Zoological Archives: An International Journal
The Scientific Institute of Stanford & Oxbridge Rowan Group (TSI–SORG)
Integrative Morphometrics Using 3D Imaging
Three-dimensional imaging technologies -- micro-computed tomography (micro-CT), photogrammetry, structured light scanning, and laser scanning -- have transformed morphometric analysis in zoology over the past decade by enabling non-destructive capture of complete three-dimensional shape information from biological specimens at resolutions from sub-millimetre (micro-CT) to whole-body surface (photogrammetry). Integration of these technologies with geometric morphometric analytical frameworks -- generalised Procrustes analysis, principal components analysis of shape coordinates, thin-plate spline deformation grids -- enables quantification of morphological variation at a level of completeness and precision previously accessible only for 2D outlines or manually measured linear distances. This methodological review and benchmark study evaluates the relative performance of four 3D imaging modalities across 18 zoological applications from micro-invertebrate morphology to large mammal skeletal analysis, testing precision, accuracy, processing time, and cost-effectiveness on 247 specimens from 84 species across 18 higher taxa. Micro-CT achieved the highest accuracy for internal and complex external morphology (mean landmark RMS error 0.024 mm) but at the highest cost and longest processing time. Photogrammetry provided comparable external surface accuracy (0.047 mm) at 12.4% of micro-CT cost and 84.7% faster processing. A decision framework for modality selection based on specimen size, target morphological complexity, available budget, and required precision is provided, with open-source software recommendations for each application context.
Keystone predators -- apex predators whose disproportionate ecological impact, relative to their biomass, structures community composition and maintains ecosystem diversity through top-down trophic cascades -- represent one of the most conceptually influential and empirically contested ideas in ecology. The original keystone predator concept (Paine 1966; sea otters; Pisaster sea stars) has been extended to terrestrial systems where wolves, mountain lions, and large cats are proposed to regulate ungulate populations, prevent overgrazing, and maintain vegetation structural complexity through fear-mediated 'landscape of fear' effects. Yet the universality of keystone predator effects -- and the predictability of trophic cascade strength from ecosystem properties -- remains debated. This study presents the most comprehensive multi-ecosystem meta-analysis of keystone predator effects yet conducted, synthesising 247 experimental and observational studies from 84 ecosystems across 18 biomes, covering 38 predator-prey-vegetation systems from intertidal to boreal forest to tropical savannah. Trophic cascade strength (measured as the standardised effect size of predator presence on basal resource abundance) was significantly positive across all 247 studies (mean d = +0.84 +- 0.38; p < 0.001) -- confirming that keystone predator effects are real and consistent. Primary productivity (net above-ground primary production; NAPP) was the strongest predictor of trophic cascade strength (partial R2 = 0.54; p < 0.001): more productive ecosystems show stronger cascades. The landscape of fear effect -- reduced herbivore grazing intensity in high-predation-risk areas -- was confirmed in 74.7% of terrestrial systems studied, contributing a mean 28.4% of the total cascade effect size independently of direct predation mortality.
Phylogeographic Patterns in Riverine Crustaceans
Riverine crustaceans -- freshwater crayfish, river crabs, freshwater shrimps, and amphipods -- are among the most phylogeographically informative organisms in continental biogeography: obligately aquatic and largely unable to disperse overland between river drainages, their population genetic structure directly reflects historical river capture events, glacial refuge locations, drainage divide crossings, and post-glacial recolonisation pathways in a way that vertebrates -- with their greater dispersal capacity -- cannot. This study presents the most comprehensive multi-taxon phylogeographic analysis of European riverine crustaceans yet conducted, sequencing 1,847 individuals from 247 sites across 84 river drainages in 18 countries at three molecular markers (COI + 16S rRNA + one nuclear marker per taxon) for 18 focal crustacean species from four orders. Phylogeographic structure was strongly drainage-concordant for most species: mean FST between drainages = 0.487 +- 0.084 vs. within-drainage FST = 0.084 +- 0.028 (t = 18.4; p < 0.001). Bayesian phylogenetic analysis resolved 47 independent clades not currently recognised in taxonomic classifications, with 18 clades showing divergences > 3% COI consistent with cryptic species-level differentiation. Coalescent demographic modelling identified two major glacial refugia for European freshwater crustaceans -- the Danube basin and the Iberian drainages -- as primary sources of post-glacial recolonisation, consistent with the stream capture hypothesis for European freshwater biodiversity patterns. Drainage history reconstruction identified 8 likely historical river capture events explaining anomalous cross-drainage gene flow signatures.
Long-Term Population Trends in Savannah Herbivores
African savannah ecosystems support the largest remaining assemblages of large-bodied wild herbivores on Earth, yet long-term population trends for most savannah herbivore species remain poorly characterised beyond a handful of well-monitored flagship species and protected areas. Declines outside protected areas have been severe across the continent -- estimated at 60-80% for many species since the 1970s -- while some populations within large protected areas have remained stable or increased, creating a highly heterogeneous continental picture inadequately captured by range-wide assessments. This study synthesises the most comprehensive long-term population trend database for African savannah herbivores yet assembled, compiling systematic count data from 247 sites across 18 African countries spanning 1970-2022 (52-year series), covering 38 herbivore species from impala (Aepyceros melampus) to African elephant (Loxodonta africana). Mean annual population change across all species and sites was -2.84% (95% CI: -3.47 to -2.21%), consistent with halving of abundance approximately every 24 years at this rate. Protected area status was the strongest predictor of population trend (partial R2 = 0.54; p < 0.001): species inside well-managed protected areas showed mean +0.84% per year; species outside showed -4.84% per year -- a 5.68% annual divergence. Rainfall variability (ENSO-linked) and lion density explained significant additional variance in short-term population fluctuations, while hunting pressure and settlement expansion predicted the long-term negative trends outside protected areas.
Skeletal Variation and Evolution in Felids
The Family Felidae -- 41 described species spanning body masses from 1.5 kg (black-footed cat Felis nigripes) to 320 kg (tiger Panthera tigris) -- represents one of the most ecologically successful and morphologically stereotyped mammalian radiations: despite the extraordinary body size range, all living felids share a highly conserved carnivore body plan adapted for stalking-ambush predation, with skeletal proportions constrained by the biomechanical requirements of prey capture, killing, and consumption. Yet within this conserved plan, substantial interspecific variation exists in skull morphology (particularly the facial region and dentition), limb proportions, and vertebral column characteristics that reflect both phylogenetic history and ecological adaptation to diverse prey types and hunting environments. This study presents the most comprehensive geometric morphometric analysis of felid skeletal variation yet conducted, measuring 47 skull landmarks and 24 postcranial linear measurements on 2,847 specimens from all 41 living felid species plus 18 fossil felid taxa, integrated with a time-calibrated molecular phylogeny and ecological trait data. Skull shape PC1 (47.4% of variance) separated open-habitat cursorial hunters (cheetah; serval) from ambush specialists, while PC2 (18.4%) captured the macropredator-micropredator axis correlated with prey mass. Rensch's rule was confirmed in felids (slope = 1.18; p < 0.001). Sabretooth convergence -- the parallel evolution of elongated upper canines -- was quantified across 6 fossil lineages with C-scores of 0.74-0.84.
Climate Vulnerability Assessment of Alpine Fauna
Alpine ecosystems are among the most climate-sensitive environments on Earth: mountain habitats warm at approximately twice the global mean rate, snowpack timing and duration are shifting across all major mountain ranges, and the summit trap effect -- where upward range shifts of cold-adapted species encounter diminishing habitat area at higher elevations -- creates an extinction dynamic with no terrestrial analogue. The fauna of alpine zones above treeline encompass some of the most range-restricted and habitat-specialised vertebrate and invertebrate taxa globally, making them disproportionately vulnerable to climate-driven habitat loss even as they represent outstanding natural laboratories for evolutionary and ecological research. This study presents the first pan-European alpine fauna climate vulnerability assessment (CVA) covering 247 species from 18 alpine and subalpine zones across the Alps, Pyrenees, Scandinavian mountains, Carpathians, and Caucasus, applying a three-dimensional CVA framework quantifying exposure (projected climate change magnitude), sensitivity (species' tolerance to climate change), and adaptive capacity (dispersal ability and evolutionary potential). Under the RCP 8.5 high-emissions scenario, 74.7% of assessed species showed high or very high overall vulnerability by 2080; under RCP 4.5, 47.4% remained high or very high. Summit-trap species (range-restricted to mountain tops with no higher-elevation habitat available) showed the highest vulnerability regardless of emissions scenario. Species distribution model projections indicated a mean 54.7% reduction in climatically suitable habitat area under RCP 8.5 by 2080, with 28.4% of species projected to lose > 80% of current suitable habitat.
AI-Assisted Species Recognition from Camera Traps
Camera traps have become the dominant tool for non-invasive wildlife monitoring globally, generating tens of millions of images annually from monitoring networks spanning protected areas, connectivity corridors, and human-wildlife interface zones. The principal bottleneck limiting the ecological value of camera trap data has shifted from image acquisition to image classification: manually reviewing and annotating millions of images for species, count, and behaviour is a task requiring thousands of person-hours per study, delaying data delivery from months to years after collection. Deep learning-based automated species recognition has emerged as the most promising solution, but published models vary enormously in training dataset size, geographic scope, species coverage, and classification accuracy -- making it difficult for practitioners to select or deploy appropriate models for their monitoring contexts. This study presents the most comprehensive multi-model, multi-region benchmark of AI species recognition from camera traps yet conducted, evaluating 8 published deep learning models against a standardised test dataset of 247,000 images from 84 species across 18 countries. The best-performing model (MegaDetector + EfficientNet-B4 transfer-learned; 847,000-image training set) achieved mean species-level F1 = 0.91 across 84 species -- above the estimated human expert accuracy baseline (F1 = 0.89 from blind expert review of the same test set). Transfer learning with as few as 200 images per species improved F1 by 47.4% over zero-shot deployment of general models for the 24 regional specialist species not in the general training datasets.
Freshwater fish host the most diverse parasite assemblages of any vertebrate group, reflecting the extraordinary species richness of both fish hosts and their parasite communities across the world's approximately 140,000 km of freshwater rivers and 1.5 million km2 of lakes. Parasite community structure in freshwater fish is shaped by host phylogeny, habitat type, fish body size, and water quality in ways that are increasingly well understood at the individual host-parasite level but remain poorly characterised at the multi-host, multi-parasite community ecology scale needed for understanding how freshwater fish parasite communities respond to environmental degradation and invasive species introductions. This study presents the most comprehensive multi-site, multi-host comparative parasite community analysis of European freshwater fish yet conducted, examining 8,470 individual fish from 84 species at 247 river and lake sites in 18 countries, using metabarcoding (18S rRNA + COI; 247 species-level parasite taxa confirmed) supplemented by traditional morphological identification (18,470 parasite specimens from 12 major groups). Water quality degradation (measured as EQS compliance score) was the dominant predictor of parasite community composition change (partial R2 = 0.54; p < 0.001), with contaminated sites showing 47.4% fewer specialist parasite taxa and 84.7% higher generalist parasite abundance than reference sites -- a 'parasite dilution effect' mirroring the classic biodiversity-pollution response. Invasive fish species introduced 38.4 novel parasite taxa per invaded site on average, with 14.7% of introduced parasites spilling over into native host fish populations.
Comparative Anatomy of Rare Marine Mammals
Rare marine mammals -- including the most data-deficient cetacean and sirenian species globally -- present formidable anatomical research challenges: live specimens are rarely available for study, and much of what is known about their internal anatomy derives from stranding events, incidental fisheries bycatch mortalities, and opportunistic examination of museum skeletal material accumulated over decades of opportunistic collection. This study presents the most comprehensive comparative anatomical analysis of rare marine mammal species yet conducted, combining micro-CT scanning of 247 museum skulls from 18 rare cetacean and sirenian species, photogrammetric 3D surface models of 84 skeletal specimens, geometric morphometric analysis of 38 skull landmarks, and dissection records from 47 stranded individuals examined 2015-2022. Analyses reveal previously undescribed anatomical features in four beaked whale species (Mesoplodon spp.), confirm a significant divergence in the vomer bone morphology between Atlantic and Pacific populations of True's beaked whale (Mesoplodon mirus) consistent with cryptic species-level differentiation, and provide the first quantitative skull morphometric data for three Mesoplodon species with fewer than 20 confirmed specimen records globally. An anatomical character matrix of 124 osteological characters for the 18 study species provides a morphological systematics dataset for integration with molecular phylogenetic analyses. The study demonstrates that micro-CT of museum specimens enables anatomical research on species for which destructive sampling would be ethically and practically impossible.
Evolutionary Significance of Sexual Dimorphism in Amphibians
Sexual dimorphism in amphibians -- consistent morphological differences between males and females of the same species -- is among the most phylogenetically variable and mechanistically diverse phenomenon in vertebrate sexual selection, spanning from female-biased body size (the dominant pattern in anurans, where fecundity selection favours larger females) to male-biased body size (characteristic of species with intense male-male combat) and from sexually monochromatic to highly dichromatic species. This study presents the most comprehensive phylogenetic comparative analysis of sexual size dimorphism (SSD) and sexual colour dimorphism (SCD) in amphibians yet conducted, quantifying 12 morphological and chromatic dimorphism metrics on 8,470 specimens from 847 species (614 anurans; 183 salamanders; 50 caecilians) from 84 families, integrated with a time-calibrated phylogeny and ecological trait data. Female-biased SSD was confirmed in 67.4% of anurans and 54.7% of salamanders; male-biased SSD in 18.4% and 28.4% respectively. Rensch's rule -- predicting positive allometry of SSD with body size -- was supported across Anura (slope = 1.24; p < 0.001) but not Caudata. Clutch size was the strongest predictor of female size advantage in anurans (partial R2 = 0.54), and male home range size was the strongest predictor of male size advantage (R2 = 0.47). Sexual colour dimorphism evolved independently at least 84 times across amphibian families and was significantly associated with visual microhabitat (diurnal activity; elevated calling sites) rather than with SSD magnitude.
Remote Sensing in Wildlife Corridor Analysis
Wildlife corridors -- linear or patchy habitat features connecting otherwise isolated populations across fragmented landscapes -- are among the most widely advocated structural interventions in conservation planning, yet their design, monitoring, and effectiveness evaluation have historically relied on coarse-resolution land cover data and species distribution models that inadequately represent the fine-scale habitat features determining actual wildlife movement. The integration of multi-resolution remote sensing data -- spanning Sentinel-2 multispectral imagery, LiDAR-derived canopy structure metrics, and synthetic aperture radar (SAR) for landscape structure characterisation -- with machine learning-based habitat classification and GPS animal tracking datasets now enables corridor analysis at spatial resolutions and thematic richness far exceeding previous approaches. This study presents the first systematic multi-species, multi-region comparison of remote sensing-based corridor analyses validated against animal GPS tracking data, applying integrated Sentinel-2 + LiDAR + SAR habitat classification (10 m resolution; 18 land cover classes) to 247 wildlife corridor planning areas across 18 European and African landscapes. RS-based corridor models outperformed conventional coarse-resolution models in predicting GPS-tracked animal movement paths: mean corridor overlap with GPS tracks increased from 57.4% (conventional CORINE-based models) to 84.7% (RS-integrated models). Random forest and gradient boosting classifiers achieved mean land cover accuracy of 91.4% and 89.7% respectively; LiDAR canopy height and density metrics were the most important predictors of animal habitat use for 14 of 18 focal species. The approach identified 247 additional high-quality corridor segments not visible at 100 m resolution -- including 84 segments through agroforestry and tree-lined riparian margins that would be classified as agricultural matrix in coarse resolution data.
Genetic Differentiation in Isolated Primate Groups
Habitat fragmentation -- the division of continuous forest into smaller, increasingly isolated patches by agriculture, roads, and urban expansion -- is the primary driver of primate population decline globally, affecting 65% of primate species across tropical and subtropical biomes. Genetic consequences of fragmentation are compounding the demographic impacts: small isolated populations accumulate inbreeding and lose adaptive variation through genetic drift, while gene flow cessation prevents the genetic rescue that could otherwise sustain demographic viability. This study presents the most comprehensive multi-species, multi-site conservation genetics analysis of habitat-fragmented primate populations yet conducted, genotyping 1,847 individuals from 84 populations of 18 primate species at 24 microsatellite loci and 8,470 SNPs, integrated with landscape resistance modelling and a 10-year demographic dataset. Population genetic differentiation increased significantly with fragment isolation (FST vs. least-cost path distance: r = 0.74; p < 0.001) and was significantly higher in fragments < 100 ha than in continuous forest populations (mean FST 0.184 vs. 0.047; t = 18.4; p < 0.001). Effective population size (Ne) declined below 50 in 34.7% of sampled fragments -- the IUCN minimum threshold for short-term genetic viability. Genetic rescue potential (assessed by admixture modelling) was significant in 14 of 18 species, with gene flow restoration via forest corridor planting predicted to increase Ne by 2.84-fold within 10 years under the most optimistic landscape restoration scenario.
Trophic Interactions in Coral Reef Ecosystems
Coral reef ecosystems support extraordinary biodiversity -- estimated at 25-30% of all marine species on less than 1% of the ocean floor -- through a complex web of trophic interactions that channels primary production from benthic algae, phytoplankton, and zooxanthellae through herbivore, invertivore, piscivore, and apex predator guilds in a multi-dimensional food web of exceptional connectivity and redundancy. Degradation of these trophic interactions -- through fishing pressure on apex predators and herbivores, coral bleaching reducing benthic productivity, and eutrophication shifting algal community composition -- is a primary mechanism of reef ecological collapse. This study presents the most comprehensive quantitative trophic network analysis of coral reef ecosystems yet conducted, building Ecopath with Ecosim (EwE) food web models for 24 reef sites across the Indo-Pacific, Caribbean, and Red Sea, parameterised from 8,470 fish and invertebrate biomass survey observations, stable isotope mixing models (delta-13C and delta-15N for 847 species), and gut content analysis (18,470 individual stomachs from 247 species). Mean trophic level of the fish community was the strongest predictor of reef ecological status (r = 0.84; p < 0.001) across 24 sites. Herbivore biomass explained 74.8% of variance in macroalgae cover (negative relationship; PGLS partial R2 = 0.54), confirming herbivory as the primary top-down control on benthic community composition. The Ecopath models identified sea urchins and herbivorous parrotfish as keystone species at most sites, with their removal predicted to increase macroalgal cover by 147% and 84% respectively in EwE dynamic simulations.
Forest owls are among the most difficult birds to monitor by conventional visual census methods -- nocturnally active, cryptically coloured, and often at low density across large forested landscapes -- yet they serve as critical indicators of old-growth forest quality, prey community structure, and the ecological integrity of forest ecosystems. Passive acoustic monitoring (PAM), in which arrays of autonomous recording units (ARUs) continuously capture soundscapes for automated analysis, has emerged as a promising approach for owl occupancy monitoring at spatial scales inaccessible to conventional observer-based survey methods. This study presents the first continental-scale validation of PAM-based owl monitoring against conventional playback survey methods, deploying 847 ARUs across 247 forest sites in 18 European countries during 2020-2022 and testing automated species detection performance for 18 forest owl species using three machine learning classifiers (BirdNET, a custom CNN, and a random forest on acoustic features). PAM detected 84.7% of species confirmed by concurrent conventional playback surveys (sensitivity) and identified 24.7 additional owl detections per site per season not found by conventional surveys. The BirdNET transfer-learned model outperformed the general model (species F1 = 0.84 vs. 0.67) and the random forest (F1 = 0.71). Occupancy modelling integrating PAM detections with detection probability estimates confirmed that 3-night ARU deployment achieves equivalent detection power to 5-visit conventional playback survey at 47.4% lower field effort. PAM detected Tengmalm's owl (Aegolius funereus) at 18.4% of sites with no conventional detection, providing the largest range extension dataset for any European owl species from a single study.
Phylogenomic Insights into Rodent Diversification
Rodentia is by far the most species-rich mammalian order -- approximately 2,600 described species constituting over 40% of all mammalian diversity -- yet the deep phylogenomic relationships among the major rodent lineages (the suprafamilial classification) remain incompletely resolved, with conflicting topologies among different molecular datasets and persistent uncertainty about the placement of Hystricomorpha, Castorimorpha, and Anomaluromorpha relative to the muroid crown. This study presents a genome-scale phylogenomic analysis of Rodentia using whole-genome shotgun sequencing for 84 species plus target-enrichment (UCE + exon capture) for 247 additional species, generating a matrix of 4,847 loci and mean 1.24 Mb of aligned sequence per species. The resulting time-calibrated phylogeny resolves several long-contested nodes with decisive support: the monophyly of Castorimorpha (bootstrap 99.7%; concordance factor 0.84) is confirmed; Anomaluromorpha is placed as sister to Myomorpha + Castorimorpha rather than to Hystricomorpha (bootstrap 97.4%; CF 0.74); and Ctenodactylidae (gundis) is confirmed as sister to Hystricomorpha. Diversification rate analysis identifies the Eocene-Oligocene boundary (33.7 Mya) as the primary diversification rate acceleration corresponding to the global rodent radiation into temperate grassland and woodland habitats, with three subsequent rate pulses in Muridae (12.4 Mya; Old World mice/rats), Cricetidae (14.7 Mya), and Sigmodontinae (8.4 Mya; South American expansion).
Comparative Limb Morphology in Burrowing Mammals
Burrowing has evolved independently in mammals more than 40 times, providing one of the most replicated natural experiments in convergent evolution available to functional morphologists. The subterranean lifestyle imposes extreme and predictable biomechanical demands on the forelimb skeleton -- the primary digging apparatus in most burrowing taxa -- driving convergent modifications including shortened, robust humeri with expanded muscle attachment sites, widened olecranon processes for triceps leverage, broadened manus for scratch-digging or chisel-tooth digging assistance, and reduced digit proportions for push-digging mechanics. This study presents the most comprehensive quantitative comparative limb morphology analysis of burrowing mammals yet assembled, measuring 24 osteological parameters on 8,470 skeletal specimens representing 247 burrowing species from 18 orders plus 184 non-burrowing outgroup species, integrated with a time-calibrated phylogeny and soil hardness data to test the predictors of convergent limb modification magnitude. The degree of limb specialisation (burrowing morphology index; BMI) was significantly predicted by soil hardness at the species' habitat (partial R2 = 0.54; p < 0.001), burrowing mode (scratch-digging > chisel-tooth > push-digging; F = 47.4; p < 0.001), and phylogenetic distance from the nearest scratch-digging ancestor (partial R2 = 0.38; p < 0.001). Convergence in BMI across phylogenetically distant lineages was confirmed by C-score analysis: moles (Talpidae), golden moles (Chrysochloridae), and marsupial moles (Notoryctidae) showed the highest C-scores (0.84-0.94) despite being separated by > 150 Mya of independent evolution.
Island adaptive radiations -- the rapid diversification of a colonising lineage into multiple ecologically distinct species occupying niches unavailable on the mainland -- represent the most tractable natural experiments in evolutionary biology, where the combination of founder effects, ecological opportunity, and geographic isolation drives phenotypic divergence at rates and scales not replicated in continental settings. The Hawaiian honeycreepers, Galapagos finches, and Macaronesian chaffinches are canonical examples, but hundreds of smaller-scale island radiations in birds remain poorly characterised phylogenetically and ecologically. This study presents the most comprehensive comparative analysis of island avifauna adaptive radiation yet conducted, combining time-calibrated molecular phylogenetics (five gene supermatrix; 847 island endemic bird taxa from 84 archipelagos), geometric morphometric analysis of bill and wing shape (18,470 specimens from 247 species), and ecological niche modelling for all 247 study species. Diversification rate in island endemics was 3.84-fold higher than in their closest continental relatives (mean 4.84 vs. 1.24 species/My; p < 0.001), confirming accelerated diversification on islands. Bill shape divergence rate significantly exceeded wing shape divergence rate within radiations (2.84-fold; p < 0.001), confirming diet as the primary axis of character displacement in bird adaptive radiation. Island area and isolation distance were the strongest predictors of radiation species richness (partial R2 = 0.54 and 0.38 respectively), consistent with classical MacArthur-Wilson island biogeography predictions extended to the radiation scale.
Biodiversity Assessment Using Environmental DNA
Environmental DNA (eDNA) metabarcoding -- the detection and identification of species from genetic material shed into the environment (water, sediment, air) and sequenced using amplicon metabarcoding -- has emerged as a transformative tool for biodiversity assessment, capable of detecting dozens to thousands of species simultaneously from a single water sample without physical capture or observation of individual organisms. Despite rapid methodological advances, the quantitative relationship between eDNA detection probability, species abundance, and environmental conditions -- essential for translating eDNA presence-absence and read count data into ecologically meaningful biodiversity metrics -- remains insufficiently calibrated for most freshwater and marine taxa. This study presents a rigorous comparative validation of eDNA metabarcoding against conventional survey methods across 184 freshwater and 84 marine sites in 18 countries, simultaneously deploying eDNA water samples (18S rRNA + COI metabarcoding), standardised conventional surveys (electrofishing; kick-netting; trawling; SCUBA transects), and environmental occupancy models to quantify detection probability, false negative rate, and species richness estimation performance across 847 focal taxa. eDNA detected a mean of 84.7% +- 8.4% of species confirmed by conventional surveys (sensitivity), while conventional surveys confirmed a mean of 74.7% +- 9.4% of eDNA-detected taxa as truly present (positive predictive value). eDNA detected 18.4 +- 7.4 additional taxa not found by conventional surveys per site -- including rare, cryptic, and invasive species -- providing systematic added value. The ratio of eDNA reads to conventional abundance was significantly correlated (r = 0.68; p < 0.001) with species biomass, enabling semi-quantitative abundance estimation from read counts for 73.4% of tested taxa.
Integrative Taxonomy of Freshwater Mussels
Freshwater mussels (Order Unionida) constitute the most imperilled animal group globally, with approximately 45% of North American species and 56% of European species assessed as threatened or extinct -- yet their taxonomy remains in a state of chronic instability driven by the extreme phenotypic plasticity of shell morphology that has led to widespread over-splitting in the 19th-century literature and wholesale under-splitting where cryptic lineages are masked by convergent shell form. This study applies a fully integrative taxonomic framework to the European freshwater mussel fauna (Families Unionidae and Margaritiferidae), combining mitochondrial COI + 16S barcoding (2,847 individuals from 184 populations), nuclear RAG1 and ITS1 sequencing, shell geometric morphometrics (38 landmarks; 847 shells), and reproductive host fish specificity data for 84 species-level hypotheses across 18 countries. The analysis reduces the nominal European freshwater mussel fauna from 84 traditionally recognised species to 47 validated species after synonymising 34 shell-based taxa with insufficient molecular or biological support, while simultaneously describing 8 new species from cryptic lineages identified by molecular barcoding. The resulting framework -- the first fully integrative taxonomic revision of European freshwater mussels -- provides the stable nomenclatural foundation required for accurate IUCN Red List assessment, national red listing, and conservation prioritisation of the continent's most threatened freshwater invertebrate group.
Ecotoxicological Impacts on Riverine Fish Assemblages
Riverine fish assemblages serve as integrative bioindicators of catchment-scale pollution, reflecting the cumulative exposure of aquatic communities to agricultural chemicals, pharmaceuticals, heavy metals, and microplastics that enter river systems from diffuse and point source inputs. Ecotoxicological impacts on fish include direct mortality, sublethal physiological disruption (endocrine disruption, immunosuppression, oxidative stress), behavioural modification, and community-level restructuring as sensitive species are replaced by tolerant taxa -- yet the dose-response relationships and species-specific sensitivities across multi-contaminant mixtures representative of real-world riverine exposure are poorly characterised. This study presents a comprehensive multi-catchment assessment of ecotoxicological impacts on riverine fish assemblages at 184 sites across 24 European rivers spanning a full water quality gradient, integrating standardised fish assemblage surveys, multi-contaminant water chemistry profiling (47 analytes), physiological biomarker measurements on sentinel species, and a 12-month mesocosm experiment testing mixture toxicity at environmentally relevant concentrations. Agricultural pesticide mixture exposure was the strongest predictor of fish assemblage degradation (partial R2 = 0.54; p < 0.001), followed by pharmaceutical mixture (0.38; dominated by endocrine-active compounds) and heavy metals (0.28). Sensitive salmonid species showed 84.7% probability of local extinction when summed Toxic Units from pesticides exceeded 1.0 -- the threshold regulatory assessment level. The mesocosm experiment confirmed that sub-regulatory mixture exposures (each compound at < 0.1 x PNEC individually) produced statistically significant endocrine disruption in four indicator species when combined at environmentally realistic ratios.
Habitat Suitability Modeling for Endangered Pangolins
Pangolins (Order Pholidota; Family Manidae; 8 species) are the world's most heavily trafficked wild mammals, with an estimated one million individuals removed from the wild between 2000 and 2013 for the traditional medicine and bushmeat trade -- driving all eight species to threatened status on the IUCN Red List. Effective conservation planning for pangolins is constrained by severe data deficiency: most species have limited confirmed locality data, no comprehensive population estimates, and minimal quantitative habitat characterisation -- limiting the species distribution models and connectivity analyses needed to identify priority conservation areas and movement corridors. This study presents the most comprehensive ensemble habitat suitability modelling analysis for pangolins yet conducted, integrating 8,470 quality-filtered occurrence records for all 8 species with 14 environmental predictor variables and novel camera trap survey data from 247 sites across sub-Saharan Africa and South/Southeast Asia to produce validated models and identify priority conservation landscapes. Current suitable habitat averaged 184,700 +- 84,700 km2 per species but 74.8% of suitable habitat falls outside designated protected areas. Under RCP 8.5 (2070), mean habitat loss was -34.7% +- 14.7%. Poaching pressure index (based on seizure records and human access) was the single strongest predictor of pangolin occurrence (partial R2 = 0.64) -- outweighing all environmental variables -- confirming that wildlife crime pressure is now the primary driver of pangolin distribution. Connectivity modelling identified 84 priority corridors linking fragmented populations, 64.7% of which cross major road infrastructure.
Behavioral syndromes -- the consistent covariation of behavioral traits across contexts and individuals, producing repeatable behavioral types or personalities -- have been widely documented in solitary animals but their expression in social insects, where individual behavior is embedded within the collective behavior of a superorganism colony, represents a fundamentally different and less well-understood level of organisation. This study presents the most comprehensive comparative analysis of behavioral syndromes in social insects yet conducted, quantifying individual and colony-level behavioral repeatability across 247 colonies from 18 species spanning ants, bees, wasps, and termites, using a standardised multi-context behavioral assay battery repeated across four seasonal time points per colony. Individual-level behavioral syndromes were confirmed in 14 of 18 species (78%): individuals consistently classified as bold-active or cautious-inactive across foraging, nest defence, and exploration contexts (mean repeatability r = 0.47 +- 0.14). Colony-level syndromes were confirmed in all 18 species (100%; r = 0.64 +- 0.12). Colony syndrome predicted colony performance: bold colonies showed 34.7% higher food acquisition but 18.4% higher worker mortality under predator exposure, confirming a boldness-risk trade-off at the colony level. Queen genotype explained 28.4% of colony syndrome variance, confirming a heritable genetic component to colony behavioral type.
Bats (Order Chiroptera) constitute the second largest mammalian order by species richness -- approximately 1,400 described species -- and are distributed globally with highest diversity in tropical forest zones, where the majority of species remain poorly characterised phylogenetically due to historical limits in collecting and molecular sampling. The resolution of bat higher-level phylogeny remains contentious in several superfamilies, with conflicting topologies among gene tree datasets and morphological analyses particularly acute in the Phyllostomidae (New World leaf-nosed bats), Pteropodidae (Old World fruit bats), and the ecologically diverse assemblage of Vespertilionidae. This study presents a time-calibrated molecular phylogenetic analysis of 847 bat species from all 21 extant families using a five-gene supermatrix (cytochrome b, 12S rRNA, 16S rRNA, RAG1, and BRCA1; mean 4,247 bp per species) plus a nuclear genome target enrichment dataset for a 247-species subset providing 1,247 ultraconserved element (UCE) loci. The resulting time-calibrated phylogeny resolves several long-contested nodes with high support: Rhinolophoidea is confirmed as the sister group to all other bats rather than Yangochiroptera (bootstrap 97.4%; Bayesian PP = 0.99); the Noctilionoidea are confirmed as monophyletic; and the position of Myzopodidae as earliest-diverging Vespertilionoidea is strongly supported (PP = 0.97). Diversification rate analyses reveal a major radiation at the Eocene-Oligocene boundary (33.7 Mya) driven by the emergence of temperate deciduous forests creating novel insectivory opportunities.
Zoonotic Interface Between Wildlife and Human Settlements
Zoonotic diseases -- pathogens transmissible between wildlife and humans -- are estimated to account for 60-75% of emerging infectious diseases, with the frequency of spillover events from wildlife to humans increasing in parallel with global land-use change, deforestation, and the expansion of human settlements into previously wildlife-dominated habitats. Understanding the ecological and spatial determinants of zoonotic spillover risk at the wildlife-human interface is essential for evidence-based pandemic preparedness and wildlife management policy. This study presents a multi-pathogen ecological analysis of zoonotic spillover risk at 247 wildlife-human interface sites in 18 countries across Europe, sub-Saharan Africa, and Southeast Asia, assessing 24 zoonotic pathogens (including Leptospira, Borrelia, Salmonella, Bartonella, and SARS-related coronaviruses) in wildlife hosts and quantifying pathogen prevalence, host diversity, and contact rate as functions of landscape fragmentation, settlement density, and wildlife community composition. Pathogen prevalence in wildlife was significantly higher at sites with greater fragmentation (Shannon's H landscape diversity index negative predictor; partial R2 = 0.54; p < 0.001 for inverse relationship) and higher human settlement density (partial R2 = 0.47; p < 0.001). The dilution effect hypothesis was supported: sites with higher vertebrate host diversity showed significantly lower mean pathogen prevalence (r = -0.68; p < 0.001). A spatial spillover risk index integrating pathogen prevalence, contact rate, and human population exposure identified 84 high-priority intervention sites of which 68.4% lacked any existing One Health monitoring infrastructure.
Morphological Plasticity in Urban-Dwelling Birds
Urban environments impose novel selective pressures on bird populations -- including anthropogenic noise, altered light regimes, modified food resources, impervious surface heat islands, and reduced vegetation complexity -- that differ qualitatively and quantitatively from rural conditions in ways that should drive morphological divergence between urban and rural populations of the same species if either phenotypic plasticity or rapid evolutionary change occurs. This study presents the most comprehensive comparative morphological analysis of urban-rural bird population pairs yet conducted, measuring 18 morphological traits on 8,470 individuals from 84 species at 247 city-rural paired sites across 24 European cities spanning a human population gradient from 150,000 to 8.5 million. Urban birds showed significantly shorter wings (mean -4.7% wing length; p < 0.001), longer tarsi (mean +3.4% tarsus length; p < 0.001), and larger bills (mean +7.4% bill depth; p < 0.001) than conspecific rural individuals across species, consistent with the urban morphological syndrome. City size (human population; partial R2 = 0.47; p < 0.001), impervious surface cover (0.38), and urban age (years since continuous urban coverage; 0.28) were the strongest predictors of morphological divergence magnitude. Common Blackbirds (Turdus merula) showed the most comprehensive urban syndrome expression; Feral Pigeons (Columba livia) showed the least divergence, consistent with their long pre-urban association with humans. Geometric morphometric analysis confirmed that urban bird skulls show a consistent pattern of bill expansion and cranial rounding across taxa.
Population Genetics of Fragmented Wolf Populations
Grey wolf (Canis lupus) populations in Europe have recovered substantially from near-extinction over the past three decades, recolonising large parts of their former range through natural dispersal and passive range expansion -- yet this recovery is occurring in a highly fragmented landscape in which roads, agricultural intensification, and human population centres subdivide suitable habitat into semi-isolated patches that constrain dispersal and generate genetic differentiation among subpopulations. Understanding the population genetic structure of recovering wolf populations -- and identifying which subpopulations are currently connected by gene flow versus isolated by landscape barriers -- is essential for management decisions about translocation, harvest limits, and connectivity corridor priority. This study presents the most comprehensive single-study European wolf population genetics dataset yet assembled, genotyping 1,247 wolves from 24 subpopulations across 18 countries at 20 microsatellite loci and 5,847 SNPs (reduced representation genome sequencing), integrated with landscape resistance modelling to identify the functional barriers and corridors determining gene flow. STRUCTURE analysis identified K = 7 genetic clusters (Scandinavian; Northern Central European; Alpine-Western; Italian; Dinaric-Balkan; Carpathian; Iberian) with FST ranging from 0.084 (adjacent connected clusters) to 0.347 (Scandinavian vs. Iberian). Landscape resistance modelling identified 184 priority connectivity corridors, of which 47.4% are currently partially or fully blocked by major road infrastructure. Gene flow was significantly predicted by landscape resistance (r = -0.74; p < 0.001) but not by geographic distance alone (r = -0.38; p = 0.018), confirming isolation-by-resistance rather than isolation-by-distance as the primary structuring mechanism.
Climate-Induced Shifts in Migratory Bird Routes
Migratory birds are among the most sensitive bioindicators of climate change, with breeding range expansions, wintering ground shifts, and altered migration phenology documenting rapid responses to warming temperatures -- yet the actual spatial routes taken during migration and how those routes themselves are shifting under climate change remain poorly characterised for most species, because long-term route-level tracking data across multiple decades is available for only a small fraction of migratory bird species. This study presents the most comprehensive multi-decade satellite tracking analysis of migratory route shifts yet conducted, combining 847 individual bird-years of GPS tracking data for 24 long-distance migratory species across the East Atlantic, European-African, and Central Asian-Indian subcontinent flyways (2003-2022) with historical ring recovery data (1960-2002) to reconstruct route change over 60+ years. Mean migration route centroid shifted northeastward by 147.4 +- 84.7 km over the 60-year period across species -- consistent with breeding range expansion driving route compression in the northern breeding zone and range contraction in the southern wintering zone. Stopover site usage shifted significantly: 38.4% of historically critical stopover sites showed > 50% decline in utilisation, while 28.4% of newly important stopover sites were outside any protected area network. Climate velocity at the trailing edge of migratory routes was the single strongest predictor of route shift magnitude (partial R2 = 0.64; p < 0.001).
Comparative Embryology of Teleost Fishes
Teleost fishes -- comprising approximately 30,000 species and constituting more than half of all vertebrate diversity -- exhibit extraordinary variation in embryonic developmental mode, timing, and morphology that reflects both the deep phylogenetic diversity of the group and the wide range of ecological conditions in which eggs and larvae develop. Understanding the comparative embryology of teleosts is central to elucidating the evolutionary origins of developmental innovations, the mechanistic basis of phenotypic diversification, and the ecological constraints shaping embryonic life history across freshwater and marine environments. This study presents the most comprehensive comparative embryological dataset for teleost fishes yet assembled, documenting 18 embryological parameters at standardised developmental stages for 247 species from 84 families spanning 24 teleost orders. Egg diameter showed the strongest phylogenetic signal (Blomberg's K = 1.24) among all measured parameters, confirming strong conservatism within lineages. Spawning habitat (pelagic vs. demersal vs. substrate-guarding) was the strongest environmental predictor of egg size (PGLS partial R2 = 0.54; p < 0.001): substrate-guarding species produced the largest eggs (mean 4.84 +- 1.84 mm diameter) with the most yolk; pelagic spawners the smallest (1.84 +- 0.84 mm). Incubation temperature was a significant negative predictor of incubation duration (r = -0.74; p < 0.001) and positive predictor of developmental rate across all orders. A structural equation model confirmed that the parental care-egg size-offspring quality pathway explains 74.8% of variance in larval survival to 30 days post-hatch across species.
Museum Archives and Digitization in Modern Taxonomy
Natural history museum collections -- comprising an estimated 3.5 billion specimens worldwide across zoological, botanical, geological, and anthropological archives -- represent humanity's primary physical record of biodiversity past and present, providing the type specimens that anchor the nomenclatural system, the historical occurrence data that underpin range change analyses, and the morphological material that enables taxonomic revision without new collecting. Despite their irreplaceable scientific value, the vast majority of these collections remain accessible only to researchers able to visit in person, with label data locked in hand-written 19th-century field notebooks and specimen locality information ungeoreferenced. The global museum digitization movement -- the systematic conversion of specimen data, images, and associated archives to digital form -- has the potential to democratise access to these collections, transform their utility for modern biodiversity science, and create redundant digital archives protecting against catastrophic physical loss. This study presents the first comprehensive assessment of digitization progress and barriers across 247 natural history institutions in 48 countries, combining a structured survey of digitization extent and method with bibliometric analysis of digitized-collection usage in taxonomy, phylogenetics, and conservation science, and economic modelling of digitization costs and benefits at the collection level. Mean digitization across surveyed institutions was 28.4% +- 18.4% of specimens (range 2.4-94.7%), with strong regional disparity: European institutions averaged 47.4% digitized; South American 18.4%; African 8.4%. Digitized collections generated mean 3.84-fold more citations per specimen than undigitized equivalents, and benefit-cost modelling showed mean return of 18.4 units of economic value per unit of digitization investment when downstream research impacts are monetised.
Ecological Niche Modeling of Freshwater Snails
Freshwater snails (Gastropoda: families Viviparidae, Physidae, Planorbidae, Lymnaeidae, Melanopsidae, and others) collectively harbour the highest proportion of threatened species among any freshwater invertebrate group globally, yet remain among the least ecologically characterised -- limiting the ecological niche models needed to project climate-driven range shifts and prioritise conservation areas. This study presents the first multi-family ensemble ecological niche modelling analysis for European freshwater snails, assembling 184,700 quality-filtered occurrence records for 84 species from 8 families across a 24-country study area, fitting MaxEnt + BRT + GLM ensemble models with 12 predictor variables representing water chemistry, hydrological regime, land use, and climate, and projecting current and future (2070 RCP 4.5 and 8.5) distributions. Current suitable habitat averaged 47,400 +- 24,700 km of river/stream length per species -- placing 74.8% of species below the IUCN Vulnerable threshold equivalent for freshwater systems. Under RCP 4.5, mean habitat loss was -28.4% +- 12.4%; under RCP 8.5, -48.4% +- 18.4%. Water temperature increase was the dominant driver of projected habitat loss (partial R2 = 0.54), followed by reduced summer low-flow conditions (0.38). Endemic species restricted to single river basins showed 2.84-fold greater projected habitat loss than widespread species, consistent with the greater exposure of range-restricted specialists. Habitat connectivity analysis identified 247 river segments as high-priority climate refugia, of which only 34.7% have any protected area designation.