Taxonomic Concepts Research Articles

Updating splits, lumps, and shuffles: Reconciling GenBank names with standardized avian taxonomies

Abstract Biodiversity research has advanced by testing expectations of ecological and evolutionary hypotheses through the linking of large-scale genetic, distributional, and trait datasets. The rise of molecular systematics over the past 30 years has resulted in a wealth of DNA sequences from around the globe. Yet, advances in molecular systematics also have created taxonomic instability, as new estimates of evolutionary relationships and interpretations of species limits have required widespread scientific name changes. Taxonomic instability, colloquially “splits, lumps, and shuffles,” presents logistical challenges to large-scale biodiversity research because (1) the same species or sets of populations may be listed under different names in different data sources, or (2) the same name may apply to different sets of populations representing different taxonomic concepts. Consequently, distributional and trait data are often difficult to link directly to primary DNA sequence data without extensive and time-consuming curation. Here, we present RANT: Reconciliation of Avian NCBI Taxonomy. RANT applies taxonomic reconciliation to standardize avian taxon names in use in NCBI GenBank, a primary source of genetic data, to a widely used and regularly updated avian taxonomy: eBird/Clements. Of 14,341 avian species/subspecies names in GenBank, 11,031 directly matched an eBird/Clements; these link to more than 6 million nucleotide sequences. For the remaining unmatched avian names in GenBank, we used Avibase’s system of taxonomic concepts, taxonomic descriptions in Cornell’s Birds of the World, and DNA sequence metadata to identify corresponding eBird/Clements names. Reconciled names linked to more than 600,000 nucleotide sequences, ~9% of all avian sequences on GenBank. Nearly 10% of eBird/Clements names had nucleotide sequences listed under 2 or more GenBank names. Our taxonomic reconciliation is a first step towards rigorous and open-source curation of avian GenBank sequences and is available at GitHub, where it can be updated to correspond to future annual eBird/Clements taxonomic updates.

Modeling Taxon Concepts: A new approach to an old problem

Although the biodiversity informatics community has recognized and understood the complexity of modeling information about scientific names and associated taxonomic concepts for more than three decades, many of the original questions and problems remain unresolved today. Because most biodiversity data is anchored to scientific names, and these names are governed by Codes of nomenclature, most effort and progress has focused on data structures centered around scientific names, rather than taxonomic concepts. But, as has been well documented in biodiversity data standards communities (e.g., Berendsohn (1995), Patterson et al. (2010), Pyle et al. (2021)), the relationship between the text-string scientific-name labels and the circumscribed conceptual taxa they are intended to represent is highly imprecise. Many attempts have been made to develop data models to represent taxonomic concepts as discrete, identifiable units to which biodiversity data can be linked. However, none has gained wide-spread adoption, often due to inherent subjective interpretations and the degree of taxonomic expertise required to define and interpret the individual units – aspects that limit their practical scalability. Similarly, previous efforts to develop taxon concept data models conflate properties of circumscription, classification, and nomenclature, resulting in overloaded notions of taxa that quickly become intractable. We describe an approach that mirrors centuries of actual taxonomic practice, rooted in fundamental properties of Code-regulated scientific names, which can leverage sources of existing digital information to represent taxonomic concepts in a highly structured, objective and computable way. It isolates the properties of circumscription from those of classification and nomenclature, but enables algorithmic integration of these three separate facets of taxonomic information using consistent informatic structures.

An Introduction to Scientific Names of Organisms, and the Taxon Concepts they Represent

In many ways, taxonomy and nomenclature lie at the center of all of biodiversity science. Most data concerning biodiversity is given context through scientific names, which follow a basic standard of nomenclature and classification that has endured for more than a quarter of a millennium. This standard has endured not only the test of time, but also major shifts in thinking about biodiversity, such as the revolutionary notion of evolution by natural selection, which were introduced a full century after the standard had been adopted. The system of scientific names now faces a similar paradigm-shifting challenge as the world of science transitions to the age of digitization and DNA sequences. Although most people are familiar with the practice of assigning scientific names to organisms, many are not aware of the history of the practice, the current rules and regulatory bodies for assigning scientific names to organisms, the subtle but important distinctions between “taxonomic names” and “taxonomic concepts” (and the corresponding implications for biodiversity informatics), or the minefield of potential pitfalls surrounding the ambiguous and inconsistent terminology used in associated discussions. From an informatics perspective, there has been a great deal of discussion on the difference between scientific names of organisms, and the taxonomic concepts they are intended to represent. Although in many ways the debates of more than two decades ago continue today, there have been some tangible steps forward, and we may be approaching a moment when the informatics of scientific names and taxon concepts achieves a new level of utility.

Extended Taxonomic Curation: Moving beyond species lists to linking species data

Taxonomy is at the center of modern biodiversity science. No species can be systematically studied until it is defined, and no observation can be linked to related data without a taxonomic label. However, taxonomy is also a science in constant flux—even well-studied groups like Mammalia have fluctuated by >25% in recognized species in the last decade (Burgin et al. 2018, MDD 2022a, MDD 2022b). As a result, there are calls to create a “global list of accepted species” to increase taxonomic stability, particularly for policy decisions in biodiversity conservation and management (Garnett et al. 2020). The counterargument notes that forcing definitional consensus is likely to further inequities, and that a pluralistic, coordinated approach to taxonomy can be achieved with innovative cyberinfrastructure designs and services (Sterner et al. 2020, Franz and Sterner 2018). Here, we propose that digitally “extended” taxonomic curation can play new and innovative roles in linking observational data to alternative taxonomic concepts; and enabling fit-for-use taxonomy to inform policy decisions. linking observational data to alternative taxonomic concepts; and enabling fit-for-use taxonomy to inform policy decisions. Taxonomic curators (TCs) have traditionally limited their activities to making lists of accepted species and higher taxa. However, most of today's biodiversity questions require observational data (e.g., specimen occurrences) that are taxonomically coherent, not just name lists, and for those linked data to be digitally available in public databases. If the collective activities of TCs can be effectively unified across distributed networks, they might facilitate the transition to Extended Specimen Networks of taxonomically coherent biodiversity data, a core goal of current research initiatives (e.g., Lendemer et al. (2020)). Beyond lists of species names is the domain of what names mean in practice (i.e., taxonomic concepts), which often differs by author (Fig. 1). Here we argue that curating the various lines of evidence that represent taxonomic concepts—what we call Species Meaning Artifacts (SMArts)—is a promising strategy for keeping track of how species splits and lumps will affect observational data records in the Global Biodiversity Information Facility (GBIF) or National Center for Biotechnology Information (NCBI). Instead of labeling records by a static name, records can be digitally associated with SMArt evidence from alternative taxonomies (e.g., geographic range maps before/after a species split). Networks of TCs curating digital SMArts will enable 'taxonomically intelligent' data aggregation (Bisby 2000), a long-pursued goal in biodiversity data science that, once realized, promises to enable investigations ranging from viral spillover to biodiversity loss (Upham et al. 2021).

Peningkatan Profesionalisme Guru MGMP Biologi-SMA Kota Jayapura Melalui Pelatihan Aplikasi Taksonomi Numerik

Biology practicum activities in high school generally follow the cookbook method. The method contains a practicum manual that contains complete information on the sequence of practicum procedures that must be carried out by students. In addition, this method may cause student boredom and is also less challenging, less inspiring, and motivational to develop investigative skills. Therefore, a Biology teacher is required to innovate in developing inspiring teaching methods. To support these Biology teachers, they need to be equipped with knowledge and skills through courses or training with the material in the curriculum so that they can master the concepts of knowledge that are more up to date. This training activity aims to guide high school Biology MGMP teachers in designing and making learning innovations in Biodiversity material and to train them in applying numerical taxonomy concepts to Biodiversity material in the classroom. The method of activity used is direct observation and practice in the field by utilizing samples of fungi, plants, or animals in the surrounding environment. The teachers made and observed several herbarium specimens to obtain the morphological characters of these specimens. Furthermore, they have applied the concept of numerical taxonomy manually or by using the NTSYS-Program software. The final result of this activity has been composed of two modules and one numerical taxonomy practicum guide that can be used by Biology teachers and students.Keyword: Biology; numerical; taxonomy; training; teachers.Â

Priabonian non-geniculate coralline algae from the Central Carpathian Paleogene Basin

Encrusting coralline algae are important rock-building organisms of the lower Priabonian limestones from the Central Carpathian Paleogene Basin. Despite the effort of early palaeontologists, former classifications lacked many diagnostic characteristics and modern taxonomic concepts, which hinders their use for modern palaeontological interpretations. The situation is further complicated as recent DNA analyses of extant coralline algae highlight the limits of the morpho-anatomical classification and identify many coralline algal genera which can also be recognized in the fossil record. Because palaeontology deals exclusively with the morpho-anatomical characteristics, a synthesis of the new discoveries in molecular phylogenetic analyses with morphology-based palaeontological classifications is necessary. Our palaeontological study based on published investigations on coralline molecular genetics enabled: 1) the identification of seventeen coralline algal morphological species grouped in six genera: Sporolithon lugeonii, Sporolithon nummuliticum, Sporolithon sp. 1, Sporolithon sp. 2, Lithothamnion camarasae, Lithothamnion cf. corallioides, Lithothamnion prascoi, Lithothamnion cf. ramosissimum, Lithothamnion roveretoi, Lithothamnion sp., Phymatolithon sp., Mesophyllum fructiferum, Mesophyllum cf. engelhartii, Mesophyllum sp., Chamberlainium lemoinei, Lithoporella melobesioides, and Lithoporella cf. minus ; 2) the description of Chamberlainium lemoinei (Miranda) comb. nov. known from the Bartonian, and 3) the identification of a unique encrusting coralline alga tentatively assigned to the genus Lithothamnion.

Adapting mark-recapture methods to estimating accepted species-level diversity: a case study with terrestrial Gastropoda.

We introduce a new method of estimating accepted species diversity by adapting mark-recapture methods to comparisons of taxonomic databases. A taxonomic database should become more complete over time, so the error bar on an estimate of its completeness and the known diversity of the taxon it treats will decrease. Independent databases can be correlated, so we use the time course of estimates comparing them to understand the effect of correlation. If a later estimate is significantly larger than an earlier one, the databases are positively correlated, if it is significantly smaller, they are negatively correlated, and if the estimate remains roughly constant, then the correlations have averaged out. We tested this method by estimating how complete MolluscaBase is for accepted names of terrestrial gastropods. Using random samples of names from an independent database, we determined whether each name led to a name accepted in MolluscaBase. A sample tested in August 2020 found that 16.7% of tested names were missing; one in July 2021 found 5.3% missing. MolluscaBase grew by almost 3,000 accepted species during this period, reaching 27,050 species. The estimates ranged from 28,409 ± 365 in 2021 to 29,063 ± 771 in 2020. All estimates had overlapping 95% confidence intervals, indicating that correlations between the databases did not cause significant problems. Uncertainty beyond sampling error added 475 ± 430 species, so our estimate for accepted terrestrial gastropods species at the end of 2021 is 28,895 ± 630 species. This estimate is more than 4,000 species higher than previous ones. The estimate does not account for ongoing flux of species into and out of synonymy, new discoveries, or changing taxonomic methods and concepts. The species naming curve for terrestrial gastropods is still far from reaching an asymptote, and combined with the additional uncertainties, this means that predicting how many more species might ultimately be recognized is presently not feasible. Our methods can be applied to estimate the total number of names of Recent mollusks (as opposed to names currently accepted), the known diversity of fossil mollusks, and known diversity in other phyla.

Genomic insights into recent species divergence in Nicotiana benthamiana and natural variation in Rdr1 gene controlling viral susceptibility.

SUMMARYOne of the most commonly encountered and frequently cited laboratory organisms worldwide is classified taxonomically as Nicotiana benthamiana (Solanaceae), an accession of which, typically referred to as LAB, is renowned for its unique susceptibility to a wide range of plant viruses and hence capacity to be transformed using a variety of methods. This susceptibility is the result of an insertion and consequent loss of function in the RNA‐dependent RNA polymerase 1 (Rdr1) gene. However, the origin and age of LAB and the evolution of N. benthamiana across its wide distribution in Australia remain relatively underexplored. Here, we have used multispecies coalescent methods on genome‐wide single nucleotide polymorphisms (SNPs) to assess species limits, phylogenetic relationships and divergence times within N. benthamiana. Our results show that the previous taxonomic concept of this species in fact comprises five geographically, morphologically and genetically distinct species, one of which includes LAB. We provide clear evidence that LAB is closely related to accessions collected further north in the Northern Territory; this species split much earlier, c. 1.1 million years ago, from their common ancestor than the other four in this clade and is morphologically the most distinctive. We also found that the Rdr1 gene insertion is variable among accessions from the northern portions of the Northern Territory. Furthermore, this long‐isolated species typically grows in sheltered sites in subtropical/tropical monsoon areas of northern Australia, contradicting the previously advanced hypothesis that this species is an extremophile that has traded viral resistance for precocious development.

The nature of dispersal barriers and their impact on regional species pool richness and turnover

AbstractAimWe document realized and potential global species ranges based on empirically vetted species concepts in conjunction with global climate databases and climate suitability modelling. From this we investigate the nature of dispersal barriers and illustrate how they generate ecological uniqueness.LocationHolarctic.MethodsFifty‐two small body‐size (i.e. < 5 mm) land snail taxa within the genera Euconulus, Pupilla and Vertigo were considered. These represent ~10% of all small body‐size Holarctic land snails and are among the most proficient known passive dispersers. Their potential climatic ranges were determined using Maxent modelling based on 9205 occurrence records. From these we inferred the location, width and nature of isolating barriers and tested for their effects on regional species pool richness and turnover.ResultsUse of unvetted traditional taxonomic concepts and unverified occurrence records would have created up to threefold higher or lower estimates of species‐specific climatic tolerances than the actual values. Modelling must thus only use high quality occurrence data. All but one taxon were shown at a global scale to possess multiple isolated areas of appropriate climate. While oceans represented the most common barrier (37%), intra‐continental barriers were in total almost twice as frequent (inappropriate climate – 29%, habitat/history – 27% and the Greenland ice sheet – 7%). These barriers restricted taxa to only a subset of their potential range, with European taxa possessing approximately twice the global occupancy rates as North American ones (median scores of 62 vs. 34%). As a result, regional taxa pools were three times smaller than their potential sizes, with 50% change in composition occurring over ~2600‐km distances.Main conclusionsEven for these readily dispersing taxa, isolation barriers prevented species from saturating their potential global range, reduced the size of regional species pools by 2/3, and generated ecological uniqueness between them.

The nature of innovation in hospital building design: a mixed grounded theory study

PurposeDespite the undeniable need for innovation in hospital building design, the literature highlights the disconnect between research and practice as the primary knowledge gap hindering such innovation. This study shows this focus to be an oversimplification, for the complex processes that trigger design innovations and impact their ecosystems need to be examined from a systemic perspective. This paper aims to conceptualise the evolution of hospital building design and identify and explain the main factors triggering design and construction innovations over the past 100 years.Design/methodology/approachA novel hybrid research design to mixed grounded theory (MGT) methodology, with Charmaz constructivist paradigm, is developed as a new systematic way of constructing and interpreting the concepts and interconnections among them that triggered design innovation.FindingsThis study represents a taxonomy of concepts and an explanatory innovation framework, containing 617 interconnections between 146 factors classified across 14 categories. The complex innovation ecosystem comprises multi-faceted processes between heterogenous factors with both individual and collective impacts on design innovations.Originality/valueThis research highlights the main components of the innovation ecosystem and its overall behaviour in this field, and the most influential and interrelated contextual factors, as well as representing and mapping generative interactions that support innovation processes. This knowledge can help hospital researchers, designers, policymakers and stakeholders adopt a multidimensional outlook to analyse the strength of all influential factors, introduce potential novel ways of collaborating, conceptualise an organisational approach, re-formulate research questions through transdisciplinary methods and introduce interdisciplinary courses and programs in architecture schools, thereby contributing to timely design innovation.

Five New Species of Fissidens Hedw. (Fissidentaceae, Bryophyta), Taxonomic Notes and a New Species Record for South Africa

In this paper, three topics concerning the genus Fissidens Hedw. are addressed. Firstly, description of five new species of the genus, viz. the Malagasy Fissidens arboricola Brugg.-Nann. and F. granulidens Brugg.-Nann., the Mauritian F. papillisetus Brugg.-Nann., the Tanzanian F. rotundifolius Brugg.-Nann. and the Brazilian F. pseudoscindulatus Brugg.-Nann. All five belong to F. subgen. Polypodiopsis (Müll. Hal.) Broth. sect. Antennidens (Müll.Hal.) Paris, are corticolous and have anomalous peristomes. Secondly, taxonomic studies revealed that F. subgen. Aloma (Kindb.) Pursell & Brugg.-Nann. is subsumed under F. subgen. Polypodiopsis (Müll.Hal.) Broth. and F. sect. Semilimbidium Müll.Hal. under sect. Antennidens (Müll.Hal.) Paris and their names are considered new synonyms of the names of the respective infrageneric taxa. Fissidens jonesii Bizot ex Pócs, previously considered conspecific with F. lagenarius Mitt. is re-instated as a good species, described, illustrated and compared to F. lagenarius. Thirdly, Fissidens lagenarius is newly recorded for the Republic of South Africa and its African distribution is amended and updated, with consideration of the revised taxonomic concept of F. jonesii.

New insights into the Barremian–lower Aptian calcareous nannofossils of the Mediterranean Tethys: Chronostratigraphic and paleobiogeographic implications

A detailed study of calcareous nannofossil assemblages from twelve uppermost lower Barremian–lower Aptian sections in the Subbetic Domain of the Betic Cordillera was performed. Seven new nannofossil species (Crucibiscutum bastetanum, Crucibiscutum gracile, Chiastozygus lamprostauros, Cyclagelosphaera platyaspis, Lithraphidites aichmoides, Lithraphidites pugio, and Rhagodiscus sicutclipeus) are described, one species is emended (Lithraphidites magnus) and the taxonomic concept of the marker species Hayesites irregularis is discussed and clarified. The detailed stratigraphic ranges of the new species, together with those of other relevant taxa, are determined and correlated to standard ammonite biostratigraphy. Age estimates of biostratigraphically relevant calcareous nannofossil biohorizons are calculated using astrochronologically tuned cyclostratigraphic data. Five new calcareous nannofossil subzones are proposed which enhance upper Barremian biostratigraphic resolution at a regional scale and are directly correlated with respect to the standard Tethyan ammonite zonation. Two of the new species described here are used as biostratigraphic markers for the newly proposed subzones. The duration of each subzone is provided through astrochronological calibration. This study allows the refinement of the calcareous nannofossil zonation for the Mediterranean–Atlantic province of the Tethyan Realm. The implications of these new results are discussed regarding the extant definition and use of the Barremian/Aptian boundary. The morpho-evolutionary trends of selected nannofossil groups are reviewed in relation to the latest Barremian–Aptian paleogeographic changes, showing these were a prominent factor controlling calcareous nannoplankton evolution and biogeographical distribution in the west European-Atlantic region.

Developing a National Trauma Research Action Plan: Results from the Pediatric Research Gap Delphi Survey.

In 2016, the National Academies of Sciences, Engineering, and Medicine trauma report recommended a National Trauma Research Action Plan to "strengthen trauma research and ensure that the resources available for this research are commensurate with the importance of injury and the potential for improvement in patient outcomes." With a contract from the Department of Defense, the Coalition for National Trauma Research created 11 expert panels to address this recommendation, with the goal of developing a comprehensive research agenda, spanning the continuum of trauma and burn care. This report outlines the work of the group focused on pediatric trauma. Experts in pediatric trauma clinical care and research were recruited to identify gaps in current clinical pediatric trauma research, generate research questions, and establish the priority of these questions using a consensus-driven Delphi survey approach. Using successive surveys, participants were asked to rank the priority of each research question on a 9-point Likert scale categorized to represent priority. Consensus was defined as >60% agreement within the priority category. Priority questions were coded based on a dictionary of 118 National Trauma Research Action Plan taxonomy concepts in 9 categories to support comparative analysis across all panels. Thirty-seven subject matter experts generated 625 questions. A total of 493 questions (79%) reached consensus on priority level. Of those reaching consensus, 159 (32%) were high, 325 (66%) were medium, and 9 (2%) were low priority. The highest priority research questions related to surgical interventions for traumatic brain injury (intracranial pressure monitoring and craniotomy); the second highest priority was hemorrhagic shock. The prehospital setting was the highest priority phase of care. This diverse panel of experts determined that most significant pediatric trauma research gaps were in traumatic brain injury, hemorrhagic shock, and the prehospital phase of care. These research domains should be top priorities for funding agencies. Therapeutic / Care Management; Level IV.

The impact of empirically unverified taxonomic concepts on ecological assemblage patterns across multiple spatial scales

Accurate ecological assemblage analysis requires that underlying taxonomic divisions reflect biological reality. However, the validity of many taxonomic hypotheses have never been rigorously confronted with replicable data. As a result, these categories might say more about human psychology than biology. We consider here the ways that statistically unchallenged taxonomic concepts can bias observed ecological pattern across multiple spatial scales. We compared assemblage lists for a group of Holarctic land snail species/subspecies hypotheses both before and after empirical confrontation. Of the 124 taxa initially believed to exist, only 105 were validated, with 34 being oversplit, another 15 being incorrectly lumped within 11 taxa and a final 33 having incorrect identification features. This led to considerable scale‐dependent alteration in assemblage patterns across 2528 sites within 42 regions and 9 biogeographic zones: depending upon location up to 90% of sites had revised composition with 10% showing a reduction in richness. Additionally, 6–60% of site pairs had altered turnover. These impacts became larger and more frequent with increasing sample grain and extent: 80–90% of regions and 100% of global biogeographic zones demonstrated altered composition, with 70–80% of regions and 100% of zones having changed richness. Reductions in richness also became more prevalent with increasing scale. Likewise, 80–94% of regional and zone pairs were found to have altered turnover, with increased similarity predominating at small and decreased similarity at large extents. Because these issues appear general and are not limited to land snail taxonomy, it is crucial for macroecologists to consider how unchallenged taxonomic concepts might bias their results. The use of objective and replicable data‐driven validation of all recognized taxonomic concepts is thus an essential foundation for accurate ecological hypothesis testing.

Re-discovery of the type series of the Indian freshwater mussel Parreysia corrugata (O. F. Müller, 1774) with the designation of the lectotype (Bivalvia: Unionidae: Parreysiinae)

ABSTRACT India represents a tropical biodiversity hotspot, harbouring a unique and largely endemic fauna of freshwater mussels (Bivalvia: Unionidae). Unfortunately, the type series of many freshwater mussel taxa historically described from this country are thought to be lost. Here, we report on the rediscovery of the type series of Parreysia corrugata (O.F Müller, 1774) (Parreysiinae: Parreysiini) in the Natural History Museum of Denmark (NHMD), Copenhagen. It contains four syntypes (complete shells), which were examined by means of morphological and geometric morphometric techniques. We show that the nominal taxon Parreysia corrugata was established based on a composite type series, because one of the syntypes belongs to another species, Potomida semirugata (Lamarck, 1819) (Gonideinae: Lamprotulini), originating from the Middle East. To fix the taxonomic identity of the Indian species, a syntype (lot NHMD 916309) that was most likely illustrated by O.F. Müller in 1779 is designated here as the lectotype of Parreysia corrugata. The lectotype, paralectotypes and corresponding labels are illustrated in detail. Our new findings clarify the taxonomic concept of Parreysia corrugata and contribute to the further development of the Indian Unionidae taxonomy. http://www.zoobank.org/urn:lsid:zoobank.org:pub:AD4E3637-66BC-4C48-BCC6-2E910451CB89

DEVELOPING BEST PRACTICE IN MICROPALAEONTOLOGY: EXAMPLES FROM THE MID-CRETACEOUS OF THE ZAGROS MOUNTAINS

Micropalaeontological studies can provide important information on how strata correlate, age calibration, palaeoenvironmental determination, palaeobiology, evolutionary relationships of the taxa being studied, palaeogeography, and the recognition of global or regional geological events in a local succession. However, the value of micropalaeontological studies is constrained by the accuracy with which taxa are identified, the accuracy of their age interpretation, and the use of up-to-date taxonomic concepts, supported by modern research literature. Best practice implies attention to these and other details, which we illustrate with reference to published research on larger benthic foraminifera (especially orbitolinids) from the mid-Cretaceous succession of the Zagros Mountains in the Middle East. It is demonstrated that whilst there are many excellent studies, a significant number could offer more value if they were to use precise, modern taxonomic concepts applied to well-illustrated and documented unequivocal material. Poorly founded age assignments and misidentifications can lead to confusion on assessment of true stratigraphic ranges and evolutionary patterns. Moreover, they can lead to miscorrelation and erroneous modelling of the subsurface in a hydrocarbon-rich region. Integrated studies of larger benthic foraminifera with other age-diagnostic fossil groups or chemostratigraphic methods would further enhance their utility. These recommendations are applicable to micropalaeontological studies on microfossils of any type and age, from any part of the world, but we hope will promote additional rigour in studies on the micropalaeontology of the Mesozoic and Cenozoic succession of the Zagros that still have much to impart.

Cognition in Software Engineering: A Taxonomy and Survey of a Half-Century of Research

Cognition plays a fundamental role in most software engineering activities. This article provides a taxonomy of cognitive concepts and a survey of the literature since the beginning of the Software Engineering discipline. The taxonomy comprises the top-level concepts of perception, attention, memory, cognitive load, reasoning, cognitive biases, knowledge, social cognition, cognitive control, and errors, and procedures to assess them both qualitatively and quantitatively. The taxonomy provides a useful tool to filter existing studies, classify new studies, and support researchers in getting familiar with a (sub) area. In the literature survey, we systematically collected and analysed 311 scientific papers spanning five decades and classified them using the cognitive concepts from the taxonomy. Our analysis shows that the most developed areas of research correspond to the four life-cycle stages, software requirements, design, construction, and maintenance. Most research is quantitative and focuses on knowledge, cognitive load, memory, and reasoning. Overall, the state of the art appears fragmented when viewed from the perspective of cognition. There is a lack of use of cognitive concepts that would represent a coherent picture of the cognitive processes active in specific tasks. Accordingly, we discuss the research gap in each cognitive concept and provide recommendations for future research.

Diversity in sociotechnical machine learning systems

There has been a surge of recent interest in sociocultural diversity in machine learning research. Currently, however, there is a gap between discussions of measures and benefits of diversity in machine learning, on the one hand, and the broader research on the underlying concepts of diversity and the precise mechanisms of its functional benefits, on the other. This gap is problematic because diversity is not a monolithic concept. Rather, different concepts of diversity are based on distinct rationales that should inform how we measure diversity in a given context. Similarly, the lack of specificity about the precise mechanisms underpinning diversity’s potential benefits can result in uninformative generalities, invalid experimental designs, and illicit interpretations of findings. In this work, we draw on research in philosophy, psychology, and social and organizational sciences to make three contributions: First, we introduce a taxonomy of different diversity concepts from philosophy of science, and explicate the distinct epistemic and political rationales underlying these concepts. Second, we provide an overview of mechanisms by which diversity can benefit group performance. Third, we situate these taxonomies of concepts and mechanisms in the lifecycle of sociotechnical machine learning systems and make a case for their usefulness in fair and accountable machine learning. We do so by illustrating how they clarify the discourse around diversity in the context of machine learning systems, promote the formulation of more precise research questions about diversity’s impact, and provide conceptual tools to further advance research and practice.

Open Research Data in the Open Science Ecosystem and Business Environment

Today, one can observe shifts in the research landscape, which is formed by digitization and open science principles. The open science movement continues to gain momentum, attention and debate. In parallel with the principle of unity, open science gives rise to a taxonomy of several related ideas, guidelines and concepts, such as open access, open replicable research and open data. Over the past fifteen years, research institutions have focused on open access to publications. However, recently the focus of attention has shifted to research data as a “new currency” in research activities and their distribution in open access, and the guiding principles of data management are becoming crucial for the wide implementation of open science practices and the effective use of data in research, industry, business and other sectors of the economy. In this context, it is relevant to carry out a thorough study of primary scientific works on open science issues and to study the role of the concept of “open research data” in the paradigm of a holistic ecosystem of open science and business ecosystem. In this work, it is proposed to use the methods of quantitative and qualitative bibliometric analysis, which allows to identify the main trends and form the basis for further research. The information base for this work was the international scientometric database Scopus, which enables to analyze bibliographic data using built-in tools and import them for external use in the VOSviewer software. The study revealed an increasing trend in the number of publications on the subject under study, with the highest annual growth rate in 2017 (76%) and 2019 (66%). Qualitative bibliographic analysis made it possible to analyze the most cited and, therefore, trending works on the selected topic. In terms of the number of citations per year, the results show that the studies with such directions in open science as open program code (open source); data/research reproducibility, research data management; open access to publications (open access) are most popular. In addition, a cluster analysis of the co-prevalence of keywords was conducted. It formed clusters dedicated to both institutional and infrastructural problems of the development of open science and research data. Separately, the results of the analysis create a scientific basis for further research into the key determinants of the effectiveness of the implementation of a proper research data management system at the micro, meso, and macro levels. It will improve the effectiveness of the implementation of scientific developments from one field of knowledge to another, while achieving increased interdisciplinary research. In parallel with this, interested persons of the real sector of the economy get the opportunity to analyze scientific results, determining the possibility of their adoption in their own activities.

Open Research Data in the Open Science Ecosystem and Business Environment

Today, one can observe shifts in the research landscape, which is formed by digitization and open science principles. The open science movement continues to gain momentum, attention and debate. In parallel with the principle of unity, open science gives rise to a taxonomy of several related ideas, guidelines and concepts, such as open access, open replicable research and open data. Over the past fifteen years, research institutions have focused on open access to publications. However, recently the focus of attention has shifted to research data as a “new currency” in research activities and their distribution in open access, and the guiding principles of data management are becoming crucial for the wide implementation of open science practices and the effective use of data in research, industry, business and other sectors of the economy. In this context, it is relevant to carry out a thorough study of primary scientific works on open science issues and to study the role of the concept of “open research data” in the paradigm of a holistic ecosystem of open science and business ecosystem. In this work, it is proposed to use the methods of quantitative and qualitative bibliometric analysis, which allows to identify the main trends and form the basis for further research. The information base for this work was the international scientometric database Scopus, which enables to analyze bibliographic data using built-in tools and import them for external use in the VOSviewer software. The study revealed an increasing trend in the number of publications on the subject under study, with the highest annual growth rate in 2017 (76%) and 2019 (66%). Qualitative bibliographic analysis made it possible to analyze the most cited and, therefore, trending works on the selected topic. In terms of the number of citations per year, the results show that the studies with such directions in open science as open program code (open source); data/research reproducibility, research data management; open access to publications (open access) are most popular. In addition, a cluster analysis of the co-prevalence of keywords was conducted. It formed clusters dedicated to both institutional and infrastructural problems of the development of open science and research data. Separately, the results of the analysis create a scientific basis for further research into the key determinants of the effectiveness of the implementation of a proper research data management system at the micro, meso, and macro levels. It will improve the effectiveness of the implementation of scientific developments from one field of knowledge to another, while achieving increased interdisciplinary research. In parallel with this, interested persons of the real sector of the economy get the opportunity to analyze scientific results, determining the possibility of their adoption in their own activities.