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Naming animals in images – a new guide to the process
Added on 2021-02-15 10:06:43 by Horton, Tammy
“The beginning of wisdom is to call things by their proper name” (Confucius) … but sometimes, giving a name to something is easier said than done... When we are looking at video and photographs of the deep-sea floor, we see the animals that live there, but determining what species they are is tricky. A new publication by NOC scientists provides a guide to getting the names right.
We need to be able to identify the animals in our images, and that need is growing rapidly as we survey more and more of the deep sea using Remotely Operated Vehicles (ROVs) and Autonomous Underwater Vehicles (AUVs), to assess the biodiversity of these remote ecosystems.
When we are unsure about the identity of an animal, it is often given a name such as ‘big red prawn?’, rather than the full scientific name we use when its identity is clear. When we see the same species of animal again, even though we don’t know what it actually is, it is important that we give it the same name. This, according to Confucius, is the beginning of wisdom.
By making sure we use the same name in the same way, we can make sure that we have good biodiversity data, and that these data can be easily understood and shared.
The new guide (Horton et al., 2021) provides rules for the use of open nomenclature signs, a way of indicating the level of certainty in an identification, in image-based biodiversity studies. This is one of numerous initiatives to improve biodiversity data collection and to make them more useful to other researchers, environmental managers and policy makers.
Lead author, Dr Tammy Horton said “Image-based biodiversity work is increasingly common but will always have limitations to the level of certainty in species identification. This is particularly critical in deep-sea studies where most of the animals are poorly known and we often encounter new species that have not been described before. Developing these clear rules for the use of open nomenclature will improve the clarity, precision, and comparability of biodiversity data.”
Drawing on expertise and experience from NOC, University of Southampton, the Charles Darwin Research Station (Ecuador), National Geographic Society (USA), Flanders Marine Institute (Belgium), and the Intergovernmental Oceanographic Commission (Belgium), the guide provides a simple flow chart to help in deciding on the term to use and at which level of identification, and also gives examples of recommended use of these terms for input to online databases (e.g. Ocean Biodiversity Information System), and in the preparation of catalogues of the fauna of an area.
Detail is provided on the use of the following terms:
Recommendations for the standardisation of open taxonomic nomenclature for image-based identifications.
Tammy Horton, Leigh Marsh, Brian James Bett, Andrew Russell Gates, Daniel O B Jones, Noëlie M.A. Benoist, Simone Pfeifer, Erik Simon-Lledó, Jennifer Durden, Leen Vandepitte, Ward Appeltans.
Frontiers in Marine Science, Deep-Sea Environments and Ecology. 08 February 2021
https://doi.org/10.3389/fmars.2021.620702
Image: A ‘big red prawn’ formally known as Cerataspis monstrosus – but can you be sure just from a photograph?
We need to be able to identify the animals in our images, and that need is growing rapidly as we survey more and more of the deep sea using Remotely Operated Vehicles (ROVs) and Autonomous Underwater Vehicles (AUVs), to assess the biodiversity of these remote ecosystems.
When we are unsure about the identity of an animal, it is often given a name such as ‘big red prawn?’, rather than the full scientific name we use when its identity is clear. When we see the same species of animal again, even though we don’t know what it actually is, it is important that we give it the same name. This, according to Confucius, is the beginning of wisdom.
By making sure we use the same name in the same way, we can make sure that we have good biodiversity data, and that these data can be easily understood and shared.
The new guide (Horton et al., 2021) provides rules for the use of open nomenclature signs, a way of indicating the level of certainty in an identification, in image-based biodiversity studies. This is one of numerous initiatives to improve biodiversity data collection and to make them more useful to other researchers, environmental managers and policy makers.
Lead author, Dr Tammy Horton said “Image-based biodiversity work is increasingly common but will always have limitations to the level of certainty in species identification. This is particularly critical in deep-sea studies where most of the animals are poorly known and we often encounter new species that have not been described before. Developing these clear rules for the use of open nomenclature will improve the clarity, precision, and comparability of biodiversity data.”
Drawing on expertise and experience from NOC, University of Southampton, the Charles Darwin Research Station (Ecuador), National Geographic Society (USA), Flanders Marine Institute (Belgium), and the Intergovernmental Oceanographic Commission (Belgium), the guide provides a simple flow chart to help in deciding on the term to use and at which level of identification, and also gives examples of recommended use of these terms for input to online databases (e.g. Ocean Biodiversity Information System), and in the preparation of catalogues of the fauna of an area.
Detail is provided on the use of the following terms:
- Genus sp. The use of this ON sign alone is discouraged, as it does not indicate the reason that the identification was not determined to the species level. Instead it should be combined with one of the open nomenclature signs below.
- Indeterminabilis (indet.) The ON sign indet. is taken to mean that the taxon is indeterminable beyond a certain taxonomic level. This is relevant to image-based identifications, where diagnostic characters are often not visible or resolvable in the image, which could be owing to the resolution of the image, or the orientation of the taxon in the field of view. This ON sign can be applied at any taxonomic rank.
- Stetit (stet.): This ON sign means it stood/stays or remained here, indicating the identification stopped at this taxonomic rank. Stetit can be employed for a variety of reasons such as indicating that it is a choice to go no further, i.e. “I called this taxon ‘Ostracoda stet.’ because I did not attempt to identify the ostracods any further; I simply noted they were ostracods and stopped there”.
- Incerta (inc.): The ON sign ‘inc.’ is used to indicate ‘uncertain identification’ and to replace the use of the question mark symbol ‘?’. In image-based identifications, this ON sign can be used at all taxonomic levels (e.g. Aristidae fam. inc.), while it is less likely to be used at higher taxonomic ranks when a physical specimen is available.
- Confer (cf.): The use of this ON indicates that the identifier cannot be certain of the identity of the species (or higher taxonomic rank) until a more detailed comparison can be made, for example with some type or reference material, or to consult a taxonomic expert. Since the terms cf. and aff. are often confused and their current usage is inconsistent, the term cf. is discouraged in application to image-based identifications, and in particular for use in online datasets. Where diagnostic features are unclear, the lowest level of identification should be moved up a rank to e.g. Calamocrinus sp. indet. (or Calamocrinus diomedae sp. inc.) instead of Calamocrinus cf. diomedae, and the information regarding the likely identity of the species should be included in the identificationRemarks field and/or in the corresponding text section of an image catalogue.
- Species affinis (sp. aff.): Imaged specimens are commonly identifiable to an entity close to, or with an affinity to, a known taxon (family, genus or species), but with clear distinction from it. This ON sign is often used in the taxonomic literature to signify that the identifier believes the taxon to be a new species. We recommend that the terms ‘sp. nov.’ and ‘sp. nov. aff.’ be avoided for use in online datasets.
Recommendations for the standardisation of open taxonomic nomenclature for image-based identifications.
Tammy Horton, Leigh Marsh, Brian James Bett, Andrew Russell Gates, Daniel O B Jones, Noëlie M.A. Benoist, Simone Pfeifer, Erik Simon-Lledó, Jennifer Durden, Leen Vandepitte, Ward Appeltans.
Frontiers in Marine Science, Deep-Sea Environments and Ecology. 08 February 2021
https://doi.org/10.3389/fmars.2021.620702
Image: A ‘big red prawn’ formally known as Cerataspis monstrosus – but can you be sure just from a photograph?
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