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Free-living aquatic nematodes are abundant, diverse and of general environmental importance. However, knowledge of species distributions of both marine and freshwater nematodes is sparse. Species distribution data are crucial for evaluating environmental impacts from human activities and to conduct integrated nematode community assessments. Basic knowledge on taxonomy and species descriptions is lacking for many regions due to decreasing taxonomic expertise, yet it is essential for biodiversity research and for building molecular sequence libraries for the application of methods such as environmental DNA. In order to encourage and facilitate taxonomic and descriptive work on this understudied group, we present here a framework for nematode species description. We begin by providing a brief overview of nematology history, then provide suggestions of microscopic methods that should be used and provide a list of characters essential for morphometric species descriptions. Finally, we briefly discuss common molecular sequencing approaches that are commonly used in nematode taxonomic literature.

Hox genes are central to metazoan body plan formation, patterning and evolution, playing a critical role in cell fate decisions early in embryonic development in invertebrates and vertebrates. While the archetypical Hox gene cluster consists of members of nine ortholog groups (HOX1-HOX9), arrayed in close linkage in the order in which they have their anterior-posterior patterning effects, nematode Hox gene sets do not fit this model. The Caenorhabditis elegans Hox gene set is not clustered and contains only six Hox genes from four of the ancestral groups. The pattern observed in C. elegans is not typical of the phylum, and variation in orthologue set presence and absence and in genomic organisation has been reported. Recent advances in genome sequencing have resulted in the availability of many novel genome assemblies in Nematoda, especially from taxonomic groups that had not been analysed previously. Here, we explored Hox gene complements in high-quality genomes of 80 species from all major clades of Nematoda to understand the evolution of this key set of body pattern genes and especially to probe the origins of the "dispersed" cluster observed in C. elegans. We also included the recently available high-quality genomes of some Nematomorpha as an outgroup. We find that nematodes can have Hox genes from up to six orthology groups. While nematode Hox "clusters" are often interrupted by unrelated genes we identify species in which the cluster is intact and not dispersed., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Termites are important ecosystem engineers and play key roles in modulating microbial communities within and outside their mounds. Microbial diversity within termite mounds is generally lower than surrounding soils, due to termite-associated antimicrobial compounds and active sanitary behaviours. Microbial symbionts of termites can also influence the microbial landscape, by inhibiting or out-competing other microbes. Certain members of the arid habitat fungal genus Podaxis (Agaricomycetes; Agaricaceae) are symbiotic with savannah specialist grass-cutting termites, and have the potential to influence mound-associated microbiomes. To test this, we characterized fungal (ITS2) and bacterial (16S rRNA) communities within and outside 49 Trinervitermes trinervoides mounds with and without Podaxis fruiting bodies across a 1000 km transect in South Africa. We predicted that Podaxis would be a dominant member of the fungal communities in mounds and negatively impact microbial diversity. Further, we explored how environmental variables shaped microbial communities, including whether soil elemental composition affected Podaxis presence. As expected, we observed less diverse fungal communities, but not bacterial communities, within than outside mounds, while microbial communities differed by sampling regions and mound compartments. Podaxis sequences were present in 48 out of 49 mounds in low relative abundances, and neither fruiting body presence nor sequence abundance were associated with microbial diversity or composition. There was, however, an overall association between the presence of Podaxis fruiting bodies and elemental composition, with different elements displaying varying associations depending on geographic region. Both environmental variables and soil elements were associated with fungal and bacterial taxa, indicating that they are key drivers of microbial community composition. Taken together, our findings suggest that microbial landscapes in termite mounds are not strongly influenced by Podaxis but mainly driven by termite filtering and regional abiotic variables and elemental compositions., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

Haematophagous leeches rely on a broad variety of bioactive compounds to secure a sufficient blood meal from their vertebrate prey. Both the primary (platelet aggregation) and secondary (blood coagulation) haemostasis are the main targets of action. The platelet aggregation inhibitor decorsin was first described in the North American leech, Macrobdella decora Say, 1824, whereas the bivalent thrombin inhibitor hirudin was originally identified in the European medicinal leech, Hirudo medicinalis Linnaeus, 1758. Hirudin blocks both the catalytic site and the fibrinogen-binding site (exosite I) of thrombin. Haemadin of the Indian land leech Haemadipsa sylvestris Blanchard, 1894, is also a highly efficient bivalent thrombin inhibitor but blocks exosite II of thrombin. So far, only the archetypal form of haemadin from H. sylvestris has been purified and functionally characterized, and two putative haemadins have been identified in the salivary transcriptome of Haemadipsa interrupta Moore, 1835, a terrestrial leech inhabiting mainly the Malayan peninsula. Here, we describe the identification of ten additional putative haemadins in the transcriptomic data set of H. interrupta, first generated by another study. Furthermore, we identified a putative oligomeric decorsin, which represents the first finding of this anticoagulant in a haemadipsid leech. Both the putative decorsin and a selection of haemadins were expressed, purified, and functionally characterized. The putative haemadins displayed a broad spectrum of thrombin-inhibitory potencies, whereas the putative oligomeric decorsin was indeed a weak inhibitor of platelet aggregation., Competing Interests: Declarations. Ethical approval: The study was conducted in accordance with the Declaration of Helsinki, and approved by the Institutional Review Board (or Ethics Committee) of the University Medicine Oldenburg, Carl von Ossietzky University Oldenburg (ethics vote 2024–034). Consent to participate and consent for publication: Written informed consent was obtained from all subjects involved in the study. Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Within the framework of surveys investigating the origins of Linnaean taxa, we assessed the evidence supporting historical taxonomic and nomenclatural proposals and decisions regarding the nose-horned viper (Vipera ammodytes). The viper was described as Coluber ammodytes Linnaeus, 1758 from "the Orient." Bruno (1968) assessed the pre-Systema Naturae Ed. 10 sources and designated the specimen described in detail by Linnaeus as the lectotype of the species and restricted the type locality to near Castello Nuovo di Duino (Trieste, Venezia Giulia NW), NE Italy. We used a two-pronged approach using literary sources and statistical analyses to show that previous type locality restrictions suggested by different authors (including Bruno), were made incorrectly, without a proper assessment of the history or the morphological characteristics of the existing type material. Our surveys suggest that the lectotype was collected by the Swedish diplomat Edvard Carleson (1704-1767) in Belgrad Forest (Belgrad Ormanı), Belgrad village, Istanbul Metropolitan Municipality, Türkiye, between August 1738 and June 1746. In light of our results, the populations currently known as V. a. montandoni Boulenger, 1904 become the nominotypical subspecies, with the type locality Belgrad Forest (Belgrad Ormanı), Belgrad village, Istanbul Metropolitan Municipality, Türkiye. Nose-horned viper populations from the north-western and central parts of the distribution range of the species that were regarded as nominotypical, thus become Vipera ammodytes illyrica (Laurenti, 1768).

Xenacoelomorpha are mostly microscopic, morphologically simple worms, lacking many structures typical of other bilaterians. Xenacoelomorphs -which include three main groups: Acoela, Nemertodermatida, and Xenoturbella- have been proposed to be an early diverging Bilateria, sister to protostomes and deuterostomes, but other phylogenomic analyses have recovered this clade nested within the deuterostomes, as sister to Ambulacraria. The position of Xenacoelomorpha within the metazoan tree has understandably attracted a lot of attention, overshadowing the study of phylogenetic relationships within this group. Given that Xenoturbella includes only six species whose relationships are well understood, we decided to focus on the most speciose Acoelomorpha (Acoela + Nemertodermatida). Here, we have sequenced 29 transcriptomes, doubling the number of sequenced species, to infer a backbone tree for Acoelomorpha based on genomic data. The recovered topology is mostly congruent with previous studies. The most important difference is the recovery of Paratomella as the first off-shoot within Acoela, dramatically changing the reconstruction of the ancestral acoel. Besides, we have detected incongruence between the gene trees and the species tree, likely linked to incomplete lineage sorting, and some signal of introgression between the families Dakuidae and Mecynostomidae, which hampers inferring the correct placement of this family and, particularly, of the genus Notocelis. We have also used this dataset to infer for the first time diversification times within Acoelomorpha, which coincide with known bilaterian diversification and extinction events. Given the importance of morphological data in acoelomorph phylogenetics, we tested several partitions and models. Although morphological data failed to recover a robust phylogeny, phylogenetic placement has proven to be a suitable alternative when a reference phylogeny is available., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Society of Systematic Biologists.)

Species of the genus Satonius Endrödy-Younga from China are briefly reviewed. Seven new species are described: Satonius cheni sp. nov. from Guangdong, Satonius nigriventralis sp. nov. from Shaanxi, Satonius panghongae sp. nov. from Jiangxi, Hunan, Guangxi and Zhejiang, Satonius quzhouensis sp. nov. from Zhejiang and Anhui, Satonius xinhuiensis sp. nov. from Guangdong, Satonius zhangi sp. nov. from Hunan, and Satonius zhenhuai sp. nov. from Hubei. Species diagnoses of the new species are provided, along with images of the habitus and illustrations of the aedeagus and metatrochanters for all available Chinese species. Additionally, further faunistic data of known Chinese species is supplemented. A key to all known species of the genus is also included.

Following glacial retreat after the last ice age, brown bears (Ursus arctos) recolonised Scandinavia. Previous research based on mitochondrial markers suggests that bears recolonised from both the north and the south, with a contact zone in central Scandinavia. More recently, the Scandinavian brown bear was subjected to a strong population decline with only ca. 130 remaining individuals, due to intense human persecution approximately 100 years ago. Here, we analyse 41 ancient, historical, and modern mitochondrial genomes, to examine the number of female lineages involved in the postglacial recolonisation event and temporal changes in the Scandinavian brown bears' mitochondrial genetic diversity. Our results support the bi-directional recolonisation hypothesis, indicating multiple mitochondrial lineages from clade 1a possibly followed a southern route, while only a single lineage from clade 3a appears to have followed a northern route. Furthermore, we found that the recent bottleneck had a strong impact on the southern subpopulation, resulting in only one remaining haplotype in the contemporary brown bears. For the northern subpopulation, the impact was moderate, and most haplotypes were retained throughout the bottleneck. By exploring the postglacial recolonisation and recent population pressures, our study enhances understanding of how these factors have influenced the genetic diversity of Scandinavian brown bears., (© 2024. The Author(s).)

Wadicosa arabica sp. nov. is described from material of both sexes collected in Oman and the United Arab Emirates. The species belongs to the W. fidelis group and differs from its congroupers, inter alia, by the shape of the tegular apophysis and the embolus in the male. The occurrence of W. arabica sp. nov. is restricted to the gravel, pebble and cobble beds of ephemeral and intermittent streams (wadis) in the mountains of the eastern United Arab Emirates and northern Oman (the Hajar Mountains sensu lato). There it is often common and conspicuous alongside areas of surface waters. Notes on its courtship behaviour are given.

This study exposes U(VI)-sorbed schwertmannite and jarosite to biotic reductive incubations under field-relevant conditions and examines the changes in aqueous and solid-phase speciation of U, Fe, and S as well as associated microbial communities over 180 days. The chemical, X-ray absorption spectroscopy, X-ray diffraction, and microscopic data demonstrated that the U(VI)-sorbed schwertmannite underwent a rapid reductive dissolution and solid-phase transformation to goethite, during which the surface-sorbed U(VI) was partly reduced and mostly repartitioned to monomeric U(VI)/U(IV) complexes by carboxyl and phosphoryl ligands on biomass or organic substances. Furthermore, the microbial data suggest that these processes were likely driven by the consecutive developments of fermentative and sulfate- and iron- reducing microbial communities. In contrast, the U(VI)-sorbed jarosite only stimulated the growth of some fermentative communities and underwent very limited reductive dissolution and thus, remaining in its initial state with no detectable mineralogical transformation and solid-phase U reduction/repartitioning. Accordingly, these two biotic incubations did not induce increased risk of U reliberation to the aqueous phase. These findings have important implications for understanding the interactions of schwertmannite/jarosite with microbial communities and colinked behavior and fate of U following the establishment of reducing conditions in various acidic and U-rich settings.

Three types of plant-insect interactions are identified on seeds from the lower Permian (Asselian) Shanxi and lower Shihhotse formations of the Taiyuan district, North China. This enhances the relatively meagre fossil record of seed predation in global late Paleozoic floras, adding the earliest record of granivory from Cathaysia. The dispersed seeds cannot be attributed with confidence to any particular plant group, but associated fossil leaves belong to a broad spectrum of plants, including Medullosales, Cycadales, Noeggerathiales, Gigantopteridales, Cordaitales, and Voltziales. Among 85 analysed seeds, six showed evidence of predation, referable to three damage types: DT074 and two new damage types that will be added to the forthcoming version of the fossil damage guide (DT274, DT430). These damage features indicate novel strategies of seed exploitation in the earliest Permian of China. The causal agents of the seed herbivory are difficult to resolve with certainty, but possible culprits include representatives of Palaeodictyopteroidea, although we cannot exclude other groups, such as Dictyoptera, Odonatoptera, Archaeorthoptera, Hemipteroidea or early holometabolan insects. The presence of damage features, together with a range of probable defensive structures (hairs, spines, apical horns, and thick integuments), suggests that an active arms race involving insects and plant reproductive structures was already well established by the early Permian., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Santos et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The stable isotope compositions of sulphur (δ 34 S) and oxygen (δ 18 O) in barite are frequently used as proxies for microbial sulphate reduction (MSR) in diverse environments, such as in relation to anaerobic oxidation of methane in marine cold seeps. There, isotopically heavy barite is used as a marker for MSR from a sulphate pool that has undergone semi-closed system conditions. Closed-system MSR is also a commonly observed feature in igneous rock hosted fracture aquifers, as shown by extremely 34 S-enriched pyrite. What is less well-constrained is whether δ 34 S in barite can be used as a proxy for MSR in such systems. Here we explore the microscale heterogeneity of δ 34 S and δ 18 O via secondary ion mass spectrometry and the trace element Sr via LA-ICP-MS maps in barite precipitated in granite-hosted boreholes during a 17-year experiment, at Äspö, Sweden. We compare it with δ 18 O sulfate , δ 34 S sulfate , and δ 34 S sulfide of the fracture fluids and with paragenetic pyrite with δ 34 S values reflecting closed system MSR. The δ 18 O values in barite (+9.4 to +16.9 ‰) represent two generations of barite, one with low values and one with high values. The latter are likely impacted by sulphur disproportionating or -oxidizing bacteria. The barite reflects a much smaller span in δ 34 S (+14.5 to +28.6 ‰) than the pyrite (-47.2 to +53.3 ‰). This lack of extremely high δ 34 S barite values is proposed to be due to that barite saturation only occurred in the early parts of the Rayleigh cycle. Additionally, fluid migration has affected the δ 34 S values to lower values, accompanied by higher Sr concentrations. Taken together, barite δ 34 S values cannot be regarded as a reliable independent proxy for MSR in deep sulphate-poor igneous rock hosted aquifers. However, the relation between the δ 34 S values of coeval barite and pyrite is regarded as a useful proxy for MSR-related fractionation during early stages of MSR.

The dataset presents a 43 year-long reanalysis of pollen seasons for three major allergenic genera of trees in Europe: alder (Alnus), birch (Betula), and olive (Olea). Driven by the meteorological reanalysis ERA5, the atmospheric composition model SILAM predicted the flowering period and calculated the Europe-wide dispersion pattern of pollen for the years 1980-2022. The model applied an extended 4-dimensional variational data assimilation of in-situ observations of aerobiological networks in 34 European countries to reproduce the inter-annual variability and trends of pollen production and distribution. The control variable of the assimilation procedure was the total pollen release during each flowering season, implemented as an annual correction factor to the mean pollen production. The dataset was designed as an input to studies on climate-induced and anthropogenically driven changes in the European vegetation, biodiversity monitoring, bioaerosol modelling and assessment, as well as, in combination with intra-seasonal observations, for health-related applications., (© 2024. The Author(s).)

Uropygial gland secretions of birds consist of host and bacteria derived compounds and play a major sanitary and feather-protective role. Here we report on our microbiome studies of the New Guinean toxic bird Pachycephala schlegelii and the isolation of a member of the Amycolatopsis genus from the uropygial gland secretions. Bioactivity studies in combination with co-cultures, MALDI imaging and HR-MS/MS-based network analyses unveil the basis of its activity against keratinolytic bacteria and fungal skin pathogens. We trace the protective antimicrobial activity of Amycolatopsis sp. PS_44_ISF1 to the production of rifamycin congeners, ciromicin A and of two yet unreported compound families. We perform NMR and HR-MS/MS studies to determine the relative structures of six members belonging to a yet unreported lipopeptide family of pachycephalamides and of one representative of the demiguisins, a new hexapeptide family. We then use a combination of phylogenomic, transcriptomic and knock-out studies to identify the underlying biosynthetic gene clusters responsible for the production of pachycephalamides and demiguisins. Our metabolomics data allow us to map molecular ion features of the identified metabolites in extracts of P. schlegelii feathers, verifying their presence in the ecological setting where they exert their presumed active role for hosts. Our study shows that members of the Actinomycetota may play a role in avian feather protection., (© 2024. The Author(s).)

Molecular techniques like metabarcoding, while promising for exploring diversity of communities, are often impeded by the lack of reference DNA sequences available for taxonomic annotation. Our study explores the benefits of combining targeted DNA barcoding and morphological taxonomy to improve metabarcoding efficiency, using beach meiofauna as a case study. Beaches are globally important ecosystems and are inhabited by meiofauna, microscopic animals living in the interstitial space between the sand grains, which play a key role in coastal biodiversity and ecosystem dynamics. However, research on meiofauna faces challenges due to limited taxonomic expertise and sparse sampling. We generated 775 new cytochrome c oxidase I DNA barcodes from meiofauna specimens collected along the Netherlands' west coast and combined them with the NCBI GenBank database. We analysed alpha and beta diversity in 561 metabarcoding samples from 24 North Sea beaches, a region extensively studied for meiofauna, using both the enriched reference database and the NCBI database without the additional reference barcodes. Our results show a 2.5-fold increase in sequence annotation and a doubling of species-level Operational Taxonomic Units (OTUs) identification when annotating the metabarcoding data with the enhanced database. Additionally, our analyses revealed a bell-shaped curve of OTU richness across the intertidal zone, aligning more closely with morphological analysis patterns, and more defined community dissimilarity patterns between supralittoral and intertidal sites. Our research highlights the importance of expanding molecular reference databases and combining morphological taxonomy with molecular techniques for biodiversity assessments, ultimately improving our understanding of coastal ecosystems., (© 2024 The Author(s). Molecular Ecology Resources published by John Wiley & Sons Ltd.)

Phylogenomic approaches have recently helped elucidate various insect relationships, but large-scale comprehensive analyses on relationships within sawflies and woodwasps are still lacking. Here, we infer the relationships and long-term biogeographic history of these hymenopteran groups using a large dataset of 354 UCE loci collected from 385 species that represent all major lineages. Early Hymenoptera started diversifying during the Early Triassic ∼249 Ma and spread all over the ancient supercontinent Pangaea. We recovered Xyeloidea as a monophyletic sister group to other Hymenoptera and Pamphilioidea as sister to Unicalcarida. Within the diverse family Tenthredinidae, our taxonomically and geographically expanded taxon sampling highlights the non-monophyly of several traditionally defined subfamilies. In addition, the recent removal of Athalia and related genera from the Tenthredinidae into the separate family Athaliidae is supported. The deep historical biogeography of the group is characterised by independent dispersals and re-colonisations between the northern (Laurasia) and southern (Gondwana) palaeocontinents. The breakup of these landmasses led to ancient vicariance in several Gondwanan lineages, while interchange across the Northern Hemisphere has continued until the Recent. The little-studied African sawfly fauna is likewise a diverse mixture of groups with varying routes of colonization. Our results reveal interesting parallels in the evolution and biogeography of early hymenopterans and other ancient insect groups., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Inbreeding depression has been documented in various fitness traits in a wide range of species and taxa, however, the mutational basis is not yet well understood. We investigate how putatively deleterious variation influences fitness and is shaped by individual ancestry by re-sequencing complete genomes of 37 individuals in a natural arctic fox (Vulpes lagopus) population subjected to both inbreeding depression and genetic rescue. We find that individuals with high proportion of homozygous loss of function genotypes (LoFs), which are predicted to exert a strong effect on fitness, generally have lower lifetime reproductive success and live shorter lives compared with individuals with lower proportion of LoFs. We also find that juvenile survival is negatively associated with the proportion of homozygous missense genotypes and positively associated with genome wide heterozygosity. Our results demonstrate that homozygosity of strongly and moderately deleterious mutations can be an important cause of trait specific inbreeding depression in wild populations, and mark an important step towards making more informed decisions using applied conservation genetics., (© 2024. The Author(s).)

Naturally Occurring Asbestos (NOA) has drawn the attention worldwide when investigation revealed an increased incidence of malignant mesothelioma in population living near NOA sites. In Basilicata region (South Italy), population living in the villages of Castelluccio Superiore and Inferiore, Lauria, Latronico, Episcopia, San Severino Lucano, and Francavilla in Sinni may be considered at high risk of asbestos exposure because these villages are either surrounded by or built on NOA-rich ophiolitic outcrops. In this work we investigated an asbestos tremolite sample coming from the ophiolitic rocks outcropping in the quarry of Iacolinei, widely used in the past to extract aggregates for various applications.  A detailed mineralogical characterization has been attained by using a multi-analytical approach (EMPA, SEM-EDS, TEM-EDS, Mössbauer, µ-Raman, X-ray powder diffraction, and thermal analysis). Morphological investigation highlighted that the sample is composed of long fibers (> 5 µm) with a significant fraction (ca. 55%) having width below 0.25 µm, considered the most biologically active fibers. Moreover, the crystal chemical characterization showed that Fe occurs at the octahedral sites of the tremolite structure. It should be noted that Fe plays a primary role in the toxicity of asbestos. Based on these results, the investigated asbestos tremolite may be considered a potent mesothelial carcinogen, requiring therefore special attention for public health protection purposes. Investigations using sentinel animals to assess the diffusion of the tremolite fibers into the environment from the serpentinite rocks and soils of Iacolinei quarry are in progress., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

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., (© 2024. The Author(s).)

Successful management requires information on pressures that threaten a species and areas where conservation actions are needed. The Baltic Proper harbour porpoise population was first listed as Critically Endangered by the International Union for the Conservation of Nature in 2008. Now, 16 years later, there is no change in conservation status despite ample conservation policy calling for its protection and an urgent need for management action to protect this population. Here, we provide an overview of the current status of the population, highlight knowledge gaps on the impact of pressures, and make recommendations for management of anthropogenic activities. Based on an exceeded limit for anthropogenic mortality, the high concentrations of contaminants in the Baltic Sea, combined with reductions in prey availability and increases in underwater noise, it is inferred that this population is likely still decreasing in size and conservation action becomes more urgent. As bycatch and unprotected underwater explosions result in direct mortality, they must be reduced to zero. Inputs of contaminants, waste, and existing and emerging noise sources should be minimised and regulated. Additionally, ecosystem-based sustainable management of fisheries is paramount in order to ensure prey availability, and maintain a healthy Baltic Sea. Stranding networks to routinely assess individuals for genetic population assignment and health need to be expanded, to identify rare samples from this population. Knowledge is still scarce on the population-level impact of each threat, along with the cumulative impact of multiple pressures on the population. However, the current knowledge and management instruments are sufficient to apply effective protection for the population now. While bycatch is the main pressure impacting this population, urgent conservation action is needed across all anthropogenic activities. Extinction of the Baltic Proper harbour porpoise population is a choice: decision-makers have the fate of this genetically and biologically distinct marine mammal population in their hands., Competing Interests: The authors declare no competing interested., (© 2024 The Author(s). Ecology and Evolution published by John Wiley & Sons Ltd.)

The molluskan order Neogastropoda encompasses over 15,000 almost exclusively marine species playing important roles in benthic communities and in the economies of coastal countries. Neogastropoda underwent intensive cladogenesis in the early stages of diversification, generating a "bush" at the base of their evolutionary tree, which has been hard to resolve even with high throughput molecular data. In the present study to resolve the bush, we use a variety of phylogenetic inference methods and a comprehensive exon capture dataset of 1817 loci (79.6% data occupancy) comprising 112 taxa of 48 out of 60 Neogastropoda families. Our results show consistent topologies and high support in all analyses at (super)family level, supporting monophyly of Muricoidea, Mitroidea, Conoidea, and, with some reservations, Olivoidea and Buccinoidea. Volutoidea and Turbinelloidea as currently circumscribed are clearly paraphyletic. Despite our analyses consistently resolving most backbone nodes, 3 prove problematic: First, the uncertain placement of Cancellariidae, as the sister group to either a Ficoidea-Tonnoidea clade or to the rest of Neogastropoda, leaves monophyly of Neogastropoda unresolved. Second, relationships are contradictory at the base of the major "core Neogastropoda" grouping. Third, coalescence-based analyses reject monophyly of the Buccinoidea in relation to Vasidae. We analyzed phylogenetic signal of targeted loci in relation to potential biases, and we propose the most probable resolutions in the latter 2 recalcitrant nodes. The uncertain placement of Cancellariidae may be explained by orthology violations due to differential paralog loss shortly after the whole genome duplication, which should be resolved with a curated set of longer loci., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Society of Systematic Biologists.)

Between the 8th and 11th centuries CE, the Iberian Peninsula underwent profound upheaval due to the Umayyad invasion against the Visigoths, resulting in population shifts and lasting demographic impacts. Our understanding of this period is hindered by limited written sources and few archaeogenetic studies. We analyzed 33 individuals from Las Gobas, a necropolis in northern Spain, spanning the 7th to 11th centuries. By combining archaeological and osteological data with kinship, metagenomics, and ancestry analyses, we investigate conflicts, health, and demography of these individuals. We reveal intricate family relationships and genetic continuity within a consanguineous population while also identifying several zoonoses indicative of close interactions with animals. Notably, one individual was infected with a variola virus phylogenetically clustering with the northern European variola complex between ~885 and 1000 CE. Last, we did not detect a significant increase of North African or Middle East ancestries over time since the Islamic conquest of Iberia, possibly because this community remained relatively isolated.

Venom systems are complex traits that have independently emerged multiple times in diverse plant and animal phyla. Within each venomous lineage there typically exists interspecific variation in venom composition where several factors have been proposed as drivers of variation, including phylogeny and diet. Understanding these factors is of broad biological interest and has implications for the development of antivenom therapies and venom-based drug discovery. Because of their high species richness and the presence of several major evolutionary prey shifts, venomous marine cone snails (genus Conus) provide an ideal system to investigate drivers of interspecific venom variation. Here, by analyzing the venom gland expression profiles of ∼3,000 toxin genes from 42 species of cone snail, we elucidate the role of prey-specific selection pressures in shaping venom variation. By analyzing overall venom composition and individual toxin structures, we demonstrate that the shifts from vermivory to piscivory in Conus are complemented by distinct changes in venom composition independent of phylogeny. In vivo injections of venom from piscivorous cone snails in fish further showed a higher potency compared with venom of nonpiscivores demonstrating a selective advantage. Together, our findings provide compelling evidence for the role of prey shifts in directing the venom composition of cone snails and expand our understanding of the mechanisms of venom variation and diversification., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Increasing food production while avoiding negative impacts on biodiversity constitutes one of the main challenges of our time. Traditional silvopastoral systems like Iberian oak savannas ("dehesas") set an example, where free-range livestock has been reared for centuries while preserving a high natural value. Nevertheless, factors decreasing productivity need to be addressed, one being acorn losses provoked by pest insects. An increased and focalized grazing by livestock on infested acorns would kill the larvae inside and decrease pest numbers, but increased livestock densities could have undesired side effects on ground arthropod communities as a whole. We designed an experimental setup including areas under trees with livestock exclosures of different ages (short-term: 1-year exclusion, long-term: 10-year exclusion), along with controls (continuous grazing), using DNA metabarcoding (mitochondrial markers COI and 16S) to rapidly assess arthropod communities' composition. Livestock removal quickly increased grass cover and arthropod taxonomic richness and diversity, which was already higher in short-term (1-year exclosures) than beneath the canopies of control trees. Interestingly, arthropod diversity was not highest at long-term exclosures (≥10 years), although their community composition was the most distinct. Also, regardless of treatment, we found that functional diversity strongly correlated with the vegetation structure, being higher at trees beneath which there was higher grass cover and taller herbs. Overall, the taxonomic diversity peak at short term exclosures would support the intermediate disturbance hypothesis, which relates it with the higher microhabitat heterogeneity at moderately disturbed areas. Thus, we propose a rotatory livestock management in dehesas: plots with increased grazing should co-exist with temporal short-term exclosures. Ideally, a few long-term excluded areas should be also kept for the singularity of their arthropod communities. This strategy would make possible the combination of biological pest control and arthropod conservation in Iberian dehesas., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

A central objective of historical biogeography is to understand where clades originated and how they moved across space and over time. However, given the dynamic history of ecosystem changes in response to climate change and geological events, the manifold long-distance dispersals over evolutionary timescales, and regional and global extinctions, it remains uncertain how reliable inferences based solely on extant taxa can be achieved. Using a novel species-level phylogeny of all known extant and extinct species of the mammalian order Carnivora and related extinct groups, we show that far more precise and accurate ancestral areas can be estimated by fully integrating extinct species into the analyses, rather than solely relying on extant species or identifying ancestral areas only based on the geography of the oldest fossils. Through a series of simulations, we further show that this conclusion is robust under realistic scenarios in which the unknown extinct taxa represent a biased subset of all extinct species. Our results highlight the importance of integrating fossil taxa into a phylogenetic framework to further improve our understanding of historical biogeography and reveal the dynamic dispersal and diversification history of carnivores.

In the period between 5,300 and 4,900 calibrated years before present (cal. BP), populations across large parts of Europe underwent a period of demographic decline 1,2 . However, the cause of this so-called Neolithic decline is still debated. Some argue for an agricultural crisis resulting in the decline 3 , others for the spread of an early form of plague 4 . Here we use population-scale ancient genomics to infer ancestry, social structure and pathogen infection in 108 Scandinavian Neolithic individuals from eight megalithic graves and a stone cist. We find that the Neolithic plague was widespread, detected in at least 17% of the sampled population and across large geographical distances. We demonstrate that the disease spread within the Neolithic community in three distinct infection events within a period of around 120 years. Variant graph-based pan-genomics shows that the Neolithic plague genomes retained ancestral genomic variation present in Yersinia pseudotuberculosis, including virulence factors associated with disease outcomes. In addition, we reconstruct four multigeneration pedigrees, the largest of which consists of 38 individuals spanning six generations, showing a patrilineal social organization. Lastly, we document direct genomic evidence for Neolithic female exogamy in a woman buried in a different megalithic tomb than her brothers. Taken together, our findings provide a detailed reconstruction of plague spread within a large patrilineal kinship group and identify multiple plague infections in a population dated to the beginning of the Neolithic decline., (© 2024. The Author(s).)

Reconstructing the tree of life and understanding the relationships of taxa are core questions in evolutionary and systematic biology. The main advances in this field in the last decades were derived from molecular phylogenetics; however, for most species, molecular data are not available. Here, we explore the applicability of two deep learning methods - supervised classification approaches and unsupervised similarity learning - to infer organism relationships from specimen images. As a basis, we assembled an image dataset covering 4144 bivalve species belonging to 74 families across all orders and subclasses of the extant Bivalvia, with molecular phylogenetic data being available for all families and a complete taxonomic hierarchy for all species. The suitability of this dataset for deep learning experiments was evidenced by an ablation study resulting in almost 80% accuracy for identifications on the species level. Three sets of experiments were performed using our dataset. First, we included taxonomic hierarchy and genetic distances in a supervised learning approach to obtain predictions on several taxonomic levels simultaneously. Here, we stimulated the model to consider features shared between closely related taxa to be more critical for their classification than features shared with distantly related taxa, imprinting phylogenetic and taxonomic affinities into the architecture and training procedure. Second, we used transfer learning and similarity learning approaches for zero-shot experiments to identify the higher-level taxonomic affinities of test species that the models had not been trained on. The models assigned the unknown species to their respective genera with approximately 48% and 67% accuracy. Lastly, we used unsupervised similarity learning to infer the relatedness of the images without prior knowledge of their taxonomic or phylogenetic affinities. The results clearly showed similarities between visual appearance and genetic relationships at the higher taxonomic levels. The correlation was 0.6 for the most species-rich subclass (Imparidentia), ranging from 0.5 to 0.7 for the orders with the most images. Overall, the correlation between visual similarity and genetic distances at the family level was 0.78. However, fine-grained reconstructions based on these observed correlations, such as sister-taxa relationships, require further work. Overall, our results broaden the applicability of automated taxon identification systems and provide a new avenue for estimating phylogenetic relationships from specimen images., (© The Author(s) 2024. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

A number of species have recently recovered from near-extinction. Although these species have avoided the immediate extinction threat, their long-term viability remains precarious due to the potential genetic consequences of population declines, which are poorly understood on a timescale beyond a few generations. Woolly mammoths (Mammuthus primigenius) became isolated on Wrangel Island around 10,000 years ago and persisted for over 200 generations before becoming extinct around 4,000 years ago. To study the evolutionary processes leading up to the mammoths' extinction, we analyzed 21 Siberian woolly mammoth genomes. Our results show that the population recovered quickly from a severe bottleneck and remained demographically stable during the ensuing six millennia. We find that mildly deleterious mutations gradually accumulated, whereas highly deleterious mutations were purged, suggesting ongoing inbreeding depression that lasted for hundreds of generations. The time-lag between demographic and genetic recovery has wide-ranging implications for conservation management of recently bottlenecked populations., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth's death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale., Competing Interests: Declaration of interests E.L.A., M.T.P.G., and L.D. are on the scientific advisory board of Colossal Biosciences and hold stock options. From 2021 to 2023, M.A.M.-R. received consulting honoraria from Acuity Spatial Genomics. E.L.A. and O.D. are inventors on US provisional patent applications 16/308,386 (E.L.A. and O.D., filed 12/7/2018), 16/247,502 (E.L.A. and O.D., 1/14/2019), and PCT/US2020/064704 (E.L.A., 12/11/2020) by the Baylor College of Medicine and the Broad Institute, relating to the assembly methods in this manuscript., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Male and female birds have different roles in reproduction and, thereby in their reproductive investment, which in turn may increase negative effects of poorer breeding conditions caused by e.g., climate change or ecosystem regime shifts. By using a 33-year time series of resightings of Atlantic puffins Fratercula arctica individually colour-ringed as breeders in previous years, we showed that the difference in colony attendance of male and female birds depended on the environmental conditions for raising young, proxied by the average duration of the chick period and size of the herring Clupea harengus fed to the chicks in the colony each year. The longer the chick period, the more was the sex ratio of adults sitting visibly in the colony biased in favour of males. An increase in herring size, indicating better feeding conditions for raising chicks, led to more observations of both sexes. Additionally, we found that birds were observed less with age and females more so than males. We discuss the results in relation to general life-history theory on sexual differences in trade-offs between individual investment in breeding and own survival. Our results suggest that females are increasingly more willing than males to invest in provisioning for the chick the more and longer the chick needs such care., Competing Interests: None declared., (© 2024 The Author(s). Ecology and Evolution published by John Wiley & Sons Ltd.)

Hybridization can result in the transfer of adaptive genetic material from one species to another, known as adaptive introgression. Bottlenecked (and hence genetically depleted) species are expected to be particularly receptive to adaptive introgression, since introgression can introduce new or previously lost adaptive genetic variation. The Alpine ibex (Capra ibex), which recently recovered from near extinction, is known to hybridize with the domestic goat (Capra aegagrus hircus), and signals of introgression previously found at the major histocompatibility complex were suggested to potentially be adaptive. Here, we combine two ancient whole genomes of Alpine ibex with 29 modern Alpine ibex genomes and 31 genomes representing six related Capra species to investigate the genome-wide patterns of introgression and confirm the potential relevance of immune loci. We identified low rates of admixture in modern Alpine ibex through various F statistics and screening for putative introgressed tracts. Further results based on demographic modelling were consistent with introgression to have occurred during the last 300 years, coinciding with the known species bottleneck, and that in each generation, 1-2 out of 100 Alpine ibex had a domestic goat parent. The putatively introgressed haplotypes were enriched at immune-related genes, where the adaptive value of alternative alleles may give individuals with otherwise depleted genetic diversity a selective advantage. While interbreeding with domestic species is a prevalent issue in species conservation, in this specific case, it resulted in putative adaptive introgression. Our findings highlight the complex interplay between hybridization, adaptive evolution, and the potential risks and benefits associated with anthropogenic influences on wild species., (© 2024 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.)

Motivation: The alignment of sequencing reads is a critical step in the characterization of ancient genomes. However, reference bias and spurious mappings pose a significant challenge, particularly as cutting-edge wet lab methods generate datasets that push the boundaries of alignment tools. Reference bias occurs when reference alleles are favoured over alternative alleles during mapping, whereas spurious mappings stem from either contamination or when endogenous reads fail to align to their correct position. Previous work has shown that these phenomena are correlated with read length but a more thorough investigation of reference bias and spurious mappings for ancient DNA has been lacking. Here, we use a range of empirical and simulated palaeogenomic datasets to investigate the impacts of mapping tools, quality thresholds, and reference genome on mismatch rates across read lengths., Results: For these analyses, we introduce AMBER, a new bioinformatics tool for assessing the quality of ancient DNA mapping directly from BAM-files and informing on reference bias, read length cut-offs and reference selection. AMBER rapidly and simultaneously computes the sequence read mapping bias in the form of the mismatch rates per read length, cytosine deamination profiles at both CpG and non-CpG sites, fragment length distributions, and genomic breadth and depth of coverage. Using AMBER, we find that mapping algorithms and quality threshold choices dictate reference bias and rates of spurious alignment at different read lengths in a predictable manner, suggesting that optimized mapping parameters for each read length will be a key step in alleviating reference bias and spurious mappings., Availability and Implementation: AMBER is available for noncommercial use on GitHub (https://github.com/tvandervalk/AMBER.git). Scripts used to generate and analyse simulated datasets are available on Github (https://github.com/sdolenz/refbias_scripts)., (© The Author(s) 2024. Published by Oxford University Press.)