Metadata Made Easy: Develop and Use Domain‐Specific Metadata Schemes by following the dmdScheme approach

1. Metadata plays an essential role in the long‐term preservation, reuse, and interoperability of data. Nevertheless, creating useful metadata can be sufficiently difficult and weakly enough incentivized that many datasets may be accompanied by little or no metadata. One key challenge is, therefore, how to make metadata creation easier and more valuable. We present a solution that involves creating domain‐specific metadata schemes that are as complex as necessary and as simple as possible. These goals are achieved by co‐development between a metadata expert and the researchers (i.e., the data creators). The final product is a bespoke metadata scheme into which researchers can enter information (and validate it) via the simplest of interfaces: a web browser application and a spreadsheet.
2. We provide the R package dmdScheme (dmdScheme: An R package for working with domain specific MetaData schemes (Version v0.9.22), 2019) for creating a template domain‐specific scheme. We describe how to create a domain‐specific scheme from this template, including the iterative co‐development process, and the simple methods for using the scheme, and simple methods for quality assessment, improvement, and validation.
3. The process of developing a metadata scheme following the outlined approach was successful, resulting in a metadata scheme which is used for the data generated in our research group. The validation quickly identifies forgotten metadata, as well as inconsistent metadata, therefore improving the quality of the metadata. Multiple output formats are available, including XML.
4. Making the provision of metadata easier while also ensuring high quality must be a priority for data curation initiatives. We show how both objectives are achieved by close collaboration between metadata experts and researchers to create domain‐specific schemes. A near‐future priority is to provide methods to interface domain‐specific schemes with general metadata schemes, such as the Ecological Metadata Language, to increase interoperability.

The article describes a methodology to develop, enter, and validate domain specific metadata schemes which is suitable to be used by nonmetadata specialists. The approach uses an R package which forms the backend of the processing of the metadata, uses spreadsheets to enter the metadata, and provides a server based approach to distribute and use the developed metadata schemes.     

Assessing diversity in plant communities: The importance of within-species variation

While the measurement of plant species diversity continues to play a central role in ecology and conservation, few formal attempts have been made at defining the concept of diversity, and, specifically, at evaluating the utility of taxonomic species as units for diversity indices. Ecological diversity is defined here as a measure of the degree of biotic and/or abiotic dissimilitude within a community that is perceivable and utilizable by organisms. Although indices based merely on ‘species’ may be useful for cataloging taxonomic diversity in communities, plant taxa are generally unreliable units for quantifying the ecological diversity perceived and utilized by most organisms in communities. Recent research highlights the shortcomings of the unit of species for characterizing ecological diversity, and we advocate the further exploration of alternative diversity classes with which to describe plant communities.     

Foraminiferal zonation of late Paleozoic depositional sequences

From the later part of the Devonian through the Permian, calcareous foraminifers became abundant and evolved rapidly. This rapid evolution of taxa forms the basis of a detailed zonation through the Carboniferous and Permian. Comparison of this evolutionary history of foraminifers, their biostratigraphic zonation, and the depositional sequences in which they occur suggests that sea-level events in late Paleozoic depositional history contributed significantly in subdividing a fairly continuous evolutionary record into a succession of about 75 identifiable foraminiferal zones during a 100–125 Myr time span. Although variable in terms of duration and vertical occurrences, the more completely recorded high-stand intervals give brief histories of the foraminiferal evolutionary record and are sandwiched between the poorly recorded or unrecorded low-stand intervals. Many of the individual foraminiferal zones are confined to a single depositional sequence.The late Paleozoic carbonate foraminiferal fossil record, as with the rest of the fossil record, is strongly affected by sediment deposition-nondeposition as a result of major changes in sea level. This incomplete fossil record is the result of repeated depositional breaks because of the way that depositional sequences form. It is not possible to ascribe macromutations, ‘punctuated’ evolution or ‘punctuated gradualism’ as the cause of this evolutionary pattern of the shelf-carbonate fossil record. This pattern is distinctive and we refer to it as ‘sequence evolution’ and ‘sequence extinction’. In the later part of the Middle Permian and in the Late Permian, the fossil record clearly illustrates that a series of faunal losses through ‘sequence extinctions’ progressively exceeded faunal replacements and new species through ‘sequence evolution’, but not a ‘mass extinction’ as is commonly ascribed to the end of the Permian Period. Most Permian faunas became extinct in the interval of 8 to 4 million years before the end of the Late Permian.     

The expansion of information in ecological systems: Emergence as a quantifiable state

Although the term ‘emergence’ has received wide attention in the literature, most of this attention has been focused on epistemological discussions about the nature of what might be considered emergent behavior in self-organizing systems. For the concept of emergence to have any great utility for biologists, it must (1) be perceptible as a physical, quantitative property rather than just a philosophical one; (2) have a quantitative definition applicable to all levels of biological organization; and (3) be an essential component of biological system performance or evolution. Using an independent, cellular population model (running in the StarLogo system), we have developed a mutual information calculation to measure the information expansion when considering the interactions between a population of herbivores and an environment in comparison to the interactions between the individual herbivores and that environment. In self-organizing biological systems, the collective action of massively parallel units generates a greater potential complexity in the information processing capacity of the ‘whole’ system relative to the ‘individual’ parts, and as such, there is a demonstrable increase in mutual information content. From this perspective, we consider emergence to exist as a simple information expansion that is a default behavior of any system with multiple, component parts governed by a simple, probabilistic rule set. It is not a first principle of self-organizing biological systems, but rather a collective behavior that can be quantitatively described in practical terms for experimental biologists. With a quantitative formulation, the concept of emergence may become a useful information statistic in assessing the structure of biological systems.     

Vicariance and dispersal form a ring distribution in nightsnakes around the Gulf of California

Plate tectonics can have profound effects on organismal distribution and is often the driving force in speciation. Through geologic processes, the Baja California Peninsula depicts two faunal patterns: one through southern vicariance with Cape separation, and the other through dispersal onto the northern peninsula, referred to as a ‘dual-peninsular effect.’ Here we apply a hierarchical sampling strategy that combines population-level sequence data (800 bp, nad4 region) with complete mt-genome data (aligned 15,549 bp) and 5 nuclear protein encoding loci (3315 bp), to test whether both patterns have occurred in one group of nightsnakes (Hypsiglena). The geologic formation of the peninsula is thought to have occurred in three stages: (1) Cape separation from mainland Mexico; (2) the northern peninsula separated, forming the northern Gulf of California; and (3) the peninsula was united through volcanic activity, while moving northward causing collision with southern California. However, the timing of events is debated. We explore phylogenetic relationships and estimate dates of divergence for nightsnakes using our hierarchical sampling strategy. Our data support both ‘southern-vicariance’ and ‘northern-dispersal’ have occurred in nightsnakes, forming a ring distribution around the Gulf of California. Two divergent forms are sympatric on the southern half of the peninsula with no indication of hybridization. Nightsnakes represent the first group to depict the ‘dual-peninsular effect’ with extensive overlap on the Baja California Peninsula.     

Polymer Gard: Computer Simulation of Covalent Bond Formation in Reproducing Molecular Assemblies

The basic Graded Autocatalysis Replication Domain (GARD) model consists of a repertoire of small molecules, typically amphiphiles, which join and leave a non-covalent micelle-like assembly. Its replication behavior is due to occasional fission, followed by a homeostatic growth process governed by the assembly’ s composition. Limitations of the basic GARD model are its small finite molecular repertoire and the lack of a clear path from a ‘monomer world’ towards polymer-based living entities.We have now devised an extension of the model (polymer GARD or P-GARD), where a monomer-based GARD serves as a ‘scaffold’ for oligomer formation, as a result of internal chemical rules. We tested this concept with computer simulations of a simple case of monovalent monomers, whereby more complex molecules (dimers) are formed internally, in a manner resembling biosynthetic metabolism. We have observed events of dimer ‘take-over’ – the formation of compositionally stable, replication-prone quasi stationary states (composomes) that have appreciable dimer content. The appearance of novel metabolism-like networks obeys a time-dependent power law, reminiscent of evolution under punctuated equilibrium. A simulation under constant population conditions shows the dynamics of takeover and extinction of different composomes, leading to the generation of different population distributions. The P-GARD model offers a scenario whereby biopolymer formation may be a result of rather than a prerequisite for early life-like processes.     

A probability-based indicator of ecological condition

We introduce a new method for quantifying the ecological condition (C) of sites based on documented species’ responses to environmental stress. Preliminary research is needed to establish species-specific logistic functions, representing probabilities of finding individual species across an explicit reference gradient, ranging from maximally stressed (C = 0) to minimally stressed (C = 10) localities. Each function takes into account the species’ tolerance to stress, the species’ overall ubiquity, and the probability of detecting the species when it is present. Given a set of standardized species-specific functions, the ecological condition of any site can be derived by iteration, converging on the value of C that best “predicts” the species that are actually present. Species from multiple taxonomic groups can be included in the calculations, and results are not directly affected by species richness or sampling area. We demonstrate a successful application of this method for bird species assemblages in the U.S. portion of the Great Lakes coastal zone. Approximately, 28% of the bird species observed in the Eastern Deciduous Forest Ecological Province and 35% of the species in the Laurentian Mixed Forest Ecological Province showed strong relationships with a reference gradient of land cover variables. Functional stress–response relationships of these species can be used effectively to estimate ecological condition at new sites. The estimated condition based on bird species generally mirrors the reference condition, but deviations from the expected 1:1 relationship provide meaningful insights about ecological condition of the target areas. Sensitivity analysis using different numbers of species shows that our method is robust and can be applied consistently with 25–30 species exhibiting strong stress–response functions.     

Molecular Systematics of Middle American Cichlid Fishes and the Evolution of Trophic-Types in ‘Cichlasoma(Amphilophus)’ and ‘C.(Thorichthys)’

The majority of Middle American cichlids are placed in the informal assemblage ‘Cichlasoma.’ The group is divided into eight sections which appear to be based primarily on trophic morphology. Although several members of ‘Cichlasoma’ have been used in ecomorphological, behavioral, and biogeographic studies, no phylogenetic hypotheses for the group exist. In an attempt to develop a better understanding of the phylogenetic relationships of ‘cichlasomine’ cichlids, we examined the evolution of the trophic specialization, substratum-sifting, in two sections, ‘Cichlasoma(Thorichthys)’ and ‘C.(Amphilophus),’ to determine whether the trait reflects common ancestry. We sequenced the complete mitochondrial cytochromebgene for 19 cichlids representing six sections of ‘Cichlasoma,’ and representatives of other Neotropical Cichlidae. Additional cichlid, and noncichlid outgroup sequences were included for a total of 22 taxa. The molecular phylogeny supports the recognition of the section ‘C.(Thoricthys)’ as a natural group, and we place those cichlids in the genusThorichthys.The phylogeny also depicts ‘C.(Amphilophus)’ as paraphyletic, with substratum-sifters and generalized predators forming separate nonsister clades. We recommend that the substratum-sifting clade of the section ‘C.(Amphilophus)’ be placed in the resurrected genusAstatheros.The generalized predator clade of ‘C.(Amphilophus)’ contains only two species, ‘C. (A.) citrinellum’ and ‘C. (A.) labiatum,’ which we place in the genusAmphilophus.The phylogenetic hypotheses generated indicate that the substratum-sifting generaThorichthysandAmphilophusdo not share a common ancestor. Reconstruction of the evolution of substratum-sifting is equivocal, requiring either the independent evolution of the trait on two separate occasions or its presence in a more inclusive clade and subsequent loss in nonsubstratum sifting species.     

Devonohexapodus bocksbergensis is a synonym of Wingertshellicus backesi (Euarthropoda) – no evidence for marine hexapods living in the Devonian Hunsrück Sea

The Devonian Hunsrück Slate fossil Devonohexapodus bocksbergensis Haas, Waloszek & Hartenberger, 2003 has been interpreted as a stem-lineage representative of the Hexapoda, implying their marine origin and independent terrestrialisation within the ‘Atelocerata’. Devonohexapodus bocksbergensis was based on a single specimen embedded in a lateral position. Reinvestigation of that holotype and of all known specimens of the Hunsrück Slate arthropod Wingertshellicus backesi Briggs & Bartels, 2001 demonstrates that all this material represents a single species. The latter is redescribed, its taxonomic diagnosis is emended, and the name Devonohexapodus bocksbergensis is treated as a junior synonym of Wingertshellicus backesi. The phylogenetic position of W. backesi neither is that of a stem-lineage representative of Hexapoda, nor does it fall within the crown group Mandibulata. The Hunsrück Slate provides no evidence of an independent terrestrialisation within the ‘Atelocerata’ or of a marine origin of the Hexapoda.     

No substantial excess all-cause mortality among cardiac implantable electronic device patients during the first COVID‑19 lockdown in the Leiden area

In the Netherlands, the coronavirus disease 2019 (COVID‑19) pandemic has resulted in excess mortality nationwide. Chronic heart disease patients are at risk for a complicated COVID‑19 course. The current study investigates all-cause mortality among cardiac implantable electronic device (CIED) patients during the first peak of the pandemic and compares the data to the statistics for the corresponding period in the two previous years. Data of adult CIED patients undergoing follow-up at the Leiden University Medical Centre were analysed. All-cause mortality between 1 March and 31 May 2020 was evaluated and compared to the data for the same period in 2019 and 2018. At the beginning of the first peak of the pandemic, 3,171 CIED patients (median age 70 years; 68% male; 41% ischaemic aetiology) were alive. Baseline characteristics of the 2019 (n = 3,216) and 2018 (n = 3,169) cohorts were comparable. All-cause mortality during the peak of the pandemic was 1.4% compared to 1.6% and 1.4% in the same period in 2019 and 2018, respectively (p = 0.84). During the first peak of the COVID‑19 pandemic, there was no substantial excess mortality among CIED patients in the Leiden area, despite the fact that this is group at high risk for a complicated course of a COVID‑19 infection. Strict adherence to the preventive measures may have prevented substantial excess mortality in these vulnerable patients.Supplementary InformationThe online version of this article (10.1007/s12471-021-01650-y) contains supplementary material, which is available to authorized users.     

Top-down controls on bacterial community structure: microbial network analysis of bacteria,T4-like viruses and protists

Characterizing ecological relationships between viruses, bacteria and protists in the ocean are critical to understanding ecosystem function, yet these relationships are infrequently investigated together. We evaluated these relationships through microbial association network analysis of samples collected approximately monthly from March 2008 to January 2011 in the surface ocean (0–5 m) at the San Pedro Ocean Time series station. Bacterial, T4-like myoviral and protistan communities were described by Automated Ribosomal Intergenic Spacer Analysis and terminal restriction fragment length polymorphism of the gene encoding the major capsid protein (g23) and 18S ribosomal DNA, respectively. Concurrent shifts in community structure suggested similar timing of responses to environmental and biological parameters. We linked T4-like myoviral, bacterial and protistan operational taxonomic units by local similarity correlations, which were then visualized as association networks. Network links (correlations) potentially represent synergistic and antagonistic relationships such as viral lysis, grazing, competition or other interactions. We found that virus–bacteria relationships were more cross-linked than protist–bacteria relationships, suggestive of increased taxonomic specificity in virus–bacteria relationships. We also found that 80% of bacterial–protist and 74% of bacterial–viral correlations were positive, with the latter suggesting that at monthly and seasonal timescales, viruses may be following their hosts more often than controlling host abundance.     

Protein-mediated electron transfer

The concept of proteins as ‘conducting glassees’ rather than ‘conducting pathways’ is reviewed in the light of recent experimental evidence on biological electron-transfer rates and their dependence on driving force, reorganization energy, and the distance and coupling between partners. The dependence of midpoint potential and reorganization energy on protein dielectric properties is also reviewed.     

The ‘Orsten’—More than a Cambrian Konservat-Lagerstätte yielding exceptional preservation

In several areas of southern Sweden, limestone nodules, locally called Orsten occur within bituminous alum shales. These shales and nodules were deposited under dysoxic conditions at the bottom of what was most likely a shallow sea during the late Middle to Upper Cambrian (ca. 500 million years ago). Subsequently, the name ‘Orsten’ has been referred to particular, mainly arthropod, fossils from such nodules, and, in a wider sense, to the specific type of preservation of minute fossil through secondarily phosphatization. This preservation is exceptional in yielding uncompacted and diagenetically undeformed three-dimensional fossils. ‘Orsten’-type preservation resulted from incrustation of a thin external layer and also by impregnation by calcium phosphate and, therefore, mineralization of the surface of the former animals during early diagenesis. Primarily, this type of preservation seems to have affected only cuticle-bearing metazoans such as cycloneuralian nemathelminths and arthropods. ‘Orsten’ preservation in this sense seems to be limited by size, in having yielded no partial or complete animals larger than 2 mm. On the other end of the scale, even larvae 100 μm long are preserved, often more complete than larger specimens, and details such as setules and pores smaller than 1 μm can be observed. Fossils preserved in such a manner are almost exclusively hollow carcasses, but can be filled secondarily; less common are completely phosphatized compact specimens. The high quality of preservation makes the Swedish ‘Orsten’ a typical Konservat-Lagerstätte. Yet, its special type of preservation is more widespread in time and geographical distribution than assumed initially, and the origin of the phosphate is not necessarily restricted just to one source. Subsequent to the first discoveries of limb fragments of Cambrian arthropods in 1975, animals in this special preservational type have been discovered in several continents and across a broad stratigraphic range including even Proterozoic strata. The latter have yielded early cleavage and metazoan embryonic stages, expanding knowledge on the preservational capacities of the ‘Orsten’. Here, we report the recent status of our research on the ‘Orsten’ and give perspectives for future exploration on a worldwide scale, particularly in light of a recently formed international research group named Center of Orsten Research and Exploration (C.O.R.E.).     

Database design for ecologists: Composing core entities with observations

The ecoinformatics community recognizes that ecological synthesis across studies, space, and time will require new informatics tools and infrastructure. Recent advances have been encouraging, but many problems still face ecologists who manage their own datasets, prepare data for archiving, and search data stores for synthetic research. In this paper, we describe how work by the Canopy Database Project (CDP) might enable use of database technology by field ecologists: increasing the quality of database design, improving data validation, and providing structural and semantic metadata — all of which might improve the quality of data archives and thereby help drive ecological synthesis.The CDP has experimented with conceptual components for database design, templates, to address information technology issues facing ecologists. Templates represent forest structures and observational measurements on these structures. Using our software, researchers select templates to represent their study’s data and can generate normalized relational databases. Information hidden in those databases is used by ancillary tools, including data intake forms and simple data validation, data visualization, and metadata export. The primary question we address in this paper is, which templates are the right templates.We argue for defining simple templates (with relatively few attributes) that describe the domain's major entities, and for coupling those with focused and flexible observation templates. We present a conceptual model for the observation data type, and show how we have implemented the model as an observation entity in the DataBank database designer and generator. We show how our visualization tool CanopyView exploits metadata made explicit by DataBank to help scientists with analysis and synthesis. We conclude by presenting future plans for tools to conduct statistical calculations common to forest ecology and to enhance data mining with DataBank databases.DataBank could be extended to another domain by replacing our forest–ecology-specific templates with those for the new domain. This work extends the basic computer science idea of abstract data types and user-defined types to ecology-specific database design tools for individual users, and applies to ecoinformatics the software engineering innovations of domain-specific languages, software patterns, components, refactoring, and end-user programming.     

The distribution of zinc, cadmium, lead and copper within the hepatopancreas of a woodlouse

The distribution of metals within the hepatopancreas of Oniscus asellus (Crustacea, Isopoda) from two uncontaminated sites, and two sites contaminated with zinc, cadmium and lead, has been studied by atomic absorption spectrophotometry, light microscopy, transmission and scanning electron microscopy and X-ray microanalysis. The hepatopancreas contains two types of intracellular granule. The first type, in the S cells, are spherical granules which contain copper, sulphur and calcium. In woodlice from contaminated sites, these ‘copper’ granules, also contain zinc, cadmium and lead. The second type, in the B cells, are flocculent deposits which contain iron. In woodlice from contaminated sites, these ‘iron’ granules also contain zinc and lead. Moribund woodlice from contaminated sites have large numbers of ‘copper’ and ‘iron’ granules in the hepatopancreas and a fine deposit of zinc and lead on the membranes of the cells. There are numerous microorganisms in close association with the microvillous border of the hepatopancreas of woodlice from all four sites. Within the microorganisms of Oniscus asellus from contaminated sites, there are deposits of material which contain zinc, lead, calcium and phosphorus ‘Copper’ and ‘iron’ granules could have evolved as storage sites for essential metals to be utilized when demand from the body exceeds uptake from the food. Woodlice in contaminated sites may be able to ‘detoxify’ potentially harmful amounts of essential and non-essential metals by storing them in a relatively insoluble form within these granules.