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Coral reefs are under intense pressure from anthropogenically induced climate warming and habitat destruction. It has been suggested that coral reefs in deeper waters may provide a refuge less affected by human development and climate change. Rocha et al. , however, show that shallow and deep reefs are biologically different. Furthermore, deep (or mesophotic) reefs are also suffering from human impacts. Thus, deep reefs do not represent a potential refuge for other reef ecosystems. Indeed, they too are threatened and need protection. Science , this issue p. 281 Deep water reefs will not provide a refuge for shallow reef ecosystems. The rapid degradation of coral reefs is one of the most serious biodiversity problems facing our generation. Mesophotic coral reefs (at depths of 30 to 150 meters) have been widely hypothesized to provide refuge from natural and anthropogenic impacts, a promise for the survival of shallow reefs. The potential role of mesophotic reefs as universal refuges is often highlighted in reef conservation research. This hypothesis rests on two assumptions: (i) that there is considerable overlap in species composition and connectivity between shallow and deep populations and (ii) that deep reefs are less susceptible to anthropogenic and natural impacts than their shallower counterparts. Here we present evidence contradicting these assumptions and argue that mesophotic reefs are distinct, impacted, and in as much need of protection as shallow coral reefs.

Lists of species underpin many fields of human endeavour, but there are currently no universally accepted principles for deciding which biological species should be accepted when there are alternative taxonomic treatments (and, by extension, which scientific names should be applied to those species). As improvements in information technology make it easier to communicate, access, and aggregate biodiversity information, there is a need for a framework that helps taxonomists and the users of taxonomy decide which taxa and names should be used by society whilst continuing to encourage taxonomic research that leads to new species discoveries, new knowledge of species relationships, and the refinement of existing species concepts. Here, we present 10 principles that can underpin such a governance framework, namely (i) the species list must be based on science and free from nontaxonomic considerations and interference, (ii) governance of the species list must aim for community support and use, (iii) all decisions about list composition must be transparent, (iv) the governance of validated lists of species is separate from the governance of the names of taxa, (v) governance of lists of accepted species must not constrain academic freedom, (vi) the set of criteria considered sufficient to recognise species boundaries may appropriately vary between different taxonomic groups but should be consistent when possible, (vii) a global list must balance conflicting needs for currency and stability by having archived versions, (viii) contributors need appropriate recognition, (ix) list content should be traceable, and (x) a global listing process needs both to encompass global diversity and to accommodate local knowledge of that diversity. We conclude by outlining issues that must be resolved if such a system of taxonomic list governance and a unified list of accepted scientific names generated are to be universally adopted.

Modern advances in DNA sequencing hold the promise of facilitating descriptions of new organisms at ever finer precision but have come with challenges as the major Codes of bionomenclature contain poorly defined requirements for species and subspecies diagnoses (henceforth, species diagnoses), which is particularly problematic for DNA-based taxonomy. We, the commissioners of the International Commission on Zoological Nomenclature, advocate a tightening of the definition of “species diagnosis” in future editions of Codes of bionomenclature, for example, through the introduction of requirements for specific information on the character states of differentiating traits in comparison with similar species. Such new provisions would enhance taxonomic standards and ensure that all diagnoses, including DNA-based ones, contain adequate taxonomic context. Our recommendations are intended to spur discussion among biologists, as broad community consensus is critical ahead of the implementation of new editions of the International Code of Zoological Nomenclature and other Codes of bionomenclature.

For more than 250 years, the taxonomic enterprise has remained almost unchanged. Certainly, the tools of the trade have improved: months-long journeys aboard sailing ships have been reduced to hours aboard jet airplanes; advanced technology allows humans to access environments that were once utterly inaccessible; GPS has replaced crude maps; digital hi-resolution imagery provides far more accurate renderings of organisms that even the best commissioned artists of a century ago; and primitive candle-lit microscopes have been replaced by an array of technologies ranging from scanning electron microscopy to DNA sequencing. But the basic paradigm remains the same. Perhaps the most revolutionary change of all - which we are still in the midst of, and which has not yet been fully realized - is the means by which taxonomists manage and communicate the information of their trade. The rapid evolution in recent decades of computer database management software, and of information dissemination via the Internet, have both dramatically improved the potential for streamlining the entire taxonomic process. Unfortunately, the potential still largely exceeds the reality. The vast majority of taxonomic information is either not yet digitized, or digitized in a form that does not allow direct and easy access. Moreover, the information that is easily accessed in digital form is not yet seamlessly interconnected. In an effort to bring reality closer to potential, a loose affiliation of major taxonomic resources, including GBIF, the Encyclopedia of Life, NBII, Catalog of Life, ITIS, IPNI, ICZN, Index Fungorum, and many others have been crafting a \"Global Names Architecture\" (GNA). The intention of the GNA is not to replace any of the existing taxonomic data initiatives, but rather to serve as a dynamic index to interconnect them in a way that streamlines the entire taxonomic enterprise: from gathering specimens in the field, to publication of new taxa and related data.

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.

A nanopublication is the smallest unit of publishable information: a scientifically meaningful assertion about anything that can be uniquely identified and attributed to its author(s) and serve to communicate a single statement, its original source ( provenance ) and citation record ( publication info ) (Mons and Velterop 2009, Kuhn et al. 2021). Nanopublications are fully expressed in both human-readable and machine-interpretable formats and can be cited thorugh their unique URI identifiers (IDs). The development of the concept, formats and use cases of biodiversity-specific nanopublications started back in 2016 (Penev et al. 2016). Recently, Pensoft and Knowledge Pixels created a workflow to publish nanopublications related to a published article (Fig. 1). At its core, the generic biodiversity nanopublication consists of a triple structure with a Subject element, a Relation element, and an Object element. The Subject element refers to a specific organism identified by an Organism ID, or groups of organisms (Taxa, identified by Taxon Concept IDs). Universal Unique Identifiers (UUIDs) are minted for both in all cases, although if the given organism already has an identifier, e.g., from digitised collections or observations, then this identifier can be specified too. The Organism is linked via class membership (rdf:type) to a Taxon Concept, which is identified with another UUID that is minted upon nanopublication creation. The need to mint IDs is due to the fact that Organism or Taxon Concept IDs (which refer to taxon names but also details about their interpretation and use) are not currently available in any comprehensive vocabulary or database. The minted Taxon Concept IDs are further defined by linking them to a Taxon Name ID from Catalogue of Life / ChecklistBank (via a relation called \"has Taxon Name\") and by linking to Taxon Name's concept (interpretation of the name) by a publication's Digital Object Identifier (DOI) or TreatmentBank entry (via a relation called \"used as defined in\"). Apart from assigning a Taxon Concept, the subject organism can optionally be linked to a life cycle stage (based on the Uber-anatomy (UBERON) Ontology) and to occurrence data via Occurrence ID. The Relation element expresses the association between Subject and Object, according to a particular ontology (e.g., Relation Ontology). The Object element may have different formats. In the template “Association between organisms\" the Object has the same structure as the Subject; while in the template “Association between an organism and environment”, the Object is a type of habitat available from the Environment Ontolog (ENVO). In addition to an assertion , a nanopublication has a provenance record (e.g., DOI of the article where the assertion has been published) and the type of evidence entered in the BasisOfRecord field. The publication info always contains the ORCID (Open Researcher and Contributor ID) of the nanopublication's creator, and the timestamp of creation. Another type of nanopublication template annotates an entire article or selected text from it by using the ORCID of the creator as the Subject, the article's DOI as the Object, and the Citation Typing Ontology (CiTO) to express evaluation of the article (e.g., “supports”, “agrees with”, “discusses”). These templates are complemented by free text comments and are available under the Nanopub tab on the article webpages at several Pensoft journals (see example and blog). Nanopublications can also prompt other types of publications, e.g., hypotheses, to become more machine-interpretable, as discussed for invasion biology (Heger et al. 2023).

Three new species of Chromis (Perciformes, Pomacentridae) from the Philippines, collected between 75–150 m depth, are described by a combination of morphological features and their coloration. Chromisgunting sp. n. was found in Batangas and Oriental Mindoro, and differs from its congeners in body depth (2.1–2.2 in SL), and color of adults, light brown, with a silver area on the anterior end and a bilateral black margin along the exterior side of the tail. It is most similar to C.scotochiloptera , with a 5.3% genetic divergence in COI. Chromishangganan sp. n. was found around Lubang Island. Body depth (1.9–2.0 in SL) and adult coloration (yellowish with dark black outer margins on dorsal and anal fins) also separate this species from its congeners. It is most similar to C.pembae , with a 2.5% genetic divergence. Chromisbowesi sp. n. was found in Batangas, and also differs from its congeners by the combination of body depth (1.5–1.6 in SL), and color of adults (brownish grey in the dorsal side to whitish on the ventral side, with alternating dark and light stripes in the sides of body). It is most similar to C.earina , with a 3.6% genetic divergence in COI.

Coral reefs are widely regarded as one of the top science and conservation priorities globally, as previous research has demonstrated that these ecosystems harbor an extraordinary biodiversity, myriad ecosystem services, and are highly vulnerable to human stressors. However, most of this knowledge is derived from studies on nearshore and shallow-water reefs, with coral reef ecosystems remaining virtually unstudied in marine areas beyond national jurisdiction (ABNJ), commonly known as the high seas. We reviewed information on the spatial distribution of reef-building corals throughout their depth range, and compiled a total of 537,782 records, including 116 unique records from ABNJ at depths between 218-5,647 m. The majority of reef-building coral records in ABNJ were in association with geomorphological features that have steep topographies. These habitats, which include escarpments, seamounts, and submarine ridges accounted for >74% of the records in international waters. Such geomorphological features, particularly those that occur within close proximity to the sea surface, should be prioritized for future scientific exploration. The majority of the reef-building coral records in ABNJ (>77%) were recorded in unprotected waters, and this study discusses the challenges and opportunities for protecting marine biodiversity in ABNJ. Finally, this study offers a definition of high seas coral reefs, and provides a framework to better understand and conserve these fragile ecosystems.

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.

Although the existence of coral-reef habitats at depths to 165 m in tropical regions has been known for decades, the richness, diversity, and ecological importance of mesophotic coral ecosystems (MCEs) has only recently become widely acknowledged. During an interdisciplinary effort spanning more than two decades, we characterized the most expansive MCEs ever recorded, with vast macroalgal communities and areas of 100% coral cover between depths of 50–90 m extending for tens of km 2 in the Hawaiian Archipelago. We used a variety of sensors and techniques to establish geophysical characteristics. Biodiversity patterns were established from visual and video observations and collected specimens obtained from submersible, remotely operated vehicles and mixed-gas SCUBA and rebreather dives. Population dynamics based on age, growth and fecundity estimates of selected fish species were obtained from laser-videogrammetry, specimens, and otolith preparations. Trophic dynamics were determined using carbon and nitrogen stable isotopic analyses on more than 750 reef fishes. MCEs are associated with clear water and suitable substrate. In comparison to shallow reefs in the Hawaiian Archipelago, inhabitants of MCEs have lower total diversity, harbor new and unique species, and have higher rates of endemism in fishes. Fish species present in shallow and mesophotic depths have similar population and trophic (except benthic invertivores) structures and high genetic connectivity with lower fecundity at mesophotic depths. MCEs in Hawai‘i are widespread but associated with specific geophysical characteristics. High genetic, ecological and trophic connectivity establish the potential for MCEs to serve as refugia for some species, but our results question the premise that MCEs are more resilient than shallow reefs. We found that endemism within MCEs increases with depth, and our results do not support suggestions of a global faunal break at 60 m. Our findings enhance the scientific foundations for conservation and management of MCEs, and provide a template for future interdisciplinary research on MCEs worldwide.