Contributions to the biodiversity of Vietnam – Results of VIETBIO inventory work and field training in Cuc Phuong National Park

VIETBIO [Innovative approaches to biodiversity discovery and characterisation in Vietnam] is a bilateral German-Vietnamese research and capacity building project focusing on the development and transfer of new methods and technology towards an integrated biodiversity discovery and monitoring system for Vietnam. Dedicated field training and testing of innovative methodologies were undertaken in Cuc Phuong National Park as part and with support of the project, which led to the new biodiversity data and records made available in this article collection. VIETBIO is a collaboration between the Museum für Naturkunde Berlin – Leibniz Institute for Evolution and Biodiversity Science (MfN), the Botanic Garden and Botanical Museum, Freie Universität Berlin (BGBM) and the Vietnam National Museum of Nature (VNMN), the Institute of Ecology and Biological Resources (IEBR), the Southern Institute of Ecology (SIE), as well as the Institute of Tropical Biology (ITB); all Vietnamese institutions belong to the Vietnam Academy of Science and Technology (VAST). The article collection "VIETBIO" (https://doi.org/10.3897/bdj.coll.63) reports original results of recent biodiversity recording and survey work undertaken in Cuc Phuong National Park, northern Vietnam, under the framework of the VIETBIO project. The collection consist of this “main” cover paper – characterising the study area, the general project approaches and activities, while also giving an extensive overview on previous studies from this area – followed by individual papers for higher taxa as studied during the project. The main purpose is to make primary biodiversity records openly available, including several new and interesting findings for this biodiversity-rich conservation area. All individual data papers with their respective primary records are expected to provide useful baselines for further taxonomic, phylogenetic, ecological and conservation-related studies on the respective taxa and, thus, will be maintained as separate datasets, including separate GUIDs also for further updating.

Early-Middle Ordovician cephalopods from Ny Friesland, Spitsbergen – a pelagic fauna with Laurentian affinities

The collection of cephalopods from eight sampling horizons within the Olenidsletta Member, Valhallfonna Formation, Floian–Dapingian, from Profilstranda and nearby Profilbekken, Ny Friesland, Spitsbergen, resulted in the detection of 31 species, 20 genera, and 12 families from the Ellesmerocerida, Endocerida, Riocerida, Dissidocerida, Orthocerida, Tarphycerida, and Oncocerida. Of these, five genera (Ethanoceras gen. nov., Hinlopoceras gen. nov., Nyfrieslandoceras gen. nov., Olenidslettoceras gen. nov., Svalbardoceras gen. nov.) and 19 species (Bactroceras fluvii sp. nov., Buttsoceras buldrebreenense sp. nov., Cycloplectoceras hinlopense sp. nov., Cyclostomiceras profilstrandense sp. nov., Deltoceras beluga sp. nov., Eosomichelinoceras borealis sp. nov., Ethanoceras solitudines gen. et sp. nov., Hemichoanella occulta sp. nov., Hinlopoceras tempestatis gen. et sp. nov., H. venti gen. et sp. nov., Lawrenceoceras ebenus sp. nov., L. larus sp. nov., Litoceras profilbekkenense sp. nov., Nyfrieslandoceras bassleroceroides gen. et sp. nov., Olenidslettoceras farmi gen. et sp. nov., Protocycloceras minor sp. nov., Proterocameroceras valhallfonnense sp. nov., Svalbardoceras sterna gen. et sp. nov., S. skua gen. et sp. nov.) are new. The diagnoses of the Cyptendoceratidae, Bactroceratidae and of Deltoceras Hyatt, 1894 are emended. Well preserved early growth stages in several species are remarkable. Turnover between the sampling horizons and between sampling intervals is high. The differences in composition, diversity and evenness of the assemblages are interpreted as reflecting changing depth and oxygenation depositional bottom conditions. The co-occurrence of endemic and cosmopolitan species is interpreted as resulting from a high vertical niche differentiation and from eustatically generated lateral shifts of facies zones. Based on calculations of phragmocone implosion depths, depositional depths of 50–130 m are plausible for the Olenidsletta Member, supporting independent evidence from biomarker signatures. Several cephalopod species of the Olenidsletta Member represent odd mosaics of morphological features of previously known cephalopods which cannot be unambiguously assigned to one of the existing cephalopod higher taxa. Results from a cladistic analysis shed new light on the early evolution of the Oncocerida and Orthocerida.

Comparison of NF-κB from the protists Capsaspora owczarzaki and Acanthoeca spectabilis reveals extensive evolutionary diversification of this transcription factor

We provide a functional characterization of transcription factor NF-κB in protists and provide information about the evolution and diversification of this biologically important protein. We characterized NF-κB in two protists using phylogenetic, cellular, and biochemical techniques. NF-κB of the holozoan Capsaspora owczarzaki (Co) has an N-terminal DNA-binding domain and a C-terminal Ankyrin repeat (ANK) domain, and its DNA-binding specificity is more similar to metazoan NF-κB proteins than to Rel proteins. Removal of the ANK domain allows Co-NF-κB to enter the nucleus, bind DNA, and activate transcription. However, C-terminal processing of Co-NF-κB is not induced by IκB kinases in human cells. Overexpressed Co-NF-κB localizes to the cytoplasm in Co cells. Co-NF-κB mRNA and DNA-binding levels differ across three Capsaspora life stages. RNA-sequencing and GO analyses identify possible gene targets of Co-NF-κB. Three NF-κB-like proteins from the choanoflagellate Acanthoeca spectabilis (As) contain conserved Rel Homology domain sequences, but lack C-terminal ANK repeats. All three As-NF-κB proteins constitutively enter the nucleus of cells, but differ in their DNA-binding abilities, transcriptional activation activities, and dimerization properties. These results provide a basis for understanding the evolutionary origins of this key transcription factor and could have implications for the origins of regulated immunity in higher taxa.

Optimization of primer and polymerase chain reaction conditions to amplify COI locus for identification of Purnajiwa (Euchresta horsfieldii (Lesch.) Benn.) collected from Bedugul, Bali

The polymerase chain reaction (PCR) has been used for molecular research to amplify DNA fragments, especially from a small amount of genetic material. PCR has been applied for numerous researches, including for plant molecular identification. A good PCR product is dependent on good amplification of the DNA segment in optimum condition. This research was conducted to optimize the primer combination, and the annealing temperature for DNA barcoding application of Balinese rare medicinal plant (Euchresta horsfieldii (Lesch.) Benn.) collected from Bedugul. COI is a suitable primer to identify unknown species to higher taxa levels and species with high phenotypic plasticity. The range of annealing temperatures was tested to amplify the combination of five COI primers: GWSF and GWSF5 for forwarding primers and GWSR, GWSR3, and GWSR5 for reverse primers. The annealing temperature was 52, 54, 56, 58, 60°C for 30 seconds. The result showed that GWSF-GWSR, GWSF-GWSR5, GWSF5-GWSR, GWSF5-GWSR5, and GWSF5-GWSR3 produced multiple bands, the double band that cannot be cut, multiple bands, faint amplification band for GWSF5-GWSR5 and GWSF5-GWSR3, respectively. Primer combination of GWSF-GWSR3 with an annealing temperature of 52°Cproduced double bands that were available to have proceeded for sequencing. In conclusion, the combination of GWSF-GWSR3 that is annealed at 52°C produced the best amplification band. The primer combinations and conditions can be used for further identification of Purnajiwa collected from Bedugul.

Assemblages of Acari in shallow burials: mites as markers of the burial environment, of the stage of decay and of body-cadaver regions

The burial of a cadaver results in reduced arthropod activity and disruptions in colonisation patterns. Here, the distribution and diversity of mite taxa was studied across decomposition stages of shallowly buried pig carcasses (Sus scrofa domesticus). In total 300 mites (88 species) were collected from three pig shallow graves compared to 129 mites (46 species) from control (bare) soil samples at the same depth. A successional pattern of Acari higher taxa and families was observed, and species richness and biodiversity fluctuated throughout decomposition, whereas active decay showed the greatest biodiversity. Mesostigmata mites were the most abundant in ‘cadaver soils’ with a significant difference in the abundance of Parasitidae mites, whereas Oribatida mites (true soil mites) were the most abundant in control soils. Certain mite species were significantly associated with decay stages: Cornigamasus lunaris with ‘bloated’, Gamasodes spiniger with ‘active’, Eugamasus sp. and Lorryia reticulata with ‘advanced’, and Macrocheles matrius and Ramusella clavipectinata in ‘dry’. Scheloribates laevigatus was a marker of bare soil at a shallow depth and Vulgoramasus remberti of buried decomposition, not specific to any decay stage. Analysis of mite assemblages associated with head, torso and posterior body showed that Parasitus evertsi and M. matrius are attracted to beneath the thighs, whereas L. reticulata to beneath the head. This study highlights the value of mites as indicator species of decomposition and its stages, confirming (1) a succession of Acari on buried remains and (2) species specificity to body regions.

The Univocity of Real Essence in Locke

I argue that Locke’s various descriptions of real essence pick out one and the same thing, namely a nature that can be ascribed to many things, and in terms of which we can get matters of classification right or wrong. On my reading, Locke does not attack real essences of the sort that are the essences of real species, but rather the presumption that a sorting according to our species concepts and their names is a sorting of things according to their real essences. And the lesson of Locke’s empirical argument against that presumption, I argue, is that our species concepts often function more like higher taxa, grouping together things that knowledge of their real essences would distinguish into distinct lowest species.

Species from the viewpoint of biocoenology

Some questions of the use of the “species” concept in biocoenology and hydrobiology are considered. The existence of certain difficulties and ambiguities in the use of this concept is shown. It is proposed to clarify the goals and objectives of identifying the species structure of biocoenoses. The examples show that ecomorphs and coeno-ecomorphs are not less important elements of a biocenotic system and require thorough research. The question of the possibility and feasibility of definitions "to species level" of all members of the community is considered. The ecological niche concept is associated with species, although there is also the guild concept that unites species according to the principle of convergent similarity of trophic, topical, or other preferences. Various systems of bioindication have become widespread, which are based on the principle of compliance of a particular species population to certain conditions. First of all, we are talking about disturbed conditions, including various impacts by pollution. It was shown that not only species, but also more easily identifiable higher taxa could be used as bioindicators of certain conditions.

Herpetological higher taxa nomina. 7. Lissamphibia Gadow, 1898

A taxon encompassing all recent taxa of amphibians and their close fossil relatives is highly supported as holophyletic in all recent phylogenetic analyses of amphibians. Under the Duplostensional Nomenclatural System, among twenty nomina available for this taxon, only one, Lissamphibia Gadow, 1898, qualifies as a sozodiaphonym and appears to be the one that should be used for this taxon, traditionally referred to the rank order. However, because of the current uncertainties in the phylogenetic relationships among basal amphibians, the allocation of this nomen to this taxon is still questionable. If it turned out to apply in fact to another, more comprehensive, taxon, its stabilisation under its current acceptation should be realised through an act of archoidy.

Herpetological higher taxa nomina. 6. Gymnophiona Rafinesque, 1814

A taxon, traditionally referred to the rank order, encompassing all recent taxa of caecilians and their close fossil relatives, is highly supported as holophyletic in all recent cladistic analyses of Amphibia. Under the Duplostensional Nomenclatural System, among 12 nomina available in the literature, only one, Gymnophiona Rafinesque, 1814, qualifies as a sozodiaphonym and should be used for this amphibian taxon. We show here that the authorship of this nomen, as well as of 32 other nomina published in 1814, is ‘Rafinesque’, not ‘Rafinesque-Schmaltz’. The nomen Apoda Oppel, 1811, that has often been used for this taxon, proves to be a distagmonym and a junior homonym of Apodes Linnaeus, 1758 and five other distagmonyms, and as such it is invalid under DONS. In total, we identified 34 distinct class-series nomina derived from the stems ἄπους (apous) or Apus in 13 distinct zoological groups, only two of which are valid under DONS Criteria: Apodiformia Wetmore, 1947, for the suborder of Aves currently known as Apodi Wetmore, 1947, and Apodomorpha Sibley, Ahlquist & Monroe, 1988 for the order of Aves currently known as Apodiformes Peters, 1940. Several other nomenclatural findings were made in the course of this study: [1] in the Teleostei, the nomina "Eupercaria" and "Syngnatharia", like all the other new nomina proposed in the paper by Betancur-R. et al. (2017) are anoplonyms and cannot be used as valid; [2] in the Mammalia, the nomina Cetus and Cetacea should be credited to Brisson (1759); [3] in the Holothuroidea, the nomen Apoda Claus, 1868, currently considered valid under the apograph Apodida, is invalid and should be replaced by the nomen Paractinopoda Ludwig, 1891; [4] in the Isopoda, the subordinal nomen Cymothoida Wägele, 1989 should be replaced by its senior synonym Darwinida Lakshminarayana & Rama Rao, 1977.

Herpetological higher taxa nomina. 8. Amphibia Blainville, 1816

Under the Duplostensional Nomenclatural System, the valid nomen of the class including all recent amphibians and all the Palaeozoic groups of anamniote tetrapods subsequent to the ‘lissamphibian-amniote phylogenetic split’ is the sozodiaphonym Amphibia Blainville, 1816. This corresponds to the usage that has been in force for two centuries in thousands of publications, and it should not be challenged, as this would entail instability and confusion.