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bioRxiv2024

Late Quaternary millennial-scale stability of the feeding strategy of the gray brocket deer in Southeastern Brazil.

There is only limited evidence (contemporary or archaeological/paleontological) regarding the feeding ecology of the gray brocket deer (Subulo gouazoubira) in Brazil's Cerrado biome. Using stable carbon ({delta}13C) and oxygen ({delta}18O) isotope analyses of dental enamel from individuals recovered from Cuvieri Cave, Minas Gerais, we explore dietary and environmental changes between the Late Pleistocene and Holocene epochs for S. gouazoubira living in this biome. {delta}13C data suggest no significant shift in feeding strategy between the Late Pleistocene and Holocene, with both sets of individuals displaying carbon isotope values consistent with browsing in open environments rather than closed canopy forests. A shift in {delta}18O values, on the other hand, indicates climatic changes in the area of Cuvieri Cave from the late Pleistocene to Holocene epoch. This study highlights the stability in the feeding behavior of the gray brocket deer despite biotic and abiotic changes between the epochs.

paleontology↗

bioRxiv2024

Selection, Evolution and Persistence of Paleoecological Systems

1The Phanerozoic fossil record can be organized as a nested set of persistent paleoecological units, ranging from paleocommunities to the Evolutionary Faunas. This paper argues that the basis for ecological persistence on geological timescales is rooted in the robustness of ecological communities, that is, the resistance and resilience of communities when perturbed by the environment. Here I present the Ecological Functional Networks Hypothesis (EFNH) that proposes that networks of species functions, or Ecological Functional Networks (EFNs), underlie ecological stasis and persistence, and that EFNs are both subject to selection and evolve. An EFN varies if the species composition and hence functional structures of its constituent communities vary, and EFNs may differ from each other based on the robustness of those constituent communities, numerical representation, and biogeographic distribution. That variation is subject to selection acting on EFN community composition, and determines both the persistence of an EFN and the differential persistence among multiple EFNs. Selection pressures on EFNs in turn exert top-down influence on species evolution and extinction. Evidence is presented to both establish the reality of EFNs in the fossil record, for example community structures that persist even as species composition changes, and the selection of EFNs, which is apparent during and after episodes of severe biotic turnover such as mass extinctions. Finally, tests are suggested that make the EFNH falsifiable, including testing the correlation between EFNs or EFN emergent traits and geological persistence, and using models of paleocommunity dynamics to examine the relationship between community or EFN robustness and geological persistence. The tests should be applied broadly throughout the Phanerozoic and diverse environments. The EFNH is part of a growing body of hypotheses that address multilevel selection and evolution of non-reproducing systems, including ecosystems and entire biospheres, and addresses those concepts on geological timescales.

paleontology↗

bioRxiv2024

Rapid riparian ecosystem recovery in low-latitudinal North China following the end-Permian mass extinction

The greatest mass extinction at the end of the Permian, ca. 252 million years ago, led to a tropical dead zone on land and sea. The speed of recovery of life has been debated, whether fast or slow, and terrestrial ecosystems are much less understood than marine. Here, we show fast reestablishment of riparian ecosystems in low-latitude North China as little as [~]2 million years after the end-Permian mass extinction. The initial ichnoassemblages in shallow lacustrine and fluvial facies of late Smithian age are monospecific, devoid of infaunalization, with apparent size reduction. In the following Spathian, relatively complex, multi-level, structured riverain ecosystems had been rebuilt including medium-sized carnivores, plant stems, root traces, increased ichnological complexity, and significantly increased infaunalization. Specifically, burrowing behavior had re-emerged as a key life strategy not only to minimize stressful climatic conditions, but possibly to escape predation.

paleontology↗

bioRxiv2024

StratPal: An R package for creating stratigraphic paleobiology modeling pipelines

O_LIThe fossil record is an important source of information to understand biological processes that take place over timescales not accessible to human observation or experiments. Fossil data is not a perfect reflection of past biological change, but a joint expression of stratigraphic, ecological, evolutionary, and taphonomic effects. Stratigraphic biology is a field dedicated to identifying these effects and accounting for them. C_LIO_LIWe present StratPal, a R package in which stratigraphic, ecological, evolutionary, and taphonomic modules can be combined into modeling pipelines for stratigraphic paleobiology. C_LIO_LIWe describe the types of data that can be modified and transformed using this approach, and briefly discuss potential extensions. C_LIO_LIAs working examples, we show how the pipeline can be used to model clustering of last occurrences at hiatuses and condensation surfaces, leading to artefactual "extinction events" caused by stratigraphic gaps. C_LI

paleontology↗

bioRxiv2024

The tetrapod fauna of the upper Permian Naobaogou Formation of China: a new mid-sized pareiasaur Yinshanosaurus angustus gen. et sp. nov. and its implication for the phylogenetic relationship of pareiasaurs

Pareiasauria is a specialized clade of herbivorous tetrapods that existed throughout Pangaea during the mid to late Permian period. The phylogenetic relationships of Chinese pareiasaur species remain controversy for several decades, primarily due to the poor preservation of known specimens. Until the report of Shihtienfenia completus in 2019, no complete skull had been documented for Chinese pareiasaurs. The present study describes a mid-sized pareiasaur, Yinshanosaurus angustus gen. et sp. nov., based on a nearly complete skull and an articulated partial postcranial skeleton collected from the Naobaogou Formation in 2018. It presents several significant new morphological features such as high and narrow skull, with the length of the skull table exceeding the width between the two quadratojugals; snout dimension as high as wide; long frontal with a length-to-width ratio of [~]3.0; U-shaped paraoccipital process in occipital view; and maxillary teeth oriented vertically, with only 7-9 cusps. Although the phylogenetic framework of pareiasaurs still requires further refinement, the current analysis yields distinct phylogenetic positions for Chinese pareiasaurs and establishes a new monophyletic clade that includes S. completus and Y. angustus.

paleontology↗

bioRxiv2024

Stepwise Assembly Of Crown Reptile Anatomy Clarified By Late Paleozoic Outgroups Of Neodiapsida

Living reptiles include more than 20,000 species with disparate ecologies. Direct anatomical evidence from Neodiapsida, which includes the reptile crown-group and its closest extinct relatives, shows that this diversity originates from a single common ancestor that lived some over 255 million years ago in the Paleozoic. However, the evolutionary assembly of crown reptile traits is poorly understood due to the lack of anatomically close relatives of Neodiapsida1-7. We present a substantially revised phylogenetic hypothesis, informed by new anatomical data from high-resolution synchrotron tomography of Paleozoic stem reptiles8-9. We find strong evidence placing the clade Millerettidae as the sister group to Neodiapsida, which uniquely share a suite of derived features. This grouping, for which we name the new clade Parapleurota, replaces previous phylogenetic paradigms by rendering the group Parareptilia as a polyphyletic assemblage of stem-reptiles, of which millerettids are the most crownward. Our findings address long-standing issues in Paleozoic reptile evolution10-17, such as firm support for the placement of captorhinids outside of crown Amniota and most varanopids as synapsids. These results greatly improve the fit of early amniote phylogeny to the observed stratigraphic record and reveal stepwise origin of crown reptile anatomy, including a middle Permian origin of tympanic hearing and loss of the lower temporal bar. This evolutionary framework provides a platform for investigating the diversification of the reptile crown group in the Early Triassic that was foundational to the origins of important living and extinct groups including dinosaurs (including birds), marine reptiles, crocodilians, and lepidosaurs.

paleontology↗

bioRxiv2024

Buca della Iena and Grotta del Capriolo: new chronological, lithic, and faunal analyses of two late Mousterian sites in Central Italy

New radiocarbon, lithic, faunal, and documentary analyses of two sites, Buca della Iena and Grotta del Capriolo, excavated in the 1970s, enhance our understanding of late Neanderthal settlement in the northwestern Italian peninsula and provide insights into their demise. Reassessment of stratigraphical and fieldwork documentation identified areas of stratigraphic reliability, supporting robust interpretations. Radiocarbon dating reveals broadly contemporaneous occupations at both sites between 50-40 ka cal BP, with Buca della Iena showing occupation from approximately 47 to 42.5 ka cal BP. Lithic analyses demonstrate the consistent application of the same chaine operatoire across both sites. Faunal analyses indicate that carnivores, particularly Crocuta spelaea, were the dominant accumulating agents in Buca della Iena, while limited preservation at Grotta del Capriolo prevents detailed taxonomic determination. However, hominin presence at both sites is evidenced by cut-marked bones. This study provides new perspectives on the Middle-to- Upper Palaeolithic transition in the northwestern Italian peninsula.

paleontology↗

bioRxiv2024

Sorting the mob: using geometric morphometrics and machine learning to differentiate kangaroo postcrania for zooarchaeological applications

Taxonomic identification of bone is one of the building blocks of zooarchaeological research into human foraging behaviour. However, it can prove difficult in regions, such as Australia, that have biodiverse taxa that are difficult to differentiate using bone morphology. One such case are the kangaroos and wallabies (macropods), one of the most speciose groups of marsupials whose remains are frequently recovered from Australian archaeological sites. Despite their clear importance to Indigenous economies, little research has been undertaken on how to reliably differentiate the postcranial remains of extant macropods. Here we address this gap by applying three-dimensional geometric morphometrics to describe how the astragalus and calcaneus differs between several large macropod genera. We describe taxonomically diagnostic anatomical attributes between genera and identify the size related (allometric) shape variation that could be mistaken for taxonomic differences. We then compare several machine learning models to demonstrate how these can be applied to geometric morphometric data to statistically classify unknown specimens from palaeozoological contexts with a high degree of accuracy. Our results show that non-linear methods of supervised machine learning outperform classical discriminant function analysis when used on our geometric morphometric data. Statistical classification of palaeozoological specimens has the potential to be a valuable tool, where differentiating skeletal remains of closely related taxa continues to prove challenging.

paleontology↗

bioRxiv2024

Convincing Evidence of Carnivorous Diet in Alvarezsaurian Dinosaur

A dietary shift from carnivory to insectivore has been proposed to explain the dramatic morphological evolution of alvarezsaurians, particularly the adaptation related to the manual digital reduction and body size miniaturization. However, based solely on morphological shifts, this hypothesis lacked direct dietary evidence to support either carnivory or insectivore. Here, we present the first convincing dietary evidence for alvarezsaurians, derived from the intestinal contents of the Early Cretaceous Bannykus wulatensis. Our analysis revealed significantly higher levels of calcium and phosphorus in the intestinal contents compared to the surrounding sandstone. Scanning electron microscopy identified hard tissue debris and possible soft tissues surrounding by phosphatized bacteria and tightly packed hollow microspheres, suggesting that the intestinal contents were strongly pseudomorphed by phosphatized microbes during fossilization. Raman spectroscopy showed characteristic peaks indicative of bone-derived material, consistent with the hard tissue debris appeared in the intestinal contents. Our results suggest that Bannykus had a carnivorous diet with strong chemical digestion, which likely compensated for its delicate cranial structures and small teeth. These results imply that if a dietary shift to insectivore occurred, it likely took place later in alvarezsaurian evolution, probably coinciding with a reduction in body size.

paleontology↗

bioRxiv2024

NOTE ON A SMALL FRUIT-EATING BAT FROM THE MIDDLE HOLOCENE OF LAGOA SANTA, EASTERN BRAZIL

Bats represent the second most diverse order of mammals; however, their fossil and subfossil remains are still relatively understudied. In Brazil, numerous living species have been identified in cave deposits, although few fossils have been dated, with none originating from the Holocene. This study presents a specimen from the Middle Holocene, collected from Cuvieri Cave. The fossil consists of an incomplete, U-shaped mandible that includes the first molars. The specimen was identified as Artibeus sp., a genus of fruit-eating bats that is currently widespread across Brazilian territory. This specimen dates to a poorly understood period in the Lagoa Santa region, when human populations had abandoned the area (referred to as the Archaic Gap) and during which the faunal population of Cervidae experienced a notable decline in the number of fossil records. The genus Artibeus is widely distributed in tropical regions and is commonly found in environments ranging from semi-arid regions to savannas and dense forests. It is not considered a paleoenvironmental indicator.

paleontology↗

bioRxiv2024

Fossil Freshwater Fishes from the Pliocene of northern Colombia and the Palaeogeography of northern South America

1Freshwater fishes from northern Colombia are reported from the Sincelejo and Ware formations, of Pliocene age. A total of ten taxa have been identified comprising two orders, five families, and nine genera. Characters from dental morphology, fin spines, and cranial bones are provided as taxonomic tools for the study of fossil fishes. All of the taxa are members of groups currently restricted to drainages east of the Andes, suggesting that physical drainage connection was still present by the Pliocene between the Amazon-Orinoco and trans-Andean drainages such as the Magdalena-Cauca, or that these groups persisted in the trans-Andean region at least until Pliocene times. The genera Hemidoras, Serrasalmus, and Trachely-opterichthys are new records for the fossil fish fauna of South America. The genus Zungaro represents a new record for the trans-Andean region, whereas the genus Platysilurus is for the first time in Colombia. Most of these occurrences also represent the youngest occurrences in the fossil record. Literature records are reidentified as Pygocentrus from the La Venta fauna and the earily Oligocene in Peru. These assemblages suggest that the Sincelejo and Ware formations were deposited in rivers of large size that were part of a large drainage network connected to the Amazon-Orinoco despite being currently located west of the Andes. These findings suggest that the Cordillera Oriental and the Merida Andes were not dividing yet the drainage network in northern South America by the middle to late Miocene.

paleontology↗

bioRxiv2024

Uncovering Ancient DNA in Petroleum: Insights into Earth Hidden Life Events and Geological History

Specific macromolecules in petroleum, preserved through geological processes from ancient organisms, are recognized as molecular fossils or geochemical markers (GMs). Our selected GMs indicate that the source rocks of Nanyang Oilfield formed in an anoxic, saline, and stratified lacustrine environment with marine influence. Contrary to science fiction notions that oil originates from ancient large animals, mainstream academia has consistently asserted that oil is derived from the organic matter of lower life forms, formed over extended geological processes, with intact DNA no longer persisting in oil post-formation. However, this study successfully extracted 3,159,020 DNA fragments from the petroleum samples using the nanoparticle affinity bead technology, followed by sequencing and classification via the mega screen method. These fragments, categorized as original in situ DNA (oriDNA), recent environmental DNA (preDNA), and paleo-environmental DNA (paeDNA), exhibit a "Genome Accumulated over Time" (GAT) pattern of "old-less, new-many". This aligns with findings from GMs while offering more specific genetic information. The analysis reveals evidence of historical events, including animal extinctions, marine invasions, ancient bird species presence, Asian Homo erectus activities, and modern human influences in preDNA. Notably, the mitogenomic data positions Asian Homo erectus closer to modern humans than to chimpanzees at the maternal basis. The absence of deamination in petroleum ancient DNA (aDNA) fragments is likely due to the anaerobic, anhydrous environment and the screening process that excludes degraded fragments. Consequently, the authenticity criteria and scope of application of traditional aDNA methods require reevaluation. Surprisingly, the near-absence of oriDNA has impeded our efforts to determine the specific biological origins of the oil. These findings position petroleum as a novel, non-skeletal source of aDNA, offering insights into ancient animal activities, geological changes, and human origins while underscoring its potential as an untapped resource for studying genetic preservation across geological timescales.

paleontology↗

bioRxiv2024

A new metoposaurid (Temnospondyli) bonebed from the lower Popo Agie Formation (Carnian, Triassic) and an assessment of skeletal sorting in temnospondyls

Metoposaurid-dominated bonebeds are relatively commonplace in Upper Triassic continental deposits with at least ten monodominant, densely populated bonebeds globally. The biostratinomy of several classic localities in India, North America, and Poland have been explored in detail, however, variability in methods and resultant conclusions point to the need for a more nuanced approach to understanding both the taphonomic and the ecological origins of metoposaurid-dominated bonebeds. Here we present the first monodominant metoposaurid mass mortality assemblage from the Late Triassic Popo Agie Formation and the stratigraphically lowest known record of several fauna from the Popo Agie Fm including the first occurrence of the Buettnererpeton bakeri in Wyoming. We employ previously used binning methods based on perceived hydrodynamic equivalence ("Voorhies groups") to assess pre-burial skeletal sorting. We suggest a simple counting and normalization method that avoids the inherent bias introduced by the interpretation of hydrodynamic equivalence of skeletal elements in taxa that lack actualistic experimental data. In contrast to other North American metoposaurid bonebeds, the sedimentology and skeletal sorting analyses of the Nobby Knob quarry support an autochthonous origin of this assemblage in a fluvio-lacustrine system with relatively little pre-burial sorting. Despite differences in underlying assumptions regarding the dispersal potential of specific skeletal elements, binning methods tend to follow similar trends regardless of framework used to assess different assemblages.

paleontology↗

bioRxiv2025

Morphology of male genitalia and legs reveals the classification of Mesozoic Zoraptera (Insecta)

Zoraptera is a small insect order with less than 50 described species from mostly tropical and subtropical regions of the World. The current system of extant Zoraptera is based on the results of molecular phylogeny combined with the morphology of male genitalia, and supplemented by the characters on the male abdomen and a number of metatibial spurs. However, fossil representatives of Zoraptera have not yet been classified into the modern system and most of them remained in the collecting genus Zorotypus Silvestri, 1913, because the genitalia were not observable or examined in detail. In this study, for the first time, we describe and critically evaluate the male genitalia and other principal diagnostic characters of all available Mesozoic Zoraptera. Our results lead to the first proposal of the generic classification of Mesozoic Zoraptera. We describe two new genera, Cretozoros gen. nov. and Burmazoros gen. nov., reinstate Paleospinosus Kaddumi, 2005, stat. restit. from synonymy with the subgenus Octozoros Engel, 2003 (in Zorotypus), and elevate Octozoros Engel, 2003 to a genus level. Cretozoros gen. nov., Paleospinosus stat. restit. and Octozoros stat. nov. are classified in Spiralizoridae: Latinozorinae, while Burmazoros gen. nov. and Xenoburmiticus Engel & Grimaldi, 2002 are classified in Zorotypidae: Zorotypinae. Altogether, it was possible to classify nine out of the 11 currently recognized species of Mesozoic Zoraptera. Zorotypus hukawngi Chen & Su 2019 is synonymized with Cretozoros acanthothorax (Engel & Grimaldi, 2002), comb. nov. and Zorotypus hirsutus Mashimo, 2018 is synonymized with Octozoros robustus (Liu, Zhang, Cai & Li, 2018), stat. restit., comb. nov., which is simultaneously restituted from the synonymy with Octozoros cenomanianus (Yin, Cai & Huang, 2018), comb. nov. The classification of Mesozoic Zoraptera into the modern system enables us to better understand the diversity of their internal lineages during the early evolution of this enigmatic insect order.

paleontology↗

bioRxiv2025

The influence of reproductive mode on resource competition and diversity patterns in Ediacaran early animal communities

The appearance of the oldest known animals during the late Ediacaran ([~]574 million years ago [Ma])1-4 was followed by a phase of little change5. This period, which lasted [~]14 million years, ended with a burst of rapid diversification known as the Ediacaran "Second Wave". The reasons for these diversity patterns are poorly understood. Here we investigate how reproductive mode mediated community dynamics, and in turn macroevolutionary change, in the Ediacaran. We show that widespread reproduction via stolon (namely via filaments connecting clones) in the first animals limited intra-specific competition among neighbours, leading to inter-specific competition acting at smaller-spatial scales than intra-specific competition, a phenomenon called heteromyopia6. Heteromyopia enables co-existence of sub-optimal competitors because the dispersal limitation of the dominant species means that they do not inhabit all the optimal habitat, so that lesser competitors can still exist within the same community, operating under reduced selection pressure. We explored the consequences of this dispersal limitation on community diversity using Approximate Bayesian Computation to estimate the posterior distributions of dispersal with a spatially explicit model fitted to the three Ediacaran assemblages and showed that the change from stoloniferous to sexual reproduction that coincided with the Second Wave could explain the sudden increase in alpha diversity observed in the fossil record. We conclude that widespread asexual reproduction via stolon likely constrained early animal evolution, limiting diversification until the onset of mobility and widespread sexual reproduction7-9.

paleontology↗

bioRxiv2025

Global plate model choice impacts reconstructions of the latitudinal biodiversity gradient

The latitudinal gradient of declining species richness from the Equator towards the poles is one of the most pervasive macroecological patterns on Earth today. However, the ubiquity of this trend over geological timescales remains unclear. One reason for this uncertainty is that palaeobiologists need Global Plate Models (GPMs) to estimate the latitudinal position of organisms remains at time of deposition. However, as GPMs constitute hypotheses for how tectonic plates have moved over Earths history, reconstructions of the latitudinal biodiversity gradient (LBG) might also vary based on the GPM used. Here, using the fossil record of five major marine invertebrate groups, we evaluate the impact of GPM choice on reconstructions of the LBG over the Phanerozoic. Our results show that GPM choice can lead to different conclusions about the shape and strength of LBGs in deep time, even at a coarse spatial scale. These findings suggest additional caution is needed when reconstructing deep-time biogeographic patterns and macroevolutionary events, such as the origin of the present-day LBG. We therefore advocate for future palaeobiogeographic studies to conduct sensitivity analyses investigating the impact of GPM choice on their conclusions, and for greater interdisciplinary collaboration between palaeobiologists and palaeogeographic modellers to avoid common issues in the use of GPMs.

paleontology↗

bioRxiv2025

Where were the Caribbean mangroves during the Last Glacial Maximum?

During the Last Glacial Maximum (LGM), when global sea levels dropped by [~]132 m, the Caribbean continental shelf was fully exposed, which drastically reduced the flat topographical habitat necessary for mangrove growth. It has been proposed that mangroves survived in flat microsites beyond the shelf break and later expanded from these microrefugia to their current distribution after the LGM. However, this hypothesis remains untested. This study aims to identify potential refugia by locating flat areas around the -132 m isobath using Global Multiresolution Topography (GMRT) images. A significant [~]200-km-long potential refugium was identified on the northern Trinidad (NT) shelf, along with several scattered kilometer-scale microrefugia near the Cariaco Basin (CB) in northeastern Venezuela. Additionally, two isolated prospective microrefugia were detected in northern Colombia (NC) and western Hispaniola (WH). Bioclimatically, all these potential LGM refugia were suitable for mangrove growth. The remaining LGM Caribbean coasts were considered unsuitable for mangrove growth. The NT refugium, along with the CB microrefugia, may have served as the primary sources for subsequent mangrove expansion. This expansion was likely facilitated by postglacial sea-level rise and the SE-NE Caribbean Current (CC), which would have acted as a major agent for propagule dispersal. This microtopographical survey not only supports the microrefugial hypothesis but also narrows the focus to the most promising areas, significantly reducing the time, effort and resources required for future seismic and coring campaigns.

paleontology↗

bioRxiv2025

Arrow heads at Obi-Rakhmat (Uzbekistan) 80 ka ago

When they are occasionally found in Middle Palaeolithic Neanderthal settlements, lithic weapons heads are large and do not differ in size, shaping or type from those used for activities other than hunting, such as plant gathering or butchery. The presence in a same assemblage of various types of armatures, some of which are microlithic and designed for this purpose, has only been documented in Modern Humans sites. Recent studies show that light projectile points, which were to become the structuring element of Upper Palaeolithic lithic industries, were already present in its formative stages. However, they remain marginal in debates regarding the Middle to Upper Paleolithic transition. We present here the first results of a search for weapon heads in the oldest layers of the Obi-Rakhmat rock shelter, at around 80 ka. This site, located in the western foothills of the Tian Shan Mountains, northeastern Uzbekistan, has yielded a blade-based lithic industry which is forming part of the continuity of the Levantine Early Middle Paleolithic but with several innovative traits. The assemblage is based on a systematic blade production (regular thick narrow blades from unipolar and bipolar sub-prismatic and narrow-faced cores, thin and wide blades from flat-faced Levallois-like cores) along with shorter pieces from convergent or centripetal Levallois cores, and bladelets from burin-cores and other small cores. Three types of projectile armature are identified from their impact marks: retouched points, bladelets and raw micropoints which were so far unseen due to their fragmentary state. The micropoints are too narrow for having been fitted to anything other than arrow shafts. They are similar to the armatures described in a pioneer settlement by Sapiens in the Rhone Valley, France, 25,000 years later.

paleontology↗