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bioRxiv2020

Micro-XRF study of the troodontid dinosaur Jianianhualong tengi reveals new biological and taphonomical signals

Jianianhualong tengi is a key taxon for understanding the evolution of pennaceous feathers as well as troodontid theropods, and it is known by only the holotype, which was recovered from the Lower Cretaceous Yixian Formation of western Liaoning, China. Here, we carried out a large-area micro-X-Ray fluorescence (micro-XRF) analysis on the holotypic specimen of Jianianhualong tengi via a Brucker M6 Jetstream mobile XRF scanner. The elemental distribution measurements of the specimen show an enrichment of typical bones couponing elements such as S, P and Ca allowing to visualize the fossil structure. Additionally, to this, the bones are enriched in several heavier elements such as Sr, Th, Y and Ce over the surrounding rocks. The enrichment is most likely associated to secondary mineralization and the phosphates from the bones. Interestingly the plumage shape correlates with an enrichment in elements such as Cu, Ni and Ti, consistent with a previous study [1] on Archaeopteryx using synchrotron imaging. The analysis presented here provide new biological and taphonomic information of this fossil. An in-situ and nondestructive micro-XRF analysis is currently the most ideal way to map the chemistry of fossils, so far this is manly restricted to small samples. Larger samples usually required a synchrotron facility for analysis. Our study demonstrated that laboratory-based large-area micro-XRF scanner can provides a practical tool for the study of large large-sized specimens allowing collect full chemical data for a better understanding of evolutionary and taphonomic processes.

paleontology↗

bioRxiv2020

Are local dominance and inter-clade dynamics causally linked when one fossil clade displaces another?

Disputing the supposition that ecological competition drives macroevolutionary patterns is now a familiar goal in many fossil biodiversity studies. But it is an elusive goal, hampered by patchy sampling, few assemblage-level comparative analyses, unverified ecological equivalence of clades and a dearth of appropriate statistical tools. We address these concerns with a fortified and vetted compilation of 40190 fossil species occurrences of cyclostome and cheilostome bryozoans, a canonical example of one taxonomically dominant clade being displaced by another. Dramatic increases in Cretaceous cheilostome genus diversification rates begin millions of years before cheilostomes overtake cyclostomes in local species proportions. Moreover, analyses of origination and extinction rates over 150 Myr suggest that inter-clade dynamics are causally linked to each other, but not to changing assemblage-level proportions. One Sentence SummaryGlobal fossil diversification rates and local taxonomic dominance are not causally linked.

paleontology↗

bioRxiv2020

Extinct species identification from Upper Pleistocene bone fragments not identifiable from their osteomorphological studies by proteomics analysis

The ancient preserved molecules offer the opportunity to gain a better knowledge on the biological past. In recent years, bones proteomics has become an attractive method to study the animal biological origin, extinct species and species evolution as an alternative to DNA analysis which is limited by DNA amplification present in ancient samples and its contamination. However, the development of a proteomic workflow remains a challenge. The analysis of fossils must consume a low quantity of material to avoid damaging the samples. Another difficulty is the absence of genomic data for most of the extinct species. In this study, a proteomic methodology was applied to mammalian bones of 130,000 years old from the earlier Upper Pleistocene site of Scladina Cave (Belgium). Starting from 5 milligram samples, our results show a large majority of detected peptides matching collagen I alpha 1 and alpha 2 proteins with a sequence coverage up to 60%. Using sequence homology with modern sequences, a biological classification was successfully achieved and the associated taxonomic ranks to each bone were identified consistently with the information gained from osteomorphological studies and palaeoenvironmental and palaeodietary data. Among the taxa identified are the Felidae family, Bovinae subfamily, Elephantidae family and the Ursus genus. Amino acid substitutions on the collagens were identified providing new information on extinct species sequences and also helping in taxonomy-based clustering. Considering samples with no osteomorphological information, such as two bone retouchers, proteomics successfully identified the bovidae and ursidae families providing new information to the paleontologists on these objects. Combining osteomorphology studies and amino acid variations identified by proteomics, one retoucher was identified to be potentially from the Ursus spelaeus species.

paleontology↗

bioRxiv2020

Holocephali From The Irati Formation (Parana Basin), Brazil: Origin, Paleogographical And Paleoenvironmental Considerations

The Permian (Cisuralian) Irati Formation, from the Brazilian southeastern Parana Basin bears, at some levels, Chondrichthyes, besides other vertebrates. Outcrops of this unit are frequent at the state of Sao Paulo eastern belt. Two members of the Irati are recognized at this state, Assistencia, the upper, and Taquaral. A sandy facies, mostly at the base of the Taquaral, is noteworthy by the richness of the Chondrichthyes, mainly Holocephali. The Petalodontiformes are the Chondrichthyes most abundant, so far referred to Itapyrodus punctatus. Recent studies of several specimens revealed that some morphotypes must belong to different species of the genus Itapyrodus. Others are akin to this genus, justifying a proposition of an endemic family Itapyrodidae. The presence of this endemic family is an argument, among others, for a proposed isolation of two Brazilan Basins northeast Parnaiba and southeast Parana, during the time of deposition of the Irati, inasmuch as Itapyrodidae are present in both basins.

paleontology↗

bioRxiv2020

A crocodylian-style cloaca in a non-avialan dinosaur

Our knowledge of the reproductive biology of dinosaurs covers a range of aspects, from brooding behaviour to nesting style and the timing of sexual maturity. Yet, the basic anatomy and function of the cloaca in non-avialan dinosaurs remains unknown. Here, we describe the outer morphology of the only known non-avialan dinosaur cloaca, preserved in an exceptional specimen of the early-diverging ceratopsian dinosaur Psittacosaurus. We clarify the position of the cloaca with respect to the ischia and caudal vertebrae and document the scales immediately adjacent to the abdomen and tail. We find that the cloaca is from a near-sexually mature subadult individual and is most similar to the cloaca of crocodylians, to the exclusion of lepidosaurians and birds. However, the sex of SMF R 4970 could not be determined as the cloaca and the rest of the specimen does not yield any sexually dimorphic information. This study highlights the ongoing role of exceptional specimens in providing rare soft tissues that help to bridge longstanding gaps in our knowledge of the basic biology of dinosaurs and other extinct reptiles.

paleontology↗

bioRxiv2020

Exceptional Late Devonian arthropods document the origin of decapod crustaceans

With over 15,000 extant species, Decapoda--or ten-legged crustaceans such as crabs, shrimp, lobsters, and relatives-- are among the most speciose and economically important group of crustaceans. Despite of their diversity, anatomical disparity, and remarkable fossil record extending back to the Late Paleozoic, the origins of Decapoda and their phylogenetic relationships with eumalacostracans remains elusive and inconclusive. Molecular dating suggests that decapods originated in the Late Ordovician (~450 Mya), but no reliable fossil crown groups are found until the Late Devonian. Moreover, there is no consensus on which lineages belong to stem groups, obscuring our understanding of the roots of the ten-legged decapod body plans as a whole, and how they relate to other non-decapod crustaceans. We present new, exceptional fossils from the Late Devonian of Czech Republic and Poland that belong to {dagger}Angustidontida, an odd shrimp-looking crustacean with a combination of anatomical features unlike those of any crown eumalacostracan known--extinct or extant. Our phylogenetic analyses, including representatives of all major lineages of crown eumalacostracans plus {dagger}Angustidontida, identify angustidontids as the only known stem-group decapod, and give hints about the transformation series, polarity of change, and evolutionary pathways leading to the modern decapod body plans seen today.

paleontology↗

bioRxiv2020

Bioarchaeological sex prediction from central Italy using generalized low rank imputation for cross-validated metric craniodental supervised ensemble machine learning with missing data

I use a novel supervised ensemble machine learning approach to verify sex estimation of archaeological skeletons from central Italian bioarchaeological contexts with large amounts of missing data present. Eighteen cranial interlandmark distances and five maxillary metric distances were recorded from n = 240 estimated males and n = 180 estimated females from four locations at Alfedena (600-400 BCE) and two locations at Campovalano (750-200 BCE and 9-11th Century CE). A generalized low rank model (GLRM) was used to impute missing data and 20-fold external stratified cross-validation was used to fit an ensemble of eight machine learning algorithms to six different subsets of the data: 1) the face, 2) vault, 3) cranial base, 4) combined face/vault/base, 5) dentition, and 6) combined cranianiodental. Area under the receiver operator characteristic curve (AUC) was used to evaluate the predictive performance of six constituent algorithms, the discrete algorithmic winner(s), and the SuperLearner weighted ensembles classification of males and females from these six bony regions. This approach is useful for predicting male/female sex from central Italy. AUC for the combined craniodental data was the highest (0.9722), followed by the combined cranial data (0.9644), the face (0.9426), vault (0.9116), base (0.9060), and dentition (0.7421). Cross-validated ensemble machine learning of cranial and dental data shows strong potential for estimating sex in the bioarchaeological record and can contribute additional perspectives to help refine our understanding of human sex estimation. Additionally, GLRMs have the potential to handle missing data in ways previously unexplored in the discipline. The main limitation is that the biological sexes of the individuals estimated in this study are not certain, but were estimated macroscopically using common bioarchaeological methods. However, these methods show great promise for estimation of sex in bioarchaeological and forensic contexts and should be investigated on known-sex reference samples for confirmation.

paleontology↗

bioRxiv2020

Pushing Raman spectroscopy over the edge: purported signatures of organic molecules in fossils are instrumental artefacts

Claims for the widespread preservation of fossilized biomolecules in many fossil animals have recently been reported in six studies, based on Raman microspectroscopy. Here, we show that the putative Raman signatures of organic compounds in these fossils are actually instrumental artefacts resulting from intense background luminescence. Raman spectroscopy relies upon the detection of photons scattered inelastically by matter as a result of its interaction with a laser beam. For many natural materials, this interaction also generates a luminescence signal that is often orders of magnitude more intense than the light produced by Raman scattering. Such luminescence, coupled with the transmission properties of the spectrometer, induced quasi-periodic ripples in the measured spectra that have been incorrectly interpreted as Raman signatures of organic molecules. Although several analytical strategies have been developed to overcome this common issue, Raman microspectroscopy as used in the studies questioned here cannot be used to identify fossil biomolecules.

paleontology↗

bioRxiv2020

Dietary and body mass reconstruction of the Miocene neotropical bat Notonycteris magdalenensis (Phyllostomidae) from La Venta, Colombia

The middle Miocene La Venta bat fauna is the most diverse bat palaeocommunity in South America, with at least 14 species recorded. They include the oldest plant-visiting bat in the New World, and some of the earliest representatives of the extant families Phyllostomidae, Thyropteridae and Noctilionidae. La Ventas Notonycteris magdalenensis is an extinct member of the subfamily Phyllostominae, a group of modern Neotropical animalivorous and omnivorous bats, and is commonly included in studies of the evolution of Neotropical bats, but aspects of its biology remain unclear. In this study, we used a multivariate dental topography analysis (DTA) to reconstruct the likely diet of N. magdalenensis by quantitatively comparing measures of molar complexity with that of 25 modern phyllostomid and noctilionid species representing all major dietary habits in bats. We found clear differences in molar complexity between dietary guilds, indicating that DTA is potentially an informative tool to study bat ecomorphology. Our results suggest N. magdalenensis was probably an omnivore or insectivore, rather than a carnivore like its modern relatives Chrotopterus auritus and Vampryum spectrum. Also, we reconstructed the body mass of N. magdalenensis to be [~]50 g, which is larger than most insectivorous bats, but smaller than most carnivorous bats. Our results confirm that Notonycteris magdalenensis was probably not a specialised carnivore. It remains to be demonstrated that the specialised carnivory ecological niche was occupied by the same lineage of phyllostomines from at least the middle Miocene. Combining our diet and body mass reconstructions, we suggest that N. magdalenensis exhibits morphological pre-adaptations crucial for the evolution of specialised carnivory.

paleontology↗

bioRxiv2020

The first dinosaur egg remains a mystery

A recent study by Norell et al. (2020) described new egg specimens for two dinosaur species, identified as the first soft-shelled dinosaur eggs. The authors used phylogenetic comparative methods to reconstruct eggshell type in a sample of reptiles, and identified the eggs of dinosaurs and archosaurs as ancestrally soft-shelled, with three independent acquisitions of a hard eggshell among dinosaurs. This result contradicts previous hypotheses of hard-shelled eggs as ancestral to archosaurs and dinosaurs. Here we estimate the ancestral condition for dinosaur and archosaur eggs by reanalyzing the original data from Norell et al. and that from a recent study on reptile eggshells (Legendre et al., 2020) with the addition of these new dinosaur specimens. We show that the recovery of dinosaur eggs as ancestrally soft-shelled is conditioned by the discretization of a continuous character (eggshell thickness), the exclusion of turtle outgroups from the original sample, and a lack of branch length information. When using a larger sample, calibrated trees, and a definition of hard-shelled eggs referencing their unique prismatic structure, we recover dinosaur and archosaur eggs as either hard-shelled or uncertain (i.e. equal probability for hard- and soft-shelled). This remaining ambiguity is due to uncertainty in the assessment of eggshell type in two dinosaur species, i.e. [~]1% of the total sample. We conclude that more reptile egg specimens and a strict comparative framework are necessary to decipher the evolution of dinosaur eggs in a phylogenetic context.

paleontology↗

bioRxiv2020

Revisiting the phosphorite deposit of Fontanarejo (central Spain): new window into the early Cambrian evolution of sponges and into the microbial origin of phosphorites

Fossils within early Cambrian phosphorites worldwide are often well preserved due to early diagenetic permineralization. Here, we examine the fossil record contained within phosphorites of the Lower Cambrian Pusa Formation (late Fortunian to Cambrian Stage 2) in Fontanarejo, central Spain. The sedimentology and age of these phosphorites have been controversial and are here reviewed and discussed, providing also a updated geological map. The Pusa Formation is composed of fine clastic sediments that are partly turbiditic, with channels of quartz-rich conglomerates and abundant phosphorites in the upper part of the succession. The microfacies and mineralogy of these channel deposits are studied here for the first time in detail, showing that they are mainly composed of subspherical apatite clasts, with minor mudstone intraclasts, quartzite and mica grains. Numerous sponge spicules, as well as entirely preserved hexactinellid sponges and demosponges, were collected within these phosphorites and likely represent stem groups. In addition to sponges, other fossils, such as small shelly fossils (SSF) of the mollusk Anabarella sp., were found. The phosphorites exhibit multiple evidence of intense microbial activity, including diverse fabrics (phosphatic oncoidal-like microbialites, thrombolites, stromatolites, and cements) and abundant fossils of filamentous microbes that strongly resemble sulfur oxidizing bacteria. Our findings strongly suggest that microbial processes mediated the rapid formation of most of the Fontanarejo apatite, probably accounting for the exceptional preservation of fragile fossils such as sponge skeletons. The apparent presence of taxonomically diverse hexactinellid and demosponge communities by the lowermost Cambrian further corroborates a Precambrian origin of the phylum Porifera.

paleontology↗

bioRxiv2020

Tooth size apportionment, Bayesian inference, and the phylogeny of Homo naledi

This study has three main objectives--two methodological and one summative, namely, further characterization of Homo naledi ([~]335-236 ka) to more firmly establish its evolutionary history. Using mathematically-corrected mesiodistal and buccolingual crown dimensions, the species was compared with samples of Pan troglodytes, Australopithecus africanus, A. afarensis, Paranthropus robustus, P. boisei, H. habilis, H. ergaster, H. erectus, H. heidelbergensis, H. neanderthalensis, and H. sapiens; the correction yields equivalently scaled samples unaffected by significant interspecific size differences. After initial cluster analysis, the data were used in tooth size apportionment analysis to determine how size is distributed relatively in each species dentition, while visualizing this variation in a sample scatterplot. The first main objective then, after quantitative coding, is evaluating the utility of these characters to estimate phylogenetic relationships, here using Bayesian inference with an Mkv model. The second objective, for the first time in paleoanthropological study, is estimating relationships using continuous characters, i.e., the scaled data, through Bayesian inference under a Brownian-motion model. This strategy facilitates maximum reception of potential phylogenetic signal. The final objective based on all analyses, though principally continuous Bayesian inference, is to elucidate the phylogeny of H. naledi. Relationships are largely congruent across methods and, with markedly higher node support, most of those inferred in prior systematic studies using qualitatively discretized traits. The present results place H. naledi as a sister taxon to H. habilis (node support [~]70-99%), with a plesiomorphic pattern of relative tooth size. It is nested within a clade comprising australopiths and early Homo dating 3.3 Ma to [~]800 ka, distinct from younger H. erectus through H. sapiens. This suggests that H. naledi originated well before the geological date range associated with the Dinaledi Chamber, from which the remains in this study were recovered, to represent a long-lived side branch in the genus.

paleontology↗

bioRxiv2021

Comparing frontal inclination angles measured from digital 3D models and 2D photographs of dry male and female crania from Croatia

The frontal bone is one of the sexually dimorphic elements of the human skull that can be used for sex estimation of unidentified human remains. Numerous morphological features of the frontal bone, such as its angle of inclination, maximum anterior projection (glabella), and rounded elevations (frontal eminences) have been shown to differ between males and females. Various approaches have been developed to assess the frontal inclination in particular, and recently a method has been proposed where the angle of the frontal slope is measured from snapshots of digital three-dimensional (3D) models of human crania. However, as 3D-based investigations of skeletal material can be time-consuming and expensive, we here compare measurements of frontal angle inclination from 3D model snapshots to measurements from 2D photographs for a large sample (61 females and 61 males) of dry archaeological crania from medieval Croatia. Although angles measured from 3D snapshots and 2D photographs produced discriminant functions that classified crania by sex with similar accuracy (around 73%), the angles recorded from the 2D photographs were systematically one degree smaller than the angles recorded from the 3D images. Thus, even though both data sets were useful for sex estimation, we conclude that angles measured with the two different techniques should not be combined.

paleontology↗

bioRxiv2021

Sexual dimorphism in mastoid process volumes measured from 3D models of dry crania from medieval Croatia

3D analysis of skeletal volumes has become an important field in digital anthropology studies. The volume of the mastoid process has been proposed to display significant sexual dimorphism, but it has a complex shape and to date no study has quantified the full mastoid volume for sex estimation purposes. In this study we compared three different ways to isolate the volume of the mastoid process from digital 3D models of dry crania, and then evaluated the performance of the three different volume definitions for sex estimation purposes. A total of 170 crania (86 male, 84 females) excavated from five medieval Croatian sites were CT-scanned and used to produce 3D stereolitographic models. The three different isolation techniques were based on various anatomical landmarks and planes, as well as the anatomy of the mastoid process itself. Measurements of the three different mastoid volumes yielded different accuracies and precisions. Interestingly, anatomical structures were sometimes more useful than classical landmarks as demarcators of mastoid volume. For all three volume definitions, male mastoid volumes were significantly larger than female volumes, in both relative and absolute numbers. Sex estimation based on mastoid volume showed a slightly higher precision and better accuracy (71 % correct classifications) than visual scoring techniques (67 %) and linear distance measurements (69 %) of the mastoid process. Sex estimation based on cranial size performed even better (78 %), and multifactorial analysis (skull size + mastoid volume) reached up to 81% accuracy. These results show that measurements of the mastoid volume represent a promising metric to be used in multifactorial approaches for sex estimation of human remains.

paleontology↗

bioRxiv2021

Differential taphonomic effects of petroleum seeps and karstic sinkholes on ancient dire wolf teeth: Hydrocarbon impregnation preserves fossils for chemical and histological analysis

Histological analysis of teeth can yield information on an organisms growth and development, facilitating investigations of diet, health, environment, and long-term responses to selective pressures. In the Americas, an extraordinary abundance of Late Pleistocene fossils including teeth has been preserved in petroleum seeps, constituting a major source of information about biotic changes and adaptations at the end of the last glacial period. However, the usefulness of these fossils for histological studies is unclear, due to the unknown taphonomic effects of long-term deposition in petroleum. Here, we compare histological and chemical analyses on dire wolf (Canis dirus) teeth obtained from two different environments, i.e. a petroleum seep (Rancho La Brea tar pits, California) and a carstic sinkhole (Cutler Hammock sinkhole, Florida). Optical and scanning electron microscopy (SEM) together with X-ray diffraction (XRD) analysis revealed excellent preservation of dental microstructure in the seep sample, and the petroleum-induced discoloration was found not to interfere with the histological and chemical examination. By comparison, teeth from the sinkhole sample showed severe degradation and contamination of the dentine by exogenous substances. These results indicate that petroleum seep assemblages are useful, or even ideal, environments for preserving the integrity of fossil material for chemical and histological analysis.

paleontology↗

bioRxiv2021

Rhizoliths identified as prehistoric filing tools for fishhook production on San Nicolas Island, California

Chemical analysis of archeological objects can provide important clues about their purpose and function. In this study, we used scanning electron microscopy (SEM) and chemical spectroscopy (SEM-EDS and XRD) to identify a white residue present on cylindrical rhizoliths from a component at an archaeological site (CA-SNI-25) on San Nicolas Island, California, dated ca. AD 1300 to 1700. The residue was found to consist of biogenic calcite and aragonite particles, different in composition and morphology from the CaCO3 particles in the rhizoliths, but identical to marine shell material. These results, together with observations of surface micro-wear patterning on fishhooks and rhizoliths, replicative experiments, in situ spatial analysis, and other archaeological evidence, show that rhizoliths were used as files in a larger tool kit for crafting shell fishhooks. Our findings shed new light on the technological innovations devised by Native Americans to exploit the rich marine resources surrounding the Channel Islands, and provide the first analytical evidence for the use of rhizoliths as a production tool.

paleontology↗

bioRxiv2021

The extinction and survival of sharks across the end-Cretaceous mass extinction

Sharks (Selachimorpha) are iconic marine predators that have survived multiple mass extinctions over geologic time. Their fossil record is represented by an abundance of teeth, which traditionally formed the basis for reconstructing large-scale diversity changes among different selachimorph clades. By contrast, corresponding patterns in shark ecology, as measured through morphological disparity, have received comparatively limited analytical attention. Here, we use a geometric morphometric approach to comprehensively examine the dental morphology of multiple shark lineages traversing the catastrophic end-Cretaceous mass extinction -- this event terminated the Mesozoic Era 66 million years ago. Our results show that selachimorphs maintained virtually static levels of dental disparity in most of their constituent clades during the Cretaceous/Paleogene transition. Nevertheless, selective extinctions did impact on apex predator lineages characterized by triangular blade-like teeth, and in particular, lamniforms including the dominant Cretaceous anacoracids. Other groups, such as, triakid carcharhiniforms, squalids, and hexanchids, were seemingly unaffected. Finally, while some lamniform lineages experienced morphological depletion, others underwent a post-extinction disparity increase, especially odontaspidids, which are typified by narrow-cusped teeth adapted for feeding on fishes. This disparity shift coincides with the early Paleogene radiation of teleosts, a possible prey source, as well as the geographic relocation of shark disparity hotspots, perhaps indicating a regionally disjunct pattern of extinction recovery. Ultimately, our study reveals a complex morphological response to the end-Cretaceous mass extinction event, the dynamics of which we are only just beginning to understand.

paleontology↗

bioRxiv2021

Validation of biosignatures confirms the informative nature of fossil organic Raman spectra

Raman spectroscopy has facilitated rapid progress in the understanding of patterns and processes associated with biomolecule fossilization and revealed the preservation of biological and geological signatures in fossil organic matter. Nonetheless six large-scale statistical studies of Raman spectra of carbonaceous fossils, selected from a number of independent assessments producing similar trends, have been disputed. Alleon et al. (21) applied a wavelet transform analysis in an unconventional way to identify frequency components contributing to two baselined spectra selected from these studies and claimed similarities with a downloaded edge filter transmission spectrum. On the basis of indirect comparisons and qualitative observations they argued that all spectral features detected, including significant mineral peaks, can be equated to edge filter ripples and are therefore artefactual. Alleon et al. (21) extrapolated this conclusion to dispute not only the validity of n>200 spectra in the studies in question, but also the utility of Raman spectroscopy, a well established method, for analysing organic materials in general. Here we test the claims by Alleon et al. (21) using direct spectral comparisons and statistical analyses. We present multiple independent lines of evidence that demonstrate the original, biologically and geologically informative nature of the Raman spectra in question. We demonstrate that the methodological approach introduced by Alleon et al. (21) is unsuitable for assessing the quality of spectra and identifying noise within them. Statistical analyses of large Raman spectral data sets provide a powerful tool in the search for compositional patterns in biomaterials and yield invaluable insights into the history of life.

paleontology↗