Taxonomic Standards Research Articles

Improved thermal preferences and a stressor index derived from modeled stream temperatures and regional taxonomic standards for freshwater macroinvertebrates of the Pacific Northwest, USA

Benthic macroinvertebrate taxa vary in their sensitivities to water quality and habitat conditions, contributing to their extensive use as ecological indicators. As climate change and landscape alteration increasingly impact stream temperatures, interest is growing in expanding our knowledge of how macroinvertebrates are affected by current and future thermal conditions. Using samples from 3501 sites, we evaluated relationships between macroinvertebrate taxa and modeled stream temperatures across Oregon and Washington, in the U.S. Pacific Northwest. We used Maximum Weekly Maximum Temperature (MWMT) values from the NorWeST temperature dataset, which is the same metric used for numeric water temperature standards in Oregon and Washington. MWMT captures peak thermal stress, when cold-water adapted aquatic biota are closest to their upper physiological limits. For each macroinvertebrate taxon, we characterized relationships between MWMT and their distributions with three measures: 1) central thermal tendency, based on weighted average (WA) optima calculations and relative abundance data; 2) lower and upper thermal limits, based on the 10th and 90th percentiles of taxon occurrence, using presence data; and 3) thermal sensitivity curve shape, based on Generalized Additive Model (GAM) plots. We assigned 521 taxa, from species to phyla, to seven thermal preference categories, ranging from cold and warm stenotherms (narrow range) to eurythermal (wide range). Thermal sensitivity and variability within each taxonomic group were identified for establishing taxonomic targets for regional monitoring programs. We also developed the Macroinvertebrate Thermal Tolerance Index (MTTI) to represent the assemblage-level response to available thermal habitats, using WA optima and relative abundances for 324 taxa. The MTTI model had a strong relationship with modeled temperatures (R2 = 0.68) and a root-mean-square-error of 2.5 °C. Our work builds on previous regional and national efforts to identify thermal indicator taxa by using modeled stream network temperatures and a thermal metric that corresponds directly to regional water temperature standards. Both the taxa thermal preferences and the MTTI can be used to help identify causes of biological impairment, prioritize restoration and protection actions, and monitor assemblage-wide changes in thermal tolerance over time.

Tightening the requirements for species diagnoses would help integrate DNA-based descriptions in taxonomic practice.

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.

BENFEP: a quantitative database of benthic foraminifera from surface sediments of the eastern Pacific

Abstract. Benthic foraminifera are important components of the ocean benthos and play a major role in ocean biogeochemistry and ecosystem functioning. Generating ecological baselines for ocean monitoring or biogeographical distributions requires a reference dataset of recent census data. Moreover, the information from their modern biogeography can be used to interpret past environmental changes on the seafloor. In this study, we provide the first comprehensive quantitative benthic foraminifera database from surface sediments of the eastern Pacific (BENFEP). Through the collation of archival quantitative data on species abundance and their homogenization according to the most recent taxonomic standards, we are able to provide a database with 3077 sediment samples, corresponding to 2509 georeferenced stations of wide geographical (60∘ N–54∘ S) and water depth (0–7280 m) coverage. The quantitative data include living, dead, and living plus dead assemblages obtained from 50 published and unpublished documents. As well as describing the data collection and subsequent harmonization steps, we provide summarized information on metadata, examples of species' distributions, potential applications of the database, and recommendations for data archiving and publication of benthic foraminiferal data. The database is enriched with meaningful metadata for accessible data management and exploration with R software and geographical information systems. The first version of the database (BENFEP_v1, Diz et al., 2022a, https://doi.org/10.1594/PANGAEA.947086) is provided in short and long format, and it will be upgraded with new entries and when changes are needed to accommodate taxonomic revisions.

IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata.

Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration of the global virosphere, progressively revealing the extensive genomic diversity of viruses on Earth and highlighting the myriad of ways by which viruses impact biological processes. IMG/VR provides access to the largest collection of viral sequences obtained from (meta)genomes, along with functional annotation and rich metadata. A web interface enables users to efficiently browse and search viruses based on genome features and/or sequence similarity. Here, we present the fourth version of IMG/VR, composed of >15 million virus genomes and genome fragments, a≈6-fold increase in size compared to the previous version. These clustered into 8.7 million viral operational taxonomic units, including 231 408 with at least one high-quality representative. Viral sequences in IMG/VR are now systematically identified from genomes, metagenomes, and metatranscriptomes using a new detection approach (geNomad), and IMG standard annotation are complemented with genome quality estimation using CheckV, taxonomic classification reflecting the latest taxonomic standards, and microbial host taxonomy prediction. IMG/VR v4 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.

An assessment of terminology for intraspecific diversity in fishes, with a focus on "ecotypes" and "life histories".

Understanding and preserving intraspecific diversity (ISD) is important for species conservation. However, ISD units do not have taxonomic standards and are not universally recognized. The terminology used to describe ISD is varied and often used ambiguously. We compared definitions of terms used to describe ISD with use in recent studies of three fish taxa: sticklebacks (Gasterosteidae), Pacific salmon and trout (Oncorhynchus spp., “PST”), and lampreys (Petromyzontiformes). Life history describes the phenotypic responses of organisms to environments and includes biological parameters that affect population growth or decline. Life‐history pathway(s) are the result of different organismal routes of development that can result in different life histories. These terms can be used to describe recognizable life‐history traits. Life history is generally used in organismal‐ and ecology‐based journals. The terms paired species/species pairs have been used to describe two different phenotypes, whereas in some species and situations a continuum of phenotypes may be expressed. Our review revealed overlapping definitions for race and subspecies, and subspecies and ecotypes. Ecotypes are genotypic adaptations to particular environments, and this term is often used in genetic‐ and evolution‐based journals. “Satellite species” is used for situations in which a parasitic lamprey yields two or more derived, nonparasitic lamprey species. Designatable Units, Evolutionary Significant Units (ESUs), and Distinct Population Segments (DPS) are used by some governments to classify ISD of vertebrate species within distinct and evolutionary significant criteria. In situations where the genetic or life‐history components of ISD are not well understood, a conservative approach would be to call them phenotypes.

Species concepts of Dothideomycetes: classification, phylogenetic inconsistencies and taxonomic standardization

Species concepts of Dothideomycetes: classification, phylogenetic inconsistencies and taxonomic standardization

Redescription of Promecostethus unifalculatus, the only known harvestman from Crozet Islands (Opiliones: Triaenonychidae).

Promecostethus unifalculatus Enderlein, 1909, is the only representative of the order Opiliones from the Crozet Islands. The species belongs to the family Triaenonychidae and is biogeographically interesting because it is a candidate for transoceanic dispersal, a very rare event in this ancient family. Despite this significance, P. unifalculatus is taxonomically still poorly known, and a redescription of this species using modern taxonomic standards is urgently needed. Here we redescribe the species, offer the first description and illustrations of the male genitalia and provide a full exomorphological survey of the species using scanning electron microscopy. Furthermore, we provide an emended diagnosis for the genus Promecostethus and discuss its relationship with some morphologically similar genera.

The correlation of Azerbaijan arid soils with WRB-2014

The geographical principles are used in grouping of the soils the highest taxonomic standards in the soviet soil scientists works concerning the classification. But the Azerbaijan soil classification is based on genetic profile. Traditionally – topographic, color, climate and so on names are used in this classification, which in the soils genetic types idea is assumed as a basis. The International classification system is identified on the basis of the diagnostic parameters in the field researches and specified as a result of the laboratory analyses. The Azerbaijan soil classification consists of eight taxonomic level and a high taxonomic level is considered- soil class, section, genetic soil type, low soil taxa - soil gender, sort, diversity, row, soil variants. Mainly used central taxon is soil type. An aim of the research is to determine correlative chances of WRB-2015 International soil classification system with the Azerbaijan soil classification. It was detected that a correlation of both soil classifications is possible. The correlation is taken place in different taxon levels. Therefore, the soils were analysed at a type and subtype standard besides high taxas when the soils were correlated. As a result of correlation, it was defined that irrigated meadow-grey soils should be correlated Anthrosols, but meadow-grey soils concerned Calcisols and Gleysols.

Two genes involved in clindamycin resistance of Bacillus licheniformis and Bacillus paralicheniformis identified by comparative genomic analysis.

We evaluated the minimum inhibitory concentrations of clindamycin and erythromycin toward 98 Bacillus licheniformis strains isolated from several types of fermented soybean foods manufactured in several districts of Korea. First, based on recent taxonomic standards for bacteria, the 98 strains were separated into 74 B. licheniformis strains and 24 B. paralicheniformis strains. Both species exhibited profiles of erythromycin resistance as an acquired characteristic. B. licheniformis strains exhibited acquired clindamycin resistance, while B. paralicheniformis strains showed unimodal clindamycin resistance, indicating an intrinsic characteristic. Comparative genomic analysis of five strains showing three different patterns of clindamycin and erythromycin resistance identified 23S rRNA (adenine 2058-N6)-dimethyltransferase gene ermC and spermidine acetyltransferase gene speG as candidates potentially involved in clindamycin resistance. Functional analysis of these genes using B. subtilis as a host showed that ermC contributes to cross-resistance to clindamycin and erythromycin, and speG confers resistance to clindamycin. ermC is located in the chromosomes of strains showing clindamycin and erythromycin resistance and no transposable element was identified in its flanking regions. The acquisition of ermC might be attributable to a homologous recombination. speG was identified in not only the five genome-analyzed strains but also eight strains randomly selected from the 98 test strains, and deletions in the structural gene or putative promoter region caused clindamycin sensitivity, which supports the finding that the clindamycin resistance of Bacillus species is an intrinsic property.

Birds of the World: A global reference for avian life histories and a case study of incompatible taxonomies

Life history accounts and taxonomic monographs are a series of publications covering a higher taxonomic group where each account is a compilation of existing knowledge detailing many aspects of a species life history. These life history accounts are extensively used by researchers, ornithologists and conservationists as a main source for the current state of knowledge of a species. Birds, being one of the more easily seen and studied taxa, have a number of specialized life history accounts where data from a wide variety of disciplines are combined into a single easily accessible resource. The Cornell Lab of Ornithology (CLO) currently manages two of these series focused on different regions of the world, Birds of North America (BNA) and Neotropical Birds (NB). Lynx Edicions has published the Handbook of Birds of the World (HBW), an extensive set of avian monographs covering every species of bird in the world. A recently announced collaboration between CLO and Lynx Edicions provides us with the opportunity to bring together the extreme detail of the life history accounts from Birds of North America with the global coverage of HBW to produce a global, in-depth treatment of every species of bird in the world. The integration of life history information from these existing projects with different underlying taxonomies presents a variety of real-world examples of the challenges to be overcome to bring these life history accounts into alignment and provide the scientific and lay communities with taxonomically accurate and up to date information. The Handbook of Birds of the World currently follows the HBW and BirdLife Taxonomic Checklist v3 (with 11,126 species recognized) while Birds of North America and Neotropical Birds both follow the eBird/Clements checklist of birds of the world: v2018 (with 10,585 species recognized). Of the roughly 11,000 species of birds, nearly 9,500 are direct matches between HBW/BirdLife and Clements at the species or species to subspecies levels. The remaining concept mismatches fall into several basic categories including lump and split differences as well as differences in which subspecies are included or excluded. In this talk we will discuss the challenges we have faced with managing and merging life history accounts where the underlying taxonomies are fundamentally different. With a requirement to ensure that life history accounts remain accurate when the underlying concepts of the original sources differ, we employ a variety of processes, some very labor intensive and some requiring in-depth taxonomic knowledge to produce consolidated species accounts. Existing resources are integral to these type of integrations and in addition to the taxonomies themselves, cross-taxonomy mapping databases such as Avibase are key. Working through this process of consolidating life history accounts highlights the basic need for taxonomic management and publication toolsets built on underlying taxonomic and life history standards. Cross institutional collaboration to produce these toolsets will be key to their development and successful adoption across the biodiversity and taxonomic communities. I will also discuss and propose a set of taxonomic management tools based on taxonomic concepts, some which already exist and are used by bird taxonomists to annually update the Clements Checklist and some which need to be implemented before we can accurately manage and consolidate biodiversity information and the evolving taxonomies on which those data are based.

More Than Names: The role of updated taxonomy in palaeontology collections

The accuracy on taxonomic determinations of palaeontology collections may have significant consequences in estimations of organism diversity through time. This justifies the need of taxonomic standardization of palaeontological collections. The perception of palaeodiversity through Phanerozoic time has significantly improved since the Sepkoski showed the marine invertebrate taxonomic data in diversity graphs, organized in orders (Sepkoski 1978) and families (Sepkoski 1979, Sepkoski 1984). The visual impact of these graphs engaged palaeontologists into gathering quantitative macroevolution in order to better understand marine palaeodiversity. Alroy et al. (2008) presented a rebuilt diversity curve based on genus-level in a large sample record. These and other statistically sound and standardized datasets of fossil occurrences have combined sources as literature, databases, and museum collections data as a foundation. Integration of these datasets with the entire fossil record based on individual specimens in space and time would be the ideal approach to species-level taxonomy standards determinations. An example showing how this approach may be achieved is the use of initiatives such as the Web-based data facility Palaeontology Database (PdB) which includes a large amount of fossil record data from throughout the world. The major advantage of that is to gather institucional and also private palaeontological collections with taxonomy experts validation. The core of these datasets is the taxon, with the species as the expected most reliable unit. Taxonomy is therefore the discipline enrolled in the process with the taxonomist at the centre of the process. Updated taxonomy is crucial to create reliable datasets and a careful approach should prevent biased data due to under- or overestimation of diversity. Palaeontological museum collections are known to be one of the largest repositories of fossil data. Taxonomic standardization of palaeontology collections in the context of a museum should: Engage taxonomists in revising fossil clades of the museum material; Promote networking and museum researcher peers involved in similar collections activities; Avoid replication of errors in taxonomic determinations (e.g. exclusive use of Web-based databases sources of taxonomy); Use type material to compare with the collection specimens; Critically analyse previous taxonomic determinations on old labels and associated specimen information; Promote the accessibility of the collection to the research community; Emphasize digitisation of specimen catalogue records as well as 2D imaging of the specimens. Engage taxonomists in revising fossil clades of the museum material; Promote networking and museum researcher peers involved in similar collections activities; Avoid replication of errors in taxonomic determinations (e.g. exclusive use of Web-based databases sources of taxonomy); Use type material to compare with the collection specimens; Critically analyse previous taxonomic determinations on old labels and associated specimen information; Promote the accessibility of the collection to the research community; Emphasize digitisation of specimen catalogue records as well as 2D imaging of the specimens. These practices are valuable complements to current methodologies adopted to improve the taxonomy of collections, resulting in more reliable data which further enables museum-based research focusing on palaeodiversity estimations.

Overlooked diversity in exotic Taraxacum in British Columbia, Canada

In almost all North American literature, including in British Columbia, weedy Taraxacum species have been named as Taraxacum officinale F.H.Wigg and Taraxacum erythrospermum Andrz. ex Besser (or Taraxacum laevigatum DC.). This coarse taxonomic approach ignores great diversity in morphology, ecology, and geographical distributions among the exotic established species. Taxonomic refinement would facilitate floristics and ecological studies when exotic Taraxacum species are involved, and the taxonomy of native Taraxacum must first determine which are and which are not native species, which in turn requires knowledge of sectional identity of any specimen. Exotic Taraxacum specimens were identified to species and taxonomic sections using refined species and sectional concepts that align with taxonomic standards used in the native ranges of the species in Europe. Seven exotic sections and one informally named group are found to be present in British Columbia (Borea, Boreigena, Celtica, Erythrosperma, Hamata, Naevosa, Taraxacum, and the Taraxacum fulvicarpum group). The number of exotic Taraxacum species known to occur in British Columbia to date exceeds 100. A key to the exotic sections of British Columbia Taraxacum is presented and the sections are characterized. Species known to date are listed by their sectional placement. Notes are also presented on distinguishing native from exotic Taraxacum in British Columbia.

Preservation of three-dimensional anatomy in phosphatized fossil arthropods enriches evolutionary inference.

External and internal morphological characters of extant and fossil organisms are crucial to establishing their systematic position, ecological role and evolutionary trends. The lack of internal characters and soft-tissue preservation in many arthropod fossils, however, impedes comprehensive phylogenetic analyses and species descriptions according to taxonomic standards for Recent organisms. We found well-preserved three-dimensional anatomy in mineralized arthropods from Paleogene fissure fillings and demonstrate the value of these fossils by utilizing digitally reconstructed anatomical structure of a hister beetle. The new anatomical data facilitate a refinement of the species diagnosis and allowed us to reject a previous hypothesis of close phylogenetic relationship to an extant congeneric species. Our findings suggest that mineralized fossils, even those of macroscopically poor preservation, constitute a rich but yet largely unexploited source of anatomical data for fossil arthropods.

Commentary on: Are we overpathologizing everyday life? A tenable blueprint for behavioral addiction research.

This commentary supports the argument that there is an increasing tendency to subsume a range of excessive daily behaviors under the rubric of non-substance related behavioral addictions. The concept of behavioral addictions gained momentum in the 1990s with the recent reclassification of pathological gambling as a non-substance behavioral addiction in DSM-5 accelerating this process. The propensity to label a host of normal behaviors carried out to excess as pathological based simply on phenomenological similarities to addictive disorders will ultimately undermine the credibility of behavioral addiction as a valid construct. From a scientific perspective, anecdotal observation followed by the subsequent modification of the wording of existing substance dependence diagnostic criteria, and then searching for biopsychosocial correlates to justify classifying an excessive behavior resulting in harm as an addiction falls far short of accepted taxonomic standards. The differentiation of normal from non-substance addictive behaviors ought to be grounded in sound conceptual, theoretical and empirical methodologies. There are other more parsimonious explanations accounting for such behaviors. Consideration needs to be given to excluding the possibility that excessive behaviors are due to situational environmental/social factors, or symptomatic of an existing affective disorder such as depression or personality traits characteristic of cluster B personalities (namely, impulsivity) rather than the advocating for the establishment of new disorders.

East Asian pollen database: modern pollen distribution and its quantitative relationship with vegetation and climate

AbstractAimOur aims were to provide new pollen data for establishing a sub‐continental surface pollen database (East Asian Pollen Database, EAPD) and to study relationships between vegetation and climate.LocationThe sample sites covered most regions of East Asia, including China, Mongolia, the Russian Far East, Vietnam, Cambodia and Thailand.MethodsData quality control procedures were applied, including taxonomic standardization, removal of duplicates, and adjustment of geographical coordinates. Vegetation types and climate parameters were assigned to each sample. Modern pollen distribution maps were drawn using circle scattergrams. The plots of pollen percentages versus climate variables allowed quantitative estimates of climate values. The modern analogue technique (MAT) was used to predict modern biomes and climate parameters.ResultsPollen assemblages extracted from 2858 sites were used to model the geographical distribution of selected taxa and their relationships with climate. For most taxa, the reconstructed range fitted the observed geographical distribution rather well. Arboreal pollen (AP) and Pinus dominated the transition zone between forest and steppe. Use of the MAT revealed that the predicted and observed biomes matched in 71% of the cases. The warm temperate evergreen broadleaf forest had the best agreement between predictions and observations. Climate values reconstructed using MAT were highly correlated with observed values in January temperature. The correlation coefficient of the temperature variables ranged from 0.799 to 0.930 and was as high as 0.939 for precipitation.Main conclusionsThis paper documents a new modern pollen database for East Asia and makes the data readily available. The reconstructed biomes and climate variables are significantly correlated with the observed values, thus demonstrating the utility of the pollen database for future multiscale palaeoenvironmental studies.

Rubus gizellae (Rosaceae), a bramble species from southeastern Europe—identification history, neotypification, and taxonomic notes

The genus Rubus Linnaeus (1753: 492) with nearly 700 species in Europe (Kurtto et al. 2010) constitutes an extraordinarily taxonomically critical group within the Rosaceae (Rosoideae). The richness of morphotypes combined with a poor understanding of the breeding system of apomictic brambles has resulted in the description of thousands of entities. Lack of taxonomic standards and an overwhelming number of scientific names has caused nomenclatorial chaos, which mainly has been resolved by the modern species concept developed in Europe in the late 1900s (“Weberian reform”, Weber 1999; Haveman & de Ronde 2012). However, the review of older names is an extended process and re-evaluation of names has often failed due to lack of type material.

New records and redescription of Halcurias pilatus and Halcurias mcmurrichi (Actiniaria, Endocoelantheae)

We redescribe and illustrate Halcurias pilatus McMurrich, 1893 and H. mcmurrichi Uchida, 2004 (Endocoelantheae, Halcuriidae) from newly collected specimens from Southern Chile and deep-water reefs off Florida, respectively. Halcurias pilatus was previously considered to have a disjunct distribution until Uchida (2004) described a new species for the material from the Bahamas. However, the description of H. mcmurrichi does not meet modern taxonomic standards. We provide new anatomical and cnidae data for H. pilatus and H. mcmurrichi. Both species differ in the distribution and cnidom of nematocyst batteries in the column, development of microcnemes mesenteries, cnidae and geographical distribution. We find that H. pilatus can have a weak mesogleal marginal sphincter and amend accordingly the diagnoses of the genus Halcurias, family Halcuriidae, and suborder Endocoelantheae. These new records represent the first time both species have been collected since their original descriptions.

Jizz and the joy of pattern recognition: Virtuosity, discipline and the agency of insight in UK naturalists’ arts of seeing

Approaches to visual skilling from anthropology and STS have tended to highlight the forces of discipline and control in understanding how shared visual accounts of the world are created in the face of potential differences brought about by multi-sensorial perception. Drawing upon a range of observational and interview material from an immersion in naturalist training and biological recording activities between 2003 and 2009, I focus upon jizz, a distinct form of gestalt perception much coveted by naturalist communities in the UK. Jizz is described as a tacit and embodied way of seeing that instantaneously reveals the identity of a species, relying upon but simultaneously suspending the arduous and meticulous study of an organism's diagnostic characteristics. I explore the potential and limitations of jizz to allow for both visual precision and an enchanted and varied form of encounter with nature. In so doing, I explore how the specific characteristics of wild, intangible and irreverent virtuoso performance work closely together with disciplining taxonomic standards. As such, discipline and irreverence work together, are mutually enabling, and allow for an accommodation rather than a segregation of potential difference brought about by perceptual variety.

Ecoinformatics and global change – an overdue liaison

AbstractThe field of ecoinformatics provides concepts, methods and standards to guide management and analysis of ecological data with particular emphasis on exploration of co‐occurrences of organisms and their linkage to environmental conditions and taxon attributes. In this editorial, introducing the Special Feature ‘Ecoinformatics and global change’, we reflect on the development of ecoinformatics and explore its importance for future global change research with special focus on vegetation‐plot data. We show how papers in this Special Feature illustrate important directions and approaches in this emerging field. We suggest that ecoinformatics has the potential to make profound contributions to pure and applied sciences, and that the analyses, databases, meta‐databases, data exchange formats and analytical tools presented in this Special Feature advance this approach to vegetation science and illustrate and address important open questions. We conclude by describing important future directions for the development of the field including incentives for data sharing, creation of tools for more robust statistical analysis, utilities for integration of data that conform to divergent taxonomic standards, and databases that provide detailed plot‐specific data so as to allow users to find and access data appropriate to their research needs.

Towards standardization of the description and publication of next‐generation sequencing datasets of fungal communities

Towards standardization of the description and publication of next‐generation sequencing datasets of fungal communities