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Abstract
Taxonomic data are a scientific common. Unlike nomenclature, which has strong governance institutions, there are currently no generally accepted governance institutions for the compilation of taxonomic data into an accepted global list. This gap results in challenges for conservation, ecological research, policymaking, international trade, and other areas of scientific and societal importance. Consensus on a global list and its management requires effective governance and standards, including agreed mechanisms for choosing among competing taxonomies and partial lists. However, governance frameworks are currently lacking, and a call for governance in 2017 generated critical responses. Any governance system to which compliance is voluntary requires a high level of legitimacy and credibility among those by and for whom it is created. Legitimacy and credibility, in turn, require adequate and credible consultation. Here, we report on the results of a global survey of taxonomists, scientists from other disciplines, and users of taxonomy designed to assess views and test ideas for a new system of taxonomic list governance. We found a surprisingly high degree of agreement on the need for a global list of accepted species and their names, and consistent views on what such a list should provide to users and how it should be governed. The survey suggests that consensus on a mechanism to create, manage, and govern a single widely accepted list of all the world's species is achievable. This finding was unexpected given past controversies about the merits of list governance.
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Tightening the requirements for species diagnoses would help integrate DNA-based descriptions in taxonomic practice. PLoS Biol 2023; 21:e3002251. [PMID: 37607211 PMCID: PMC10443861 DOI: 10.1371/journal.pbio.3002251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023] Open
Abstract
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.
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Renaming taxa on ethical grounds threatens nomenclatural stability and scientific communication. Zool J Linn Soc 2023. [DOI: 10.1093/zoolinnean/zlac107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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The Herbarium 2021 Half-Earth Challenge Dataset and Machine Learning Competition. FRONTIERS IN PLANT SCIENCE 2022; 12:787127. [PMID: 35178056 PMCID: PMC8846375 DOI: 10.3389/fpls.2021.787127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/20/2021] [Indexed: 05/17/2023]
Abstract
Herbarium sheets present a unique view of the world's botanical history, evolution, and biodiversity. This makes them an all-important data source for botanical research. With the increased digitization of herbaria worldwide and advances in the domain of fine-grained visual classification which can facilitate automatic identification of herbarium specimen images, there are many opportunities for supporting and expanding research in this field. However, existing datasets are either too small, or not diverse enough, in terms of represented taxa, geographic distribution, and imaging protocols. Furthermore, aggregating datasets is difficult as taxa are recognized under a multitude of names and must be aligned to a common reference. We introduce the Herbarium 2021 Half-Earth dataset: the largest and most diverse dataset of herbarium specimen images, to date, for automatic taxon recognition. We also present the results of the Herbarium 2021 Half-Earth challenge, a competition that was part of the Eighth Workshop on Fine-Grained Visual Categorization (FGVC8) and hosted by Kaggle to encourage the development of models to automatically identify taxa from herbarium sheet images.
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The Habitat Persistence Hypothesis: a new perspective on the distribution of coral-reef organisms. FRONTIERS OF BIOGEOGRAPHY 2022. [DOI: 10.21425/f5fbg57427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Towards a global list of accepted species I. Why taxonomists sometimes disagree, and why this matters. ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00495-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Mesophotic.org: a repository for scientific information on mesophotic ecosystems. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5677403. [PMID: 31836897 PMCID: PMC6911162 DOI: 10.1093/database/baz140] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 10/04/2019] [Accepted: 11/13/2019] [Indexed: 11/30/2022]
Abstract
Mesophotic coral ecosystems (MCEs) and temperate mesophotic ecosystems (TMEs) occur at depths of roughly 30–150 m depth and are characterized by the presence of photosynthetic organisms despite reduced light availability. Exploration of these ecosystems dates back several decades, but our knowledge remained extremely limited until about a decade ago, when a renewed interest resulted in the establishment of a rapidly growing research community. Here, we present the ‘mesophotic.org’ database, a comprehensive and curated repository of scientific literature on mesophotic ecosystems. Through both manually curated and automatically extracted metadata, the repository facilitates rapid retrieval of available information about particular topics (e.g. taxa or geographic regions), exploration of spatial/temporal trends in research and identification of knowledge gaps. The repository can be queried to comprehensively obtain available data to address large-scale questions and guide future research directions. Overall, the ‘mesophotic.org’ repository provides an independent and open-source platform for the ever-growing research community working on MCEs and TMEs to collate and expedite our understanding of the occurrence, composition and functioning of these ecosystems. Database URL: http://mesophotic.org/
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A New Species of Fairy Wrasse (Teleostei: Labridae: Cirrhilabrus) from Mesophotic Coral Ecosystems of the Verde Island Passage, Philippines. COPEIA 2020. [DOI: 10.1643/ci-19-297] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Three new species of Chromis (Teleostei, Pomacentridae) from mesophotic coral ecosystems of the Philippines. Zookeys 2019; 835:1-15. [PMID: 31043847 PMCID: PMC6477865 DOI: 10.3897/zookeys.835.27528] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 02/24/2019] [Indexed: 11/12/2022] Open
Abstract
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. Chromisguntingsp. 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. Chromishangganansp. 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. Chromisbowesisp. 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.
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Tosanoidesannepatrice, a new basslet from deep coral reefs in Micronesia (Perciformes, Percoidei, Serranidae). Zookeys 2018:139-153. [PMID: 30310352 PMCID: PMC6177527 DOI: 10.3897/zookeys.786.28421] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/09/2018] [Indexed: 11/28/2022] Open
Abstract
The new species Tosanoidesannepatricesp. n. is described from four specimens collected at depths of 115–148 m near Palau and Pohnpei in Micronesia. It differs from the other three species of this genus in life color and in certain morphological characters, such as body depth, snout length, anterior three dorsal-fin spine lengths, caudal-fin length, and other characters. There are also genetic differences from the other four species of Tosanoides (d ≈ 0.04–0.12 in mtDNA cytochrome oxidase I). This species is presently known only from Palau and Pohnpei within Micronesia, but it likely occurs elsewhere throughout the tropical western Pacific.
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Mesophotic coral ecosystems are threatened and ecologically distinct from shallow water reefs. Science 2018; 361:281-284. [DOI: 10.1126/science.aaq1614] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 05/22/2018] [Indexed: 12/13/2022]
Abstract
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.
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Tosanoides obama, a new basslet (Perciformes, Percoidei, Serranidae) from deep coral reefs in the Northwestern Hawaiian Islands. Zookeys 2017:165-181. [PMID: 28138296 PMCID: PMC5240353 DOI: 10.3897/zookeys.641.11500] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 12/15/2016] [Indexed: 11/30/2022] Open
Abstract
The new species Tosanoidesobama is described from two specimens collected at a depth of 90–92 m off Kure Atoll and Pearl and Hermes Atoll, Northwestern Hawaiian Islands. It differs from the other two species of this genus in life color and in certain morphological characters, such as number of pored lateral-line scales, pectoral-fin rays, snout length, anterior three dorsal-fin spine lengths, dorsal-fin profile, and other characters. There are also substantial genetic differences from the other two species of Tosanoides (d ≈ 0.10 in mtDNA cytochrome oxidase I). The species is presently known only from the Northwestern Hawaiian Islands within the Papahānaumokuākea Marine National Monument.
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A comprehensive investigation of mesophotic coral ecosystems in the Hawaiian Archipelago. PeerJ 2016; 4:e2475. [PMID: 27761310 PMCID: PMC5068450 DOI: 10.7717/peerj.2475] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 08/23/2016] [Indexed: 11/21/2022] Open
Abstract
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 km2 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.
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Prognathodes basabei, a new species of butterflyfish (Perciformes, Chaetodontidae) from the Hawaiian Archipelago. Zookeys 2016:137-52. [PMID: 27667937 PMCID: PMC5027661 DOI: 10.3897/zookeys.614.10200] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 08/22/2016] [Indexed: 12/05/2022] Open
Abstract
A new species of the butterflyfish genus Prognathodes is described from specimens collected at a depth of 55–61 m off Pearl and Hermes Atoll, Northwestern Hawaiian Islands. This species has been observed by mixed-gas divers and from submersibles at depths ranging from 45–187 m throughout the Hawaiian Archipelago, with shallower sightings in the Northwestern Hawaiian Islands and deeper in the Main Hawaiian Islands. It is similar to Prognathodesguezei (Maugé and Bauchot 1976) from the western Indian Ocean, and at least one other undescribed species of Prognathodes from Palau, differing from these species in the number of soft dorsal-fin rays, size of head, and body depth. There are also differences in the life color, and a substantial genetic difference from the Palauan species (d » .08 in mtDNA cytochrome oxidase I).
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Towards a Global Names Architecture: The future of indexing scientific names. Zookeys 2016; 550:261-81. [PMID: 26877664 PMCID: PMC4741226 DOI: 10.3897/zookeys.550.10009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 05/20/2015] [Indexed: 01/30/2023] Open
Abstract
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.
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A common registration-to-publication automated pipeline for nomenclatural acts for higher plants (International Plant Names Index, IPNI), fungi (Index Fungorum, MycoBank) and animals (ZooBank). Zookeys 2016; 550:233-46. [PMID: 26877662 PMCID: PMC4741224 DOI: 10.3897/zookeys.550.9551] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 03/10/2015] [Indexed: 11/30/2022] Open
Abstract
Collaborative effort among four lead indexes of taxon names and nomenclatural acts (International Plant Name Index (IPNI), Index Fungorum, MycoBank and ZooBank) and the journals PhytoKeys, MycoKeys and ZooKeys to create an automated, pre-publication, registration workflow, based on a server-to-server, XML request/response model. The registration model for ZooBank uses the TaxPub schema, which is an extension to the Journal Tag Publishing Suite (JATS) of the National Library of Medicine (NLM). The indexing or registration model of IPNI and Index Fungorum will use the Taxonomic Concept Transfer Schema (TCS) as a basic standard for the workflow. Other journals and publishers who intend to implement automated, pre-publication, registration of taxon names and nomenclatural acts can also use the open sample XML formats and links to schemas and relevant information published in the paper.
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Luzonichthysseaver, a new species of Anthiinae (Perciformes, Serranidae) from Pohnpei, Micronesia. Biodivers Data J 2015:e4902. [PMID: 25941454 PMCID: PMC4411493 DOI: 10.3897/bdj.3.e4902] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 04/25/2015] [Indexed: 11/12/2022] Open
Abstract
Luzonichthysseaver, n. sp., is described from two specimens, 42-46 mm standard length (SL) collected from Pohnpei, Micronesia. Collections were made by divers on mixed-gas closed-circuit rebreathers using hand nets at depths of 90-100 m. Luzonichthysseaver is distinct from all other species of the genus in the characters of lateral line scales, gill rakers, pelvic fin length, caudal concavity and coloration. Of the six species of Luzonichthys, it appears to be morphologically most similar to L.earlei and L.whitleyi.
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Community next steps for making globally unique identifiers work for biocollections data. Zookeys 2015:133-54. [PMID: 25901117 PMCID: PMC4400380 DOI: 10.3897/zookeys.494.9352] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 03/17/2015] [Indexed: 11/12/2022] Open
Abstract
Biodiversity data is being digitized and made available online at a rapidly increasing rate but current practices typically do not preserve linkages between these data, which impedes interoperation, provenance tracking, and assembly of larger datasets. For data associated with biocollections, the biodiversity community has long recognized that an essential part of establishing and preserving linkages is to apply globally unique identifiers at the point when data are generated in the field and to persist these identifiers downstream, but this is seldom implemented in practice. There has neither been coalescence towards one single identifier solution (as in some other domains), nor even a set of recommended best practices and standards to support multiple identifier schemes sharing consistent responses. In order to further progress towards a broader community consensus, a group of biocollections and informatics experts assembled in Stockholm in October 2014 to discuss community next steps to overcome current roadblocks. The workshop participants divided into four groups focusing on: identifier practice in current field biocollections; identifier application for legacy biocollections; identifiers as applied to biodiversity data records as they are published and made available in semantically marked-up publications; and cross-cutting identifier solutions that bridge across these domains. The main outcome was consensus on key issues, including recognition of differences between legacy and new biocollections processes, the need for identifier metadata profiles that can report information on identifier persistence missions, and the unambiguous indication of the type of object associated with the identifier. Current identifier characteristics are also summarized, and an overview of available schemes and practices is provided.
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Neoniphonpencei, a new species of holocentrid (Teleostei: Beryciformes) from Rarotonga, Cook Islands. Biodivers Data J 2015:e4180. [PMID: 25698898 PMCID: PMC4319167 DOI: 10.3897/bdj.3.e4180] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/22/2015] [Indexed: 11/23/2022] Open
Abstract
Neoniphonpencei, n. sp., is described from thirteen specimens, 132-197 mm standard length (SL) collected from mesophotic coral ecosystems (MCEs) at Rarotonga, Cook Islands by divers using mixed-gas closed-circuit rebreathers. It differs from all other species of the genus in number of lateral line scales, scales above and below lateral line, elements of life color, and in COI and cytochrome b DNA sequences. Of the five other known species of Neoniphon, it is most similar to the Indo-Pacific N.aurolineatus and the western Atlantic N.marianus both morphologically and genetically.
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Phylogeographic analyses of submesophotic snappers Etelis coruscans and Etelis "marshi" (family Lutjanidae) reveal concordant genetic structure across the Hawaiian Archipelago. PLoS One 2014; 9:e91665. [PMID: 24722193 PMCID: PMC3982960 DOI: 10.1371/journal.pone.0091665] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 02/13/2014] [Indexed: 11/18/2022] Open
Abstract
The Hawaiian Archipelago has become a natural laboratory for understanding genetic connectivity in marine organisms as a result of the large number of population genetics studies that have been conducted across this island chain for a wide taxonomic range of organisms. However, population genetic studies have been conducted for only two species occurring in the mesophotic or submesophotic zones (30+m) in this archipelago. To gain a greater understanding of genetic connectivity in these deepwater habitats, we investigated the genetic structure of two submesophotic fish species (occurring ∼200-360 m) in this archipelago. We surveyed 16 locations across the archipelago for submesophotic snappers Etelis coruscans (N = 787) and E. "marshi" (formerly E. carbunculus; N = 770) with 436-490 bp of mtDNA cytochrome b and 10-11 microsatellite loci. Phylogeographic analyses reveal no geographic structuring of mtDNA lineages and recent coalescence times that are typical of shallow reef fauna. Population genetic analyses reveal no overall structure across most of the archipelago, a pattern also typical of dispersive shallow fishes. However some sites in the mid-archipelago (Raita Bank to French Frigate Shoals) had significant population differentiation. This pattern of no structure between ends of the Hawaiian range, and significant structure in the middle, was previously observed in a submesophotic snapper (Pristipomoides filamentosus) and a submesophotic grouper (Hyporthodus quernus). Three of these four species also have elevated genetic diversity in the mid-archipelago. Biophysical larval dispersal models from previous studies indicate that this elevated diversity may result from larval supplement from Johnston Atoll, ∼800 km southwest of Hawaii. In this case the boundaries of stocks for fishery management cannot be defined simply in terms of geography, and fishery management in Hawaii may need to incorporate external larval supply into management plans.
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Xanthichthysgreenei, a new species of triggerfish (Balistidae) from the Line Islands. Biodivers Data J 2013:e994. [PMID: 24723781 PMCID: PMC3964694 DOI: 10.3897/bdj.1.e994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 09/11/2013] [Indexed: 12/02/2022] Open
Abstract
Xanthichthysgreenei sp. n. is described from six specimens, 97-154 mm standard length (SL) collected from mesophotic coral ecosystems (90-100 m) at Kiritimati (Christmas Island), Line Islands, part of the Republic of Kiribati in the Central Pacific. Of the six species of Xanthichthys, it is most similar to the Atlantic Xanthichthysringens and the Indo-West Pacific Xanthichthyslineopunctatus, sharing with these species the character of three pigmented cheek grooves. It is distinctive in its low body scale row count (33-35, other Xanthichthys species with 39 or more), small size (maximum SL 154 mm, other species over 225 mm), and color pattern of scattered dark spots sub-dorsally and no other spots or lines on body.
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Names are key to the big new biology. Trends Ecol Evol 2010; 25:686-91. [PMID: 20961649 DOI: 10.1016/j.tree.2010.09.004] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Revised: 09/20/2010] [Accepted: 09/21/2010] [Indexed: 10/18/2022]
Abstract
Those who seek answers to big, broad questions about biology, especially questions emphasizing the organism (taxonomy, evolution and ecology), will soon benefit from an emerging names-based infrastructure. It will draw on the almost universal association of organism names with biological information to index and interconnect information distributed across the Internet. The result will be a virtual data commons, expanding as further data are shared, allowing biology to become more of a 'big science'. Informatics devices will exploit this 'big new biology', revitalizing comparative biology with a broad perspective to reveal previously inaccessible trends and discontinuities, so helping us to reveal unfamiliar biological truths. Here, we review the first components of this freely available, participatory and semantic Global Names Architecture.
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Candidate gene expression analysis of toxin-induced dilated cardiomyopathy in the turkey (Meleagris gallopavo). Poult Sci 2007; 85:2216-21. [PMID: 17135679 DOI: 10.1093/ps/85.12.2216] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Dilated cardiomyopathy (DCM), a heart disease, affects many vertebrates including humans and poultry. The disease can be either idiopathic (IDCM) or toxin-induced (TIDCM). Although genetic and other studies of IDCM are extensive, the specific etiology of TIDCM is still unknown. In this study, we compared mRNA levels of cardiac troponin T (cTnT) and phospholamban (PLN) in turkeys affected and unaffected by TIDCM. Cardiac TnT and PLN were chosen because their altered expression has been observed in IDCM-affected birds. A total of 72 birds, 44 affected and 28 unaffected with TIDCM, were used. Differences in the mRNA levels of cTnT and PLN between affected and unaffected turkeys were significant only for cTnT. The sequence of the turkey PLN showed significant similarity at the nucleotide level to the reference chicken sequence and to those of other species. In addition to implicating cTnT in TIDCM, the present work describes a partial turkey PLN coding sequence that could be useful for future studies.
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Transmission of male infertility and intracytoplasmic sperm injection (mini-review). FIZIOLOHICHNYI ZHURNAL (KIEV, UKRAINE : 1994) 2006; 52:110-8. [PMID: 16909765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The fact that genetic aetiology is responsible for approximately one third of all kinds of male sterility has led to concerns regarding the application of artificial reproductive technologies in the cases of azoospermia and severe oligozoospermia. Congenital sterility could be caused by gene mutation, quantitative or structural abnormality of sexual chromosomes or autosomes. The possibility of inherited transmission of male sterility within the context of applying artificial reproductive technologies is analysed in the article. Klinefelter's syndrome, mutation of cystic fibrosis transmembrane conductance regulator (CFTR) gene, which causes cystic fibrosis, and mutation of azoospermia factor zone (AZF) of Y-chromosome are among the most frequent genetic causes of severe oligozoospermia and azoospermia. The probability of a mutation of the CFTR gene being transmitted to the next generation is 50%. The probability of inherit transmission of Klinefelter's syndrome of mosaic karyotype could reach 70%. The probability of transmission of AZF mutation to children of male sex, generated with ICSI, is 100%. The percent of men with AZF mutation among users of ICSI centers, ranges from 3.2% to 14%. It means that at least 3.2 % of all boys conceived with ICSI will be sterile because of mutation in the AZF zone of Y-chromosome. It should be noted that genetic analysis and counselling do not always occur before the beginning of artificial fertilization cycles. Parents-to-be do not always have an opportunity to learn about the genetic risks of their unborn child and make any subsequent and responsible decisions. Among the decisions is a choice of not resorting to ART, but to live with the infertility and explore other opportunities for parenthood. Responsibility for high risk of conceiving a child with genetic anomalies rests not only with the parents, but also with all of society, including those responsible for research, technology, and legislation, in the health care profession.
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Abstract
The preparation and application of anatomic models and phantoms to facilitate learning diagnostic ultrasound is described. Imaging with diagnostic ultrasound requires mastery of many skills, along with knowledge of sound-tissue interactions which contribute to the formation of diagnostic images and artifacts. Understanding the genesis of artifacts encountered during ultrasound scanning can avoid misinterpretation and aid diagnosis. In addition, development of machine related knowledge and skills, including manipulation of the transducer and the selection of correct settings for variables such as gain, power, time-gain compensation, and transducer type, is dependent on an understanding of how these factors affect the image. The normal appearance of an organ relates to both its echogenicity and morphologic characteristics, and confirmation of the nature of an abnormality often requires ultrasound guided biopsy. The use of anatomic models and phantoms in ultrasound instruction allows principles to be demonstrated, knowledge acquired, and biopsy procedures practiced and mastered in a controlled setting. This can minimize live animal use, and enhance the knowledge base and skills of the clinician prior to applying this diagnostic technique to the clinical patient.
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Interpreting low-intensity cardiac murmurs in dogs predisposed to subaortic stenosis. J Am Anim Hosp Assoc 2000; 36:379-82. [PMID: 10997510 DOI: 10.5326/15473317-36-5-379] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Hoplolatilus pohle, a New Species of Sand Tilefish (Perciformes: Malacanthidae) from the Deep Reefs of the D'Entrecasteaux Islands, Papua New Guinea. COPEIA 1997. [DOI: 10.2307/1447758] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Abstract
OBJECTIVE The current status of the research knowledge on the psychotherapy of bulimia nervosa is reviewed. METHODS Published studies using randomization to treatment are discussed. RESULTS The existing research data speak convincingly to the efficacy of cognitive behavioral treatment (CBT); however, certain important questions remain unanswered. DISCUSSION The current deficiencies in the field are underscored.
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Abstract
Eighty-three obese subjects with binge eating disorder (BED) were compared with 99 obese subjects not meeting criteria for BED on the Toronto Alexithymia Scale (TAS). Overall, the subjects in our sample were not significantly alexithymic, the mean global TAS score being 62.8 (SD = 10.2) which is comparable with the values found in non-patient control samples. Furthermore, the mean TAS scores did not differ between obese subjects with and without BED. However, we found a slightly higher prevalence of alexithymia (TAS total score 74 and above) in BED subjects compared with non-BED subjects (24.1% and 11.1%, respectively). A series of stepwise multiple regression analyses were run, exhibiting a significant relationship between the TAS and educational level and the Eating Disorder Inventory (EDI) subscales Interpersonal Distrust and Ineffectiveness. Age, body mass index, measures of depression, and eating pathology did not predict TAS scores.
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Abstract
One hundred obese women with a mean age of 39.2 years, and a mean body mass index (BMI) of 35.9 kg/m2 were evaluated before entering a treatment study for weight reduction. According to the results of a structured interview, subjects were divided into four groups: (1) no overeating episodes, (2) episodic overeating episodes without the feeling of loss of control, (3) overeating plus the sense of loss of control (binge eating), and (4) full diagnostic criteria for binge eating disorder (BED). One-way analyses of variance (ANOVAs) revealed significant positive associations between binge eating and eating/weight-related characteristics such as a history of frequent weight fluctuations, the amount of time spent dieting, drive for thinness, and a tendency for disinhibition of eating. Furthermore, subjects exhibited more feelings of ineffectiveness, stronger perfectionistic attitudes, more impulsivity, less self-esteem, and less interoceptive awareness the more problems with binge eating they reported. The results support the idea that binge eaters might be a distinct subgroup among the obese population, and corroborate the utility of a diagnosis of BED in identifying the most disturbed obese subjects with regard to the variables tested.
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Abstract
We assessed the correlation between a self-report questionnaire and an expert-rating including an initial interview and a longitudinal evaluation on the diagnosis of binge eating disorder (BED) in a sample of 100 obese women participating in a treatment program for weight reduction. The level of diagnostic agreement between patient-rating and expert-rating with regard to the presence or absence of BED was modest, with a kappa value of .57. According to Shrout, Spitzer, and Fleiss (Archives of General Psychiatry, 44, 172-177, 1987) this represents fair to good agreement beyond chance. The self-report instrument did not produce higher estimates of the frequency of BED in this selected sample of treatment seekers than the expert-rating, as observed in studies on the epidemiology of bulimia nervosa in community samples. The questionnaire identified 40 cases of BED, the expert-rating 43 cases. The results indicate that the disagreement between self-report and interview was mainly due to discordances in three of the diagnostic criteria of BED--namely loss of control, marked distress regarding binge eating, and the frequency requirement of two binge eating episodes per week for a 6-month period. Inconsistencies between subjects and clinicians with regard to the definition of an overeating episode and with regard to the behavioral indicators of loss of control did not lead to differences between self-report and observer-rating in the final diagnosis of BED.
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Abstract
Although much of the psychotherapy for psychiatric disorders is conducted on a weekly basis, several researchers in the field of bulimia nervosa have utilized a more intensive approach as a means to strengthen treatment effects. A second issue concerns the amount of emphasis that should be placed on encouraging the interruption of bulimic symptoms early in treatment. In the current study we systematically studied these two issues. Subjects were randomly assigned to one of four forms of cognitive-behavioral group psychotherapy, the four cells differing on the variables of intensity and emphasis on abstinence. The results indicate that a high intensity approach, an early abstinence approach, or a combination of these two approaches are all significantly more effective in inducing remission in patients with bulimia nervosa compared with a weekly psychotherapy that uses the same manual-based cognitive-behavioral therapy approach.
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Abstract
A reanalysis of treatment response and relapse was performed using survival analysis in a 12-week clinical trial of cognitive behavioral group psychotherapy for the treatment of bulimia nervosa. One hundred forty-three (143) bulimic women with high incidence of binge eating, self-induced vomiting, and/or laxative abuse were randomly assigned to one of four possible treatment conditions that consisted of a combination of two factors: (1) emphasis on abstinence (high and low), and (2) treatment intensity (high and low). "Initial" and "maintained" response to treatment based on "total" and "near" abstinence criteria were determined using self-reported binge eating, vomiting, and laxative use data. Results suggest that an emphasis on abstinence appears important in achieving initial abstinence, whereas intensity of treatment may be important in maintaining abstinence.
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Abstract
This study compared the shoplifting patterns of 27 bulimic and 25 nonbulimic shoplifters. Bulimic shoplifters often stole food, but usually also stole other items. Nonbulimic shoplifters reported starting to steal at an earlier age, weighed more than bulimic shoplifters, and were more likely to endorse antisocial reasons for shoplifting.
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Abstract
The authors describe a series of 14 patients with bulimia nervosa who regularly spent long periods of time in saunas as a weight-control technique. This practice is probably more common in parts of the world where Finnish saunas are in widespread use. Many of these patients also engaged in other behaviors that resulted in dehydration, such as diuretic abuse and laxative abuse.
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Estimated lifetime prevalence of trichotillomania in college students. J Clin Psychiatry 1991; 52:415-7. [PMID: 1938977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND Trichotillomania, a disorder of hair pulling, has been considered a rare condition. Estimations of the prevalence of this disorder have been based largely on clinical experience, and there have been no estimates of its prevalence based on data collected from a large, nonclinical population. METHOD 2579 freshman college students at two state universities and one liberal arts college were asked to provide written responses to questions designed to practically apply DSM-III-R criteria for trichotillomania and estimate the prevalence of trichotillomania in this population. RESULTS 2534 students (97.9% of the study population) responded. We found a 0.6% lifetime prevalence of DSM-III-R trichotillomania for both male and female respondents. Hair pulling resulting in visible hair loss, but failing to meet full DSM-III-R criteria, was identified in 1.5% of males and 3.4% of females. CONCLUSION Trichotillomania may not be as rare as previously suspected and may affect males as often as females.
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Abstract
Bulimic subjects who responded to intensive group psychotherapy plus imipramine or placebo or to imipramine alone (N = 68) were assigned to 4-month maintenance with weekly support groups and/or medication (placebo or imipramine) and were evaluated 6 months after initial treatment (N = 61). Thirty percent of the subjects relapsed during the 6 months. Initial treatment with group psychotherapy plus placebo or imipramine was associated with a lower relapse rate than initial treatment with imipramine alone. Neither attendance at the maintenance group sessions nor imipramine maintenance was associated with better outcome.
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Abstract
Patients who have bulimia nervosa and are overweight have received little attention in the medical literature. The authors identified 25 patients who weighed greater than or equal to 130% of their ideal body weight out of a series of 591 patients with bulimia nervosa. This subgroup was contrasted with a sample of 25 patients with bulimia nervosa who were 90% to 110% of their ideal body weight. Members of the overweight bulimia nervosa group were binge-eating and vomiting less frequently than the comparison group but were more likely to be abusing laxatives, and to report a history of self-injurious behavior and suicide attempt(s). Both groups reported frequent binge-eating.
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Abstract
This study compared two subgroups of women of normal weight with bulimia nervosa: those with a history of anorexia nervosa and those without such a history. Those with a history of anorexia nervosa indicated a desired body weight significantly lower than those without the history. Those with a history of anorexia nervosa were more likely to abuse laxatives and less likely to self-induce vomiting. Both groups reported feeling fat and worrying a great deal about weight and shape issues.
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A comparison study of antidepressants and structured intensive group psychotherapy in the treatment of bulimia nervosa. ARCHIVES OF GENERAL PSYCHIATRY 1990; 47:149-57. [PMID: 2405806 DOI: 10.1001/archpsyc.1990.01810140049008] [Citation(s) in RCA: 130] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Previous research on the treatment of outpatients with bulimia nervosa has focused on two treatment strategies: (1) drug therapy, primarily using tricyclic antidepressants, and (2) psychotherapy, often employing behavioral and cognitive behavioral techniques. We report here the short-term treatment outcome of a 12-week comparison trial of bulimic outpatients who were randomly assigned to one of four treatment cells: (1) imipramine hydrochloride treatment, (2) placebo treatment, (3) imipramine treatment combined with intensive group psychotherapy, and (4) placebo treatment combined with intensive group psychotherapy. All three active treatment cells resulted in significant reductions in target-eating behaviors and in a significant improvement in mood relative to placebo treatment. However, the results also suggested that the amount of improvement obtained with the intensive group psychotherapy component was superior to that obtained with antidepressant treatment alone. The addition of antidepressant treatment to the intensive group psychotherapy component did not significantly improve outcome over intensive group psychotherapy combined with placebo treatment in terms of eating behavior, but did result in more improvement in the symptoms of depression and anxiety.
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Abstract
In a review of the records of 454 patients with bulimia nervosa, 87 (19.2%) reported having a history of weight greater than 130% ideal body weight, although they were normal weight at evaluation. As contrasted to patients who had no history of having been overweight, this group of patients had a later onset of bulimia symptoms, weighed more and were more likely to be very dissatisfied with their current weight and to fear becoming overweight. The eating problems were similar in both groups.
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The changing population of bulimia nervosa patients in an eating disorders program. HOSPITAL & COMMUNITY PSYCHIATRY 1989; 40:1188-9. [PMID: 2807227 DOI: 10.1176/ps.40.11.1188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Response to alternative antidepressants in imipramine nonresponders with bulimia nervosa. J Clin Psychopharmacol 1989; 9:291-3. [PMID: 2671061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The authors report the results of open-label antidepressant trials in a series of normal weight bulimic women who showed an inadequate response to an initial trial of imipramine hydrochloride as part of a treatment comparison study. The results indicate that a significant percentage of subjects responded to a second trial of an alternative agent. Overall, 47% had a complete remission of symptoms during the second trial, usually with a monoamine oxidase inhibitor or fluoxetine. The authors stress the importance of persisting in trials of alternative agents if bulimic patients fail to respond to an initial trial.
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