Abstract: Land‐use change and habitat degradation are among the biggest drivers of aboveground biodiversity worldwide but their effects on soil biodiversity are less well known, despite the importance of soil organisms in developing soil structure, nutrient cycling and water drainage. Combining a global compilation of biodiversity data from soil assemblages collated as part of the PREDICTS project with global data on soil characteristics, we modelled how taxon richness and total abundance of soil organisms have responded to land use. We also estimated the global Biodiversity Intactness Index (BII)—the average abundance and compositional similarity of taxa that remain in an area, compared to a minimally impacted baseline, for soil biodiversity. This is the first time the BII has been calculated for soil biodiversity. Relative to undisturbed vegetation, soil organism total abundance and taxon richness were reduced in all land uses except pasture. Soil properties mediated the response of soil biota, but not in a consistent way across land uses. The global soil BII in cropland is, on average, a third of that originally present. However, in grazed sites the decline is less severe. The BII of secondary vegetation depends on age, with sites with younger growth showing a lower BII than mature vegetation. We conclude that land‐use change has reduced local soil biodiversity worldwide, and this further supports the proposition that soil biota should be considered explicitly when using global models to estimate the state of biodiversity.

We present a genome assembly from a female specimen of <ns3:italic>Ampedus sanguinolentus sanguinolentus</ns3:italic> (click beetle; Arthropoda; Insecta; Coleoptera; Elateridae). The assembly contains two haplotypes with total lengths of 1,574.76 megabases and 1,572.87 megabases. Most of haplotype 1 (97.13%) is scaffolded into 10 chromosomal pseudomolecules, while haplotype 2 is a scaffold-level assembly. The mitochondrial genome has also been assembled and is 15.99 kilobases in length.

Abstract Background: Acanthocephalans of the genus <jats:italic>Bolbosoma</jats:italic> Porta, 1908 are trophically transmitted parasites that infect marine mammals (mostly cetaceans and less frequently pinnipeds) worldwide. There are 12 species currently considered as valid; however, most records lack information on the maturity stage of the specimens. This, coupled with the scarce phylogenetic information available, hinders a correct understanding of their patterns of host specificity, evolutionary history, and taxonomy. A particularly intriguing case is that of <jats:italic>Bolbosoma vasculosum</jats:italic> (Rudolphi, 1819), which has been frequently reported in odontocetes but rarely as an adult, having been suggested to be synonymous with <jats:italic>Bolbosoma capitatum</jats:italic> (von Linstow, 1880). Methods: We used a comprehensive approach to investigate the concept of <jats:italic>Bolbosoma</jats:italic>. First, we conducted a bibliographic review of records of <jats:italic>Bolbosoma</jats:italic> spp. to clarify which are the final hosts for each species. We paid particular attention to <jats:italic>B. vasculosum</jats:italic>, using morphological and molecular analyses to compare it with <jats:italic>B. capitatum</jats:italic>. Second, we characterized the complete mitochondrial genome of <jats:italic>Bolbosoma balaenae</jats:italic> (Gmelin, 1790), <jats:italic>Bolbosoma turbinella</jats:italic> (Diesing, 1851), <jats:italic>B. capitatum</jats:italic>, and <jats:italic>B. vasculosum</jats:italic>. Then, we reconstructed the phylogenetic relationships of <jats:italic>Bolbosoma</jats:italic> spp. and related taxa using full mitochondrial genomes (or only <jats:italic>cox1</jats:italic> when full mitogenomes were unavailable) and nuclear ribosomal genes (18S and 28S). Results: Bolbosoma</jats:italic> spp. exhibit high specificity for cetaceans, with no confirmed records of adult specimens in other host groups. Within this genus, <jats:italic>B. vasculosum</jats:italic> appears to be conspecific with <jats:italic>B. capitatum</jats:italic> based on both morphological and molecular evidence. This species shows high affinity to odontocetes, while the remaining species are specific to mysticetes. Phylogenetic analyses showed strong support for the monophyly of <jats:italic>Bolbosoma</jats:italic> spp., which appeared as sister taxa to <jats:italic>Corynosoma</jats:italic> spp. and <jats:italic>Andracantha</jats:italic> spp.. The resulting topology aligns with the patterns of specificity indicated by host records, revealing two distinct clades for species specific to odontocetes and mysticetes, respectively. Conclusions: The phylogenetic relationships obtained support the hypothesis that the association of <jats:italic>Bolbosoma</jats:italic> spp. with cetaceans originated through a host-switching event from aquatic birds.

The geophilomorph Mesoschendyla javanica (Attems, 1907) was originally described from a small number of males collected from bat guano in Tjompea (Ciampea), Java. Subsequently, no additional material was identified. The type series remained the only specimens belonging to this genus known from Asia. Mesoschendyla javanica is re-discovered 118 years after its original description amongst centipedes collected from soil cores taken during the 1977–1978 Royal Geographical Society Gunung Mulu Expedition to Sarawak (Borneo, East Malaysia) and is deposited in the collection of the Natural History Museum (London). The new material comprising 49 specimens, amongst which are the first known females, is described and illustrated, shedding light on intraspecific morphological variation. The syntypes and sole previously available specimens are redescribed and illustrated, completing the summary original description of the species. Ecological and biogeographical notes are provided for Sarawak specimens.

The available information regarding bryozoans in coastal areas of Pakistan is limited. This research paper presents the first record of Calyptotheca alexandriensis from Ras Juddi (Pasni) along the Makran coast, and the second record globally of this species. This species was first reported in the Eastern Harbor of Alexandria, Egypt, as a distinctive deep orange erect foliaceous bryozoan and was observed abundantly on various hard substrates, such as rocks, ropes, metal pipes supporting marina piers, and ship hulls. The discovery adds a new record of the family, Lanceoporidae, and genus, Calyptotheca, to the bryozoan fauna of Pakistan, expanding its known distribution to the Northern Arabian Sea. The present specimens were collected during December 2021–October 2022 and subjected to detailed taxonomic analysis using light microscopy and scanning electron microscopy (SEM). This study contributes to the understanding of bryozoan biodiversity in the region and highlights the potential for further discoveries along the unexplored coastal areas of Pakistan.

Abstract: The “second wave” of Ediacaran evolution (∼558–548 Ma) was characterized by the appearance of macroscopic organisms in shallow marine settings, where they formed communities with high morphological and ecological diversity, including new and more complex modes of life. Based on analogy with modern marine ecosystems, these early shallow water communities could have substantially modified local hydrodynamic conditions and influenced resource availability, but we know very little about how they interacted with their fluid environment at larger spatial scales. Here, we use computational fluid dynamics to investigate the hydrodynamics of different shallow marine Ediacaran communities based on fossil surfaces from Russia and South Australia. Our results reveal considerable hydrodynamic variability among these communities, ranging from unobstructed flow, to enhanced mixing, to very low in-canopy flow. This variability represents a noticeable shift from the more conserved hydrodynamic conditions reconstructed for older Ediacaran communities from deep water settings. The variation in how shallow marine Ediacaran communities affected local hydrodynamics could have given rise to notable differences in the distribution of crucial water-borne resources such as organic carbon and oxygen. We therefore hypothesize that increasing variability in community hydrodynamics was an important source of habitat heterogeneity during the late Ediacaran. On long timescales, this heterogeneity may have helped sculpt ecological opportunity, fostering the radiation of animals.

Named in 1856, West African Rock Dove Columba livia gymnocycla differs markedly in appearance from other Rock Dove subspecies. Recent DNA analyses have revealed that gymnocycla is also genetically very different from Columba livia, warranting species status for this taxon. The species was never abundant in its small distribution, and only a small number of specimens are present in museum collections. A search for the species in Senegambia in 2024 was unsuccessful and C. gymnocycla may have already vanished from much or all of its distribution.

Abstract: Morphological variation in the hominoid capitate has been linked to differences in habitual locomotor activity due to its importance in movement and load transfer at the midcarpal joint proximally and carpometacarpal joints distally. Although the shape of bones and their articulations are linked to joint mobility, the internal structure of bones has been shown experimentally to reflect, at least in part, the loading direction and magnitude experienced by the bone. To date, it is uncertain whether locomotor differences among hominoids are reflected in the bone microarchitecture of the capitate. Here, we apply a whole‐bone methodology to quantify the cortical and trabecular architecture (separately and combined) of the capitate across bipedal (modern<jats:italic>Homo sapiens</jats:italic>), knuckle‐walking (<jats:italic>Pan paniscus</jats:italic>,<jats:italic>Pan troglodytes</jats:italic>,<jats:italic>Gorilla</jats:italic>sp.), and suspensory (<jats:italic>Pongo</jats:italic>sp.) hominoids (<jats:italic>n</jats:italic> = 69). It is hypothesized that variation in bone microarchitecture will differentiate these locomotor groups, reflecting differences in habitual postures and presumed loading force and direction. Additionally, it is hypothesized that trabecular and cortical architecture in the proximal and distal regions, as a result of being part of mechanically divergent joints proximally and distally, will differ across these portions of the capitate. Results indicate that the capitate of knuckle‐walking and suspensory hominoids is differentiated from bipedal<jats:italic>Homo</jats:italic>primarily by significantly thicker distal cortical bone. Knuckle‐walking taxa are further differentiated from suspensory and bipedal taxa by more isotropic trabeculae in the proximal capitate. An allometric analysis indicates that size is not a significant determinate of bone variation across hominoids, although sexual dimorphism may influence some parameters within<jats:italic>Gorilla</jats:italic>. Results suggest that internal trabecular and cortical bone is subjected to different forces and functional adaptation responses across the capitate (and possibly other short bones). Additionally, while separating trabecular and cortical bone is normal protocol of current whole‐bone methodologies, this study shows that when applied to carpals, removing or studying the cortical bone separately potentially obfuscates functionally relevant signals in bone structure.</jats:p>

Abstract Motivation: In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced “Poisson Tree Processes” (PTP) method is a phylogeny-aware approach that does not rely on such thresholds. Yet, two weaknesses of PTP impact its accuracy and practicality when applied to large datasets; it does not account for divergent intraspecific variation and is slow for a large number of sequences. Results: We introduce the multi-rate PTP (mPTP), an improved method that alleviates the theoretical and technical shortcomings of PTP. It incorporates different levels of intraspecific genetic diversity deriving from differences in either the evolutionary history or sampling of each species. Results on empirical data suggest that mPTP is superior to PTP and popular distance-based methods as it, consistently yields more accurate delimitations with respect to the taxonomy (i.e., identifies more taxonomic species, infers species numbers closer to the taxonomy). Moreover, mPTP does not require any similarity threshold as input. The novel dynamic programming algorithm attains a speedup of at least five orders of magnitude compared to PTP, allowing it to delimit species in large (meta-) barcoding data. In addition, Markov Chain Monte Carlo sampling provides a comprehensive evaluation of the inferred delimitation in just a few seconds for millions of steps, independently of tree size. Availability and Implementation: mPTP is implemented in C and is available for download at http://github.com/Pas-Kapli/mptp under the GNU Affero 3 license. A web-service is available at http://mptp.h-its.org. Supplementary information: Supplementary data are available at Bioinformatics online.