MicroCT data provide evidence correcting the previous misidentification of an Eocene amber beetle (Coleoptera, Cicindelidae) as an extant species.

The fossil record suggests some insect species have a marked longevity. The oldest fossils purported to represent extant insect species are from the Oligocene and Eocene. One of the most cited fossils is the extant tiger beetle Tetracha carolina (Coleoptera: Cicindelidae) that was identified over a century ago by Walther Horn in Eocene Baltic amber. We examined this and compared it to the previously described cincindelid Baltic amber fossil Palaeoiresina cassolai using X-ray microscopy and 3D imaging techniques. We conclude that Horn's fossil tiger beetle specimen is conspecific with the Eocene P. cassolai and is a member of an extinct stem group lineage of Cicindelidae. Based on a review of all the tiger beetle fossils described from Cretaceous and Paleogene deposits, we found that the assignment of these fossil species to extant lineages is not supported. There are currently no synapomorphies known from fossils that can provide evidence for Cretaceous Manticorni or Megacephalini nor is there evidence for Eocene Iresina. We provide evidence that rejects the idea of a recent beetle species persisting since the Eocene period, which is crucial for using the currently known fossil Cicindelidae species to calibrate divergence dating of beetle phylogenies.

Complete sequences of six major histocompatibility complex haplotypes, including all the major MHC class II structures.

Accurate and comprehensive immunogenetic reference panels are key to the successful implementation of population-scale immunogenomics. The 5Mbp Major Histocompatibility Complex (MHC) is the most polymorphic region of the human genome and associated with multiple immune-mediated diseases, transplant matching and therapy responses. Analysis of MHC genetic variation is severely complicated by complex patterns of sequence variation, linkage disequilibrium and a lack of fully resolved MHC reference haplotypes, increasing the risk of spurious findings on analyzing this medically important region. Integrating Illumina, ultra-long Nanopore, and PacBio HiFi sequencing as well as bespoke bioinformatics, we completed five of the alternative MHC reference haplotypes of the current (GRCh38/hg38) build of the human reference genome and added one other. The six assembled MHC haplotypes encompass the DR1 and DR4 haplotype structures in addition to the previously completed DR2 and DR3, as well as six distinct classes of the structurally variable C4 region. Analysis of the assembled haplotypes showed that MHC class II sequence structures, including repeat element positions, are generally conserved within the DR haplotype supergroups, and that sequence diversity peaks in three regions around HLA-A, HLA-B+C, and the HLA class II genes. Demonstrating the potential for improved short-read analysis, the number of proper read pairs recruited to the MHC was found to be increased by 0.06%-0.49% in a 1000 Genomes Project read remapping experiment with seven diverse samples. Furthermore, the assembled haplotypes can serve as references for the community and provide the basis of a structurally accurate genotyping graph of the complete MHC region.

Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning.

MOTIVATION: Current state-of-the-art tools for the de novo annotation of genes in eukaryotic genomes have to be specifically fitted for each species and still often produce annotations that can be improved much further. The fundamental algorithmic architecture for these tools has remained largely unchanged for about two decades, limiting learning capabilities. Here, we set out to improve the cross-species annotation of genes from DNA sequence alone with the help of deep learning. The goal is to eliminate the dependency on a closely related gene model while also improving the predictive quality in general with a fundamentally new architecture. RESULTS: We present Helixer, a framework for the development and usage of a cross-species deep learning model that improves significantly on performance and generalizability when compared to more traditional methods. We evaluate our approach by building a single vertebrate model for the base-wise annotation of 186 animal genomes and a separate land plant model for 51 plant genomes. Our predictions are shown to be much less sensitive to the length of the genome than those of a current state-of-the-art tool. We also present two novel post-processing techniques that each worked to further strengthen our annotations and show in-depth results of an RNA-Seq based comparison of our predictions. Our method does not yet produce comprehensive gene models but rather outputs base pair wise probabilities. AVAILABILITY AND IMPLEMENTATION: The source code of this work is available at https://github.com/weberlab-hhu/Helixer under the GNU General Public License v3.0. The trained models are available at https://doi.org/10.5281/zenodo.3974409. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Constant morphological patterns in the hemolymph vascular system of crayfish (Crustacea, Decapoda).

We present a study of the hemolymph vascular system of the marbled crayfish, Procambarus fallax f. virginalis, the only crayfish species known to be parthenogenetic. To identify potential evolutionary patterns, we compared data from a total of 48 specimens of P. fallax with 22 specimens of Orconectes limosus. Visualizations (2D and 3D) were carried out using a combination of classical and modern morphological techniques. Our data were compared to the existing literature. Like all Decapoda, both P. fallax and O. limosus have a hemolymph vascular system, consisting of a globular heart with seven off-branching arteries. We were able to visualize in detail the heart of crayfish for the first time, i.e., the myocard with its clusters of muscles running through the lumen of the heart, the valves and flaps of ostia and arteries. Furthermore, the branching patterns of the seven artery systems were analyzed. Anatomical structures identified to be consistent in all specimens of both species were combined as ground pattern of hemolymph vascular system features for Astacida.

The First Organ-Based Ontology for Arthropods (Ontology of Arthropod Circulatory Systems - OArCS) and its Integration into a Novel Formalization Scheme for Morphological Descriptions.

Morphology, the oldest discipline in the biosciences, is currently experiencing a renaissance in the field of comparative phenomics. However, morphological/phenotypic research still suffers on various levels from a lack of standards. This shortcoming, first highlighted as the "linguistic problem of morphology", concerns the usage of terminology and also the need for formalization of morphological descriptions themselves, something of paramount importance not only to the field of morphology but also when it comes to the use of phenotypic data in systematics and evolutionary biology. We therefore argue, that for morphological descriptions, the basis of all systematic and evolutionary interpretations, ontologies need to be utilized which are based exclusively on structural qualities/properties and which in no case include statements about homology and/or function. Statements about homology and function constitute interpretations on a different or higher level. Based on these "anatomy ontologies", further ontological dimensions (e.g., referring to functional properties or homology) may be exerted for a broad use in evolutionary phenomics. To this end we present the first organ-based ontology for the most species-rich animal group, the Arthropoda. Our Ontology of Arthropod Circulatory Systems (OArCS) contains a comprehensive collection of 383 terms (i.e., labels) tied to 296 concepts (i.e., definitions) collected from the literature on phenotypic aspects of circulatory organ features in arthropods. All of the concepts used in OArCS are based exclusively on structural features, and in the context of the ontology are independent of homology and functional assumptions. We cannot rule out that in some cases, terms are used which in traditional usage and previous accounts might have implied homology and/or function (e.g. heart, sternal artery). Concepts are composed of descriptive elements that are used to classify observed instances into the organizational framework of the ontology. That is, descriptions in ontologies are only descriptions of individuals if they are necessary/and or sufficient representations of attributes (independently) observed and recorded for an individual. In addition, we here present for the first time an entirely new approach to formalizing phenotypic research, a semantic model for the description of a complex organ system in a highly disparate taxon, the arthropods. We demonstrate this with a formalized morphological description of the hemolymph vascular system in one specimen of the European garden spider Araneus diadematus. Our description targets five categories of descriptive statement: "position", "spatial relationships", "shape", "constituents", and "connections", as the corresponding formalizations constitute exemplary patterns useful not only when talking about the circulatory system, but also in descriptions in general. The downstream applications of computer-parsable morphological descriptions are widespread, with their core utility being the fact that they make it possible to compare collective description sets in computational time, that is, very quickly. Among other things, this facilitates the identification of phenotypic plasticity and variation when single individuals are compared, the identification of those traits which correlate between and within taxa, and the identification of links between morphological traits and genetic (using GO, Gene Ontology) or environmental (using ENVO, Environmental Ontology) factors. [Arthropoda; concept; function; hemolymph vascular system; homology; terminology.].

Hemodynamic effects of dobutamine and dopexamine after cardiopulmonary bypass in pediatric cardiac surgery.

BACKGROUND: After surgical repair of congenital heart disease, inotropic support is sometimes necessary to wean from cardiopulmonary bypass. In pediatric cardiac surgery, dobutamine and dopamine are often used as inotropic support. Dopexamine is a synthetic catecholamine, which has positive inotropic and vasodilating properties. Because the hemodynamic effects of catecholamines are modified after cardiopulmonary bypass, the aim of this study was to investigate the effects of dobutamine and dopexamine on cardiac index and systemic vascular resistance index after cardiopulmonary bypass in pediatric cardiac surgery. METHODS: The study was performed in a prospective, randomized, and double-blinded cross-over design. The investigation included 11 children for elective, noncomplex congenital heart surgery. After weaning from cardiopulmonary bypass and a 20-min period of steady state, children received either 2.5 microg x kg(-1) x min(-1) dobutamine or 1 microg x kg(-1) x min(-1) dopexamine for 20 min. Cardiac index (transpulmonary thermodilution), mean arterial pressure, central venous pressure, stroke volume, systemic vascular resistance, and central venous oxygen saturation were determined. The primary outcome variable was cardiac index. RESULTS: No difference in cardiac index was observed between the two groups (P = 0.594). Both drugs increased cardiac index, dopexamine from 3.9 +/- 0.6 to 4.7 +/- 0.8 l x min(-1) x m(-2) (P = 0.003) and dobutamine from 4.1 +/- 0.7 to 4.8 +/- 0.7 l x min(-1) x m(-2) (P = 0.004). During treatment with dobutamine, children presented with significantly higher mean arterial pressure (P = 0.003) and systemic vascular resistance index (P = 0.026). CONCLUSIONS: This trial demonstrates that low-dose dobutamine and dopexamine both increase cardiac index during pediatric cardiac surgery but with different hemodynamic effects.

The POETICs of industrial carbon dioxide emissions in Japan: an urban and institutional extension of the IPAT identity.

BACKGROUND: This study applies the POETICs framework (population, organization, environment, technology, institutions and culture) to an analysis of industrial carbon dioxide emissions in Japanese cities. The inclusion of institutional variables in the form of International Council for Local Environmental Initiatives membership, ISO 14001 implementation, and non-profit sector activity addresses the ecological limitations of the often used IPAT (impact = population x affluence x technology) approach. RESULTS: Results suggest the weak existence of an environmental Kuznets curve, in which the wealthiest cities are reducing their emissions through increased efficiency. Significant institutional impacts are also found to hold in the predicted directions. Specifically, panel and cross-sectional regressions indicate that membership in the International Council for Local Environmental Initiatives and non-profit organizational presence have negative effects on industrial carbon dioxide emissions. CONCLUSION: The presence of institutional drivers at the city level provides empirical support for the POETICs rubric, which recasts the ecological framing of the IPAT identity in a more sociological mold. The results also indicate that Japanese civil society has a role to play in carbon mitigation. More refined studies need to take into consideration an expanded set of methods, drivers, and carbon budgets, as applied to a broader range of cases outside of Japan, to more accurately assess how civil society can bridge the issue of scale that separates local level policy concerns from global level climate dynamics.

Patterns of genetic divergence of three Canarian endemic Lotus (Fabaceae): implications for the conservation of the endangered L. kunkelii.

We examined data for 11 allozyme loci in 14 populations that represent the distribution of the endangered Lotus kunkelii, the narrowly distributed L. arinagensis (both endemic to Gran Canaria), and the broad-ranging L. lancerottensis (endemic to the easternmost Canary Islands, Fuerteventura and Lanzarote) to explore and construe patterns of genetic variation and use this data to assess the controversial taxonomic status of L. kunkelii relative to L. lancerottensis. While L. kunkelii maintains low levels of variation, presumably as a consequence of prolonged inbreeding due to very low population size and sharp geographic isolation, the other two taxa have much higher indicators of polymorphism than those reported for other oceanic island endemics. Lotus arinagensis has the highest genetic polymorphism and the lowest interpopulation differentiation, presumably because of its considerable antiquity and habitat stability, despite recent fragmentation. The high interpopulation differentiation in L. lancerottensis is attributed to the Atlantic acting as a barrier, reducing gene flow within islands. Evolutionary analysis of the allozyme evidence indicates that L. kunkelii is genetically closer to L. arinagensis than to L. lancerottensis, thereby dispelling the taxonomic uncertainty and supporting L. kunkelii as a distinct species, warranting legal protection in the forthcoming catalog of threatened Canarian species.