found a 1:1 correspondence between BIN and traditionally recognized species for 69 species (89%). Low interspecific distances with maximum pairwise K2P values below 2.2% were found for three species pairs, including two species pairs with haplotype sharing (Bembidion atrocaeruleum/Bembidion varicolor and Bembidion guttula/Bembidion mannerheimii). In contrast to this, deep intraspecific sequence divergences with distinct lineages were revealed for two species (Bembidion geniculatum/Ocys harpaloides). Our study emphasizes the use of DNA barcodes for the identification of the analyzed ground beetles species and represents an important step in building-up a comprehensive barcode library for the Carabidae in Germany and Central Europe as well.

Identification of North Sea molluscs with DNA barcoding.

Sequence-based specimen identification, known as DNA barcoding, is a common method complementing traditional morphology-based taxonomic assignments. The fundamental resource in DNA barcoding is the availability of a taxonomically reliable sequence database to use as a reference for sequence comparisons. Here, we provide a reference library including 579 sequences of the mitochondrial cytochrome c oxidase subunit I for 113 North Sea mollusc species. We tested the efficacy of this library by simulating a sequence-based specimen identification scenario using Best Match, Best Close Match (BCM) and All Species Barcode (ASB) criteria with three different threshold values. Each identification result was compared with our prior morphology-based taxonomic assignments. Our simulation resulted in 87.7% congruent identifications (93.8% when excluding singletons). The highest number of congruent identifications was obtained with BCM and ASB and a 0.05 threshold. We also compared identifications with genetic clustering (Barcode Index Numbers, BINs) computed by the Barcode of Life Datasystem (BOLD). About 68% of our morphological identifications were congruent with BINs created by BOLD. Forty-nine sequences were clustered in 16 discordant BINs, and these were divided in two classes: sequences from different species clustered in a single BIN and conspecific sequences divided in more BINs. Whereas former incongruences were probably caused by BOLD entries in need of a taxonomic update, the latter incongruences regarded taxa requiring further investigations. These include species with amphi-Atlantic distribution, whose genetic structure should be evaluated over their entire range to produce a reliable sequence-based identification system.