Biodiversity Data Journal :
Taxonomy & Inventories
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Corresponding author: Michele Rossini (micros.naturae@gmail.com)
Academic editor: J. Adilson Pinedo-Escatel
Received: 05 Feb 2024 | Accepted: 14 May 2024 | Published: 14 Jun 2024
© 2024 Michele Rossini, Giulio Montanaro, Olivier Montreuil, Sergei Tarasov
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Rossini M, Montanaro G, Montreuil O, Tarasov S (2024) Towards computable taxonomic knowledge: Leveraging nanopublications for sharing new synonyms in the Madagascan genus Helictopleurus (Coleoptera, Scarabaeinae). Biodiversity Data Journal 12: e120304. https://doi.org/10.3897/BDJ.12.e120304
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Numerous taxonomic studies have focused on the dung beetle genus Helictopleurus d’Orbigny, 1915, endemic to Madagascar. However, this genus stilll needs a thorough revision. Semantic technologies, such as nanopublications, hold the potential to enhance taxonomy by transforming how data are published and analysed. This paper evaluates the effectiveness of nanopublications in establishing synonyms within the genus Helictopleurus.
In this study, we identify four new synonyms within Helictopleurus: H. rudicollis (Fairmaire, 1898) = H. hypocrita Balthasar, 1941 syn. nov.; H. vadoni Lebis, 1960 = H. perpunctatus Balthasar, 1963 syn. nov.; H. halffteri Balthasar, 1964 = H. dorbignyi Montreuil, 2005 syn. nov.; H. clouei (Harold, 1869) = H. gibbicollis (Fairmaire, 1895) syn. nov. Helictopleurus may have a significantly larger number of synonyms than currently known, indicating potentially inaccurate estimates about its recent extinction.
We also publish the newly-established synonyms as nanopublications, which are machine-readable data snippets accessible online. Additionally, we explore the utility of nanopublications in taxonomy and demonstrate their practical use with an example query for data extraction.
dung beetles, taxonomy, nomenclature, machine-readable data, SPARQL, ontology, Madagascar, extinction
The dung beetle genus Helictopleurus d’Orbigny, 1915, which comprises 71 species (
A recent revision of the Helictopleurus fungicola species-group (
The potential underestimation of synonyms in Helictopleurus suggests that future research could further reduce the number of recognised species in the genus. Consequently, the reported extinction of 50% of Helictopleurus species during the 20th century (
We use nanopublications to share our results regarding the synonymies. A nanopublication represents a minimal unit of scientifically meaningful information that can be used to describe virtually anything (
The studied specimens are deposited in the following institutes:
Label data of the examined type specimens is provided in Darwin Core (DwC) format. We investigated only the genitalia of the type specimens whose identity could not be determined using external morphology alone. Specimens were photographed using a Canon EOS 5D Mark III and a Canon MP-E 65mm 2,8 1-5x macro lens. Images were edited in Adobe Photoshop. We used TaxonWorks to manage and retrieve the taxonomic history of the taxa treated in this study. The species distribution maps were generated in QGIS by assembling occurrence data from FinBIF (Finnish Biodiversity Information Facility), type and non-type specimens from the MNHN and NMPC. FinBIF data were retrieved in R, using the FinBIF package (
The nanopublications were generated using the nanodash service, offered by Knowledge Pixels. Due to a collaborative effort between Pensoft Publishers and Knowledge Pixels, this service is accessible through the Biodiversity Data Journal (BDJ) portal. It enables the creation of nanopublications that can be seamlessly integrated with conventional publications for release in BDJ, a process we utilised in this research.
Nanopublications can be queried using the endpoints at https://query.np.trustyuri.net. The exemplary SPARQL query, which is designed to retrieve all synonyms along with their corresponding valid names, is available via this link and the Supplementary Material (Suppl. material
This query uses a SPARQL endpoint provided by Knowledge Pixels to select synonyms created using the nanodash service. Specifically, it searches for nanopublications of the type OrganismTaxonToOrganismTaxonAssociation.
Helictopleurus halffteri
Type specimens of Helictopleurus.
Distribution maps of Helictopleurus.
Helictopleurus dorbignyi
Within the semivirens group, H. halffteri may be related to H. seminiger. Males can be distinguished by the clypeal tubercle simple (laterally connected to two ridges in H. seminiger) and the frontoclypeal carina trituberculate (simple in H. seminiger). No female specimens of H. seminiger are known, as the type series includes the male lectotype only (see "Taxon discussion" below).
Antsianaka and Lac Alaotra (Fig.
The Helictopleurus semivirens species-group includes 10 species: H. aeneoniger Lebis, 1960, H. cambeforti Montreuil, 2005, H. halffteri Balthasar, 1964, H. heidiae Montreuil, 2007, H. niger d’Orbigny, 1915, H. pseudoniger Montreuil, 2005, H. seminiger d’Orbigny, 1915, H. semivirens d’Orbigny, 1915, H. steineri Paulian & Cambefort, 1991 and H. tamatavensis Montreuil, 2005 (
Helictopleurus halffteri shares exclusive phenotypic traits with the members of the group, such as head ogival-shaped and elongated (unique within Helictopleurus); head of male often with clypeal tubercles, frontoclypeal carina and frontal tubercles and/or curved carina; dorsal side of the body very polished, fairly dark, dull to feebly shining; elytra visibly longer than pronotum with respect to the majority of Helictopleurus species.
The type series of H. dorbignyi is composed of the male holotype collected in Antsianaka, lake Alaotra and multiple male and female paratypes collected further south, in the Ranomafana National Park and nearby localities (Fianarantsoa) (Fig.
(i) the morphology of the female holotype of H. halffteri and its type locality suggest that this specimen is conspecific with the male holotype of H. dorbignyi. Thus, H. dorbignyi is established as junior subjective synonym of H. halffteri (H. dorbignyi syn. nov.).
(ii) The study of the female genitalia of H. halffteri and female paratypes of H. dorbignyi collected in Ranomafana indicates that they belong to different species. Therefore, a new Helictopleurus species from Ranomafana is waiting formal description.
Interestingly, the unique type specimen of H. seminiger was collected from Antsianaka – which is the same type locality as H. halffteri – and the species has never been recollected since 1892. These circumstances would make the identity of this taxon questionable. However, during our visit to the Paris museum, we could not study the genitalia of the lectotype of H. seminiger. Possibly, the differences observed on the cephalic processes between H. seminiger and H. halffteri represent a simple variation of a same species. An extensive review of the semivirens group would help to sort out unresolved questions that still hamper the correct identification of these cryptic taxa.
Oniticellus rudicollis
Liatongus rudicollis:
Helictopleurus rudicollis:
Helictopleurus hypocrita
Helictopleurus rudicollis belongs to the rudicollis group and can be readily distinguished from other members of the group, H. rubricollis and H. cribricollis, by the pronotum and elytra metallic-green and shiny and elytra with lighter spots (elytra dark, dull, not metallic and without spots in both H. rubricollis and H. cribricollis). The separation of H. rudicollis from H. splendidus is still unclear, as the male of the latter was never described. Nonetheless, the following female characters could help in separating the two species: punctation of posterior third of pronotum evenly distributed in H. rudicollis (sparser in H. splendidus); lateral pronotal angles more expanded laterally in H. splendidus; median tubercle of frontal carina simple in H. rudicollis (bilobate in H. splendidus).
This species is widely distributed across eastern Madagascar, from the Sambava to Ifanadiana District (Fig.
The Helictopleurus rudicollis group includes four species (
Helictopleurus rudicollis was described from Tamatave and Antsianaka, which correspond to today’s Toamasina and Lac Alaotra, respectively, both located in central-eastern Madagascar (
During a recent collecting expedition in Madagascar (February 2022), we collected a series of conspecific specimens in Mandraka Park (-18.914266, 47.92477098), Analamazoatra (-18.939524, 48.418760) and Mantadia (-18.84549399, 48.42834902) National Parks, including one male, that may belong to H. splendidus. However, a detailed comparison of the morphology of these specimens with the types of H. splendidus and H. rudicollis is needed to confirm this identification and the taxonomic status of H. splendidus.
Helictopleurus vadoni
Helictopleurus parvulus
Helictopleurus perpunctatus
Helictopleurus vadoni is readily distinguished from congeneric species by the following combination of characters: elytra dark, with metallic tinges and characteristic brownish-orange spots mostly concentrated on the basal half of the intervals 1–5; elytral intervals with erected setae; pronotum metallic-green, shiny, densely and evenly punctated and setose, discal punctures coarser.
This species occurs in the Sambava and Maroantsetra Districts, north-eastern Madagascar (Fig.
Helictopleurus perpunctatus was described on two female specimens, without exact collecting locality. According to
Helictopleurus vadoni and H. viridiflavus are the only members of the group that occur in the humid-most eastern Madagascar, with occasional incursions into drier regions (Fig.
Oniticellus clouei
Helictopleurus clouei:
Oniticellus gibbicollis
Helictopleurus gibbicollis
Helictopleurus clouei is distinguished from other members of the H. quadripunctatus group by the pronotum metallic-green and shining (opaque, dark green to bluish in the other species); elytra orange to dark brown (black with a medial yellow stripe in H. perrieri), with poorly-defined dark spots at the base and apex (spots more distinct in H. quadripunctatus).
This species occurs in northern Madagascar and is relatively common in open habitat (Fig.
According to
Amongst the numerous Helictopleurus authored by L. M. H. Fairmaire (1820–1906), in 1895, he described H. gibbicollis from a single male specimen collected by C. A. Alluaud (1861–1949) in Diego Suarez (
Over the years and despite the intense dung beetle surveys carried out in Diego Suarez and surroundings (e.g.
The morphological examination of the syntypes of H. clouei and H. gibbicollis allowed us to establish the latter as a junior subjective synonym of H. clouei (H. gibbicollis syn. nov.). Probably, the different colour of the elytra of the two specimens (dark brown in the syntype of H. gibbicollis and bright orange in H. clouei) might have confused former authors, who kept considering H. clouei and H. gibbicollis as distinct species. However, the shape of the cephalic ornaments (carinas and frontal horn) and pronotum, the pronotal tegument, the colour pattern of elytra and the shape of the parameres clearly indicate that the two specimens are conspecific.
This new synonymy reduces the number of species of the quadripunctatus group to three.
The latest catalogue of Helictopleurus includes 60 species (
Contrasting this view, our prior and current study (
We created the nanopublications in the nanodash platform and integrated them into this article using the ARPHA writing tool provided by Pensoft. Each of our nanopublications contains a statement like "species name X is a subjective synonym (obo:NOMEN_0000285) of species name Y, published by M. Rossini, based on this article". The identifiers for the species names are supplied by ChecklistBank. Nanopublications are written using RDF language (akin to XML) by utilising terms from established ontologies and vocabularies (
Upon creation in nanodash, nanopublications are instantly accessible via a decentralised network maintained by Knowledge Pixels, which makes them available to anyone with internet access. It is important to note that nanopublications are not peer-reviewed upon creation. This approach facilitates the rapid sharing of biological data, but it also raises significant concerns within the community about the potential contamination with low-quality data. Notably, the nanodash platform distinctly labels nanopublications as either peer-reviewed or non-peer-reviewed, enabling their straightforward separation. We therefore believe that nanopublications do not seem to pose a threat to data quality or to flooding the informational landscape with undesirable content. Nevertheless, this topic requires further discussion within the scientific community.
Peer-reviewed nanopublications are directly linked to their corresponding papers, facilitating their citation. Therefore, integration of nanopublications with taxonomy shows great potential to enhance the citation and acknowledgment of taxonomic studies (
Nanopublications streamline the traditionally labour-intensive process of updating and accessing taxonomic information. In the conventional approach, researchers must diligently surf through relevant taxonomic papers to keep data up-to-date, a task that is both time-consuming and demanding. Similarly, major data aggregators, such as GBIF or the Catalogue of Life, face challenges in extracting information from traditional publications, often relying on manual processing or use of semi-supervised tools. Besides requiring additional effort, this also leads to delays in making the new data available after they are published. Nanopublications address these challenges by making taxonomic data immediately accessible and queryable online.
There is an ongoing initiative to link nanopublications with ZooBank (International Code of Zoological Nomenclature), aiming to make taxonomic and nomenclatural information swiftly available and broadly accessible to researchers. This integration could significantly accelerate the dissemination of taxonomic knowledge across various domains of science. Generally, nanopublications hold great promise for enhancing efficiency and reducing the time and effort required in managing taxonomic data.
We extend our sincere gratitude to Tobias Kuhn (Knowledge Pixels) for designing the SPARQL query used in this paper. We thank Stéphane Boucher for the digitalisation of the Helictopleurus collection (type and non-type specimens) stored at the Paris museum. Additionally, we would like to thank Erick Omar Martínez, Dmitry Dmitriev and two anonymous reviewers for the suggestions and improvements in the manuscript. Finally, we are grateful to the Malagasy Institut pour la Conservation des Ecosystèmes Tropicaux (MICET), Ministère de l'Environnement et du Développement Durable (Madagascar), as well as the University of Madagascar and Madagascar National Parks (Mandraka, Analamazoatra, Mantadia) for logistic and bureaucratic support to obtain research permits in Madagascar (#443/21/MED/SG/DGGE/DAPRNE/SCBE.Re). The authors acknowledge the BiCIKL project, Grant No 101007492.
Collecting data in DwC format.