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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.

Abstract Background Cardiac positron emission tomography (PET) offers non-invasive assessment of perfusion and left ventricular (LV) function from a single dynamic scan. However, no prior assessment of mitral regurgitation severity by PET has been presented. Application of indicator dilution techniques and gated image analyses to PET data enables calculation of forward stroke volume and total LV stroke volume. We aimed to evaluate a combination of these methods for measurement of regurgitant volume (RegVol) and fraction (RegF) using dynamic 15O-water and 11C-acetate PET in comparison to cardiovascular magnetic resonance (CMR). Results Twenty-one patients with severe primary mitral valve regurgitation underwent same-day dynamic PET examinations (15O-water and 11C-acetate) and CMR. PET data were reconstructed into dynamic series with short time frames during the first pass, gated 15O-water blood pool images, and gated 11C-acetate myocardial uptake images. PET-based RegVol and RegF correlated strongly with CMR (RegVol: 15O-water r = 0.94, 11C-acetate r = 0.91 and RegF: 15O-water r = 0.88, 11C-acetate r = 0.84, p 30mL) was 95% for 15O-water and 92% for 11C-acetate. Conclusions LV regurgitation severity quantified using cardiac PET correlated with CMR and showed high accuracy for discriminating patients from healthy volunteers.

Abstract DNA barcoding identification needs a good characterization of intraspecific genetic divergence to establish the limits between species. Yet, the number of barcodes per species is many times low and geographically restricted. A poor coverage of the species distribution range may hamper identification, especially when undersampled areas host genetically distinct lineages. If so, the genetic distance between some query sequences and reference barcodes may exceed the maximum intraspecific threshold for unequivocal species assignation. Taking a group of Quercus herbivores (moths) in Europe as model system, we found that the number of DNA barcodes from southern Europe is proportionally very low in the Barcoding of Life Data Systems. This geographical bias complicates the identification of southern query sequences, due to their high intraspecific genetic distance with respect to barcodes from higher latitudes. Pairwise intraspecific genetic divergence increased along with spatial distance, but was higher when at least one of the sampling sites was in southern Europe. Accordingly, GMYC (General Mixed Yule Coalescent) single‐threshold model retrieved clusters constituted exclusively by Iberian haplotypes, some of which could correspond to cryptic species. The number of putative species retrieved was more reliable than that of multiple‐threshold GMYC but very similar to results from ABGD and jMOTU. Our results support GMYC as a key resource for species delimitation within poorly inventoried biogeographic regions in Europe, where historical factors (e.g., glaciations) have promoted genetic diversity and singularity. Future European DNA barcoding initiatives should be preferentially performed along latitudinal gradients, with special focus on southern peninsulas.

Abstract Background In this study, we investigate species limits in the cyanobacterial lichen genus Rostania (Collemataceae, Peltigerales, Lecanoromycetes). Four molecular markers (mtSSU rDNA, β-tubulin, MCM7, RPB2) were sequenced and analysed with two coalescent-based species delimitation methods: the Generalized Mixed Yule Coalescent model (GMYC) and a Bayesian species delimitation method (BPP) using a multispecies coalescence model (MSC), the latter with or without an a priori defined guide tree. Results Species delimitation analyses indicate the presence of eight strongly supported candidate species. Conclusive correlation between morphological/ecological characters and genetic delimitation could be found for six of these. Of the two additional candidate species, one is represented by a single sterile specimen and the other currently lacks morphological or ecological supporting evidence. Conclusions We conclude that Rostania includes a minimum of six species: R. ceranisca, R. multipunctata, R. occultata 1, R. occultata 2, R. occultata 3, and R. occultata 4,5,6. Three distinct Nostoc morphotypes occur in Rostania, and there is substantial correlation between these morphotypes and Rostania thallus morphology.

We revise the Afrotropical Agabus raffrayi species group, motivated by the discovery of new diversity in Kenya and South Africa. Whilst Agabus is mainly a holarctic genus, the Agabus raffrayi group is restricted to high altitude regions of eastern Africa and temperate parts of South Africa, from where we describe the southernmost Agabus in the world. The following new species are introduced: Agabus anguluverpus sp. nov. from Mount Kenya in central Kenya, Agabus austellus sp. nov. a widespread species in South Africa, Agabus riberae sp. nov. from the Kamiesberg and northeastern Cederberg ranges in the Northern and Western Cape Provinces of South Africa and Agabus agulhas sp. nov. from the Agulhas Plain, Western Cape Province, South Africa. We provide a distribution map, a determination key for males, quantitative measurements of diagnostic characters, habitus photos and detailed photos of male genitalia for all described species in the group, as well as images of diagnostic characters and habitats. The presence or absence of an elongated section between the subapical broadening and the base of the apical and subapical teeth of the male aedeagus is a useful novel character, first revealed by our study. In contrast with the most recent revision of Afrotropical Agabus, we show that Agabus ruwenzoricus Guignot, 1936 is restricted to eastern Africa; South African records of this species having been based on misidentifications, no species of the group being common to southern and eastern Africa. We speculate that the raffrayi group may display phylogenetic niche conservatism, being restricted, as an originally temperate taxon, to higher elevations in tropical eastern Africa, but occurring at lower altitudes in temperate South Africa.

The island nation of Madagascar was surveyed extensively through a series of expeditions to determine the fauna of Naucoridae. Previously, 17 species in four genera had been reported from the country. All taxa previously recorded from Madagascar were re-collected, with the exception of three species, Macrocoris flavicollis Signoret, Temnocoris starmuhlneri Poisson, and Tsingala nossibeanus (Bergroth). Macrocoris flavicollis is removed from the list of species occurring in Madagascar. Within Laccocorini (Laccocorinae), a new genus, Gonioathrix n.gen. is described; Temnocoris and Tsingala are revised; three new species are described in Temnocoris (T. leachi n.sp., T. montandoni n.sp., T. poissoni n.sp.) and four in Tsingala (T. angulata n.sp., T. latiforma n.sp., T. spatulata n.sp., T. trilobata n.sp.). Lectotypes are designated for Afronaucoris madagascariensis (Montandon), Tsingala humeralis (Signoret), and T. naucoroides (Montandon). In Macrocorinae, a new species of Macrocoris, M. namorona n.sp., from Ranomafana National Park is described. These taxonomic actions bring the total for the country to five genera and 25 species. Distributions, habitat associations, and a key to the species are presented.

The genus Copelatus Erichson, 1832 (Coleoptera, Dytiscidae, Copelatinae) of Madagascar is revised in two parts. This review is restricted to the Copelatus species that have fewer than ten elytral + one submarginal stria, including all species except those of the erichsonii species group. Both morphological and molecular (mitochondrial COI) data are used in an integrative taxonomic approach. Thirteen species are recognised, of which five are described as new: Copelatus ankaratra sp. nov., Copelatus kely sp. nov., Copelatus pseudostriatus sp. nov., Copelatus safiotra sp. nov. and Copelatus vokoka sp. nov. Copelatus unguicularis Régimbart, 1903 and Copelatus apicalis Fairmaire, 1898 are both transferred to the genus Madaglymbus Shaverdo & Balke, 2008 (comb. nov.). Copelatus mimetes Guignot 1957 is a junior synonym of the widespread Afrotropical–Arabian Copelatus pulchellus (Klug, 1834) (syn. nov.). Copelatus marginipennis (Laporte, 1835) is reinstated (stat. nov.) as a valid species with Copelatus aldabricus Balfour-Browne, 1950 and Copelatus aldabricus var. simplex Guignot, 1952 as junior synonyms (syn. nov.). We designate lectotypes for Colymbetes marginipennis Laporte, 1835 and Copelatus obtusus Boheman, 1848. Copelatus peridinus Guignot, 1955 is recorded for Madagascar for the first time and Copelatus nodieri Régimbart, 1895 is rejected as a species present in Madagascar.

Diving beetles are generally aquatic and live submerged in water during larval and adult stages. A few groups have colonised hygropetric habitats and fewer species still can possibly be referred to as terrestrial. Here we describe six new Copelatine species that were mainly found in dry shallow forest floor depressions in the eastern and northeastern lowland humid forests of Madagascar. Three new species are described in each of the two genera Copelatus and Madaglymbus: Copelatus amphibius sp. nov., Copelatus betampona sp. nov., Copelatus zanatanensis sp. nov., Madaglymbus kelimaso sp. nov., Madaglymbus menalamba sp. nov., and Madaglymbus semifactus sp. nov. Diagnosis, description, known distribution, ecology, and conservation notes are provided for each species. All species are illustrated with a dorsal habitus image, ventral and lateral views of the male penis, and parameres. Photographs of the unusual terrestrial habitats where the species were found are provided. Madaglymbus menalamba sp. nov. is also documented with macrophotos and videorecordings of the terrestrial locomotion and behaviour in the field. Although these species should not be classified as terrestrial, or even semi-terrestrial Dytiscidae, they seem to be specialists of very ephemeral aquatic habitats and stay put instead of disperse when the habitat dries up. It is hypothesised that this lifestyle and behaviour on Madagascar is restricted to the high-precipitation humid forest regions mainly in the east. It may also represent a transition step, or stepping-stone, towards becoming fully terrestrial, a step that the few known terrestrial Dytiscid taxa once passed through. It is very likely that this type of habitat is overlooked for aquatic beetles, not only in Madagascar, and the six species herein described may be just the “tip of the iceberg”.

We review the species of Bidessus of Madagascar and describe Bidessus anjozorobe sp. nov. from material collected in Anjozorobe forest. Anjozorobe is part of the Anjozorobe-Angavo Protected Area, which is an important corridor of transition forest between typical eastern humid forests and the residual sub-humid forest of the Central Highlands. Bidessus longistriga Régimbart, 1895 and Bidessus perexiguus Kolbe, 1883 are widespread but endemic low-altitude species on Madagascar. Bidessus nesioticus Guignot, 1956 is an alpine species described from near the peak of the Ankaratra mountain massifs at 2500 m a.s.l. We recollected the species for the first time since its description, in Ankaratra and in a new area above 2000 m a.s.l. in the Andringitra mountain further south. Bidessus cf. nero Gschwendtner, 1933 is tentatively recorded for Madagascar for the first time but further studies are needed to test the status of mainland and insular populations. Bidessus apicidens Biström & Sanfilippo, 1986 has not been recollected on Madagascar since 1970. All species are endemic to Madagascar except potentially Bidessus cf. ceratus and Bidessus cf. nero described from Uganda and the Democratic Republic of the Congo, respectively. The older records of the two non-endemic species Bidessus complicatus Sharp, 1904 and Bidessus ovoideus Régimbart, 1895 on Madagascar could not be verified.

Despite more than 250 years of taxonomic research, we still have only a vague idea about the true size and composition of the faunas and floras of the planet. Many biodiversity inventories provide limited insight because they focus on a small taxonomic subsample or a tiny geographic area. Here, we report on the size and composition of the Swedish insect fauna, thought to represent roughly half of the diversity of multicellular life in one of the largest European countries. Our results are based on more than a decade of data from the Swedish Taxonomy Initiative and its massive inventory of the country's insect fauna, the Swedish Malaise Trap Project The fauna is considered one of the best known in the world, but the initiative has nevertheless revealed a surprising amount of hidden diversity: more than 3,000 new species (301 new to science) have been documented so far. Here, we use three independent methods to analyze the true size and composition of the fauna at the family or subfamily level: (1) assessments by experts who have been working on the most poorly known groups in the fauna; (2) estimates based on the proportion of new species discovered in the Malaise trap inventory; and (3) extrapolations based on species abundance and incidence data from the inventory. For the last method, we develop a new estimator, the combined non-parametric estimator, which we show is less sensitive to poor coverage of the species pool than other popular estimators. The three methods converge on similar estimates of the size and composition of the fauna, suggesting that it comprises around 33,000 species. Of those, 8,600 (26%) were unknown at the start of the inventory and 5,000 (15%) still await discovery. We analyze the taxonomic and ecological composition of the estimated fauna, and show that most of the new species belong to Hymenoptera and Diptera groups that are decomposers or parasitoids. Thus, current knowledge of the Swedish insect fauna is strongly biased taxonomically and ecologically, and we show that similar but even stronger biases have distorted our understanding of the fauna in the past. We analyze latitudinal gradients in the size and composition of known European insect faunas and show that several of the patterns contradict the Swedish data, presumably due to similar knowledge biases. Addressing these biases is critical in understanding insect biomes and the ecosystem services they provide. Our results emphasize the need to broaden the taxonomic scope of current insect monitoring efforts, a task that is all the more urgent as recent studies indicate a possible worldwide decline in insect faunas.

The Laccophilus alluaudi species group is an interesting case of an endemic species radiation of Madagascar and the Comoros. To date, a single species, Laccophilus tigrinus Guignot, 1959 (Anjouan), is known from the Comoro Islands, with eight other species known from Madagascar. Here we review the Laccophilus alluaudi species group from the Comoro Islands based on partly new material. We recognize five species, out of which four are here described as new: L. mohelicus n. sp. (Mohéli), L. denticulatus n. sp. (Grande Comore), L. michaelbalkei n. sp. (Mayotte) and L. mayottei n. sp. (Mayotte). Based on morphology of male genitalia, we hypothesize that the five species form a monophyletic group and originated from a single colonization event from Madagascar. If confirmed, this would constitute one of the few examples of intra-archipelago diversification in the Comoros. The knowledge of species limits in relation to their distribution in the Comoros archipelago is also urgently needed in the face of rapid habitat degradation.

The larvae of the Malagasy whirligig beetle Dineutus sinuosipennis Laporte, 1840, identified using DNA sequence data, are described and illustrated for the first time, including detailed morphometric and chaetotaxic analyses of selected structures and a description of larval habitat. Larvae of the genus Dineutus Macleay, 1825 are diagnosed, and a key to identify the genera of the tribe Dineutini is presented. Larvae of Dineutus exhibit the characters traditionally recognized as autapomorphies of the Gyrinidae: body less sclerotized, egg bursters located on the parietal, one additional sensorial plate on the third antennomere, cardo and lacinia well developed, prementum completely divided, abdominal tracheal gills, and four terminal hooks on the pygopod. They also share with larvae of the other Dineutini genera these putative synapomorphies: numerous minute pore-like additional structures on the ultimate maxillary and labial palpomeres, coxal primary seta CO12 inserted submedially, and trochanteral primary seta TR2 absent. Larvae of Dineutus can be distinguished from those of other known genera of Dineutini by the posterior margin of the lacinia not dentate, tracheal gills plumose, parietal seta PA5 inserted relatively far from setae PA7–9, mandibular pores MNb and MNc inserted relatively far from each other, and tarsal seta TA1 inserted submedially.