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Abstract A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.

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Abstract Subterranean ecosystems (comprising terrestrial, semi-aquatic, and aquatic components) are increasingly threatened by human activities; however, the current network of surface-protected areas is inadequate to safeguard subterranean biodiversity. Establishing protected areas for subterranean ecosystems is challenging. First, there are technical obstacles in mapping three-dimensional ecosystems with uncertain boundaries. Second, the rarity and endemism of subterranean organisms, combined with a scarcity of taxonomists, delays the accumulation of essential biodiversity knowledge. Third, establishing agreements to preserve subterranean ecosystems requires collaboration among multiple actors with often competing interests. This perspective addresses the challenges of preserving subterranean biodiversity through protected areas. Even in the face of uncertainties, we suggest it is both timely and critical to assess general criteria for subterranean biodiversity protection and implement them based on precautionary principles. To this end, we examine the current status of European protected areas and discuss solutions to improve their coverage of subterranean ecosystems.

Centipedes of temperate regions can be found in various habitats, including forest litter, soil or caves. Slovenia, situated in the Northwestern Balkans, has rich centipede fauna, with one of the earliest scientific descriptions of a cave centipede, Lithobius stygius Latzel, 1880, from Postojnska jama. Many lithobiomorph species have been reported from Slovenian caves, but the data on their occurrence are scattered in the literature or public collections, and several specimens have even remained unexamined. Here we present the overview of lithobiomorph centipedes found in Slovenian caves. Altogether, 21 lithobiomorph species were found in 160 localities. The majority of the records, 319 out of 410, are published for the first time. Only three species are considered exclusively subterranean species, L. stygius, L. zveri and Eupolybothrus obrovensis, while other species are surface dwellers. The potential explanation of surface species presence in caves is discussed. We comment on cases of unresolved taxonomical status and present suggestions for further research needed to resolve them. Even though lithobiomorph centipedes often occur in caves, their role and importance in subterranean habitats remain to be studied.

The Western Balkan’s Vjetrenica Cave in southern Bosnia and Herzegovina is renowned for high richness of subterranean species. However, the data on its fauna have been published only in monographs printed in a small number of copies, making them hardly accessible to the wider scientific community. To overcome this issue, we compiled the data from published monographs with the data from our own recent field surveys. Further, as they are connected via water channels or small crevices in bedrock, we defined the Vjetrenica Cave System as a system comprising Vjetrenica and Bjelušica Caves and Lukavac Spring. Altogether, 93 troglobiotic, i.e., obligate subterranean aquatic (48) and terrestrial (45), taxa were reported for the system, verifying the Vjetrenica Cave System as the second richest locality in subterranean biodiversity in the world. The global uniqueness of the system is also reflected in the fact that as many as 40 troglobiotic species were described from the system. Finally, we reviewed the factors endangering this unique subterranean community and questioned whether it will withstand human-induced changes and pressures due to infrastructural development in southern Bosnia and Herzegovina.

The Dinaric Karst is a global hotspot for subterranean diversity, with two distinct peaks of species richness in the northwest and southeast, and an area of a lower species richness in the central part. In this article, we present a species list and describe the ecological conditions of the Lukina jama–Trojama cave system, located in the central part of the Dinaric Karst. This cave system is the deepest and one of the most logistically challenging cave systems sampled so far in the Dinaric Karst. Repeated sampling resulted in a list of 45 species, including 25 troglobionts, 3 troglophiles, 16 stygobionts, and 1 stygophile. Most of the recorded species are endemic to the Velebit Mountain, while three species are endemic to the Lukina jama–Trojama cave system. Within the system, species richness peaks in the deepest third of the cave, most likely reflecting the harsh ecological conditions in the upper parts, including ice, cold winds, and occasional waterfalls. Milder and more stable deeper parts of the cave contain a rich subterranean species community, part of which is associated with two very distinct aquatic habitats, the cave hygropetric and the phreatic zone. The newly recognized hotspot of subterranean biodiversity in the central Dinaric Karst, which has emerged between the two known centers of biodiversity, further highlights the species richness in large cave systems, but also challenges the diversity patterns in the Dinaric Karst overall.

Almost 200 years of continuous and systematic research in subterranean habitats of the Dinaric Karst and adjoining areas have resulted in the discovery of more than 400 specialized subterranean beetles. Among these, a special place belongs to the morphologically well distinguished and elusive, so called aphaenopsoid trechine beetles, which are characterized by a prolonged head, pronotum and appendages, and widened, ovoid-shaped elytra. Two new species of aphaenopsoid trechines – Derossiella lukici sp. n. from two deep pits on Mt Biokovo, Croatia, and Adriaphaenops petrimaris sp. n. from Pištet 4 Cave, Kameno more, Montenegro – are described, illustrated, and compared with closely related congeners. Identification keys for both genera and an annotated catalogue for all Adriaphaenops species, as well as data on the distribution and the ecology of these remarkable species, are provided and discussed.

Nemaspela Šilhavý, 1966 (Opiliones: Nemastomatidae) is a genus of exclusively troglobiotic harvestmen species inhabiting caves in the Crimea, Caucasus and Balkan Peninsula. In this paper, Nemaspela borkoae sp. nov., recently found in four caves in Montenegro, is described. The new species is characterized by its small body, 1.5–2.1 mm long, and very long, thin appendages, with legs II about 15 times as long as the body. Although very similar, Nemaspela ladae Karaman, 2013 and N. borkoae sp. nov. can be easily distinguished by the terminally rounded vs conical glans, straight vs conspicuously ventrally bent pedipalp tarsus on its proximal portion and pedipalp tarsus measuring about ½ vs ⅔ tibia length. Nemaspela ladae and N. borkoae sp. nov. constitute the western Nemaspela group, both missing the male cheliceral apophysis present in all species of the eastern Nemaspela group from the Crimea and Caucasus, except in N. femorecurvata Martens, 2006. However, according to the glans morphology, N. borkoae sp. nov. seems much more closely related to several species from the Caucasus than to N. ladae from the Balkan Peninsula. We speculate that N. ladae and N. borkoae sp. nov. might originate from two epigean ancestral lineages.

Diplura is a group of entognathous hexapods, often considered a sister group to insects. They play an important role in recycling organic matter in soil and subterranean terrestrial ecosystems. The Campodeidae is the most diverse family, divided into four subfamilies. The subfamily Plusiocampinae has a subterranean life-style with many species distributed in the Euro-Mediterranean area. The incertae sedis tachycampoids (“lignée Tachycampoïde”) is a group within the family Campodeidae that share with the Plusiocampinae a strong preference for subterranean habitats and several morphological characters, such as slender body shape, elongated appendages, considerable increment in the number of antennomeres and cercal articles, and complexity of sensorial structures. The present monograph provides a taxonomic revision of the subfamily Plusiocampinae and the genera belonging to the tachycampoid lineage from Europe and the Mediterranean region. It comprises detailed morphological descriptions and illustrations together with data on the habitats and distributions of 87 species, 10 subspecies and 11 affinis forms. Seven new species are described among those, namely: Plusiocampa (Plusiocampa) apollo Sendra, Giachino & Vailati sp. nov., P. (P.) chiosensis Sendra & Gasparo sp. nov., P. (P.) dublanskii Sendra & Turbanov sp. nov., P. (P.) hoffmanni Sendra & Paragamian sp. nov., P. (P.) rhea Sendra sp. nov., P. (P.) ternovensis Sendra & Borko sp. nov. and P. (Venetocampa) ferrani Sendra & Delić sp. nov.

Abstract Molecular taxonomy often uncovers cryptic species, reminding us that taxonomic incompleteness is even more severe than previous thought. The importance of cryptic species for conservation is poorly understood. Although some cryptic species may be seriously threatened or otherwise important, they are rarely included in conservation programs as most of them remain undescribed. We analysed the importance of cryptic species in conservation by scrutinizing the South European cryptic complex of the subterranean amphipod Niphargus stygius sensu lato. Using uni- and multilocus delineation methods we show that it consists of 15 parapatric and sympatric species, which we describe using molecular diagnoses. The new species are not mere “taxonomic inflation” as they originate from several distinct branches within the genus and coexist with no evidence of lineage sharing. They are as evolutionarily distinct as average nominal species of the same genus. Ignoring these cryptic species will underestimate the number of subterranean endemics in Slovenia by 12 and in Croatia by four species, although alpha diversity of single caves remains unchanged. The new taxonomy renders national Red Lists largely obsolete, as they list mostly large-ranged species but omit critically endangered single-site endemics. Formal naming of cryptic species is critical for them to be included in conservation policies and faunal listings.