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bioRxiv2022

Reconstructing phylogeny of the hornless rhinoceros Aceratheriinae

This study presents the first phylogenetic analysis focused on the Subfamily Aceratheriinae to date, with 391 characters coded from 43 taxa at the species level. We added 77 newly defined and 33 revised characteristics, including features of the skull, teeth, and postcranial bones. In the present analysis, the tribe Teleoceratini, as well as the tribe Aceratheriini, was reclassified within Aceratheriinae, however, the traditionally established monophyly of each tribe was decomposed. Combined with detailed morphological comparisons, we reconstructed the phylogeny of Aceratheriinae and revised the diagnosis of Aceratheriinae. The reported skull and teeth specimens of Turkanatherium from the late Early Miocene indicate that it is not an acerathere and has been placed as a basal rhinocerotid. The Aceratheriinae has undergone evolutionary adaptation several times during the early stage of evolution, and several genera from the Oligocene to the Early Miocene have been reconstructed as early diverging taxa, such as Molassitherium, Protaceratherium, Plesiaceratherium and Chilotheridium; Aprotodon and Mesaceratherium from the Late Oligocene to the Early Miocene were united as the earliest divergent clade of Aceratheriinae; meanwhile, due to the limited materials, the phylogenies of Floridaceras and Dromoceratherium are unstable in this analysis, and both have been tentatively considered as the early diverging clades of Aceratheriinae. Alicornops was reclassified a member of Teleoceratini. Aceratheriini and Teleoceratini have been redefined as two highly specialized groups. Furthermore, Aceratheriini has been divided into two/three clades based on the difference in the skull outlines and the occlusal patterns of the cheek teeth.

paleontology↗

bioRxiv2022

SOCIALITY, COMMUNITIES AND MORPHOLOGICAL FEATURES OF ANTS FROM MID-CRETACEOUS BURMESE AMBER

We consider morphological diversity of ants from mid-Cretaceous Burmese amber. An eco-ethological hypothesis concerning its origin and features of Mesozoic and Cenozoic ant communities is proposed. It appears that some morphological features of representatives of the stem taxa allow us to speak about the absence of effective communication and, subsequently, group foraging in these ants. Therefore, the diversity of primitive Cretaceous ants, as predators, reflects their food specialization according to types of prey, on condition of their social lifestyle, that results in division of the ecological space among ant species into ecological niches. The occurrence of both effective communication and group foraging (mobilization) in the crown ant taxa, as crucial adaptation, has permitted them to exceed the bounds of niches of specialized predators, since type and size of prey are not strictly correlated to size of an ant and its mandibles; it also has given a chance to maintain large colonies. Due to this, myrmecocomplexes of modern ants are arranged on the principle of colonies dominance rather than the principle of division of ecological niches, like Mesozoic.

paleontology↗

bioRxiv2022

A new pterosaur from Skye, Scotland and the early diversification of flying reptiles

The Middle Jurassic was a critical time in pterosaur evolution, witnessing the inception of major morphological innovations that underpinned successive radiations by rhamphorhynchids, basal monofenestratans and pterodactyloids. Frustratingly, this interval is particularly sparsely sampled, with a record consisting almost exclusively of isolated fragmentary remains. Here, we describe new material from the Bathonian-aged Kilmaluag Formation of Skye, Scotland, which helps to close this gap. REDACTED (gen. et sp. nov.) is based on a three-dimensionally preserved partial skeleton, which represents the first associated Middle Jurassic pterosaur. REDACTED is one of the first pterosaurs to be fully digitally prepared and CT scanning reveals multiple elements of the skeleton that remain fully embedded within the matrix, which are otherwise inaccessible. Novel anatomical features of this new Middle Jurassic pterosaur help to confirm the existence of the controversial clade Darwinoptera, greatly clarifying our understanding of Jurassic pterosaur evolution.

paleontology↗

bioRxiv2022

Integrating Fossil Flowers into the Angiosperm Phylogeny using a Total Evidence Approach

Fossil flowers are essential to infer past angiosperm evolutionary processes. The assignment of fossil flowers to extant clades has traditionally relied on morphological similarity and on apomorphies shared with extant taxa. The use of explicit phylogenetic analyses to establish their affinity has so far remained limited. In this study, we built a comprehensive framework to investigate the phylogenetic placement of 24 exceptionally preserved fossil flowers. For this, we assembled a new species-level dataset of 30 floral traits for 1201 extant species that were sampled to represent the stem and crown nodes of all angiosperm families. We explored multiple analytical approaches to integrate the fossils into the phylogeny, including different phylogenetic estimation methods, topological-constrained analyses, and a total evidence approach combining molecular and morphological data of extant and fossil species. Our results were widely consistent across approaches, with minor differences in the support of fossils at different phylogenetic positions. The placement of some fossils is in agreement with previously suggested relationships, but for others, a new placement is indicated. We also identified fossils that are well constrained within particular extant families, whereas others showed high phylogenetic uncertainty. Finally, we present recommendations for future total evidence analyses, regarding the selection of fossils and appropriate methodologies, and provide some perspectives on how to integrate fossils into the investigation of divergence times and the temporal evolution of morphological traits.

paleontology↗

bioRxiv2022

New insights into 4,000 years of resource economy across Greenland using ancient DNA

The success and failure of past cultures across the Arctic was tightly coupled to the ability of past people to exploit the full range of resources available to them, and to adapt to fluctuations in resource availability. There is substantial evidence for the hunting of birds, caribou and a wide range of marine mammals in pre-historic Greenland from bone remains preserved in ancient middens. However, the extent to which these communities relied on marine resources such as fish and large cetaceans is understudied because of the taphonomic processes and bias that affect how these taxa present themselves in the archaeological record. To address this, we analyse DNA from bulk bone samples from 12 archaeological sites across Greenland dating from Paleo-Inuit to Neo-Inuit periods. Using a combination of metabarcoding and shotgun metagenomics we identify an assemblage of 43 species consisting of birds, fish, and both marine and terrestrial mammals. We find genetic evidence of five different whale species, of which the bowhead whale (Balaena mysticetus) was the most commonly detected. Furthermore, we detect nine fish species, of which four have not previously been identified in any of the studied sites. Lastly, we identify a novel haplotype in caribou (Rangifer tarandus) at the 3,000-year-old site Itinnera, suggesting the presence of a distinct lineage of (now extinct) dwarfed caribou that colonised Greenland after the last ice age 9,000 years ago. Collectively, these findings provide a rare insight into whaling and fishing practices in Greenland and demonstrate that prehistoric Greenlandic communities had the social and technological capacity to target the largest whales available in the waters around them.

paleontology↗

bioRxiv2022

Molecular and mineral responses of corals grown under artificial Calcite Sea conditions

The formation of skeletal structures composed of different calcium carbonate polymorphs (aragonite and calcite) appears to be regulated both biologically and environmentally. Among environmental factors influencing aragonite and calcite precipitation, changes in seawater conditions - primarily in the molar ratio of magnesium and calcium during so-called "Calcite" (mMg:mCa below 2) or "Aragonite" seas (mMg:mCa above 2) - have had profound impacts on the distribution and performance of marine calcifiers throughout the Earths history. Nonetheless, the fossil record shows that some species appear to have counteracted such changes and kept their skeleton polymorph unaltered. Here, the aragonitic octocoral Heliopora coerulea and the aragonitic scleractinian Montipora digitata were exposed to Calcite Sea-like mMg:mCa with various levels of changes in magnesium and calcium concentration, and both mineralogical (i.e., CaCO3 polymorph) and gene expression changes were monitored. Both species maintained aragonite deposition at lower mMg:mCa ratios, while concurrent calcite presence was only detected in M. digitata. Despite a strong variability between independent experimental replicates for both species, the expression for a set of putative calcification-related genes, including known components of scleractinian skeleton organic matrix, was found to consistently change at lower mMg:mCa. These results support previously proposed involvements of the skeleton organic matrix in counteracting decreases in seawater mMg:mCa. Although no consistent changes in expression for calcium and magnesium transporters were observed, down-regulation calcium channels in H. coerulea in one experimental replicate and at an mMg:mCa of 2.5 might indicate the possibility of active calcium uptake regulation by the corals under altered mMg:mCa.

paleontology↗

bioRxiv2022

Earliest evidence for frugivory and seed dispersal by birds

The Early Cretaceous diversification of birds was a major event in the history of terrestrial ecosystems, occurring during the earliest phase of the Cretaceous Terrestrial Revolution. Frugivorous birds play an important role in seed dispersal today, and may have done so since their origins. However, evidence of this has been lacking. Jeholornis is one of the earliest-diverging birds, only slightly more derived than Archaeopteryx, but its cranial anatomy has been poorly understood, obscuring diet-related functional interpretations. Originally hypothesised to be granivorous based on seeds preserved as gut contents, this interpretation has become controversial. We conducted high-resolution synchrotron tomography on an exquisitely preserved new skull of Jeholornis, revealing remarkable cranial plesiomorphies combined with a specialised rostrum. We use this to provide a near-complete cranial reconstruction of Jeholornis, and exclude the possibility that Jeholornis was granivorous, based on morphometric analyses of the mandible (3D) and cranium (2D), and comparisons with the 3D alimentary contents of extant birds. We show that Jeholornis was at least seasonally frugivorous, providing the earliest evidence for fruit consumption in birds, and indicating that seed dispersal was present from early in the avian radiation. As highly-mobile seed dispersers, early frugivorous birds could expand the scope for biotic dispersal in plants, and may explain, in part, the subsequent evolutionary expansion of fruits, indicating a potential role of bird-plant interactions in the Cretaceous Terrestrial Revolution.

paleontology↗

bioRxiv2022

A Cambrian soft-bodied conical animal illustrates the origins of lophophorate phyla

The origin and early evolution of lophotrochozoans remain a difficult but crucial issue in reconstructing metazoan phylogeny. Exceptionally preserved fossils have provided hopeful information for resolving this lophotrochozoan problem. Here we identify that Conicula striata, a soft-bodied conical animal from the early Cambrian Chengjiang Lagerstatte, has mosaic characteristics of different lophophorate phyla. C. striata possesses a phoronid-like vermiform trunk housing a U-shaped gut and a coiled lophophore comprising [≥]12 arms with numerous tentacles, but it also bears brachiopod-like features including an undivided mantle enclosing lophophore and a pedicle-like protrusion on annulated trunk. Phylogenetic analysis retrieves C. striata as a total-group lophophorate and as an intermediate taxon between Phoronida and Brachiopoda. This suggests that the bivalved architecture of brachiopods originated from an undivided mantle in a phoronid-like ancestor, and that the ancestral vermiform trunk became reduced during the origin of Brachiopoda, illuminating the origins of body plans in the lophophorate phyla.

paleontology↗

bioRxiv2022

Keratose sponges in ancient carbonates - a problem of interpretation

Increasing current interest in sponge fossils includes numerous reports of diverse vermicular and peloidal structures interpreted as keratose sponges in Neoproterozoic to Mesozoic carbonates and in various open marine to peritidal and restricted settings. Reports of their occurrence are fundamental and far-reaching for understanding microfacies and diagenesis where they occur; and fossil biotic assemblages, as well as wider aspects of origins of animals, sponge evolution/ecology and the systemic recovery from mass extinctions. Keratose sponges: 1) have elaborate spongin skeletons but no spicules, thus lack mineral parts and therefore have poor preservation potential so that determining their presence in rocks requires interpretation; and 2) are presented in publications as interpreted fossil structures almost entirely in two-dimensional (thin section) studies, where structures claimed as sponges comprise diverse layered, network, particulate and amalgamated fabrics involving calcite sparite in a micritic groundmass. There is no verification of sponges in these cases and almost all of them can be otherwise explained; some are certainly not correctly identified. The diversity of structures seen in thin sections may be reinterpreted to include: a) meiofaunal activity; b) layered, possibly microbial (spongiostromate) accretion; c) sedimentary peloidal to clotted micrites; d) fluid escape and capture resulting in birdseye to vuggy porosities; and e) molds of siliceous sponge spicules. Without confirmation of keratose sponges in ancient carbonates, interpretations of their role in ancient carbonate systems, including facies directly after mass extinctions, are unsafe, and alternative explanations for such structures should be considered. This study calls for greater critical appraisal of evidence, to seek confirmation or not, of keratose sponge presence. (259/300 max, for Sedimentology)

paleontology↗

bioRxiv2022

Cuticle and cuticular sensilla in Agnostina

The microstructure of the cuticle of several Agnostina species is described. For the first time, it has been shown that their cuticle consists of three layers: thick outer and transitional layers and a thin inner layer. The layers are made up of stacks of laminae: the laminae in the outer layer are thicker than in the transitional and inner ones. The evolution of the agnostoid cuticle proceeded, apparently, in the direction of decreasing the thickness of the inner layer which in contrast to all other arthropods, is thinner than the outer layer. Apparently, the inner layer was mineralized to a lesser extent than the outer one. In the structure of the cuticle, Agnostina are close to horseshoe crabs and trilobites. On the outer and inner layers, a set of sensilla was revealed; they can be attributed to trichoid, campaniform, and digitiform sensilla (with mechanoreceptor function) and celoconic sensilla (with chemoreceptor function). Also, unique sensorial ensembles were found on cephalons and pygidia; the function of the former is probably mechanosensorial, and the purpose of the latter cannot be assumed on this material.

paleontology↗

bioRxiv2022

Large-bodied ornithomimosaurs inhabited Appalachia during the Late Cretaceous of North America

Reconstructing the evolution, diversity, and paleobiogeography of North Americas Late Cretaceous dinosaur assemblages requires spatiotemporally contiguous data; however, there remains a spatial and temporal disparity in dinosaur data on the continent. The rarity of vertebrate-bearing sedimentary deposits representing Turonian-Santonian ecosystems, and the relatively sparse record of dinosaurs from the eastern portion of the continent, present persistent challenges for studies of North American dinosaur evolution. Here we describe an assemblage of ornithomimosaurian materials from the Santonian Eutaw Formation of Mississippi. Morphological data coupled with osteohistological growth markers suggest the presence of two taxa of different body sizes, including one of the largest ornithomimosaurians known worldwide. The regression predicts a femoral circumference and a body mass of the Eutaw individuals similar to or greater than that of large-bodied ornithomimosaurs, Beishanlong grandis and Gallimimus bullatus. The paleohistology of MMNS VP-6332 demonstrates that the individual was at least 11 years of age (similar to B. grandis [[~]375 kg, 13-14 years old at death]). Additional pedal elements share some intriguing features with ornithomimosaurs yet suggest a larger-body size closer to Deinocheirus mirificus. The presence of a large-bodied ornithomimosaur in this region during this time is consistent with the relatively recent discoveries of early-diverging, large-bodied ornithomimosaurs from mid-Cretaceous strata of Laurasia (Arkansaurus fridayi and B. grandis). The smaller Eutaw taxon is represented by a tibia preserving seven growth cycles, with osteohistological indicators of decreasing growth, yet belongs to an individual with near reaching somatic maturity of the larger taxon, suggesting the co-existence of medium- and large-bodied ornithomimosaur taxa during the Late Cretaceous Santonian of North America. The Eutaw ornithomimosaur materials provide key information on the diversity and distribution of North American ornithomimosaurs and Appalachian dinosaurs and fit with broader evidence of multiple cohabiting species of ornithomimosaurian dinosaurs in Late Cretaceous ecosystems of Laurasia.

paleontology↗

bioRxiv2022

Spinosaurids as 'subaqueous foragers' undermined by selective sampling and problematic statistical inference

Fabbri et al.1 claim that the huge sail-backed dinosaur Spinosaurus aegyptiacus and the spinosaurid Baryonyx were "subaqueous foragers," diving underwater in pursuit of prey, based on their measure of bone "compactness." Using thin-sections and computed tomographic (CT) scans of thigh bone (femur) and trunk rib from various living and extinct vertebrates, they claim to be able to distinguish taxa with "aquatic habits" from others. Their conclusions are undermined by selective bone sampling, inaccuracies concerning spinosaurid bone structure, faulty statistical inferences, and novel redefinition of the term "aquatic."

paleontology↗

bioRxiv2022

Hybridization In The Late Pleistocene: Merging Morphological And Genetic Evidence

This is an exciting time for our understanding of the origin of our species. Previous scientific consensus saw human evolution as defined by adaptive differences (behavioural and/or biological) and the emergence of Homo sapiens as the ultimate replacement of non-modern groups by a modern, adaptively more competitive one. However, recent research has shown that the process underlying our origins was considerably more complex. While archaeological and fossil evidence suggests that behavioural complexity may not be confined to the modern human lineage, recent paleogenomic work shows that gene flow between distinct lineages (e.g. Neanderthals, Denisovans, early H. sapiens) occurred repeatedly in the Late Pleistocene, likely contributing elements to our genetic make-up that might have been crucial to our success as a diverse, adaptable species. Following these advances, the prevailing human origins model has shifted from one of near-complete replacement to a more nuanced view of partial replacement with considerable reticulation. Here we provide a brief introduction to the current genetic evidence for hybridization among hominins, its prevalence in, and effects on, comparative mammal groups, and especially how it manifests in the skull. We then explore the degree to which cranial variation seen in the fossil record of Late Pleistocene hominins from Western Eurasia corresponds with our current genetic and comparative data. We are especially interested in understanding the degree to which skeletal data can reflect admixture. Our findings indicate some correspondence between these different lines of evidence, flag individual fossils as possibly admixed, and suggest that different cranial regions may preserve hybridisation signals differentially. We urge further studies of the phenotype in order to expand our ability to detect the ways in which migration, interaction and genetic exchange have shaped the human past, beyond what is currently visible with the lens of ancient DNA.

paleontology↗

bioRxiv2022

Ancestral Body Plan and Adaptive Radiation of Sauropterygian Marine Reptiles

Mesozoic was the age of reptiles that not only occupied the land and sky but also adapted to the sea. Sauropterygia, from turtle-like placodonts, lizard-like pachypleurosaurs, and predatory nothosaurs to long-necked pistosaurs including plesiosaurs, is one of the most predominant lineages among secondarily aquatic reptiles. However, we know little about the early evolution of sauropterygians involving the morphological gaps among aforementioned sub-groups and their ancestral body-plan, because the Early Triassic fossil remains are scarce shortly after their origin. Here we report a skeleton from the Early Triassic in South China, representing the oldest known complete specimen related to Sauropterygia. It can be referred to Hanosaurus hupehensis and shows a mosaic morphology combining the characters of multiple sauropterygian sub-lineages. We constructed an updated character matrix obtaining the hitherto most comprehensive phylogeny of Triassic sauropterygians, and Hanosaurus hupehensis is stably resolved as the basal-most member of the Sauropterygiformes (clade nov.). Sauropterygians were previously considered using limb propulsion for the movement that is distinguishable from ichthyosaurs and other marine reptiles, but this skeleton reflects an ancestral body plan of sauropterygians unexpectedly developing an elongate trunk and four short limbs, being different from most sauropterygians but more convergently similar to the basal members of other marine reptilian lineages in body shape. After this convergence, we confirm the rapid adaptive radiation of sauropterygiform reptiles following the end-Permian mass extinction. Our results provide an evolutionary framework of sauropterygian marine reptiles and highlight the integrations of both convergences and divergences when an emerging animal lineage arises.

paleontology↗

bioRxiv2022

Sinking a giant: quantitative macroevolutionary comparative methods debunk qualitative assumptions

Myhrvold et al.1 suggest that our inference of subaqueous foraging among spinosaurids2 is undermined by selective bone sampling, inadequate statistical procedures, and use of inaccurate ecological categorizations. Myhrvold et al.1 ignore major details of our analyses and results, and instead choose to portray our inferences as if they were based on qualitative interpretations of our plots, without providing additional analyses to support their claims. In this manuscript, we thoroughly discuss all the concerns exposed by Myhrvold et al.1. Additional analyses based on our original datasets2 and novel data presented by Myhrvold et al.1 do not change our original interpretations: while the spinosaurid dinosaurs Spinosaurus and Baryonyx are recovered as subaqueous foragers, Suchomimus is inferred as a non-diving animal.

paleontology↗

bioRxiv2022

Spatio-temporal diversity of dietary preferences and stress sensibilities of early and middle Miocene Rhinocerotidae from Eurasia: impact of climate changes

Major climatic and ecological changes are documented in terrestrial ecosystems during the Miocene epoch. The Rhinocerotidae are a very interesting clade to investigate the impact of these changes on ecology, as they are abundant and diverse in the fossil record throughout the Miocene. Here, we explored the spatio-temporal evolution of rhinocerotids paleoecology during the early and middle Miocene of Europe and Pakistan. We studied the dental texture microwear (proxy for diet) and enamel hypoplasia (stress indicator) of 19 species belonging to four sub-tribes and an unnamed clade of Rhinocerotidae, and coming from nine Eurasian localities ranging from Mammal Neogene zone (MN) 2 to MN7/8. Our results suggest clear differences in the feeding ecology and thus niche partitioning at Kumbi 4 (MN2, Pakistan), Sansan (MN6, France), and Villefranche dAstarac (MN7/8, France), while overlap of the interpreted diets and subtle variations are discussed for Beon 1 (MN4, France) and Gra[c]anica (MN5/6, Bosnia-Herzegovina). All rhinocerotids studied were interpreted as browsers or mixed-feeders, and none had a grazer nor frugivore diet. The prevalence of hypoplasia was moderate ([~]10%) to high (> 20%) at all localities but Kumbi 4 ([~]6%), and documented quite well the local conditions. For instance, the high prevalence at the close to Miocene Climatic Optimum locality of Beon 1 ([~]26%) has been correlated with periodical droughts, while the moderate ones ([~]10%) at Sansan and Devinska Nova Ves Spalte (Slovakia) both dated from the MN6 (i.e., by the middle Miocene Climatic Transition, ca. 13.9 Mya) were linked to the persistence of sub-tropical local conditions. Besides locality, species and tooth locus were also important factors of variation for the prevalence of hypoplasia. The very large hippo-like Brachypotherium brachypus was one of the most affected species at all concerned localities (but Sansan), whereas early-diverging elasmotheriines were very little affected, suggesting an influence of phylogeny and/or diet in stress susceptibility.

paleontology↗

bioRxiv2022

Sampling biases obscure the early diversification of the largest living vertebrate group

Extant ray-finned fishes (Actinopterygii) dominate marine and freshwater environments, yet their spatiotemporal diversity dynamics following their origin in the Palaeozoic are poorly understood. Previous studies investigate face-value patterns of richness, with only qualitative assessment of potential biases acting on the Palaeozoic actinopterygian fossil record. Here, we investigate palaeogeographic trends and apply richness estimation techniques to a recently-assembled occurrence database for Palaeozoic ray-finned fishes. We reconstruct patterns of local richness of Palaeozoic actinopterygians, alongside sampling standardised estimates of global diversity. We identify substantial fossil record biases, such as geographic bias in the sampling of actinopterygian occurrences centred around Europe and North America. Similarly, estimates of diversity are skewed by extreme unevenness in the abundance distributions of occurrences, reflecting past taxonomic practices and historical biases in sampling. Increasing sampling of poorly represented regions and expanding sampling beyond the literature to include museum collection data will be critical in obtaining accurate estimates of Palaeozoic actinopterygian diversity. In conjunction, applying diversity estimation techniques to well-sampled regional subsets of the global dataset may identify accurate local diversity trends.

paleontology↗

bioRxiv2022

Faunal remains from the Upper Paleolithic site of Nahal Rahaf 2 in the southern Judean Desert, Israel

AO_SCPLOWBSTRACTC_SCPLOWNahal Rahaf 2 (NR2) is an Early Upper Paleolithic (ca. 35 kya) rock shelter in the southern Judean Desert in Israel. Two excavation seasons in 2019 and 2020 revealed a stratigraphical sequence composed of intact archaeological surfaces attributed to the Arkov-Divshon cultural entity of the arid southern Levant. We present the faunal assemblages from the site, which are rare among the desert sites due to preservation problems. Our results suggest that the residents of the site exploited prime adult caprines (Capra cf. Capra ibex), but were also engaged in hunting of gazelles (Gazella cf. Gazella gazella), whose carcasses were selectively transported to the site and processed for within-bone nutrients. Long-range hunting trips are suggested by the body-part selection in relatively small bovids, and by the presence of species representing wetter habitat patches 20-30 km north of the site. The bi-focal emphasis on generalized gazelle and age-specific caprine hunting, is unique among Late Pleistocene sites from the Levant. The proportion of caprines increases through the stratigraphic sequence, suggesting more specialized economy through time and in inverse relations to site use intensity.

paleontology↗