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bioRxiv2026

Latitudinal dependence of stability trends in marine plankton in the Cenozoic

The temporal stability and spatial heterogeneity of global marine ecosystems under changing climates reveal how biodiversity persists or collapses. However, the deep-time evolution of these phenomena remains poorly understood. We reconstructed the stability landscape of pelagic plankton from the Cretaceous-Paleogene extinction to the present. We find that the Cenozoic was a period of punctuated volatility with high turnover post-extinction and during the Late Neogene cooling. Spatially resolved analysis revealed latitude-dependent trends: equatorial regions stabilized over time, whereas polar communities, especially in the Southern Ocean, destabilized. Equatorial regions homogenized from initially high heterogeneity, whereas polar communities showed the opposite pattern, including a latitudinal seesaw of spatial heterogeneity over the past 30 million years. These findings illuminate temporal stability and spatial heterogeneity dynamics across geologic timescales.

paleontology↗

bioRxiv2026

Neotaphonomic characteristics of vertebrate site formation in underwater caves

Recovering well-preserved vertebrate remains from underwater caves has provided critical insights into archaeological and palaeontological records worldwide. However, understanding how bone assemblages form and are modified in underwater environments remains limited due to stable low energy burial conditions that produce time-averaged deposits, and underwater settings that hinder traditional recording and recovery methods. This study applies an actualistic taphonomic framework to three assemblages of domesticate animal bones (N = 231) from two underwater caves, Green Waterhole and Gouldens Sinkhole, near Mount Gambier, South Australia, encompassing known submerged (wet; N = 134) and dry (N = 97) burial conditions. The assemblages were examined to assess how wet and dry cave environments impact bone distribution, surface and microstructural modification. Radiocarbon dating of 41 specimens indicates that domesticate fauna were deposited over decadal and centennial timescales, allowing taphonomic signatures to be contextualised through time. Statistically significant differences were identified between wet and dry burial contexts. Bones recovered from wet contexts exhibit mostly better preservation, including skeletal elemental completeness, surface, and microstructure, than those from dry caves. However, some of the submerged specimens also have elevated frequencies of bone surface corrosion with macroscopic evidence for heterogenous black biological staining, algal or biofilm attack, and a distinctive form of circular etching. Histotaphonomy further reveals patterns of peripheral cyanobacterial tunnelling across most bones recovered from submerged contexts. Bones from dry environments were dominated by terrestrially linked tunnelling across all regions of the bone cortex. These findings can be explained by variation in light availability across different cave zones which influences biological activity and, in turn, the expression of taphonomic markers on bone externally and at the microstructural level. This is the first study to provide a benchmark bone dataset for reconstructing depositional histories and post-depositional reworking in underwater cave environments under a taphonomic framework.

paleontology↗

bioRxiv2026

No global collapse of food webs across the Permian-Triassic Mass Extinction

The Permian-Triassic mass extinction (PTME), the Earths most severe biotic crisis associated with extreme environmental perturbations, eliminated >80% of marine species1. However, whether it triggered a globally pervasive top-down collapse of marine food webs, and whether recovery proceeded through bottom-up reassembly, remain unresolved2-4. Here we reconstruct spatially explicit metacommunity food webs from seven regions spanning equatorial to high latitudes to test how extinction dynamics and ecosystem reorganization varied geographically. By integrating estimates of community structure and species interactions, we provide direct inference on trophic disruption across the PTME. Despite catastrophic species loss and flattening of the latitudinal diversity gradient5, trophic collapse was not globally uniform, and higher trophic levels were not globally truncated. Instead, extinction selectivity was spatially heterogenous and tracked environmental severity. Benthic, low-motility herbivores with limited respiratory capacity were disproportionately lost, consistent with intensified warming, deoxygenation and disruption of primary productivity under elevated pCO2. Mid-to high-latitude communities became top-heavy and structurally complex, whereas tropical systems remained bottom-heavy and less robust to secondary extinction. These results demonstrate that trophic disruption and recovery were geographically structured, mediated by environmental forcing, species traits and pre-extinction food-web architecture, with implications for predicting marine ecosystem responses to ongoing climate change.

paleontology↗

bioRxiv2026

Fossil-based analyses of clades' diversification patterns require taxonomic expertise and appropriate methodology

SummaryEstimating deep-time diversification patterns and the establishment of extant biodiversity represent major challenges in macroevolution. Fossil record data provide essential information to address these topics, but their heterogeneous temporal and geographical distributions require using analytical approaches to process these data. Gardiner et al.1 (hereafter GEA) used a deep-learning model2 and a fossil-occurrences dataset3 to estimate neoselachian richness over the last 145 myr. Results and DiscussionGEA1 found that neoselachian diversity increased throughout the Cretaceous, was little impacted by the Cretaceous-Paleogene (K/Pg) mass extinction ([~]10% species loss), and peaked in the mid-Eocene but declined until the Present. While the Cretaceous increase in neoselachian richness is well known4, the other findings of GEA1 are at odds with current knowledge. With the exception of lamniform sharks, the perceived decrease in species richness in the recent past is most likely due to a drop in available fossil record data combined with difficulties in identifying extant species in the fossil record5. Similarly, all previous analyses of the impact of the K/Pg mass extinction on elasmobranch diversification have reported high extinction rates, a marked diversity drop, and delayed recovery6-7, despite heterogeneity across clades, ecology, and geographical distribution7. Taking the K/Pg as an example, we demonstrate that the discrepancies between GEA1s results and current consensus is most likely due to a combination of incomplete, unverified, and incorrect fossil-occurrence data with inappropriate methodology.

paleontology↗

bioRxiv2026

Anthropocentrism as a source of sampling bias in the fossil record.

The fossil record is the most important tool in palaeosciences, so continually reviewing and attempting to reduce biases in its collection is necessary to curate the best possible record of past life on Earth. Biases in the fossil record are introduced through both biological processes and data collection. Here we have investigated the extent to which anthropocentric data collection has contributed to sampling bias in the assembly of the current fossil record. We have found that the current fossil record (represented in this study by the NOW database) is anthropocentrically biased, both temporally and spatially. Specifically, fossil locality density is higher in time periods when hominins are found, and in known hominin-bearing locations. This demonstrates the need to stop essentializing the narrative of human evolution in paleoscience to reduce bias in sampling of fossil localities.

paleontology↗

bioRxiv2026

Contingency Inverts Mammalian Herbivore Evolution in Australia

The rise of Neogene herbivores with high-crowned (hypsodont) molar teeth has been viewed as a mostly predictable response to abrasive grazing diets. Using kangaroos, an isolated marsupial radiation, we show that the ancestral vertical slicing function of grazing kangaroo molars prompted heavy investment from the late Miocene in thickened enamel, rather than hypsodonty. Grazing kangaroo enamel thickness overlaps some robust hominins, evincing an eclectic, thick-enamelled grazer guild. The success of vertically-chewing marsupials contrasts with their placental counterparts, which were overwhelmingly replaced by transversely-chewing ungulates. This inversion is explained by the pre-grassland extinction of most transversely-chewing marsupials, and the crucial advent of thick enamel. These results challenge the determinism of the browser-grazer transition, and implicate extinction, and ensuing innovation, as causes of unpredictability in evolution.

paleontology↗

bioRxiv2026

Linear morphometrics fail to support strong sexual dimorphism in Uintatherium anceps

Uintatheres, mammals belonging to the extinct order Dinocerata, are among the most recognizable of all Paleogene ([~]66 - 23 Ma) organisms. Unmistakable for their bizarre skulls with multiple pairs of horns and saber-like upper canines, uintatheres have captivated paleontologists since the late nineteenth century. Since their initial discovery, uintatheres have been regarded as a classic example of dramatic sexual dimorphism in the fossil record, with males purported to be larger and possess more prominent horns and canines than females. However, the hypothesis that uintatheres were highly sexually dimorphic has never been formally tested. Here, I use traditional, linear morphometrics on a collection including most known skulls of Uintatherium anceps to quantify patterns of cranial variation within this taxon. Despite using a variety of traditional and novel statistical methods, I fail to detect any evidence of strong sexual dimorphism in Uintatherium. To verify my approach, I assembled a similarly sized dataset from Bison bison as an extant analog, and found strong, consistent evidence of sexual dimorphism. In light of these findings, as well as the current understanding of uintathere systematics and paleoecology, I argue that strong sexual dimorphism should not be treated as the null hypothesis for this clade.

paleontology↗

bioRxiv2026

New insights into the postcranial morphology of Lithornis vulturinus from the Eocene London Clay

The deepest phylogenetic divergence within crown birds (Neornithes) is that between the reciprocally monophyletic Palaeognathae and Neognathae. Extant palaeognath diversity comprises the iconic flightless "ratites" (ostriches, rhea, kiwi, cassowaries, and emu), as well as 46 species of volant tinamous in Central and South America (Billerman et al., 2020). Although the earliest stages of palaeognath evolution remain shrouded in mystery due to a sparse fossil record, a group of apparently volant extinct palaeognaths from the Paleogene of Europe and North America, the lithornithids, can help to clarify palaeognath origins. Here, we use high resolution microCT scanning to characterize the morphology of two lithornithid specimens from the early Eocene (Ypresian) London Clay Formation: the neotype of Lithornis vulturinus (NHMUK A5204), from the Isle of Sheppey, Kent, England, and a newly discovered clay nodule containing lithornithid postcranial remains from the nearby locality of Seasalter. This three-dimensional dataset reveals bones from the L. vulturinus neotype that are partially or completely covered by matrix, allowing us to redescribe this critical specimen in new detail and present a revised differential diagnosis of L. vulturinus. We refer the new specimen from Seasalter to L. vulturinus on the basis of apomorphies such as a proximally directed lateral process of the coracoid, caudally divergent lateral margins of the sternum, an arcuate deltopectoral crest, as well as its provenance from a nearby penecontemporaneous locality. The Seasalter specimen contains abundant postcranial material that provides new insight into bones damaged or missing in the neotype, including two undamaged scapulae bearing the hooked acromion that is a diagnostic feature of lithornithids, two complete coracoids, and a nearly complete three-dimensionally preserved sternum. Its estimated body mass is one third larger than that of the neotype, indicating intraspecific variation within L. vulturinus that may reflect sexual dimorphism. Molecular divergence dates and Cretaceous neognath fossils indicate the presence of total-clade palaeognaths before the K-Pg mass extinction event; detailed anatomical descriptions of Paleogene palaeognaths will assist in the identification of the first total-clade palaeognaths from the Cretaceous, and provide insight into how and when flight was independently lost among Cenozoic crown palaeognaths.

paleontology↗

bioRxiv2026

Contrasting Species-Level and Genus Level Disparity Patterns within the ammonoid family Acanthoceratidae

Paleobiologists commonly use genera as a proxy for species in biodiversity studies. However, a lingering concern is that patterns among genera might not always faithfully reflect patterns among species. To date, the concern has focused chiefly on measured patterns of richness over time and on implied origination and extinction rates. However, similar issues might arise for studies of morphological disparity. Moreover, there potentially are additional implications of disparity patterns among species versus those among genera concerning the range of observable anatomical characters and whether disparity within genera is comparable to disparity among genera. If clades have some relatively slowly changing characters that workers have used to denote different genera, then we would expect to see congeneric species to cluster in morphospace; however, if such characters are rare, then within-genus disparity might approach among-genus disparity. Here, we use genus-level and species-level disparity patterns among acanthoceratid ammonoids from the Late Cretaceous. In particular, we examine whether these different level imply different evolutionary dynamics over a major ecological event (Ocean Anoxic Event 2) and how disparity within genera (i.e., among congeneric species) compares to disparity among genera. We find genus-level disparity somewhat inflates early acanthoceratid disparity but implies similar patterns over the OAE2. We also find that within-genus disparity is slightly lower than among-genus, but not hugely so. The combined results suggest that acanthoceratoid shell anatomy does not really show "genus" level characters, even if congeneric species do tend to be more similar to each other than to species in other genera. Thus, this might provide more of a warning for other types of studies using anatomical data (e.g., phylogenetic studies) than for disparity studies. Non-technical SummaryMany paleobiologists use genera to examine scientific questions. This leads to questions over whether this broader approach misses important species-level patterns. This study uses acanthoceratid ammonoids from the Late Cretaceous to examine disparity patterns at both the genus-level and the species-level. We specifically examine the disparity at both levels of this group over a time of high stress for this group, Ocean Anoxic Event 2 (OAE2). Our results show that genus-level disparity slightly exaggerates early acanthoceratid disparity but lowers to a similar pattern to the species-level disparity during OAE2. Within-genus disparity is shown to be slightly lower than among-genus, but not enough to be startling. Together, these results indicate that while some species within the same genus tend to be more alike to each other than those in other genera, there isnt a set of true "genus" level characters. This outcome leads to a warning against using anatomical data in phylogenetic studies, but less so for disparity studies.

paleontology↗

bioRxiv2026

Morphological comparison between cell-like entities from mammalian tissues and Precambrian microfossils

The fossil record of the Precambrian era preserves some of the earliest evidence of life, yet these ancient microfossils primarily reveal morphology rather than function, leaving unresolved questions about how early cells lived, replicated and evolved. The RNA world hypothesis proposes that primordial organisms relied on RNA for both information storage and catalysis, but direct living systems reflecting such biology remain poorly characterized. Here we describe cell-like entities isolated from mammalian tissues, measuring approximately 1-3 m in diameter and exhibiting morphological similarity to a range of Precambrian microfossils. Ultrastructural comparisons reveal a high degree of correspondence with fossil taxa spanning the Paleoproterozoic to Ediacaran intervals ([~]1.8 Ga to [~]551 Ma). In addition to these morphological features, the entities display biochemical characteristics, including RNA-dominant nucleic acid content and particle-associated reverse transcriptase activity. These observations indicate that the cell-like entities described are not inert, but represent biologically active systems. The combined ultrastructural and biochemical features raise the possibility that biologically active entities comparable to those observed in Precambrian microfossils may occur in contemporary biological contexts.

paleontology↗

bioRxiv2026

Rapid and robust sex determination from ancient enamel proteomes using protSexInferer

Accurate biological sex determination of ancient remains is critical for archaeological, anthropological, and forensic studies, but remains challenging for morphologically ambiguous and highly degraded endogenous DNA samples. Paleo-proteomics sex identification approaches, targeting sexually dimorphic amelogenin isoforms (AMELX and AMELY), present a promising solution. However, current workflows rely on manual verification of a few specific peptide markers, a process that lacks standardization and is susceptible to false-positive AMELY signals. To overcome these limitations, we developed protSexInferer, a lightweight, open-source bioinformatic pipeline for automated sex estimation from paleo-proteomic data. Our method uses the ratio of AMELY-specific peptides to all detected AMELY- and AMELX-specific peptides (i.e., the RAMELY value) rather than the mere presence or absence of AMELY signals for sex classification. We demonstrated that the RAMELY value clearly distinguishes male and female individuals in both reference and independent validation datasets, enabling reliable sex assignments even in cases where conventional intensity-based comparisons (e.g., AMELY-59M vs. AMELX-60) are ambiguous. This ratio-based approach effectively mitigates the impact of false-positive AMELY signals, therefore eliminating the need for time-consuming manual verification, and remains reliable even for samples with low peptide yields. Equipped with pre-constructed protein reference databases, protSexInferer provides a robust, standardized, and end-to-end solution for paleo-proteomic sex determination.

paleontology↗

bioRxiv2026

Phloem evolved gradually and asynchronously to xylem in early vascular plants

The evolution of the water-conducting xylem and sugar-conducting phloem tissues were key innovations in land plant evolution, enabling the origin of long-distance transport networks1. In extant vascular plants, phloem and xylem are linked functionally and always occur together2, though their evolutionary origin is unclear. This uncertainty is owed to the greater fossilisation potential of lignified xylem tracheids compared to thin-walled phloem cells3, 4, 5. Therefore, the fossil record of xylem is far more extensive than that of phloem, with the first definitive record of xylem being around 40 million years earlier6 than phloem7. This bias in the fossil record obscures characterisation of the origins of plant vasculature. In this study, this limitation is overcome by re-describing the "phloem-like" tissues of exceptionally preserved plants from the 407-million-year-old Rhynie chert8-15. We report that this tissue differs markedly from the phloem of extant plants, and propose its identification as a tissue of food-conducting cells (FCCs). Major histological differences were observed in the fossil plants, including no evidence for a pericycle, which in extant species delimits vascular from ground tissues, and the FCCs of the Rhynie chert plants were significantly larger in diameter than phloem cells. These differences suggest that early vascular plants lacked true phloem. However, putative sieve pores in the FCCs of Asteroxylon mackiei were identified. This represents to our knowledge the earliest record of sieve pores in the fossil record. Our results suggest an evolutionary scenario in which phloem features assembled gradually within FCCs, asynchronous to the evolution of xylem.

paleontology↗

bioRxiv2026

Developmental variation in pterygoid segmentation clarifies patterns of avian bony palate evolution

The morphology of the palate has long constituted the primary basis for differentiating between the two deepest clades of crown group birds, Neognathae and Palaeognathae. However, published literature on the bird palate is dominated by classical anatomical descriptions pre-dating the advent of contemporary three-dimensional imaging techniques, hindering our understanding of bird palate disparity and development. Pterygoid segmentation, the process by which the rostral portion of the pterygoid separates and fuses with the palatine during ontogeny in neognathous birds, remains a poorly understood aspect of avian cranial development despite giving rise to an important component of the cranial kinetic system. Here, we use micro-computed tomography to explore ontogenetic change of the palate during the process of pterygoid segmentation across an unprecedentedly broad taxonomic sample of immature and mature birds. With this large dataset, we present direct evidence for the full process of post-hatching pterygoid segmentation being exclusively restricted to the major avian subclade Neoaves. Further, our investigation helps refine several hypotheses of homology related to the pterygoid-palatine contact in crown birds and their close stem-group relatives: we hypothesise that the rostral projection of the pterygoid observed in Anseres (and potentially Anhimidae and Megapodiidae) is homologous with the hemipterygoid of neoavians, and that the discrete and unfused hemipterygoids of some crownward stem-birds suggest that a discrete hemipterygoid originated prior to the origin of the process of pterygoid segmentation. However, whether pterygoid segmentation represents a synapomorphy of Neornithes, Neognathae, or Neoaves remains ambiguous in light of elusive data from the fossil record and early stages of cranial development. Overall, our study clarifies the process of pterygoid segmentation in crown birds and raises new questions regarding the major morphological modifications that have characterized the evolutionary history of the avian bony palate.

paleontology↗

bioRxiv2026

Clade dynamics support an early origin of crown eukaryotes

The timing of the last eukaryotic common ancestor (LECA) remains a fundamental question in evolutionary biology and palaeontology. Unambiguous eukaryotic-grade fossils appear from 1780 Ma, but no crown-group supergroups are confidently identified before the end of the Mesoproterozoic (ca. 1050 Ma). The late LECA hypothesis suggests that this absence of crown-assignable fossils and biosignatures implies a late Mesoproterozoic origin of the crown. Here we show that this hypothesis is incompatible with the evolutionary dynamics of the eukaryote clade, even under the limited constraints of the fossil record. Studying stem-crown dynamics based on a birth-death model, we show that a late crown age requires diversification rates well below the minimum rate needed to generate observed living eukaryote diversity (~2.5 - 10 million species) for any plausible total group age. Our results suggest that only an early LECA can bridge evolutionary dynamics with the eukaryotic-grade fossil record, the living diversity, and the molecular clock estimates. Based on these constraints, we suggest a feasible minimum age estimate for LECA of ca. 1696 Ma, supported by current fossil evidence and supporting molecular clock estimates. These results also provide a fossil-testable prediction: crown-group eukaryotes likely exist in early Mesoproterozoic assemblages, albeit undetected with current morphology-based approaches.

paleontology↗

bioRxiv2026

Robust evidence for modest diversity loss across the K/Pg in neoselachians: Response to Guinot et al.

We reconstructed the neoselachian diversity over the past 145 million years using new occurrence dataset and DeepDive1-3. We recovered a small decline through the K/Pg following a steady increase during the Cretaceous, and a prolonged, substantial decline towards the present following a mid-Eocene peak2. Guinot et al. argue that our conclusions are compromised by problems in the underlying data and by the way extinction magnitude across the K/Pg was quantified. They cast doubt particularly on the pattern across the K/Pg, which they consider to be at odds with all previous analyses. They raise no issue with the Cretaceous trend, even though it was recovered with the same dataset and methods. We audited the alleged data issues reported in Guinot et al. and found that they mostly reflect operational choices (see Supplementary Information). However, we applied their data treatment and ran sensitivity tests to evaluate how this approach affects our results, specifically around the K/Pg. None of our tests recovered a diversity collapse for neoselachians during this interval. As such, we demonstrate that our findings are robust and consistent across different data treatments.

paleontology↗

bioRxiv2026

Mosaic terrestrial diversity dynamics through the Permo-Triassic interval

The end-Permian mass extinction (EPME) represents the most severe biotic crisis of the Phanerozoic Eon on Earth and has been well documented in marine taxa. However, its impact on terrestrial organisms and ecosystems remains incompletely understood. Here we present a high-resolution reconstruction of terrestrial diversification dynamics and spatial reorganization across the Permo-Triassic boundary (PTB) using comprehensive occurrence data of macroplants, sporomorphs and vertebrates. Terrestrial responses to the EPME show highly temporal, regional and taxonomic heterogeneities. Plants experienced a genus-level diversity loss of [~] 6.7%, across the PTB, whilst vertebrates, a lagged decline from the late Permian, peaking at a diversity loss of [~] 66.7%. Global distributions of plant and vertebrate show converging on similar latitudinal gradients post the PTB. Plant diversity loss is disproportionately high in low-latitude and tropical regions and progressively lower toward mid- and high-latitudes. Our study facilitates a fine-grained understanding to terrestrial macroevolution in geologic history through multi-analysis of a large volume of fossil data. Our findings challenge the long-held notion of global terrestrial collapse and mass extinction in plants during the PTB and offer a deep-time analogue for uneven response of extant terrestrial biodiversity to ongoing climate change.

paleontology↗

bioRxiv2026

Humans could become the greatest driver of biosphere net gain in Earth history, but we are currently the second fastest driver of biosphere loss

Human activity is transforming the shape, size, and resilience of Earths biosphere, degrading and augmenting Holocene baseline conditions at various scales, and replacing the wild biosphere with an anthropogenically modified one. We evaluate episodes of biosphere change throughout Earth history and compare them with contemporary and near-future anthropogenic changes, developing the concept of biosphere disruptors - agents that force global-scale macroevolutionary change. Transient disruptors are short-lived agents (mean 8.0x105 years), including massive volcanism and asteroid impacts. Persistent disruptors, including atmospheric and ocean oxygenation and land plant evolution, remain in the Earth System over long timescales (mean 1.6x108 years). In the geological record, transient disruptors are associated with temporary but sometimes massive biosphere degradation, whereas persistent disruptors are associated with sustained biosphere enhancement. Most anthropogenic biosphere impacts resemble those of past transient disruptors, globally degrading wild biomass and biodiversity. Humanity is driving the second highest rate of biosphere degradation in Earth history after the Cretaceous-Palaeogene bolide impact. However, humanity is the first disrupting agent capable of reflecting on and potentially transforming its impact on planetary habitability. If we can achieve this, humanity could drive the greatest rate of increase in planetary habitability in Earth history on centennial to millennial timescales.

paleontology↗

bioRxiv2026

A practical pipeline for volume rendering of trillion-voxel tomographic data

Recent advancements in tomography produce imaging data of geological materials (rocks and fossils) at trillion-voxel scales with multi-channels. Such high-resolution datasets are potentially keys to unveil evolutionary biological information with various shapes and sizes that have not been ever discovered. Volume rendering is an ideal visualization approach for them because it treats all voxels without relying on user-defined surface boundaries. However, these large-scale real-world tomographic data have rarely been volume-rendered at their native resolution, limiting the examination of rich morphological information. Here, we demonstrate a de facto standard volume-rendering pipeline running on a graphical processing unit (GPU)-equipped supercomputing system toward multi-channel, trillion-voxel tomographic data. Our workflow preserves original resolution, capturing detailed morphological information spanning microscopic to macroscopic scales. Systematic comparison of node types shows that GPU memory, rather than host memory, is the primary bottleneck. Our results establish a baseline for large-scale, multi-channel volume rendering of real tomographic data and demonstrate its applicability to geological samples. This work is presented as a practical demonstration of large-scale volume visualization.

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