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bioRxiv2026

Nineteenth-century emergence of a seafloor ecosystem beyond late Quaternary limits

Mismatches between ecological time and geologic time complicate our ability to effectively compare contemporary ecosystem changes with those of the past. We amassed sub-decadal paleoecological data from the California Current System (CCS) to examine how benthic ecosystem structure evolved over the past 34,000 years in the Santa Barbara Basin across the glacial-to-interglacial transition. Our results indicate that even deep-sea ecosystems of the anthropocene sensu lato - the past few centuries characterized by outsized human impacts - are distinct compared to any point in the last 34,000 years. Novel ecosystem states and heightened variability began in the early 1800s AD, suggesting that colonial-era human land-use drove the emergence of a novel ecosystem state more than a century before global climate warming began in earnest.

paleontology↗

bioRxiv2026

Early Vertebrates Were Not Slow: Rapid Life Histories in Devonian Agnathans

Life history strategies such as rapid growth and high population turnover rates observed in vertebrates have been thought to have emerged relatively late in evolution. However, very little direct evidence exists at the species level for early vertebrates. In this study, a large fossil collection of over 450 specimens of Protaspis spp, heterostracan agnathans from the Cottonwood Canyon Formation at Beartooth Butte, Wyoming, from the Early Devonian, was analyzed. Morphological observations, analysis of bone plate completeness, and length-frequency analyses using ELEFAN--commonly used in recent fish studies--were applied to reconstruct growth rates, cohort structure, and ontogenetic processes. Protaspis specimens exhibited a continuous growth series from juvenile to adult stages, and a clear cohort structure was identified from the length-frequency distributions. The ELEFAN analysis suggested a life-history characterized by rapid growth and a short life span, and these features remained consistent in subset analyses restricted by species or locality, confirming the robustness of the estimates. Furthermore, the integration of the dermal bone plates progressed during the late stages of ontogeny, revealing that the rapid growth during the juvenile stage preceded the completion of this defensive structure. Comparisons of their growth parameters with those of extant fishes show that Protaspis does not align with slow-growing, long-lived "living fossil" taxa, but instead clusters with small-bodied, fast-growing species. These findings suggest that life-history strategies involving rapid growth and high population turnover were already established in early jawless vertebrates, much earlier than previously assumed.

paleontology↗

bioRxiv2026

Iridescence in pterosaur pycnofibers and the evolution of integumentary coloration

The bodies of pterosaurs, the first flying vertebrates, are covered with integumentary filaments (pycnofibres) thought to be homologous to feathers in dinosaurs, but their coloration remains unknown. Here, we report a layered internal arrangement of melanosomes containing a photonic nanostructure within the monofilaments in a previously undescribed specimen of tapejarid pterosaur Sinopterus dongi from the Early Cretaceous Jehol Biota. Optical simulations showed that this structure reflects green to magenta iridescent coloration, confirming the presence of melanosome-based iridescent coloration previously thought to be unique to birds. This finding deepens our understanding of structure/color gamut relationships in amniotes, while supporting further shared characteristics associated with derived genetic and regulatory shifts in archosaurs.

paleontology↗

bioRxiv2026

Taxon-resolved sources of organic carbon preserved in lake sediments using the sedaDNA GenC pipeline

Organic carbon (OC) burial in lakes is an important component of the global carbon cycle, but the source organisms of preserved OC remain poorly resolved. Here we develop the genC pipeline, which combines sedimentary ancient DNA concentrations, read-based taxonomic assignments, and group-specific priors for DNA and cellular carbon content to derive OCDNA-projected, a semi-quantitative proxy for the magnitude and taxonomic composition of preserved sedimentary OC. We apply genC to six high-latitude lake records spanning the last 30,000 years. OCDNA-projected broadly agrees with independent proxies for total organic carbon and aquatic contribution, supporting its reliability. Our results indicate that environmental conditions, especially warming, rather than preservation alone, are the main drivers of preserved OC variation. Terrestrial sources, mainly woody plants, dominate lake sediment OC. Eukaryotic algae as well as aquatic and terrestrial bacteria become more important during the warmer Holocene. These results establish sedaDNA as a taxonomically resolved tool for reconstructing long-term changes in preserved lake-sediment OC.

paleontology↗

bioRxiv2026

A new skeleton of the gorgonopsian Aelurognathus tigriceps from the Daptocephalus Assemblage Zone (Karoo Basin, South Africa) with novel insights into the pelvic girdle, hind limbs, and tail

Gorgonopsian therapsids represent a transitional condition in the evolution of synapsid locomotion and postcranial structure. Most descriptions of gorgonopsians have focused on cranial material, however, limiting their usefulness for informing patterns of postcranial evolution on the mammal stem. While some recent work has begun to focus on postcrania, especially the pectoral girdle and forelimbs, comparatively little data are available on the pelvic girdle, hind limbs and tail. We report a new specimen of the late Permian gorgonopsian Aelurognathus tigriceps comprising a partial skull and well-preserved postcranial skeleton, including the near-complete series of dorsal vertebrae and ribs, complete pelvic girdle, hind limbs, feet, and a nearly complete tail. The tail is longer than any other published gorgonopsian. The new material presented here provides an opportunity to better establish broader patterns of morphology in the gorgonopsian postcranial skeleton.

paleontology↗

bioRxiv2026

Breaking the bottleneck: self-supervised deep learning framework for fully automated fossil CT segmentation

Semantic segmentation of domain-specific imaging data where labelled training examples are scarce and foreground-background contrast is low remains an open challenge in deep learning applied to science. Palaeontological computed tomography (CT) exemplifies this problem: digitally isolating fossilised bone from surrounding rock matrix is labour-intensive ([≥]100 hrs/dataset), subjective, and often reliant on expensive proprietary software, creating a "segmentation bottleneck" that prevents large-scale and rapid processing of CT data collections. Here we present a self-supervised, end-to-end framework combining SimCLR v1 contrastive pretraining with deterministic pseudo-label generation and U-Net refinement to fully automate fossil CT segmentation without manual annotation. Using 50,626 CT images from the Middle Jurassic Kilmaluag Formation spanning amphibians, reptiles, dinosaurs, and early mammals, the framework achieved a Dice coefficient of 93.66% and IoU of 82.42% on a held-out specimen not seen during training, comparable to the highest Dice and IoU values reported in recent Deep Learning-based fossil CT segmentation studies. Cross-taxon generalisation was validated geometrically on six fully external specimens, achieving sub-voxel mesh agreement with manually thresholded references. By eliminating the annotation requirement that has limited prior deep learning approaches in palaeontology, this framework reduces per-specimen processing from [~]100 person-hours to 6 hrs (one-time UNet training) +1-3 minutes (mesh generation per specimen), an essential first step towards batch processing and analysis of CT data for large-scale comparative and quantitative analyses.

paleontology↗

bioRxiv2026

First Plant sedaDNA assemblage from California reveals ecological stability throughout 10,000 years of human presence at Lake Elsinore

As we face the sixth mass extinction, understanding how ecosystems have persisted--or collapsed--through millennia of changing climates and human activity is critical for preventing biodiversity loss. We bolstered the past 24,000 years of plant and mammal records using targeted capture of ancient sedimentary DNA (sedaDNA) from Southern Californias Lake Elsinore, a cultural center for the Payomkawichum (Luiseno), Cahuilla, and other Peoples. Our sedaDNA approach generated a diverse dataset that included 18 plant orders not previously documented from Lake Elsinore. We paired these records with local measurements and paleo evidence of fire regimes, climate, demographic history, and ethnobotanical knowledge. We find that ecological stability persisted for 10,000 years of continuous human presence, reflecting ecosystem resilience through major climatic shifts, altered fire regimes, and varying intensities of Indigenous land use. SedaDNA revealed increased availability of food, medicinal, and utilitarian plant taxa during this period of botanical stability, shedding light on ancient fire-environment-human interactions that can inform contemporary management strategies.

paleontology↗

bioRxiv2026

Stratigraphic Paleobiology of Carbonate Systems

Stratigraphic paleobiology is a newly established interdisciplinary approach, which has demonstrated that the fossil record is a joint expression of biotic and stratigraphic change, and all inferences from it must be grounded in a solid understanding of the stratigraphic context. Fossiliferous strata can be found in all depositional systems (e.g., marine, terrestrial, or lacustrine; siliciclastics or carbonates), each having a unique characteristic timescale and set of external controls, which govern the accumulation of sedimentary particles, including fossils. Consequently, the same biotic changes are preserved differently across depositional systems. While carbonate systems form a large portion of the fossil record, most studies in stratigraphic paleobiology have focused on siliciclastic systems and are not easily generalizable. As they are predominantly formed by living organisms, carbonates are both fossils and record, opening the opportunity to study the co-dependency of life and its environment. Here, we explore the stratigraphic paleobiology of carbonate systems by combining simulations of carbonate platform and ramp geometries with synthetic fossil records. We explore the preservation of extinction patterns and rates spatially and across geometries. By examining stratigraphic biases in isolation (unconformity and condensation, ecology, and abundance biases), we find characteristic differences between ramp and platform geometries due to their differential response to sea level change, spatial variability, and differences in ecological clines. Differences in the structure of the fossil record between platform geometries are traceable to the contribution and properties of the carbonate producing organisms (carbonate factories), showing that preservation of earth system data in carbonate systems will vary both latitudinally and temporally or as a result of major perturbations of the biogeosphere. Our results show that while general rules on the structure of the fossil record can be derived for entire depositional systems, accounting for the geological and ecological dynamics of a particular sedimentary basin can hugely refine interpretations of the fossil record. That is particularly true for biogenic and biologically-mediated sediments.

paleontology↗

bioRxiv2026

Dawn of segmented bilaterians unveiled by soft-bodied fossils in microbial pseudomorphs from the Basal Cambrian

It is estimated that the evolution of segmented bilaterians occurred during the Ediacaran, whereas most of their unambiguous body fossils did not appear until Cambrian Stage 3. This fossil gap hampers our understanding of the early history of body segmentation, which is a crucial evolutionary innovation for bilaterians. Trace fossils from the late Ediacaran and basal Cambrian suggest this gap is likely to represent a taphonomic bias, implying that the progenitors of segmented bilaterians that existed within this temporal span were hardly preserved. Here, we report a variety of segmented bilaterians from the lowermost Cambrian of South China. These fossils are preserved as microbial pseudomorphs, rather than as ordinary phosphatization. These findings demonstrate that microbial pseudomorphs represent a major pathway for the preservation of segmented bilaterians during this period, as well as an effective mechanism for overcoming the taphonomic bias that affects micro-animals with delicate, non-biomineralized bodies. Moreover, the newly described animals, among the earliest segmented bilaterians, reveal a high diversity of segmented bilaterians during Ediacaran-Cambrian transition, shedding new light on the evolution of body segmentation.

paleontology↗

bioRxiv2026

Temporal resolution reshapes dynamics of inferred community structure and extinction selectivity across the Permian-Triassic mass extinction

The Permian-Triassic mass extinction fundamentally restructured ecosystems, yet it remains unresolved whether ecological collapse unfolded gradually or in discrete steps, and how extinction selectivity varied with environmental change. Here, we analyse marine food webs from Meishan (China) at high temporal resolution. We show that trophic structure destabilised prior to peak biodiversity loss, followed by a structural tipping point during the extinction interval when the community became less robust to secondary extinctions. Extinction selectivity shifted substantially across the study interval. During the extinction interval, extinction was concentrated at lower trophic levels, propagating upwards from benthic herbivores to higher-level consumers. Although coarse resolution preserves temporal trends in trophic structure and extinction selectivity, it obscures abrupt transitions, sequential extinction dynamics, and critical shifts in ecological organisation. We demonstrate that temporal resolution governs inference of extinction dynamics, with important implications for reconstructing past ecological crises and interpreting ecosystem responses to rapid environmental change.

paleontology↗

bioRxiv2026

Revisiting Cucuruchu, a Late Pleistocene site on the Venezuelan Caribbean coast with megafauna and lithic association

The study of historical documents from the original excavation led by J. M. Cruxent, of museum collections, as well as results of fieldwork, are combined to provide a revised assessment of the archeologically site of Cucuruchu, which together with those of Taima-Taima and Muaco, document megafaunal lithic remains associated from the Late Pleistocene in northern Venezuela. Six vertebrate taxa are reported for Cucuruchu: five megaherbivores (a giant sloth, Eremotherium laurillardi.; a glyptodontid, Glyptotherium cf. G. cylindricum; a macrauchenid, cf. Xenorhinotherium bahiense; a proboscidean, Notiomastodon platensis; and an equid, Equus sp.), and a turtle (Kinosternon sp.). Two fragments of El Jobo projectiles were found in situ lying among megaherbivores bones, while another unidentified projectile fragment was also found in the same layer. Although no direct evidence of human exploitation on these megaherbivores remains has been found, the presence of El Jobo projectiles in the undisturbed fossil-bearing layer some of which are associated with fossil remains, could be a suggestive of such interaction. Two new radiocarbon dates indicate ages of at least ca. 15.3-16.0 kyr cal BP for the fossil-bearing layer, contrasting with the mid to late Holocene age originally reported. Cucuruchu is a window to the past and supports the presence of hunter-gatherers of the El Jobo culture in the region at the end of the Pleistocene.

paleontology↗

bioRxiv2026

Constrained body mass evolution and decoupled morphological rates in plesiosaurs

Body size, through its links to various physiological traits, has often been hypothesized to influence evolutionary rates. Negative body size-rate correlations have been reported in the morpho-logical or molecular evolution of several extant vertebrate groups, including mammals, birds, reptiles, and teleost fishes. In this study, we estimated body masses for 89 species of plesiosaurs, a clade of Mesozoic aquatic reptiles, and found that their body size evolution conforms to a three-regime Ornstein-Uhlenbeck process, indicative of constrained evolution. Rates of morphological evolution, inferred using the skyline fossilized birth-death process and the variable-rates model, show minimal support for a correlation with body size in this clade. Our results thus serve as a counterexample, suggesting that the negative body size-rate relationship is not a universal vertebrate pattern, but rather a trend restricted to certain lineages.

paleontology↗

bioRxiv2026

Biomechanics of the extremely elongated neck of the Triassic archosauromorph Tanystropheus

Extremely elongate necks have convergently evolved in several amniote lineages, including both aquatic and terrestrial forms (Fig. 1). The development of such a feature brings with it advantages in obtaining food items, but also biomechanical challenges, such as flexibility, stability, lift, and inertia. In Tanystropheus, a particularly long-necked Triassic archosauromorph, the neck is composed of only 13, mostly extraordinarily elongated and slender cervical vertebrae and accompanying rod-like, overlapping ribs, making it arguably the most extreme example of neck elongation in tetrapod evolution (Fig. 1;1-6). Understanding the function of this remarkable neck provides insights into the limits of neck elongation in amniotes and the evolution of morphological novelties in Triassic reptiles. Here we present the first quantitative biomechanical analysis of the Tanystropheus neck using a digital model based on three-dimensionally preserved bones. We assessed its range of motion (ROM) and performed finite element analysis (FEA) on the individual cervical ribs and the neck model in different configurations. Our results indicate that the neck of Tanystropheus was not extremely stiff, as previously postulated, and the ribs likely did not impair its movements. They transferred tensile forces towards the base of the neck, similar to what hypothesized for sauropods7. This study elucidates the bauplan of an extremely specialized animal and brings us closer to understanding the patterns of achieving neck elongation in vertebrates. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/735087v1_fig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@6732a3org.highwire.dtl.DTLVardef@12d9dcdorg.highwire.dtl.DTLVardef@1d331a0org.highwire.dtl.DTLVardef@5f0a91_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Comparison of the cervical vertebral column anatomy of some long-necked tetrapods. Reconstructions not to scale. Based on: Tanystropheus conspicuus - Rytel6; Dinocephalosaurus orientalis - Spiekman et al.8; Mamenchisaurus youngi - Pi et al.9, Ouyang and Ye10; Struthio camelus - Mivart11; Quetzalcoatlus - Padian et al.12; Chelodina longicollis - Herrel et al.13; Albertonecte vanderveldei - Kubo et al.14, Sachs et al.15; Giraffa camelopardalis - Badlangana et al.16. The numbered nodes correspond to the following taxa: 1. Tetrapoda; 2. Diapsida; 3. Archosauromorpha; 4. Tanysauria; 5. Avemetatarsalia; and 6. Saurischia. C_FIG

paleontology↗

bioRxiv2026

Underwater caves preserve biochemical composition and histological structure in modern and fossil mammalian bones

Biochemical and microstructural bone degradation (diagenesis) occurs after death and is environment dependent. Existing macroscopic and histological research suggests bones submerged in water degrade differently to those in dry contexts. However, little is known about how submerged and dry degradation processes affect skeletal remains in caves, which have fundamentally different decomposition conditions to open environments. This study combines histology with laboratory-based and synchrotron-sourced Fourier-transform infrared microspectroscopy (FTIRM) to characterise bone microanatomical and biochemical degradation in bones from underwater (wet) and dry cave environments. We investigate fossil and historic mammal (ovicaprids, macropodids) bone diagenesis from Mount Gambier, South Australia, intra-skeletally and between depositional conditions. FTIRM analysis revealed greater collagen-associated amide signatures in historic wet bones than dry counterparts, while fossils showed no detectable signal. Despite biochemical differences, bone histology did not present noticeable differences between specimens, with similar birefringence levels and no radial micro-fractures across the secondary osteon border. Wet and fossil bones also exhibited comparable carbonate content despite differences in organic composition and mineral recrystallisation, suggesting submerged cave environments facilitate preservation of carbonate-bearing mineral phases within relatively closed (trapped) diagenetic systems. These findings demonstrate that underwater cave conditions support fossil preservation through complex and heterogenous organic and mineral diagenetic pathways.

paleontology↗

bioRxiv2026

Survivorship Bias Explains Age-Dependent Extinction in Fossil Genera

Fossil genera exhibit pronounced age-dependent extinction: older genera are more likely to survive extinction events than younger ones. Many biological mechanisms have been proposed that could make lineages progressively more resistant to extinction through time. However, the same pattern can also arise from survivorship bias: as more vulnerable genera are progressively eliminated, the surviving pool becomes increasingly enriched in robust lineages, even if the properties of individual lineages never change. Using the Sepkoski marine genus compendium, we construct a quantitative model based solely on survivorship bias and ask whether additional age-dependent changes are required to explain the fossil record. This model with a single fitting parameter quantitatively reproduces the full set of age-conditioned survival probabilities, together with the overall dependence of extinction risk on genus age and the genus lifetime distribution. Allowing extinction resistance to change systematically through time yields no measurable improvement, indicating that, at least at the aggregate statistical level, explicit age-dependent changes in lineage properties are not required to explain the observed patterns of extinction. These results show that our minimal one-parameter model provides a quantitative null model for age-dependent extinction, against which proposed biological mechanisms can now be tested.

paleontology↗

bioRxiv2026

Healed predation scar on a Cambrian apex predator

Predation is considered a key driver of the rapid diversification of animals during the Cambrian explosion. While the fossil record documents a plethora of evidence of successful and failed predation on biomineralized invertebrates at low trophic levels, no previous evidence of predation on larger, often soft-bodied, animals at higher trophic levels has been reported. This means that the modeled links between higher trophic levels in Cambrian food webs lack supporting fossil evidence, hindering understanding of the complexity of Cambrian trophic relationships. Here, we report a healed injury on the swimming flap of the radiodont apex predator Amplectobelua symbrachiata-- one of the largest animals in the Cambrian oceans. The diagnostic W-shape with a healed margin supports interpretation of this wound as predatory in origin, with likely attackers including larger contemporaneous radiodonts - possibly members of the same species -- or the giant lobopodian Omnidens. Evidence that apex predators were attacked provides critical empirical data informing the complexity of Cambrian food webs. This finding provides empirical support for the existence of high-level feeding loops, analogous to those in modern marine ecosystems, documenting the rapid increase in trophic complexity during the latter stages of the Ediacaran-Cambrian Transition.

paleontology↗

bioRxiv2026

Denisovan leg bones from Taiwan reveal large body size

Denisovans are an extinct archaic Homo group whose lineage diverged from the Neanderthal lineage approximately 550,000 years ago and were widely distributed across eastern Asia until [~]45,000 years ago1-7. Their morphological features are known directly from the existing cranio- dental and phalangeal remains1,2,8-12. However, the body size and postcranial morphology of the Denisovans remain largely unknown. We here report that hominin femoral and tibial fossils recovered from the Penghu Channel, Taiwan, are Denisovans in their proteomic profiles. Morphologically, these specimens are among the largest leg bones known in Pleistocene Homo. They exhibit generally archaic features, but also show some modern human-like morphology, including a strong femoral pilaster. Our findings demonstrate that the Denisovan population at the northern circle had larger body size than earlier Homo erectus as well as Late Pleistocene Homo sapiens in eastern Asia. This challenges the generally held expectation that Pleistocene Homo followed Bergmanns rule that anticipates latitudinal decline of body size, and suggests that the large Denisovan brain resulted from their large body size at least partly. The strong pilaster developed in the Penghu femur suggests some behavioral similarities between the Denisovans and the Upper Palaeolithic modern humans and/or gene flow from the latter to the former.

paleontology↗

bioRxiv2026

Habitat and feeding ecology of a Denisovan from Late Pleistocene Taiwan

Denisovans, originally identified from ancient genome from Denisova Cave in Altai, were a sister group to the Neanderthals and were once widely distributed across diverse terrains in the north and south of eastern Asia1-5. Genomic studies suggest that there were multiple events of interbreeding between modern humans (Homo sapiens) and Denisovans somewhere in Asia6. However, little is known about Denisovan living environments, diet, ecological niche, the timing of their disappearance, and the possible coexistence with modern humans in different regions. Here we report the radiocarbon age and stable isotopic signature of Penghu 3, a large Denisovan tibia from Penghu Channel, Taiwan7. The results showed that Penghu 3 dates to approximately 45,000 years ago, the time when modern humans were already widespread in southern parts of Asia. This Denisovan individual inhabited a C4-dominated ecosystem, open environments such as savannahs and floodplains, or a mixture of both, and consumed a high proportion of animal protein similar to some European Neanderthals8-10, with no clear evidence for the use of aquatic resources. These findings have implications for the behavioral flexibility, large body size7, and eventual disappearance of the Denisovans.

paleontology↗