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bioRxiv2023

Introducing Isotopia: a stable isotope database for Classical Antiquity

We present Isotopia, an open-access database compiling over 36,000 stable isotope measurements ({delta}13C, {delta}15N, {delta}18O, {delta}34S, 87Sr/86Sr, 206Pb/204Pb, 207Pb/204Pb, 208Pb/204Pb, 207Pb/206Pb, and 208Pb/206Pb) on human, animal, and plant bioarchaeological remains dating to Classical Antiquity (approximately 800 BCE - 500 CE). These were recovered from different European regions, particularly from the Mediterranean. Isotopia provides a comprehensive characterisation of the isotopic data, encompassing various historical, archaeological, biological, and environmental variables. Isotopia is a resource for meta-analytical research of past human activities and paleoenvironments. The database highlights data gaps in isotopic classical archaeology, such as the limited number of isotopic measurements available for plants and animals, limited number of studies on spatial mobility, and spatial heterogeneity of isotopic research. As such, we emphasise the necessity to address and fill these gaps in order to unlock the reuse potential of this database.

paleontology↗

bioRxiv2023

Prebiotic membrane structures mimic the morphology of purported early traces of life on Earth

Elucidating the most probable compositions of the first cell membranes prior to the origin of life, within a laboratory setting, requires experiments with organic molecules and chemical conditions representative of those present on the early Earth. As such, the membrane forming molecules used in these experiments are described as prebiotically plausible, i.e., they could have formed through abiotic reactions and be available for membrane formation prior to the emergence of biology. Similarly, the chemical properties of solutions in which these membranes are formed (e.g., pH, temperature, ionic strength) must represent the early Earth environmental conditions under investigation. Here, using a combined confocal and transmission electron microscopy approach, we show that prebiotically plausible organic molecules, in solutions representative of Hadean submarine alkaline hydrothermal vents, form aggregated structures with substantial morphological diversity. The structures hold the potential for use as traces of prebiotic processes in the ancient rock record. In addition, many of the structures are morphologically similar to those which are presented as early microfossils, thus highlighting the limitations of morphological interpretation in these types of studies. Detailed analyses of abiotic organic structures are essential for our understanding of the earliest living organisms on Earth, as well as for our interpretation of any potential biosignatures recovered in the future from extra-terrestrial bodies.

paleontology↗

bioRxiv2023

Dietary reconstructions of Magdalenian canids from SW-Germany do not indicate that the area was a centre of early European wolf domestication

In their paper A refined proposal for the origin of dogs: the case study of Gnirshohle, a Magdalenian cave site, Baumann and colleagues[1] claim that their data support the hypothesis that the Hegau Jura was a potential center of early European wolf domestication, and that such a scenario becomes plausible considering a close proximity of canids and humans thereby introducing a controlled, or at least a restrictive diet. The study focusses on fossil remains of large canids from the Gnirshohle cave site in SW Germany. Morphometric data on only one specimen, GN-999, as well as collagen {delta}15N and {delta}13C isotopic data and mitochondrial DNA analyses on the Gnirshohle specimens and a comparative sample were used to conclude that the Gnirshohle specimens shed light on the origin of dogs as purported by the title of the paper. Here we argue that the paper is fundamentally flawed and excluded available relevant data.

paleontology↗

bioRxiv2023

A Glimpse Into the Cenomanian: Palynology of the Arlington Archosaur Site, Late Cretaceous Western Interior Seaway, Texas, USA

The Arlington Archosaur Site (AAS) between Dallas and Fort Worth, Texas, is known as a rich fossiliferous section. The age of these rocks is generally considered to be mid-Cenomanian, but conflicting evidence suggests the age may be as young as the late Cenomanian-early Turonian. To address the issue, a palynological study was designed and conducted based on the close sampling of the lithofacies. Palynological samples were processed according to the standard acid preparation. The study was quantitative and focused on associations to determine the paleoenvironment, paleoclimate, biostratigraphy, and age of exposure. The rich palynological assemblages comprise spores from seedless plants, gymnosperms, angiosperms, fungi, algae, and dinoflagellate cysts. Bryophytes were abundant mainly in Facies A and B, with Zlivisporis cenomanianus taking over the bryophytes habitat in Facies D. Lycophytes abundant in the alluvial and coastal plains are considered to have been transported. Conifers were the predominant group of gymnosperms, also mainly transported into the section. Freshwater algal remains include Schizophacus laevigatus/Ovoidites parvus, Schizosporis reticulatus, Botryococcus sp., and Pediastrum sp. Acanthomorph acritarchs present in low abundance and diversity appear following shallow marine dinoflagellates spikes and before freshwater colonial algal spikes. The vegetation signal at Notos Facies A and B indicates tropical to subtropical shallow marine to coastal plains, while Notos Facies D indicates tidally influenced areas. Also, picks of the diversity and abundance of dinoflagellate cysts are interpreted as an increased marine influence and proposed as possible flooding surfaces. The results support the alternation of marine incursions within deltaic and floodplain sequences, related to regional climate oscillation that affected the vegetation on the upland drainage area. Key palynological markers point to an early Late Cenomanian age, and the presence of the Cyclonephelium compactum-C. membraniphorum (Ccm morphological plexus) signals that the incursion of boreal waters during the Plenus Cold Event of the Ocean Anoxic Event 2 may have reached as far south as the AAS area. This coincides with vegetation trends that suggest a cooler and less humid climate at the start of Facies A, where Ccm is more abundant.

paleontology↗

bioRxiv2023

Nanoscale Imaging and Microanalysis of Ice Age Bone Offers New Perspective on 'Subfossils' and Fossilization

The 3-D structure and organization of type-1 collagen protein and vasculature for a set of ancient permafrost bones is extensively documented at the nanoscale (up to 150,000x magnification) for the first time. The chemical mapping technique ToF-SIMS is additionally used to directly localize chemical signal to these structures; C:N and isotope measurements are also reported for the bulk organic bone matrix. These analyses test the hypothesis that biomolecular histology of collagen and vasculature from the permafrost bones supports their taphonomic classification as "subfossils" rather than "fossils". Results indicate the original collagenous scaffolding and vasculature are still present, the former of which is well-preserved, thus supporting the hypothesis. This study is the first to taphonomically classify a set of pre-Holocene bones as "subfossils" based on the preserved state of their biomolecular histology. These methods can be readily expanded to specimens of warmer thermal settings and earlier geologic strata. Doing so has potential to establish/formalize at what point a bone has been truly "fossilized"; that is, when it has transitioned from "subfossil" status to being a true "fossil" bone. This will elucidate the fossilization process for ancient vertebrates and lead to a deeper understanding of what it means to be a "fossil".

paleontology↗

bioRxiv2023

Not dasycladalean alga, but an Odyssey of the earliest Phanerozoic animal reef-builders

The compacted macrofossil Protomelission? sp. from the early Cambrian Xiaoshiba Lagerstatte was recently ascribed to early dasycladalean green algae and used to disprove the bryozoan affinity of coeval phosphatized microfossils, which made the puzzling question whether the bryozoans originated in early Cambrian pending again. Our new analyses of multiple specimens which are conspecific with Protomelission? from the Chengjiang Lagerstatte indicate that they are not dasycladaleans but one of the three groups of archaeocyath-like sponges that atypically inhabited siliciclastic substrates. All the archaeocyath-like fossils share the same preservation mode and exhibit archaeocyath-type external skeletal features. Particularly, the Protomellision?-like fossils preserve structures indicative of archaeocyath aquiferous system and ontogeny. They represent the first recognized one-walled archaeocyath sponges in South China and evidence the niche expansion of archaeocyaths on their way of global radiation from Siberia, 518 million years ago. The origin of the bryozoans remains a mystery.

paleontology↗

bioRxiv2023

Early Jurassic origin of avian endothermy and thermophysiological diversity in Dinosauria

A fundamental question in dinosaur evolution is how they adapted to substantial long-term shifts in Earth System during the Mesozoic and when they developed environmentally independent, avian-style acclimatization due to the evolution of an endothermic physiology. Combining fossil occurrences with macroevolutionary and paleoclimatic models, we unveil distinct evolutionary pathways in the main dinosaur lineages: ornithischians and theropods diversified across broader climatic landscapes, trending toward cooler niches. An Early Jurassic shift to colder climates in Theropoda suggests an early adoption of endothermic thermophysiology. Conversely, sauropodomorphs exhibited prolonged climatic conservatism associated with higher thermal conditions. Paleo-biome mapping emphasizes temperature, rather than plant productivity, as the primary driver of this pattern, suggesting poikilothermic physiology with a stronger dependence on higher temperatures in sauropods since the Early Jurassic. One-Sentence SummaryDinosaur climatic evolution reveals early endothermy emergence in theropods, ornithischians but heterotherm sauropodomorphs.

paleontology↗

bioRxiv2024

Distinct causes underlie double-peaked trilobite morphological disparity

Trilobite cephalic morphology impacted the autecology of individuals, and is critical for high- and low-level taxonomic assignments. Disparity in trilobite cephalon shape varied through time and was integral to the occupation of a diversity of ecological niches. To fully appreciate trilobite cephalic evolution, we must understand how this disparity varies, and what factors control cephalon morphometry. We explore the disparity of trilobite cephala through the Palaeozoic, and analyse the associations between cephalic morphometry and taxonomic assignment and geological Period, using a dataset of 983 2D trilobite cephalon outlines. Elliptical Fourier transformation visualised as a Principal Components Analysis suggests significant differences in morphospace occupation for order and Period groups, and comparisons of disparity measures also suggest significantly different disparities between the groups. Trilobite cephalic disparity peaks in the Ordovician and Devonian. The Cambrian-Ordovician expansion of morphospace occupation appears a result of radiation to new niches, and thus all trilobite orders were established by the late Ordovician. In comparison, the morphospace expansion from the Silurian to Devonian seems solely a result of within-niche diversification rather than novel niche occupation. However, analyses interrogating the regions of morphospace occupied, including centroid distances, average pairwise shape comparisons and Linear Discriminant Analysis demonstrate that, except for the order Harpida and the Cambrian and Ordovician Periods, order and geological Period could not be robustly predicted for an unknown trilobite. Further, Kmeans clustering analyses suggest the total dataset naturally subdivides into only seven groups that do not correspond with taxonomic orders, though Kmeans clusters do decrease in number through the Palaeozoic, aligning with findings of decreasing disparity.

paleontology↗

bioRxiv2024

Early evolution of the ecdysozoan body plan

Extant ecdysozoans (moulting animals) are represented by a great variety of vermiform or articulated organisms. However, controversies remain about the nature of their ancestral body plan although the vermiform hypothesis seems to prevail. We describe here Beretella spinosa gen et sp. nov. a tiny ecdysozoan from the early Cambrian, Yanjiahe Formation, South China, with an unusual sack-like appearance, single opening, and spiny ornament. Beretella has no equivalent among animals, except Saccorhytus from the basal Cambrian. Phylogenetic analyses resolve both forms as a sister group (Saccorhytida) to all known Ecdysozoa, thus suggesting that ancestral ecdysozoans may have been non-vermiform animals. Saccorhytids are likely to represent an early dead-end off-shot along the stem-line Ecdysozoa that possibly evolved through anatomical simplification (e.g. lack of anus). Although extinct during the Cambrian, this animal lineage provides precious insight into the early evolution of Ecdysozoa and the nature (possibly non-vermiform) of the earliest representatives of the group.

paleontology↗

bioRxiv2024

Assessing the Adequacy of Morphological Models used in Palaeobiology

Reconstructing the evolutionary history of different groups of organisms provides insight into how life originated and diversified on Earth. Phylogenetic trees are commonly used to estimate this evolutionary history, providing a hypothesis of the events. Within Bayesian phylogenetics a major step in estimating a tree is in choosing an appropriate model of character evolution. In the case of most extinct species, our only source of information to decipher their phylogenetic relationships is through the morphology of fossils. We therefore use a model of morphological character evolution, the most common of which being the Mk Lewis model. While it is frequently used in palaeobiology, it is not known whether the simple Mk substitution model, or any extensions to it, provide a sufficiently good description of the process of morphological evolution. To determine whether or not the Mk model is appropriate for fossil data we used posterior predictive simulations, a model adequacy approach, to estimate absolute fit of the model to morphological data sets. We first investigate the impact that different versions of the Mk model have on key parameter estimates using tetrapod data sets. We show that choice of substitution model has an impact on both topology and branch lengths, highlighting the importance of model choice. Next, we use simulations to investigate the power of posterior predictive simulations for morphology. Having validated this approach we show that current variations of the Mk model are in fact performing adequately in capturing the evolutionary dynamics that generated our data. We do not find any preference for a particular model extension across multiple data sets, indicating that there is no one size fits all when it comes to morphological data and that careful consideration should be given to choosing models of discrete character evolution. By using suitable models of character evolution, we can increase our confidence in our phylogenetic estimates, which should in turn allow us to gain more accurate insights into the evolutionary history of both extinct and extant taxa.

paleontology↗

bioRxiv2024

Hydrodynamic function of genal prolongations in trinucleimorph trilobites revealed by computational fluid dynamics

Trilobites, a diverse clade of Palaeozoic arthropods, repeatedly converged on the trinucleimorph morphology. Trinucleimorphs possessed vaulted cephala with a broad anterior fringe and prominent posteriorly orientated genal prolongations. Various functional hypotheses have been proposed for the fringe, however the possible function of the genal prolongations has received less attention. Here we use a computational fluid dynamics approach to test whether these prolongations served a hydrodynamic function: generating negative lift to allow trinucleimorphs to remain in place on the seafloor and prevent overturning within fast flowing water. We simulated the performance of cephala with broad, narrow, and absent genal prolongations in a benthic environment with flow speeds ranging from 0.05-0.5 m s-1, in two cephalic postures. The first posture had the anterior of the cephalon parallel to the seafloor, while for the second the genal prolongations were parallel to the seafloor. Posture and presence of genal prolongations were found to be important for generating negative lift, with performance improving under faster flow speeds. No significant difference between narrow and broad genal prolongations was detected. This study provides support for genal prolongations serving a hydrodynamic function, similar to the femurs of some insect larvae, however, it does not preclude prolongations also serving additional functions as snowshoes or antipredatory deterrents.

paleontology↗

bioRxiv2024

A framework for reconstructing ancient food webs using functional trait data

O_LIFood webs provide quantitative insights into the structure and dynamics of ecological communities. Previous work has shown their utility in understanding community responses to modern and ancient perturbations, including anthropogenic change and mass extinctions. However, few ancient food webs have been reconstructed due to difficulties assessing trophic interactions amongst extinct species derived from an incomplete fossil record. C_LIO_LIWe present and assess the Paleo Food web Inference Model (PFIM). PFIM uses functional trait data--predictive of interactions in modern ecosystems and commonly available for fossil organisms--to reconstruct ancient food webs. We test the model by (i) applying it to four modern ecosystems with empirical constrained food webs to directly compare PFIM-constructed networks to their empirical counterparts, (ii) by carefully comparing discrepancies between PFIM-inferred and empirical webs in one of those systems, and (iii) by comparing networks describing feasible trophic interactions ("feasible webs") with networks to which we superimpose characteristic interaction distributions derived from modern theory ("realized webs"). As a proof of concept, we then apply the method to faunal data from two Cambrian fossil deposits to reconstruct ancient trophic systems. C_LIO_LIPFIM-inferred feasible food webs successfully predict [~]70% of trophic interactions across four modern systems. Furthermore, inferred food webs with enforced interaction distributions (i.e., realized webs) accurately predict [~]90% of interactions. Comparisons with a global database of trophic interactions and other food web models, suggest that under sampling of empirical webs accounts for up to 21% of the remaining differences between PFIM and empirical food webs. C_LIO_LIFood webs can be reasonably approximated by inferring trophic interactions based upon life habit traits. This study provides the foundation to use trait-based inference models across the fossil record to examine ancient food webs and community evolution. C_LI

paleontology↗

bioRxiv2024

Optical photothermal infrared spectroscopy (O-PTIR): a promising new tool for bench-top analytical palaeontology at the sub-micron scale

The identification of preserved organic material within fossils is challenging. Well-established vibrational spectroscopy techniques, such as micro-FTIR (Fourier Transform Infra-Red spectroscopy), have been widely used to investigate organic fossils molecular composition. However, even when well-adapted to study objects several tens of micrometre across, they still suffer from limitations, notably regarding resolution and sample preparation requirements. Optical Photothermal Infrared Spectroscopy (O-PTIR), a recently developed technique, overcomes the challenges of bench-top FTIR spectroscopy. By combining an IR excitation laser with a 532 nm green probe laser, this technique allows molecular characterization at high spectral resolution (~2 cm-1) and with extremely fine spatial resolution (~500 nanometres). Additionally, problems linked with sample thickness, surface roughness and particle shape/size are mitigated when compared with FTIR or Atomic Force Microscopy-based nanoIR techniques. Here we show that O-PTIR can be used to easily and successfully map the molecular composition of small organic fossils preserved in silica matrix (chert) in petrographic thin sections. Our study reveals that O-PTIR resolves spatial heterogeneities in the preserved molecular composition of organic fossils (spores and plants) at a sub-micron scale, and that such heterogeneities occur in the cuticle in an early Devonian plant, where they suggest a structural organisation comparable to modern plants. These results on 400 million years old fossils, validate O-PTIR as a powerful and extremely promising new tool for nanoanalytical palaeontology.

paleontology↗

bioRxiv2024

Tetrapod terrestrialisation: a weight-bearing potential already present in the humerus of the stem-tetrapod fish Eusthenopteron foordi

Our study shows that the von Mises stress, induced by external load on the humerus of Eusthenopteron, dissipates through the cortex, trabeculae and the muscles of the pectoral appendage involved in elevation and protraction. As Eusthenopterons microanatomy is similar to that of Devonian tetrapods, we expect them to share the same process of load dissipation and energy absorption through 1) cortical stress distribution; and 2) longitudinal trabecular conduction. Our FE simulations in hypothetical terrestrial conditions demonstrate that this type of microanatomical architecture could withstand the weight of Tiktaalik proportionally to the size of Eusthenopteron in standing posture. This tubular arrangement, including marrow processes originally involved in long-bone elongation, would have acquired a key secondary biomechanical function to increase the resistance and strength of the cancellous bone to external compressive load. As an exaptation, this specific trabecular architecture may have played a major role in the tetrapod land exploration about 400 million years ago.

paleontology↗

bioRxiv2024

The effects of clay minerals on bacterial community composition during arthropod decay

Fossilization, or the transition of an organism from the biosphere to the geosphere, is a complex mechanism involving numerous biological and geological variables. Bacteria are one of the most significant biotic players to decompose organic matter in natural environments, early on during fossilization. However, bacterial processes are difficult to characterize as many different abiotic conditions can influence bacterial efficiency in degrading tissues. One potentially important variable is the composition and nature of the sediment on which a carcass is deposited after death. We experimentally examined this by decaying the marine shrimp Palaemon varians underwater on three different clay sediments. Samples were then analyzed using 16S ribosomal RNA sequencing to identify the bacterial communities associated with each clay system. Results show that samples decaying on the surface of kaolinite have a lower bacterial diversity than those decaying on the surface of bentonite and montmorillonite, which could explain the limited decay of carcasses deposited on this clay. However, this is not the only role played by kaolinite, as a greater proportion of gram-negative over gram-positive bacteria is observed in this system. Gram-positive bacteria are generally thought to be more efficient at recycling complex polysaccharides such as those forming the body walls of arthropods. This is the first experimental evidence of sediments shaping an entire bacterial community. Such interaction between sediments and bacteria might have contributed to arthropods exquisite preservation and prevalence in kaolinite-rich Lagerstatten of the Cambrian Explosion.

paleontology↗

bioRxiv2024

Diplopoda in the world fossil record

AbstractWe present a comprehensive catalog with an updated database of the fossil record of Diplopoda in the world. Taxonomic data was collected from descriptions and reports published from 1854 to the present. We also include new records from the Lower Miocene Mexican amber, counting 83 unknown fossil inclusions, with the first records of the orders Polyxenida, Platydesmida, and Julida, as well as the families Sphaeriodesmidae and Trichopolydesmidae within Polydesmida. According to our results, Diplopoda comprises 217 fossil records from the Middle Silurian to Upper Pleistocene, representing three subclasses, six superorders, 25 orders, one superfamily, 54 families, 90 genera, and 156 fossil species. To date, no fossils of the order Siphonocryptida have been reported. The fossil record extends over three geological eras: the Paleozoic, with 156 records; the Mesozoic, with 51; and the Cenozoic, with 77. The fossil preservation includes 87 impressions, 68 compressions, 108 amber inclusions, and 19 ichnites. Thus, this catalog allows us to estimate the size and taxonomic composition of Diplopoda in the fossil record worldwide.

paleontology↗

bioRxiv2024

Marine Origin of the Arachnid Brain Reveals Early Divergence of Chelicerata

Fossils from the lower Cambrian provide crucial insights into the diversification of arthropod lineages: Mandibulata, exemplified by centipedes, insects, and crustaceans; and Chelicerata, represented by sea spiders, horseshoe crabs, and arachnids, the last including spiders, scorpions, and ticks1. Two mid-Cambrian genera claimed as stem chelicerates are Mollisonia and Sanctacaris, defined by a carapaced prosoma equipped with clustered limbs, followed by a segmented trunk opisthosoma equipped with appendages for swimming and respiration2-4. Up to the present, the phyletic status of Mollisoniidae and Sanctacariidae has been that of a basal chelicerate2, stemward of Leanchoiliidae, whose neuromorphology resembles that of extant Merostomata (horseshoe crabs)5. Here, we identify preserved traces of neuronal tissues in Mollisonia symmetrica that crucially depart from a merostome organization. Instead, a radiating organization of metameric neuropils occupying most of its prosoma is situated behind a pair of oval unsegmented neuropils directly connected to paired chelicerae extending from the front of the prosoma. The disposition and connections of these neuropils is the neuroanatomical signature that denotes a complete reversal of the three genetically distinct domains defining arthropod brains6. Thus, in Mollisonia the deutocerebrum is the most rostral domain with the proso-and protocerebral domains folded backwards such that tracts from the principal eyes extend caudally to reach their prosocerebral destination. These defining neuromorphological features illuminate a marine origin of Arachnida from which evolved the planets most successful arthropodan predators.

paleontology↗

bioRxiv2024

Hominin brain size increase has emerged from within-species encephalization

The fact that rapid brain size increase was clearly a key aspect of human evolution has prompted many studies focussing on this phenomenon1-4, and many suggestions as to the underlying evolutionary patterns and processes5-10. No study to date has however separated out the contributions of change through time within-vs. between-hominin species whilst simultaneously incorporating effects of body size. Using a phylogenetic approach never applied before to palaeoanthropological data, we show that brain size increase across ~ 7 million years of hominin evolution arose from increases within individual species which account for an observed overall increase in relative brain size. Variation among species in brain size after accounting for this effect is associated with body mass differences but not time. In addition, our analysis also reveals that the within-species trend escalated in more recent lineages, implying an overall pattern of accelerating brain size increase through time.

paleontology↗