Soup to tree: the phylogeny of beetles inferred by mitochondrial metagenomics of a Bornean rainforest sample

In spite of the growth of molecular ecology, systematics and next-generation sequencing, the discovery and analysis of diversity is not currently integrated with building the tree-of-life. Tropical arthropod ecologists are well placed to accelerate this process if all specimens obtained via masstrapping, many of which will be new species, could be incorporated routinely in phylogeny reconstruction. Here we test a shotgun sequencing approach, whereby mitochondrial genomes are assembled from complex ecological mixtures via mitochondrial metagenomics, and demonstrate how the approach overcomes many of the taxonomic impediments to the study of biodiversity. DNA from ~500 beetle specimens, originating from a single rainforest canopy fogging sample from Borneo, was pooled and shotgun sequenced, followed by de novo assembly of complete and partial mitogenomes for 175 species. The phylogenetic tree obtained from this local sample was highly similar to that from existing mitogenomes selected for global coverage of major lineages of Coleoptera. When all sequences were combined, only minor topological changes are induced against this reference set, indicating an increasingly stable estimate of coleopteran phylogeny, whilst the ecological sample expands the tip-level representation of several lineages. Robust trees generated from ecological samples now enable an evolutionary framework for ecology. Meanwhile, the inclusion of uncharacterized samples in the tree-of-life rapidly expands taxon and biogeographic representation of lineages without morphological identification. Mitogenomes from shotgun sequencing of unsorted environmental samples and their associated metadata, placed robustly into the phylogenetic tree, constitute novel DNA ‘superbarcodes’ for testing hypotheses regarding global patterns of diversity

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Figs. 7–9 in Enneboeus marmoratus Champion New to the USA, with a World Catalog of the Family Archeocrypticidae (Coleoptera: Tenebrionoidea)

Figs. 7–9. Enneboeus caseyi, specimen from Stillwater, Payne Co., Oklahoma, USA (MLGC). 7) Dorsal habitus;Published as part of Gimmel, Matthew L., Johnston, M. Andrew & Merkl, Ottó, 2018, Enneboeus marmoratus Champion New to the USA, with a World Catalog of the Family Archeocrypticidae (Coleoptera: Tenebrionoidea), pp. 269-278 in The Coleopterists Bulletin 72 (2) on page 272, DOI: 10.1649/0010-065X-72.2.269, http://zenodo.org/record/538180

A new enigmatic lineage of Dascillidae (Coleoptera: Elateriformia) from Eocene Baltic amber described using X-ray microtomography, with notes on Karumiinae morphology and classification

Dascillidae are a species-poor beetle group with a scarcefossil record. Here, we describe Baltodascillus serraticornis gen. et sp. nov. based on a well-preservedspecimen from Eocene Baltic amber. It differs from all known Dascillidae byits reduced mandibles. After studying the specimen using light microscopyand X-ray microtomography, we tentatively place this genus in the poorlydefined subfamily Karumiinae based on the large eyes, serrate antennae, andlack of prosternal process. This is the first representative of theDascillidae formally described from Baltic amber and the first describedfossil member of the subfamily Karumiinae. We briefly discuss theproblematic higher classification of Dascillidae, along with the morphologyand biogeography of the group

Ta2O5-gates of ph-sensitive devices : comparative spectroscopic and electrical studies

Thin films of tantalum pentoxide (Ta2O5) were prepared on Si/SiO2 substrates by thermal oxidation of tantalum. In systematic oxidation studies we followed the growth of the Ta2O5/SiO2 interface. The oxide layers and their interfaces were characterized by SIMS, SAM, XPS, by comparative C-V measurements and by pH-(ISFET) sensitivities. Depending on the oxidation procedure, we find non-ideal stoichiometries of the Ta2O5/SiO2 interface, whose widths vary as a function of the oxidation time of the previously evaporated metallic tantalum. Specific annealing procedures lead to unexpectedly high leakage currents, which correlate with the formation of voids in the oxide layers. Even in the absence of voids, non-ideal interfaces provide high concentrations of electrically-active states in gate oxides of ISFETS, which in turn determine the results of C-V measurements and ISFET characteristics. For ideal stoichiometric and atomically abrupt interfaces, we observe long-term stability and ideal Nernstian behaviour in the pH-(ISFET) sensitivities