Catalogue Search | MBRL
Are you sure you want to remove the book from the shelf?
{{itemTitle}}
260
result(s) for
"Taxonomists"
Sort by:
Automatic taxonomic identification based on the Fossil Image Dataset (>415,000 images) and deep convolutional neural networks
The rapid and accurate taxonomic identification of fossils is of great significance in paleontology, biostratigraphy, and other fields. However, taxonomic identification is often labor-intensive and tedious, and the requisition of extensive prior knowledge about a taxonomic group also requires long-term training. Moreover, identification results are often inconsistent across researchers and communities. Accordingly, in this study, we used deep learning to support taxonomic identification. We used web crawlers to collect the Fossil Image Dataset (FID) via the Internet, obtaining 415,339 images belonging to 50 fossil clades. Then we trained three powerful convolutional neural networks on a high-performance workstation. The Inception-ResNet-v2 architecture achieved an average accuracy of 0.90 in the test dataset when transfer learning was applied. The clades of microfossils and vertebrate fossils exhibited the highest identification accuracies of 0.95 and 0.90, respectively. In contrast, clades of sponges, bryozoans, and trace fossils with various morphologies or with few samples in the dataset exhibited a performance below 0.80. Visual explanation methods further highlighted the discrepancies among different fossil clades and suggested similarities between the identifications made by machine classifiers and taxonomists. Collecting large paleontological datasets from various sources, such as the literature, digitization of dark data, citizen-science data, and public data from the Internet may further enhance deep learning methods and their adoption. Such developments will also possibly lead to image-based systematic taxonomy to be replaced by machine-aided classification in the future. Pioneering studies can include microfossils and some invertebrate fossils. To contribute to this development, we deployed our model on a server for public access at www.ai-fossil.com.
Journal Article
A concise review of the highly diverse genus Sargassum C. Agardh with wide industrial potential
Sargassum C. Agardh is a highly diverse genus within the brown algae, with 615 currently recognized species, varieties and forms worldwide. This high level of species diversity led early taxonomists, using morphological-anatomical criteria only, to divide the genus into up to five sub-genera and several lower-ranking taxonomic units (e.g., sections, tribes). With the advent of molecular data, subsequent authors revised this complex and archaic classification, with the genus now comprising only two sub-genera: Sargassum and Bactrophycus. Whilst most Sargassum species are benthic, only two are known to be holopelagic and responsible for strandings along tropical Atlantic coasts. The rest of the genus is cosmopolitan, occurring from tropical to temperate regions. Sargassum has not yet been reported in polar regions. Where Sargassum is present, macroalgal populations can grow in large quantities, and the resulting biomass can be valuable to the local communities for a variety of uses. Here we review the genus Sargassum from a taxonomic, ecological and physiological perspectives, and explore the different ways of taking advantage of this extraordinary biomass, which while becoming an invasive pest in some countries, could represent opportunities for coastal populations worldwide.
Journal Article
The need to employ reliable and reproducible species identifications in coralline algal research
Coralline algae perform important ecological roles in nearshore marine ecosystems globally by promoting the settlement of invertebrate larvae and enhancing biodiversity by creating habitat. However, these roles are severely threatened by global environmental changes. Most coralline algae are extremely difficult to identify, and DNA sequencing has revealed rampant inaccuracy of morpho-anatomical approaches to distinguish species, and even genera. If appropriate identification methods are not reported, or even used, we will be left with an uninterpretable body of literature where the species-specific biology of coralline algae cannot be validated. This will make it difficult to determine the impact a changing ocean may have on these ecologically important species. We reveal the magnitude of the issue in coralline algal research—both the identification methods used and the reporting of identification protocols. An analysis of 341 articles over the past decade revealed that only 7.6% used molecular methods, with over 70% not reporting any details of how species were identified. While many coralline algal taxonomists understand that the majority of species cannot be identified morphologically, this message has not disseminated to the ecological and physiological community. We provide a series of guidelines for conducting DNA-based identifications and strongly recommend the use of these methods over less informative morpho-anatomical techniques. Most importantly, the methods of identification should be adequately reported. Without following these guidelines, research on coralline algae runs the risk of collecting uninterpretable data, and conducting irreproducible science, slowing our ability to determine how these important species will respond to future ocean conditions.
Journal Article
Socio-environmental impacts of non-native and transplanted aquatic mollusc species in South America: What do we really know?
The impacts of biological invasions remain poorly known for some habitats, regions and taxa. To date, there has been no comprehensive effort to review and synthesize the impacts of invasive mollusc species in South America. In this paper, we provide a synoptic view on what is known on documented socio-ecological impacts of aquatic no-native mollusc species (NNMS) and transplanted mollusc species (TMS) from South America. An expert group involving malacologists and taxonomists from different countries, the “South America Alien Molluscs Specialists” (eMIAS), shared and summarized the scientific literature, databases, and published and unpublished information on confirmed impacts of NNMS and TMS in South America. Three broad categories, non-mutually exclusive were used as a framework: “Environmental/Biodiversity impacts”, “Economic and social effects”, and “Human health impacts”. Some 21 NNMS and seven TMS have documented impacts on at least one of those three categories. We encourage targeting the less known areas of research, such as economic valuation of human health (and veterinary) impacts attributable to NNMS or TMS and expand our knowledge of environmental impacts for the species listed in this study.
Journal Article
Publication practice in Taxonomy: Global inequalities and potential bias against negative results
There is broad recognition by practicing taxonomists that the field is going through a crisis, which has been dubbed the “taxonomic impediment”. There are many aspects involved in said crisis, but publication practices in taxonomy are often neglected or relegated to the backseat. We provide an initial foray into this topic via a worldwide survey with taxonomists, spanning all botanical and zoological groups, and career stages. Demographically, most of the respondents identified themselves as males (70%), working in Europe or North America (68%), in universities (50%) or museums (27%). Over half of the respondents are established/late-career researchers (only about 25% of full professors were female), with a low number of early-career researchers and graduate students (i.e., taxonomists in training). Nearly 61% of the men acquired their highest title at least eleven years ago, while only 41% of the women did so. Nearly 92% of the respondents have published new species descriptions, while around 60% and 26% have synonymized, respectively, species-level or subspecies-level taxa. In general, respondents perceive the act of describing new species to be easier than synonymizing species (p = 0.05). Established/late-career researchers and male researchers, particularly in Oceania and North America, found it easier to publish nomenclatural acts such as new species descriptions, while early-career researchers had their acts contested more often. Our results reaffirm the low academic recognition of the field, the lack of funding for research and publishing charges especially in the Global South, and the difficulty in finding specialized outlets (and the low impact factor of those journals) as persistent issues in taxonomy. Other significant problems raised by respondents include ethical issues in the peer-review process, a bias against newcomers in the field coming either from established researchers or committees, and taxonomic vandalism.
Journal Article
Progress and perspectives in the discovery of polychaete worms (Annelida) of the world
Despite the availability of well-documented data, a comprehensive review of the discovery progress of polychaete worms (Annelida) has never been done. In the present study, we reviewed available data in the World Register of Marine Species, and found that 11,456 valid species of Recent polychaetes (1417 genera, 85 families) have been named by 835 first authors since 1758. Over this period, three discovery phases of the fauna were identified. That is, the initial phase (from 1758 to mid-nineteenth century) where nearly 500 species were described by few taxonomists, the second phase (from the 1850’s to mid-twentieth century) where almost 5000 species were largely described by some very productive taxonomists, and the third phase (from the 1950’s to modern times) in which about 6000 species were described by the most taxonomists ever. Six polychaete families with the most species were Syllidae (993 species), Polynoidae (876 species), Nereididae (687 species), Spionidae (612 species), Terebellidae (607 species) and Serpulidae (576 species). The increase in the number of first authors through time indicated greater taxonomic effort. By contrast, there was a decline in the number of polychaete species described in proportion to the number of first authors since around mid-nineteenth century. This suggested that it has been getting more difficult to find new polychaete species. According to our modelling, we predict that 5200 more species will be discovered between now and the year 2100. The total number of polychaete species of the world by the end of this century is thus anticipated to be about 16,700 species.
Journal Article
Recovery Plan for the Endangered Taxonomy Profession
The worldwide decline in taxonomists has a broad impact on biology and society. Learning from general historical patterns of science and understanding social changes caused by growing economies, we propose changes in priorities for training taxonomists to reverse these losses. Academically trained professionals, parataxonomists (local assistants trained by professional biologists), youths educated with an emphasis on natural history, and self-supported expert amateurs are the major sources of taxonomists. Recruiting effort from each category is best determined by public attitudes toward education, as well as the availability of discretionary funds and leisure time. Instead of concentrating on descriptions of species and narrow studies of morphology and DNA, the duties of the few professional taxonomists of the future also will be to use cyberspace and a wide range of skills to recruit, train, and provide direction for expert amateurs, young students, parataxonomists, the general public, and governments.
Journal Article
Application of phylogenomic tools to unravel anthozoan evolution
Comprising approximately 7500 living species of various corals and sea anemones, Anthozoa ranks among the most ecologically and economically valuable marine taxa. However, the taxonomy and systematics of anthozoans remain in flux as several facets of their biology (e.g. cryptic speciation, hybridisation and introgression, morphological plasticity and convergence) confound taxonomists even today. Rapid advancements in molecular sequencing and analyses have made available vast quantities of genomic data on an increasing number of species across the anthozoan tree of life. While whole genome assemblies are expected to result in the most robust phylogenetic trees, reduced-representation techniques such as genome skimming, RAD-seq, phylotranscriptomics and hybrid capture have led to well-supported inferences at various taxonomic levels and may still be favoured at this stage due to the high cost associated with even a single genome assembly. Here, we examine the different genotyping and analytical approaches used in anthozoan phylogeny reconstructions, their applicability across different divergences, and the coverage of studies among anthozoan clades to date. Based on our review of 82 phylogenomic studies, we describe the suitability of methods employed relative to their aims, highlight the imbalanced coverage of taxonomic groups studied and assess immediate and long-term needs where consolidation and streamlining of approaches would further advance the field. Overall, we find that Scleractinia (Anthozoa) is the most phylogenetically sampled group and studies on Octocorallia (Anthozoa) and its subclades are emerging. Nevertheless, we emphasise the need for more phylotranscriptomic, hybrid capture and whole genome sequencing across all anthozoans to increase topological support and generate more precise divergence time estimates. The enhanced phylogenetic understanding of Anthozoa is expected to provide insights into the evolution of genes and adaptations to environmental stressors amidst the current climate and mass extinction crises.
Journal Article
From pioneers to modern-day taxonomists: the good, the bad, and the idiosyncrasies in choosing species epithets of rotifers and microcrustaceans
In the Anthropocene, scientists have an imperative to prioritize the sharing of scientific knowledge as a fundamental responsibility in fostering collective action. Scientific names are essential in communicating biodiversity, and to maximize their impact, they need to be consistently labeled across all organisms and made accessible to diverse audiences. In our study, we examined the etymological and temporal patterns in naming practices of rotifers and microcrustaceans (cladocerans and copepods). By analyzing a dataset comprising 992 species present in Brazil, but described worldwide since the eighteenth century, we identified various factors influencing specific epithets, including morphology, ecology, behavior, geography, and cultural references, as well as names honoring notable individuals. Our findings revealed that while morphology was the primary basis for etymology (62.1%) in naming rotifers, cladocerans, and copepods, its relative importance has decreased over time. We observed a significant increase in etymologies related to geography and the recognition of influential scientists in the field. Furthermore, our study unveiled a gender bias, with male scientists being more frequently honored with species names (86.4%). In addition to acknowledging the contributions made by taxonomists studying these groups, our study offers valuable insights intended to stimulate reflections on the significance of naming practices in biodiversity research and communication, in line with current social-ecological needs.
Journal Article