Recommendations for the Standardisation of Open Taxonomic Nomenclature for Image-Based Identifications

Horton, Tammy; Marsh, Leigh; Bett, Brian J.; Gates, Andrew R.; Jones, Daniel O.B.; Benoist, Noëlie M.A.; Pfeifer, Simone; Simon-Lledó, Erik; Durden, Jennifer M.; Vandepitte, L.; Appeltans, Ward

doi:10.3389/fmars.2021.620702

Cited by 76 publications

(62 citation statements)

References 47 publications

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“…genus, family, class) followed by the use of open nomenclature (ON) signs applicable to image-based faunal analyses (e.g. indet., stet., inc.) as suggested by Horton et al (2021) . The use of ON signs allows standardisation and clarification of the uncertainty inherent in identification from image-based studies, thus enabling the subsequent use and comparability of generated datasets.…”

Section: Data Resourcesmentioning

confidence: 65%

Reef benthos of Seychelles - A field guide

Fassbender¹,

Stefanoudis²,

Filander³

et al. 2021

BDJ

632

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During the 2019 First Descent: Seychelles Expedition, shallow and deep reef ecosystems of the Seychelles Outer Islands were studied by deploying a variety of underwater technologies to survey their benthic flora and fauna. Submersibles, remotely operated vehicles (ROVs) and SCUBA diving teams used stereo-video camera systems to record benthic communities during transect surveys conducted at 10 m, 30 m, 60 m, 120 m, 250 m and 350 m depths. In total, ~ 45 h of video footage was collected during benthic transect surveys, which was subsequently processed using annotation software in order to assess reef biodiversity and community composition. Here, we present a photographic guide for the visual identification of the marine macrophytes, corals, sponges and other common invertebrates that inhabit Seychelles’ reefs. It is hoped that the resulting guide will aid marine biologists, conservationists, managers, divers and naturalists with the coarse identification of organisms as seen in underwater footage or live in the field. A total of 184 morphotypes (= morphologically similar individuals) were identified belonging to Octocorallia (47), Porifera (35), Scleractinia (32), Asteroidea (19), Echinoidea (10), Actiniaria (9), Chlorophyta (8), Antipatharia (6), Hydrozoa (6), Holothuroidea (5), Mollusca (2), Rhodophyta (2), Tracheophyta (2), Annelida (1), Crinoidea (1), Ctenophora (1), Ochrophyta (1) and Zoantharia (1). Out of these, we identified one to phylum level, eight to class, 14 to order, 27 to family, 110 to genus and 24 to species. This represents the first attempt to catalogue the benthic diversity from shallow reefs and up to 350 m depth in Seychelles.

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Section: Data Resourcesmentioning

confidence: 65%

Reef benthos of Seychelles - A field guide

Fassbender¹,

Stefanoudis²,

Filander³

et al. 2021

BDJ

632

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“…Molecularly well-defined temporary names for new species are likely to become more abundant and therefore critical to our knowledge of biodiversity in the coming years, and we need to ensure they are managed carefully and consistently. Recommendations for the use of open nomenclature have been proposed recently to attempt to standardise and overcome these issues ( Sigovini, Keppel & Tagliapietra, 2016 ; Horton et al, 2021 ) and it is hoped that these standard formats will be considered for use in both BOLD and GenBank.…”

Section: Discussionmentioning

confidence: 99%

Global gap-analysis of amphipod barcode library

Jażdżewska

Tandberg

Horton

et al. 2021

PeerJ

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In the age of global climate change and biodiversity loss there is an urgent need to provide effective and robust tools for diversity monitoring. One of the promising techniques for species identification is the use of DNA barcoding, that in Metazoa utilizes the so called ‘gold-standard’ gene of cytochrome c oxidase (COI). However, the success of this method relies on the existence of trustworthy barcode libraries of the species. The Barcode of Life Data System (BOLD) aims to provide barcodes for all existing organisms, and is complemented by the Barcode Index Number (BIN) system serving as a tool for potential species recognition. Here we provide an analysis of all public COI sequences available in BOLD of the diverse and ubiquitous crustacean order Amphipoda, to identify the barcode library gaps and provide recommendations for future barcoding studies. Our gap analysis of 25,702 records has shown that although 3,835 BINs (indicating putative species) were recognised by BOLD, only 10% of known amphipod species are represented by barcodes. We have identified almost equal contribution of both records (sequences) and BINs associated with freshwater and with marine realms. Three quarters of records have a complete species-level identification provided, while BINs have just 50%. Large disproportions between identification levels of BINs coming from freshwaters and the marine environment were observed, with three quarters of the former possessing a species name, and less than 40% for the latter. Moreover, the majority of BINs are represented by a very low number of sequences rendering them unreliable according to the quality control system. The geographical coverage is poor with vast areas of Africa, South America and the open ocean acting as “white gaps”. Several, of the most species rich and highly abundant families of Amphipoda (e.g., Phoxocephalidae, Ampeliscidae, Caprellidae), have very poor representation in the BOLD barcode library. As a result of our study we recommend stronger effort in identification of already recognised BINs, prioritising the studies of families that are known to be important and abundant components of particular communities, and targeted sampling programs for taxa coming from geographical regions with the least knowledge.

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“…For microorganisms, because of the vast diversity of bacteria and microbial eukaryotes and the lack of physical characters to separate species, for practical reasons they are often identified as OTUs, so the "dark taxa" issue applies only to macrofauna and megafauna. To resolve this issue, valid, resolvable 'temporary names' are needed, used in a consistent way and linked to all key databases (Horton et al, 2021). The Genomic Standards Consortium (GSC 17 ) and the GGBN and OBIS are currently trying to standardize approaches to improved integration of occurrence and sequence data or to provide links to these data in other databases (Rabone et al, 2019).…”

Section: Accessing Specimens and Samples For Access And Benefit Sharingmentioning

confidence: 99%

Marine Genetic Resources in Areas Beyond National Jurisdiction: Promoting Marine Scientific Research and Enabling Equitable Benefit Sharing

Rogers¹,

Baco

Escobar-Briones

et al. 2021

Front. Mar. Sci.

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Growing human activity in areas beyond national jurisdiction (ABNJ) is driving increasing impacts on the biodiversity of this vast area of the ocean. As a result, the United Nations General Assembly committed to convening a series of intergovernmental conferences (IGCs) to develop an international legally-binding instrument (ILBI) for the conservation and sustainable use of marine biological diversity of ABNJ [the biodiversity beyond national jurisdiction (BBNJ) agreement] under the United Nations Convention on the Law of the Sea. The BBNJ agreement includes consideration of marine genetic resources (MGR) in ABNJ, including how to share benefits and promote marine scientific research whilst building capacity of developing states in science and technology. Three IGCs have been completed to date with the fourth delayed by the Covid pandemic. This delay has allowed a series of informal dialogues to take place between state parties, which have highlighted a number of areas related to MGR and benefit sharing that require technical guidance from ocean experts. These include: guiding principles on the access and use of MGR from ABNJ; the sharing of knowledge arising from research on MGR in ABNJ; and capacity building and technology transfer for developing states. In this paper, we explain what MGR are, the methods required to collect, study and archive them, including data arising from scientific investigation. We also explore the practical requirements of access by developing countries to scientific cruises, including the sharing of data, as well as participation in research and development on shore whilst promoting rather than hindering marine scientific research. We outline existing infrastructure and shared resources that facilitate access, research, development, and benefit sharing of MGR from ABNJ; and discuss existing gaps. We examine international capacity development and technology transfer schemes that might facilitate or complement non-monetary benefit sharing activities. We end the paper by highlighting what the ILBI can achieve in terms of access, utilization, and benefit sharing of MGR and how we might future-proof the BBNJ Agreement with respect to developments in science and technology.

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Recommendations for the Standardisation of Open Taxonomic Nomenclature for Image-Based Identifications

Cited by 76 publications

References 47 publications

Reef benthos of Seychelles - A field guide

Reef benthos of Seychelles - A field guide

Global gap-analysis of amphipod barcode library

Marine Genetic Resources in Areas Beyond National Jurisdiction: Promoting Marine Scientific Research and Enabling Equitable Benefit Sharing

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