Naturalis Biodiversity Center

Biodiversity genomics is converging from historically separate approaches — DNA barcoding and reference genome sequencing — into an integrated digital ecosystem driven by shared data stewardship principles: transparent provenance, persistent identifiers and interoperable repositories. We demonstrate how these workflows can operate within a unified informatics architecture spanning data generation, validation, publication and reuse. We describe coordinated infrastructure, including the European BOLD mirror, ERGA Genome Tracking Console and metadata platforms COPO and PlutoF. These systems employ harmonised validation pipelines, shared metadata standards that bridge the Darwin Core and Genomic Standards Consortium vocabularies and automated data exchange amongst ENA, UNITE and GBIF. Workflows in Galaxy, Nextflow and Snakemake are registered in WorkflowHub as Research Object Crates (RO-Crates), ensuring reproducibility and complete provenance. Key outcomes include comprehensive data flow documentation, automated quality control using BUSCO and ERGA Assembly Reports and robust specimen-to-data linkage. We identify challenges in metadata harmonisation, distributed tracking, collaborative attribution and infrastructure sustainability and provide recommendations for addressing them through existing platforms and emerging RO-Crate standards. This work establishes practical foundations for treating biodiversity molecular data as a continuum, demonstrating how FAIR principles can scale to continental initiatives.

Alpheus lobidens De Haan, 1849 (type locality: Japan) and A. crassimanus Heller, 1862 (type locality: Nicobar Islands, Andaman Sea), two taxonomically challenging snapping shrimps previously regarded as conspecific, are rediagnosed based on the holotype and on the newly collected material from the Andaman Sea, respectively. Most importantly, the female holotype of A. lobidens has a balaeniceps ridge on the pollex of the minor chela, whereas in A. crassimanus, the minor cheliped fingers of females are simple, devoid of balaeniceps setae. Other characters diagnostic to A. lobidens include the laterally compressed rostrum reaching the distal margin of the first article of the antennular peduncle, the highly elevated rostral carina widening posteriorly, and the broad, deeply depressed adrostral furrows. These features set A. lobidens apart from other taxa previously referred to A. lobidens or A. lobidens complex in literature. Alpheus polynesicus Banner & Banner, 1975, originally described as a subspecies of A. lobidens and later synonymised with A. lobidens, is reinstated as a full species based on evidence from literature. Four new species, which have been confused with A. lobidens, are described from Japan, based on molecular and morphological data, as well as their colour patterns in life: A. yoshigoui sp. nov., A. nigrofasciatus sp. nov., A. latifasciatus sp. nov., and A. aestuaricola sp. nov. These new species are now referred to the A. crassimanus species complex and compared with allied species, including those from outside the Indo-West Pacific. The Japanese records of A. heeia Banner & Banner, 1975 are all referred to A. nigrofasciatus sp. nov. Molecular phylogenetic analyses using two mitochondrial markers (16S rRNA and COI genes) have shown that two morphologically distinct morphs distinguished by the presence or absence of sclerotised setae on the mesial face of the third maxilliped carpus (= penultimate article) belong to the same species, A. nigrofasciatus sp. nov. The taxonomic identities of several lineages of Alpheus recovered in the phylogenetic analyses remain unresolved due to difficulties in accessing voucher specimens. References to A. lobidens and A. crassimanus have been reviewed as thoroughly as possible.

Environmental DNA (eDNA) has rapidly become a powerful method for large-scale biodiversity assessment and monitoring. Yet the reliability of eDNA data depends on high-quality reference material that can verify detections, resolve taxonomic uncertainty, and correct spatial or temporal biases. This is where global natural science collections, curated in natural history museums, herbaria, and other collection-holding institutes, play an essential role. These collections preserve centuries of information on species, traits, and ecological contexts, providing the authoritative baseline needed to interpret molecular observations and understand biodiversity change over time.Harnessing this potential requires that collection data be open, reusable, and integrated with emerging molecular approaches. Advances in imaging, computational methods, and molecular analysis have made it possible to link specimen-based knowledge with large-scale datasets. To support such integrated, data-driven research and adaptive conservation strategies, robust infrastructure is needed.The Distributed System of Scientific Collections (DiSSCo) – a European Research Infrastructure collaborating with more than 300 institutions across 23 countries – addresses this challenge by representing each specimen as a FAIR (Findable, Accessible, Interoperable, and Reusable) Digital Object. Building on existing standards, each specimen and its associated data are made FAIR, with provenance and trust explicitly encoded. Users can explore connections across data types and contribute annotations, corrections, or additional information, with AI-assisted services such as automated georeferencing, OCR, and morphology detection further enhancing data quality and completeness.Such linked and verified data provide the critical bridge between historical collections and modern eDNA workflows. Digital specimens data ground eDNA detections in validated reference material, strengthening taxonomic resolution and enabling more accurate interpretation of biodiversity patterns across spatial and temporal scales. Sequencing historical specimens enriches this further by revealing long-term population and ecosystem dynamics.By establishing an infrastructure capable of linking billions of historical specimen records with emerging molecular and environmental data, DiSSCo creates the conditions for future integration that will support predictive biodiversity assessments and global eDNA efforts.

• Integrated remote sensing and environmental data for Amazon tree diversity mapping. • Extreme gradient boosting identified as the best-performing algorithm. • Climate, soil and vegetation are influential, complementary predictors. • Generated 1 km resolution maps, showing spatial patterns at high resolution. Tropical forests are biodiversity hotspots facing increasing threats from climate change and anthropogenic pressures. Tree species diversity is a key indicator of forest biodiversity, making accurate and spatially detailed information essential for effective monitoring and conservation. For large-scale tree species diversity mapping, satellite data and machine learning offer great potential, but challenges remain, including limited field data, coarse spatial resolution, and complex relationships between in-situ diversity and remotely sensed metrics. This study investigates the potential of integrating remote sensing, environmental data and machine learning for tree species diversity mapping across the Amazon. Specifically, we 1) compared performances of widely used algorithms (random forest, extreme gradient boosting, artificial neural networks, support vector regression and ordinary least squares), 2) identified key environmental predictors, and 3) produced 1-km resolution maps to assess their spatial patterns. Our results show that extreme gradient boosting outperformed other algorithms. Climate and soil emerged as the most influential drivers of broad-scale diversity patterns, while remote sensing metrics were also influential in adding fine-scale spatial patterns. High tree diversity was associated most with climate stability, high precipitation, soil characteristics, and spatial heterogeneity of vegetation indices. The resulting maps aligned well with field observations and prior studies, while showing the potential of fine-scale mapping with competitive accuracy and low uncertainty using remotely sensed data. These findings thus demonstrate the effectiveness of integrating remote sensing, environmental data and machine learning for tree species diversity mapping in tropical forests, in support of biodiversity assessments and conservation measures.

Abstract The ontogeny of Neanderthal ( Homo neanderthalensis ) perinates is poorly understood due to the paucity of juvenile skeletal remains. Here we reconstruct fetal bone growth, and explore deciduous tooth structures, in three Neanderthal juveniles (Sesselfelsgrotte, 1, 2 and 3) (90,000–50,000 years ago) from southeastern Germany using non-destructive microcomputed tomography. Sesselfelsgrotte 1 exhibited bone tissue consistent with modern human perinatal plexiform-like structures and primary osteons. Long bones showed regions of advanced growth compared to the mandible and frontal bone, which can be explained through different processes of ossification and potentially localized faster development in Neanderthals compared to modern humans. Bone microstructure resembles that of the late third trimester of modern humans, agreeing with previous estimates based on macroscopic data. Sesselfelsgrotte 2 and 3 deciduous teeth retain hypodensities deep within the crown dentine consistent with interglobular dentine. We conclude that the fetal bone patterning is similar to modern humans with areas of advanced growth, indicating that the growth trajectory for this Neanderthal perinate was broadly equivalent to that of modern humans. The abnormal dentine mineralization points toward a possible systemic disorder.

We present a revised diagnosis of the extinct galeomorph shark †Bavariscyllium based on dental and skeletal material from the Upper Jurassic of Germany and test its purported carcharhiniform affinity through morphometric and phylogenetic analyses. Although †Bavariscyllium possesses a whisker-like throat barbel suggesting a closer relationship with orectolobiforms, our findings reveal insufficient evidence to confidently assign †Bavariscyllium to either Orectolobiformes or Carcharhiniformes. Additionally, we present quantitative evidence indicating that early galeomorphs, despite probably not being placed among extant orders, were exploring a variety of body forms, predating the divergence of most major body plans among modern representatives. †Bavariscyllium exhibits generalised clutching-type teeth with a hemiaulacorhize root characterised by strongly flared root lobes, closely resembling the supposed earliest carcharhiniforms from the Middle Jurassic. However, these features neither confirm nor refute a carcharhiniform affinity, questioning the reliability of these early galeomorphs as calibration fossils for dating the divergence of carcharhiniforms in phylogenomic analyses.

New Caledonia is a biodiversity hotspot with high levels of micro-endemism, yet its gracillariid fauna remains poorly documented. Here, two new species of Caloptilia Hübner, 1825 (Gracillariidae) are described from Glochidion J.R.Forst. & G.Forst. (Phyllanthaceae) host plants in Parc des Grandes Fougères, New Caledonia: Caloptilia augeas Guiguet, Lopez-Vaamonde, van Nieukerken & Ohshima, sp. nov., and Caloptilia ceryneia Guiguet, Lopez-Vaamonde, van Nieukerken & Ohshima, sp. nov. Both species induce leaf galls on Glochidion billardierei Baill., co-occurring on the same host species, sometimes even on the same leaf. They exhibit distinct wing patterns, but very similar male and female genitalia, and DNA barcoding supports their status as separate species. These findings provide evidence for potential within-host sympatric speciation, as documented in other gall-inducing insects. The larval biology of C. augeas and C. ceryneia reveals a unique frass disposal behaviour, whereby waste is excreted through a hole and the aperture is subsequently sealed-an adaptation not previously reported in gall-inducing Lepidoptera. Our findings double the known number of gall-inducing species in Gracillariidae, highlighting that this life history strategy may be more common than currently appreciated. We also provide new information on distribution and host plants of Caloptilia xanthopharella (Meyrick, 1880), a leaf roller found on the same host plant, G. billardierei. These findings mark the first records of the subfamily Gracillariinae in New Caledonia. This study underscores the underexplored diversity of New Caledonian gracillariids and emphasises the conservation value of Parc des Grandes Fougères. Further surveys in the Indo-Pacific region may reveal additional yet undescribed Caloptilia species associated with Phyllanthaceae and help clarify the evolutionary mechanisms underpinning their diversification.

ABSTRACT Aim The assembly of montane plant communities through time is underlain by historical and abiotic factors. However, the extent of evolutionary connectivity between ancient highland ecosystems and surrounding lowlands remains unclear. Here, we investigate the evolutionary connections between the campos rupestres , a hyperdiverse and fragmented montane vegetation complex in eastern South America, and lowland biomes surrounding it: savannas, rainforests and seasonally dry tropical forests. Location Eastern South America. Time Period Cenozoic. Major Taxa Studied Flowering plants. Methods Using phylogenetic beta diversity analyses for 13 angiosperm clades, we assess the degree of lineage dissimilarity between campos rupestres subregions and adjacent biomes. We also apply generalised dissimilarity modelling to determine the role of climate, soil and geographic distance in shaping spatial patterns of phylogenetic composition. Results Our results reveal high lineage permeability between campos rupestres and surrounding biomes, with lineage sharing largely reflecting biome adjacency. This pattern is mainly driven by shared climatic conditions, which are the strongest predictors of phylogenetic dissimilarity. Main Conclusions We highlight the importance of lineage exchange between lowland and montane environments for the assembly of highland floras. By showing that lineage movements across biome boundaries have been common over time and across spatial scales, our study challenges the idea that ancient Neotropical mountains are isolated sky‐islands. Instead, we emphasise the dynamic nature of montane plant diversity and the pivotal role of climate in shaping evolutionary connections between highlands and lowlands.

New records are given of the genus Koenikea from northern and eastern Australia. The following six new species are described: Koenikea yorkensis sp. nov., K. brachypalpis sp. nov., K. interstitialis sp. nov., K. inconspicua sp. nov., K. caniaensis sp. nov. and K. tuberculata sp. nov. The male of Koenikea piota Cook, 1986 is described for the first time. A key is provided for all Australian Koenikea species.