Sergei Tarasov

Taxonomic studies generate large amount of descriptive information, yet species treatments are usually written directly as natural-language text. This approach makes the underlying phenotypic information difficult to extract, reuse computationally, and maintain consistently across studies. We present an integrated workflow connecting Phenoscript, GitHub, and Overleaf. Species descriptions are written semantically in Phenoscript using biological ontologies, making their phenotypic content computable and reusable; they are then stored and version-controlled in GitHub and synchronized with an Overleaf manuscript, where human-readable descriptions are rendered directly for publication. The workflow reduces repetitive copying and formatting, preserves revision history, and promotes the production of FAIR phenotypic and taxonomic data. We apply this workflow to the African dung beetle genus Amietina Cambefort, 1981 (Coleoptera: Scarabaeinae: Onthophagini), and describe four new species from Tanzania— A. bondarevi n. sp ., A. grebennikovi n. sp ., A. mazumbaiensis n. sp ., and A. praedicta n. sp .—bringing the total number of recognized species to eight. We also provide new distributional records, present an updated identification key, and discuss microendemism in Amietina across the Eastern Arc Mountains.

Background: The tribal classification of scarab dung beetles (Coleoptera: Scarabaeinae) is currently largely incomplete due to the lack of robust phylogenetic evidence supporting the assignment of many Afro-Eurasian and American genera to tribes. Methods: We used ultraconserved elements (UCEs) to infer phylogenetic relationships across most Afro-Eurasian dung beetle lineages, including 25 of the 27 extant genera currently incertae sedis . Results: We recovered full support for the monophyly of previously recognised tribes and for several phylogenetically and morphologically clearly delimited new tribal-level clades, allowing us to propose a complete tribal classification for all Afro-Eurasian dung beetle genera. Thirteen new tribes are described and diagnosed: Aphengoecini trib. nov. , Bohepilissini trib. nov. , Catharsiini trib. nov. , Chalconotini trib. nov. , Circelliini trib. nov. , Dwesasilvasedini trib. nov. , Haroldiini trib. nov. , Heliocoprini trib. nov. , Janssensantini trib. nov. , Macroderini trib. nov. , Nesovinsoniini trib. nov. , Pycnopanelini trib. nov. and Tanzanolini trib. nov . The tribe Coprini sensu novo is redefined as comprising three subtribes: Coprina, Onychothecina subtrib. nov. and Pedariina subtrib. nov . The tribe Odontolomini is downranked to a subtribe of Endroedyolini sensu novo , becoming Endroedyolini Odontolomina stat. nov . The tribe Onthophagini sensu novo is redefined and divided into three subtribes: Helictopleurina stat. nov. , Oniticellina stat. nov. and Onthophagina; the remaining former subtribes of Oniticellini (Attavicinina, Drepanocerina and Liatongina) are synonymised with Oniticellina; the subtribe Alloscelina of Onthophagini is synonymised with Onthophagina ( syn. nov. ). The tribe Panelini stat. rev. and sensu novo , comprising the single genus Panelus , is revalidated and redefined. Updated morphological diagnoses of Elassocanthonini, Gymnopleurini, Onitini and Scarabaeini are provided. The genus Phaedotrogus is synonymised with Haroldius (Haroldiini) ( syn. nov. ). An identification key to all Afro-Eurasian dung beetle tribes is provided. Discussion: Our results establish a robust phylogenetic framework and revised tribal classification for Afro-Eurasian Scarabaeinae dung beetles, providing a foundation for future taxonomic, comparative and macroevolutionary research.

The historical classification of dung beetles (subfamily Scarabaeinae) based on classical morphology has been repeatedly shown to be artificial due to widespread homoplasy. Previous attempts to revise, redefine and stabilize the classification within a molecular phylogenetic framework resulted in 101 genera treated as incertae sedis. Among these unplaced taxa are all genera endemic to Australia, New Guinea, New Caledonia and New Zealand. Here we examine tribal classifications among the subfamily Scarabaeinae based on ultraconserved elements (UCEs), with a targeted sampling aimed at examining systematic relationships of the Australasian endemic genera that, until now, have remained poorly supported. On the basis of these results, we reinstate a tribal name previously synonymous with Deltochilini. Mentophilini Lacordaire stat. rest. and sensu n . includes 31 genera endemic to Australasia. Additionally, a new tribe is proposed for a distinct lineage that is supported by both morphology and phylogeny. Boletoscapterini trib. n . consists of a single Australian genus, Boletoscapter Matthews. We discuss the validity of the tribe Epilissini and recommend not recognizing the tribe until future revisionary work redefines the distinct clades. Following these taxonomic changes, 23 tribes within Scarabaeinae are recognized as valid and 47 scarabaeine genera remain unplaced.

Five indigenous species of Scarabaeinae are known from Mauritius island, classified into two genera: the monotypic Nesovinsonia Martinez & Pereira, 1958 and Nesosisyphus Vinson, 1946. This study conducts a taxonomic review of the latter genus Nesosisyphus, and evaluates its recent extinction using historical and new occurrence records, subfossils, and niche modeling. We provide the first molecular phylogeny and evaluate the evolutionary relationships of Nesosisyphus by comparing two different phylogenetic trees: the first, based on a Ultraconserved Elements (UCEs hereafter) dataset, and the second one, on three loci (28S, 16S, COI). We identify five Mauritian Nesosisyphus species, including a new extinct one, Nesosisyphus draco sp. n., from a 4,000 yr old subfossil. We diagnose, illustrate, and provide an updated key to all the sisyphine species from Mauritius, as well as the occurrence map. Our niche modeling analysis reveals a broader past distribution range for Mauritian sisyphines, now confined to small, disjunct forest patches due to extensive forest contraction and local extinctions.

Hymenoptera is a megadiverse insect order, yet the drivers of its massive radiation remain poorly understood. Here, we employ novel comparative phylogenetic methods that integrate computational ontologies with ancestral state reconstructions of 346 discrete morphological characters to investigate the tempo and mode of phenome evolution in Hymenoptera across both adults and larvae. We examine the interplay between phenotypic rates, selection, modularity, and lineage diversification over deep time. Our analyses reveal that both larval and adult phenomes experienced an early burst scenario during the Late Permian – Triassic. However, their evolution appears decoupled, which enhanced the overall evolvability of Hymenoptera. Moreover, major phenotypic transitions in the order are complex, multifaceted processes driven by directional selection. One such event—the emergence of the wasp waist— involved a fundamental reorganization of the adult phenome. This dramatic transformation shifted net diversification from negative to positive during the Triassic, thereby enabling the subsequent survival and explosive diversification of the apocritan lineage.

The dung beetle genus Scarabaeus (Coleoptera, Scarabaeinae, Scarabaeini), predominantly found in the arid regions of the Old World, includes three endemic species inhabiting the dry ecosystems of western and southern Madagascar. These species are presumed to form a monophyletic clade nested within the African Scarabaeus. Semantic modelling of phenotypes using ontologies represents a transformative approach to species description in biology, making phenotypic data FAIR and computable. The recently developed Phenoscript language enables the creation of semantic, computable species descriptions using a syntax akin to human natural language (NL). However, Phenoscript has not yet been tested as a tool for describing new taxa. In this study, we test the utility of Phenoscript by describing a new species, Scarabaeus (sensu lato) sakalava sp. nov. from Madagascar. The initial description is composed directly in Phenoscript, replacing the traditional natural language format. This Phenoscript description is then translated into a human-readable form using the Phenospy tool for publication purposes. Additionally, the Phenoscript description is converted into an RDF graph, making it understandable by computers using semantic technologies. Scarabaeus sakalava sp. nov. is found in western central Madagascar and is closely related to S. viettei (Paulian, 1953) from north-western Madagascar. We provide an updated identification key and distribution map for all Malagasy Scarabaeus and discuss their systematic placement.

Numerous taxonomic studies have focused on the dung beetle genusHelictopleurusd’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 genusHelictopleurus.In this study, we identify four new synonyms withinHelictopleurus:H. rudicollis(Fairmaire, 1898) =H. hypocritaBalthasar, 1941syn. nov.;H. vadoniLebis, 1960 =H. perpunctatusBalthasar, 1963syn. nov.;H. halffteriBalthasar, 1964 =H. dorbignyiMontreuil, 2005syn. nov.;H. clouei(Harold, 1869) =H. gibbicollis(Fairmaire, 1895)syn. nov.Helictopleurusmay 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.

Taxonomy has long struggled with analysing vast amounts of phenotypic data due to computational and accessibility challenges. Ontology-based technologies provide a framework for modelling semantic phenotypes that are understandable by computers and compliant with FAIR principles. In this paper, we explore the use of Phenoscript, an emerging language designed for creating semantic phenotypes, to produce computable species descriptions. Our case study centers on the application of this approach to dung beetles (Coleoptera, Scarabaeinae).We illustrate the effectiveness of Phenoscript for creating semantic phenotypes. We also demonstrate the ability of the Phenospy python package to automatically translate Phenoscript descriptions into natural language (NL), which eliminates the need for writing traditional NL descriptions. We introduce a computational pipeline that streamlines the generation of semantic descriptions and their conversion to NL. To demonstrate the power of the semantic approach, we apply simple semantic queries to the generated phenotypic descriptions. This paper addresses the current challenges in crafting semantic species descriptions and outlines the path towards future improvements. Furthermore, we discuss the promising integration of semantic phenotypes and nanopublications, as emerging methods for sharing scientific information. Overall, our study highlights the pivotal role of ontology-based technologies in modernising taxonomy and aligning it with the evolving landscape of big data analysis and FAIR principles.

The Phenoscape project has developed ontology-based tools and a knowledge base that enables the integration and discovery of phenotypes across species from the scientific literature. The Phenoscape TraitFest 2023 event aimed to promote innovative applications that adopt the capabilities supported by the data in the Phenoscape Knowledgebase and its corresponding semantics-enabled tools, algorithms and infrastructure. The event brought together 26 participants, including domain experts in biodiversity informatics, taxonomy and phylogenetics and software developers from various life-sciences programming toolkits and phylogenetic software projects, for an intense four-day collaborative software coding event. The event was designed as a hands-on workshop, based on the Open Space Technology methodology, in which participants self-organise into subgroups to collaboratively plan and work on their shared research interests. We describe how the workshop was organised, the projects developed and outcomes resulting from the workshop, as well as the challenges in bringing together a diverse group of participants to engage productively in a collaborative environment.