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bioRxiv2026

Enamel Palaeoproteomics Successfully Distinguishes between Denisovans and European Neandertals

Ancient DNA (aDNA) has transformed the study of hominin relationships, but its preservation in ancient fossils is often limited. Enamel palaeoproteomics offers an alternative molecular approach for taxonomic analysis. In this study, we re-analyse published DDA mass spectrometry data1 from the Denisovan-attributed Penghu 1 mandible (PXD054412)2 and a Neandertal enamel specimen from Gruta de Oliveira, Portugal (PXD038154) 3. Five AMBN peptides carrying the Valine-273 substitution (V273) were validated in the Penghu 1 enamel, three of which were independently detected in both DDA acquisitions. No V273-containing peptide signal was detected in the Neandertal dataset. Conversely, the ancestral Methionine-273 peptide REDPM[+16]AYG was detected exclusively in the Neandertal specimen. Extracted ion chromatograms, isotopic envelope confirmation, and MS2 fragmentation spectra, all support the reported peptide assignments. AMELY-specific peptides additionally support male sex assignment for both ancient individuals. Together, these results confirm the taxon-specific mutual exclusivity of AMBN V273 and M273 variants across Denisovan and Neandertal lineages, establishing AMBN M273V as a molecularly validated diagnostic marker for Denisovan identification from dental enamel. More broadly, targeted MS1 reanalysis of public proteomics datasets provides a scalable complement to ancient genomics for resolving hominin lineage identity and sex determination when DNA is not preserved

paleontology↗

bioRxiv2026

Constraining Palaeogeography and Palaeotides for the Cambrian using cnidarian medusae

The ocean tides influence key Earth system processes at a range of spatial and temporal scales. It is known that the geometry of ocean basins is the leading controller of tidal energetics, so well-constrained palaeogeographic reconstructions and tidal properties for Earths past are imperative when investigating other Earth system processes. Here, we present a novel way to constrain both deep-time tidal model results and reconstructions, by combining palaeoecology with sedimentology. We compare new palaeo-tidal model simulations for the Cambrian period, significant for the early origin and radiation of major animal fauna, to tidal proxies. One of the most abundant soft-bodied organisms preserved during this time are cnidarian medusae (jellyfish). A total of 17 cnidarian medusae localities were obtained through the literature, which had an adequate global distribution and occurred at regular intervals throughout the period of study. In some locations there were also estimates of palaeo-tidal range. Our results show a good agreement between the simulations and proxy data. In the few locations where there is disagreement, it is proposed that the palaeogeographic reconstructions are missing details, e.g., island chains, and our results allow for the palaeogeographic reconstructions to be improved. The proxy method presented is promising and can be applied to other time-periods with different marine fossils, particularly at evolutionary and extinction periods where the marginal marine environment is of importance.

paleontology↗

bioRxiv2026

Nanoscale chemical tomography reveals organic and inorganic clusters in fossilised dinosaur tooth

Mineralized dental tissues are formed through biomineralization processes involving the growth and self-organisation of hydroxylapatite (HAP) nanoscale grains. There remain open questions regarding the way elements such as Mg or Na are incorporated in the organic matter between HAP grains or within the grain structure where they influence the nucleation and growth of HAP. Here, mapping the enamel structure and composition of a well-preserved ca. 150-million-year-old Giraffatitan brancai sauropod dinosaur tooth from millimeters down to the near-atomic scale, we reveal the nanoscale accumulation of Mg at HAP grain boundaries, alongside F arising from diagenesis. Within the HAP grains and at HAP grain boundaries organic matter forms clusters that we propose contribute to the fast growth rate of the tooth. Moreover, unexpected Cu3As particles are found across the entire enamel structure. These elements are not in the dentine, that exhibits empty tubules, which suggests that they were integrated during the tooth growth itself. Our multiscale analysis provides new information encouraging to reconsider aspects of the biomineralization and fossilization processes.

paleontology↗

bioRxiv2026

Skeletal remains of a freshwater jalodontid chondrichthyan from the Upper Triassic Arden Sandstone Formation of Warwickshire, UK.

The Triassic was a significant period in the evolution of modern chondrichthyans (sharks, rays and chimaeras), bridging the gap between Paleozoic chondrichthyans and more recognizably modern Mesozoic forms. Although only a handful of Triassic skeletal fossils of chondrichthyans are known worldwide their calcified cartilages provide rare insight into their anatomy, evolution, and lifestyle. Here we use computed tomographic methods to describe six chondrichthyan skeletal fossils from the Carnian (Upper Triassic) Arden Sandstone Formation of Shrewley, Warwickshire, UK, consisting of a partial braincase, jaws, pectoral fin radials, caudal fin hypurals, and dorsal fin basal cartilages, and characterize their paleoenvironment. We assign the braincase and jaws, and tentatively assign the post-cranial remains, to the jalodontid taxon Keuperodus brodiei, previously described on the basis of teeth including those from the same locality. This represents the first known occurrence of articulated chondrichthyan skeletal remains from the Upper Triassic and the first interpretable cranial cartilages of the Order Jalodontiformes. The partial braincase of K. brodiei preserves an unusual basicranial circulation, almost completely embedded in the basicranium, and the jaws have an elongate extended shape; both features are akin to Paleozoic phoebodontid chondrichthyans. Phylogenetic analysis recovers K. brodiei as a stem-group elasmobranch with a close relationship to phoebodonts, one of several Paleozoic shark lineages to have independently survived the end-Permian mass extinction. However, unlike Phoebodontiformes and all other Jalodontiformes, K. brodiei occupied freshwater lake shorelines and associated fluvial feeder channels, revealing a possible freshwater refugium for Jalodontiformes towards at the end of their stratigraphic range.

paleontology↗

bioRxiv2026

Bone diagenesis in Iron Age Siberia: a histological and microtomographic study of Tunnug 1 (Russia, 2nd-4th c. CE)

The Siberian site of Tunnug 1, located in the Uyuk Valley (Tuva Republic, Russia), encompasses an Early Scythian burial mound (9th century BCE) and a peripheral cemetery attributed to the Kokel culture (2nd-4th centuries CE). Situated within a permafrost-affected environment, the site offers an opportunity to investigate bone preservation under long-term freeze-thaw cycle conditions and explore the relationship between funerary treatment and bone diagenesis. This study presents a combined histological and microtomographic analysis of 76 bone samples from 71 individuals across 36 burials. Transmitted light microscopy, scanning electron microscopy (SEM) and micro-computed tomography (micro-CT) were employed to document biological, chemical and physical degradation. Bone preservation was evaluated through three approaches: the traditional Oxford Histological Index (OHI), quantitative image analysis and assessment of (micro)cracking. The results revealed moderate bone preservation (OHI 2-4). Biological degradation in the form of Microscopical Focal Destruction (MFD) and chemical alteration were identified in six individuals. Enlarged canaliculi were observed in every bone sample. Microcracks were present in all individuals, visible exclusively under SEM. No clear diagenetic signatures linked to specific funerary practices were identified, though variations in preservation suggest a possible influence of burial depth. The distinct impact of permafrost and long-term freeze-thaw cycles on bone microstructure could not be isolated, underscoring the multifactorial nature of diagenesis. This study highlights the complementary value of combining multiple analytical methods assessing bone diagenesis and emphasises the need for continued experimental research into the effects of freezing environments on human remains.

paleontology↗

bioRxiv2026

Unique pattern of injuries in Olenoides serratus from the Burgess Shale elucidate moulting process in trilobites

Ecdysozoans is one of the most abundant and diverse groups of metazoans and grow through moulting the rigid exoskeleton that provided protection. But the moulting process is often dangerous, resulting in malformations or death. Injuries have been well documented in the calcitic exoskeleton of trilobites, some of which have been attributed to moulting complications when long spines are deformed. Injuries in trilobites are often found in the trunk rather than the cephalon, and abnormal genal spines are rarely documented. Here we examine injuries in eleven specimens of Olenoides serratus from the Burgess Shale (Cambrian, Wuluian) and demonstrate an increased frequency of genal spine malformations compared to other trilobites. The unusual pattern of malformations may be attributed to moulting injuries of the long and delicate genal spines in O. serratus. To moult, trilobites curved ventrally to press the anterior margin of their cephalon into the substrate and open the facial sutures. This process exerted force on the librigenae. To exit the exuvia, the genal spines were forced to bend as the old librigenae dipped ventrally along the anterior edge, resulting in the injured genal spines in O. serratus. A similar process of moulting resulting in injuries may be seen in other early Euarthropods.

paleontology↗

bioRxiv2026

A novel phylogenetic comparative model reveals strong signals for early high disparity in ichthyosaurs

Early high disparity, where clades reach maximum morphological diversity early in their history, is often observed in the fossil record. Since there are currently no suitable methods to model these Early High Disparity (EHD) processes accurately, we introduce a new phylogenetic comparative method (PCM) to address this gap by combining two evolutionary modes--Ornstein-Uhlenbeck (OU) and Early Burst (EB)--leading to an initial surge in disparity until an early maximum, driven by the EB component, after which disparity declines due to OU constraints. We tested the EHD model on ichthyosaur skull length data and found it to be the best fit in nearly all cases compared to other modes. The median time of peak disparity (TEHD) is about 231.1 million years ago, during the Triassic, roughly 12.4% into the ichthyosaur lineage. To explore how environmental and geological factors might influence peak disparity, we performed changepoint analyses on sea level, sea surface temperature, rock area, and sedimentary sequence ages. While changepoints in temperature at 237.2 Ma and sequence boundaries at 238 Ma were closest to TEHD, no significant changepoints appeared to match TEHD.

paleontology↗

bioRxiv2026

Acrean fish diversity back in time: Paleoichthyology of the Rio Acre fossil fauna in Brazil

Freshwater fishes are an important component of the Neogene fossil record of South America. They have been recorded in the Acre fossil fauna, with considerable taxonomic and ecological diversity. Novel findings from the Patos locality in Acre State have produced several specimens representing eleven taxa, including the first occurrences in the fossil record of the genera Agamyxis, Glanidium, and Trachycorystes. These taxa comprise two orders, Characiformes and Siluriformes, with four and seven taxa respectively. The taxa found in the Patos locality are representative of typical modern Amazonian assemblages found in the drainages of the region, thus suggesting substantial ecological conservatism. An updated list of the Rio Acre fossil fish fauna is consistent with previous findings in the literature regarding clustering structure in fossil assemblages during the Neogene of South America.

paleontology↗

bioRxiv2026

Protocells reproduce morphological and chemical signatures of early microfossils

Identification of early microfossils relies on morphological and chemical criteria assumed to be unique to life, but whether abiotic microstructures can satisfy these criteria has not been rigorously tested. Hydrothermal environments preserve microfossils but are also efficient geochemical reactors for abiotic reactions. Protocells form in hydrothermal conditions and represent a plausible abiotic analogue to early microfossils. Here we show that protocells form from simple organic molecules in low-temperature, alkaline hydrothermal conditions in the presence of silica and produce spheres, filaments, and lenticular structures that strongly resemble the morphology of purported microfossils in Archaean silica cherts. FTIR spectroscopy provides overlapping chemical signatures across protocells, microorganisms, and geologic microstructures. In addition, the FTIR R3/2 ratio, a chemometric index often used to discriminate domains and determine biogenicity, identifies eight different protocell systems as either bacterial, archaeal, or eukaryotic. These data suggest that protocells preserved in ancient hydrothermal deposits can satisfy current biogenicity criteria, undermining the reliability of interpretations of the early fossil record. As life detection is the primary objective for current space exploration endeavours, robust biogenicity protocols that account for abiotic signatures are essential.

paleontology↗

bioRxiv2026

The trilobite nervous system and the early evolution of the mandibulate central complex

Fossil central nervous systems (CNS) have illuminated several facets of total-group euarthropod evolution, including their phylogenetic affinities, the origin of the head, and their ancestral neuroanatomical organization. However, the CNS remains unknown in trilobites, the most diverse and earliest group of Palaeozoic euarthropods, but can potentially clarify fundamental questions that remain disputed despite thousands of described species and countless studies spanning over two centuries, such as their affinities relative to modern representatives. Here, we describe the CNS of the cheirurid Anacheirurus adserai from the Lower Ordovician Fezouata Shale. Anacheirurus features a brain with well-developed proto, deuto- and tritocerebral neuromeres, an anteriomedian protocerebral protrusion, a central complex, an esophageal foramen, and a ganglionated ventral nerve cord. The CNS is replicated in framboidal iron that differs in texture and composition from the exoskeleton and rock matrix. The overall organization of Anacheirurus's CNS most closely resembles that of Cambrian stem-group mandibulates, and critically shares the presence of a central complex with a protocerebral bridge and lateral accessory lobes with extant pancrustaceans. Our findings provide new morphological support for the hypothesis that Trilobita belongs to the mandibulate stem lineage and bring new insights into the ancestral morphology and evolutionary history of the euarthropod central complex. More broadly, our findings offer direct anatomical evidence of the key sensorimotor system innovations that originated during the Cambrian Information Revolution.

paleontology↗

bioRxiv2026

Solving Paleobotany's 200-year problem with fluorescence and artificial intelligence

Paleobotany has a 200-year problem: leaf fossils are often too poorly preserved to make proper taxonomic identification. Though they are the most abundant, and well-studied macroscopic fossil plant organ, many fossil leaves-- including specimens held in museum and university collections-- appear to lack the detailed features needed to take crucial next steps, like placement into phylogenetic context, generation of ecological interpretations, or reconstruction of paleoclimate. However, we have discovered that under UV and laser light [~]50% of leaves across a diverse survey of fossil deposits fluoresce in a way that reveals spectacularly detailed leaf venation and gross morphology that is invisible under white light. These 'Fossil Ciphers' bring new life into each step of the paleobotanical method, unlocking previously unattainable taxonomic classifications, quantitative morphometrics, and promising new avenues for the incorporation of AI into fossil leaf analyses. With the aid of fluorescence techniques, we can help solve paleobotany's 200-year problem.

paleontology↗

bioRxiv2026

Increase in sea-level and shelf area positively influenced the development of Cenozoic biodiversity hotspots by modulating turnover rate in marine benthos

Marine biodiversity is unevenly distributed across the oceans, with exceptional concentrations of species richness confined to a few hotspots. Fossil and molecular evidence indicate that marine hotspots have shifted among ocean basins throughout the Cenozoic, but the mechanisms underlying their emergence and persistence have rarely been tested across multiple marine groups. Using standardized fossil occurrence data for molluscs, cnidarians, and foraminifera, we identified marine biodiversity hotspots through the past 66 million years. We then apply a multistep framework linking environmental drivers (sea surface temperature (SST), shelf area, and sea level) to clade-specific macroevolutionary processes (origination, extinction, and immigration) to evaluate the dynamics of these hotspots. Our results reveal contrasting evolutionary dynamics across marine biodiversity hotspots of different marine groups. Benthic groups: Mollusca and Cnidaria exhibit higher evolutionary turnover in hotspots than in non-hotspot regions, whereas planktic foraminifera maintain high diversity through reduced extinction and immigration rates. Increase in the sea level and shelf area positively contribute to the development of hotspot by increasing the origination rate in mollusca and cnidaria. Our study offers an integrative framework for understanding how marine biodiversity hotspots arise through a network of interacting processes: environmental drivers shape macroevolutionary dynamics, which in turn generate clade-specific diversity trajectories; together, these processes determine whether a particular region develops into a biodiversity hotspot.

paleontology↗

bioRxiv2026

Playing by their own rules: clade-specific trends in mandibular form and function disrupt current paradigms of early tetrapod evolution

Quantitative research into the evolution of vertebrate feeding has largely focused on the mandible, using morphofunctional changes in the lower jaw as an indication of broader shifts in overall feeding mode. In the context of major ecomorphological transformations, such as the origin of tetrapods, the paradigm of a trade-off between "fast-jawed", aquatic suction-feeders versus "strong-jawed", terrestrial biters is particularly prominent. However, the assumption underlying this perspective--that the mandible constitutes a reliable proxy for overall feeding mechanisms--has yet to be rigorously validated. Here, we test this widespread notion by examining both morphology (via geometric morphometrics) and function (via commonly-used functional metrics) across a broad dataset of extant and extinct vertebrate mandibles. We find that extant clades exhibit phylogenetically-structured morphofunctional solutions to the challenge of feeding in different environments, distinct from the trends exhibited by extinct taxa, thus highlighting the need for caution when relying on mandibles for deep-time reconstructions of feeding mode. By providing the first large-scale validation of functional trait differences across vertebrate feeding mechanisms, our research offers the quantitative context needed to decipher broad macroevolutionary trends in vertebrate feeding, thus better informing events such as the tetrapod water-to-land transition.

paleontology↗

bioRxiv2026

Causal analysis of rock-biodiversity relationships over the global Phanerozoic challenges rock record bias and common cause hypothesis

Sampled marine biodiversity covaries strongly with sedimentary rock quantity over the Phanerozoic, but the respective contributions of different potential causes remain unsettled. Although regional studies show that rock-record bias accounts for more variation in sampled marine biodiversity than common-cause mechanisms, evaluating this relationship across the global Phanerozoic record remains difficult because fossil databases are inherently biased toward fossiliferous strata. To address this limitation, we compiled literature-derived measures of global marine biodiversity and sedimentary strata, along with an existing sea-level curve. Using an information-theoretic causal framework, we then evaluated the relative contributions of rock-record bias and common-cause hypotheses to Phanerozoic-scale variation in sampled marine biodiversity. Our results show a strong contemporaneous causality of marine strata on sampled biodiversity, indicating that rock record bias detected at regional scales extends to the global scale. However, neither rock record bias nor common-cause mechanisms accounts for most Phanerozoic-scale patterns in sampled biodiversity, and additional unmeasured factors likely contribute. Finally, we find tentative evidence that synergistic causality between geologically mediated sampling biases and forces shaping the underlying biological signal contributes to global Phanerozoic patterns in sampled biodiversity.

paleontology↗

bioRxiv2026

Durophagous adaptations in a new crocodyliform from the Santonian of Hungary and a systematic reassessment of European Cretaceous atoposaurids

Atoposauridae comprises a group of diminutive, semiterrestrial, brevirostrine neosuchian crocodyliforms that represents a characteristic component of European Jurassic-Cretaceous tetrapod faunas. Although frequently evaluated within the context of crown-group Crocodylia origins, their highly contested phylogenetic relationships continue to obscure their precise role in crocodylomorph evolutionary history. Particular ambiguity surrounds the monophyly of the genus Theriosuchus - with some hypotheses inferring long-term persistence of the lineage in Mesozoic Europe, whereas others interpreting select Cretaceous species as representatives of separate, even non-atoposaurid clades (e.g. Sabresuchus spp). We describe a new, stratigraphically intermediate taxon from the Santonian of Hungary based on isolated cranial elements, consistently placed as the sister taxon of Sabresuchus (Theriosuchus) sympiestodon from the Maastrichtian of Romania by our comprehensive set of phylogenetic analyses using three separate datasets. Sabresuchus tribodon sp. nov. is either recovered within Atoposauridae (global datasets) or Paralligatoridae (ingroup analysis) and can be distinguished from all other representatives of these groups by a specialized morphology consisting of massive, thick-enameled bulbous posterior maxillary teeth ornamented with apicobasal ridges, an extremely short rostrum with a reduced number of maxillary and dentary teeth, and the significantly upturned dorsal margin of the posterior dentary and surangular. Comparable anatomical adaptations are present in ecomorphologically convergent extinct crocodyliforms whose inferred feeding ecology included durophagy. However, this complete suite of characters has not been previously documented in either atoposaurids or paralligatorids. Our systematic reassessment results in an up-to-date taxonomy of Cretaceous European atoposaurids and tentatively confirms the polyphyly of Theriosuchus, though more definitive conclusions require combining individual, differently focused datasets. We reinterpret Aprosuchus ghirai from the Maastrichtian of Romania as a junior synonym of Sabresuchus sympiestodon and the putative European notosuchian Ogresuchus furatus from the Maastrichtian of Spain as an indeterminate atoposaurid.

paleontology↗

bioRxiv2026

Diversity in early animal communities of the Ediacaran, Avalon assemblage

Diversity is an emergent property of macroecological and macroevolutionary processes. The Avalon assemblage preserves near-census snapshots of Ediacaran communities, enabling tests of the drivers of diversity. However, it remains unclear how alpha diversity varied among surfaces or whether variation reflected uneven sampling, abiotic context or biotic processes. We analysed diversity for 11,342 specimens across 22 surfaces and examined abiotic and biotic correlates. Despite compositional variation, most surfaces fell into four community types dominated by Fractofusus andersoni, F. misrai and/or Pectinifrons, Bradgatia, or upright fronds, with potential substructure within the upright-frond type, whereas Clapham's Pigeon Cove and Shingle Head communities, from the oldest and youngest formations, respectively, may indicate greater community differentiation near the sampled stratigraphic limits. Sampling effort varied widely, yet taxon-area curves showed richness was well captured on 12 of 22 surfaces, and Shannon and Simpson diversity remained consistent across sampling completeness and taxonomic treatments. Diversity showed no clear associations with locality or stratigraphic affiliation, but differed among community types and declined with increasing vertical segregation. Overall, these results suggest that, among the predominantly Newfoundland communities sampled, Avalon alpha diversity may have been shaped more by local community assembly and organisation than by broader geographic, environmental and temporal context.

paleontology↗