Comparative isotope ecology of western Amazonian rainforest mammals.

Closed-canopy rainforests are important for climate (influencing atmospheric circulation, albedo, carbon storage, etc.) and ecology (harboring the highest biodiversity of continental regions). Of all rainforests, Amazonia is the world's most diverse, including the highest mammalian species richness. However, little is known about niche structure, ecological roles, and food resource partitioning of Amazonian mammalian communities over time. Through analyses of δ13Cbioapatite, δ13Chair, and δ15Nhair, we isotopically characterized aspects of feeding ecology in a modern western Amazonian mammalian community in Peru, serving as a baseline for understanding the evolution of Neotropical rainforest ecosystems. By comparing these results with data from equatorial Africa, we evaluated the potential influences of distinct phylogenetic and biogeographic histories on the isotopic niches occupied by mammals in analogous tropical ecosystems. Our results indicate that, despite their geographical and taxonomic differences, median δ13Cdiet values from closed-canopy rainforests in Amazonia (-27.4‰) and equatorial Africa (-26.9‰) are not significantly different, and that the median δ13Cdiet expected for mammalian herbivores in any closed-canopy rainforest is -27.2‰. Amazonian mammals seem to exploit a narrower spectrum of dietary resources than equatorial African mammals, however, as depicted by the absence of highly negative δ13Cdiet values previously proposed as indicative of rainforests (<-31‰). Finally, results of keratin and bioapatite δ13C indicate that the predictive power of trophic relationships, and traditional dietary ecological classifications in bioapatite-protein isotopic offset expectations, must be reconsidered.

Arothron: An R package for geometric morphometric methods and virtual anthropology applications.

OBJECTIVES: The statistical analysis of fossil remains is essential to understand the evolution of the genus Homo. Unfortunately, the human fossil record is straight away scarce and plagued with severe loss of information caused by taphonomic processes. The recently developed field of Virtual Anthropology helps to ameliorate this situation by using digital techniques to restore damaged and incomplete fossils. MATERIALS AND METHODS: We present the package Arothron, an R software suite meant to process and analyze digital models of skeletal elements. Arothron includes tools to digitally extract virtual cavities such as cranial endocasts, to statistically align disarticulated or broken bony elements, and to visualize local variations between surface meshes and landmark configurations. RESULTS: We describe the main functionalities of Arothron and illustrate their usage through reproducible case studies. We describe a tool for segmentation of skeletal cavities by showing its application on a malleus bone, a Neanderthal tooth, and a modern human cranium, reproducing their shape and calculating their volume. We illustrate how to digitally align a disarticulated model of a modern human cranium, and how to combine piecemeal shape information on individual specimens into one. In addition, we present useful visualization tools by comparing the morphological differences between the right hemisphere of the Neanderthal and the modern human brain. CONCLUSIONS: The Arothron R package is designed to study digital models of fossil specimens. By using Arothron, scientists can handle digital models with ease, investigate the inner morphology of 3D skeletal models, gain a full representation of the original shapes of damaged specimens, and compare shapes across specimens.

A new three-dimensional geometric morphometrics analysis of the Ouranopithecus macedoniensis cranium (Late Miocene, Central Macedonia, Greece).

OBJECTIVES: This study aims to virtually reconstruct the deformed face (XIR-1) and maxilla (RPl-128) of the Late Miocene hominoid Ouranopithecus macedoniensis from Greece, through the application of mirror-imaging and segmentation. Additionally, analysis was conducted through 3D geometric morphometrics, utilizing a comparative sample of fossil hominoids, extant great apes (Gorilla, Pan, and Pongo) and humans, so as to explore shape variation and phenetic similarities between them. MATERIALS AND METHODS: High-resolution computed tomography was used to create digital representations of the XIR-1 and RPl-128 specimens. The virtual reconstruction of the XIR-1 cranium was achieved by mirror-imaging, while the RPl-128 maxilla was virtually segmented and reattached in a correct anatomical position. Anatomical landmarks were registered in three dimensions on a comparative sample of adult crania of extant great apes, humans and fossil hominoids. The data were processed with Procrustes superimposition and analyzed using multivariate statistics methods. RESULTS: Results show that Ouranopithecus macedoniensis falls within or close to the Gorilla convex hull in the principal component analyses, and it is closer to the mean Procrustes shape distance of primarily Gorilla. Both specimens, XIR-1 and RPl-128, are classified as Gorilla based on discriminant function analyses. DISCUSSION: The results of our geometric morphometrics analyses indicate that Ouranopithecus macedoniensis is morphologically more similar to Gorilla than to Homo, Pan, or Pongo, results that can contribute to the evaluation of existing hypotheses about its phylogenetic position.

Inner tooth morphology of Homo erectus from Zhoukoudian. New evidence from an old collection housed at Uppsala University, Sweden.

Locality 1, in the Lower Cave of the Zhoukoudian cave complex, China, is one of the most important Middle Pleistocene paleoanthropological and archaeological sites worldwide, with the remains of c. 45 Homo erectus individuals, 98 mammalian taxa, and thousands of lithic tools recovered. Most of the material collected before World War II was lost. However, besides two postcranial elements rediscovered in China in 1951, four human permanent teeth from the 'Dragon Bone Hill,' collected by O. Zdansky between 1921 and 1923, were at the time brought to the Paleontological Institute of Uppsala University, Sweden, where they are still stored. This small sample consists of an upper canine (PMU 25719), an upper third molar (PMU M3550), a lower third premolar crown (PMU M3549), and a lower fourth premolar (PMU M3887). Some researchers have noted the existence of morpho-dimensional differences between the Zhoukoudian and the H. erectus dental assemblage from Sangiran, Java. However, compared to its chrono-geographical distribution, the Early to Middle Pleistocene dental material currently forming the Chinese-Indonesian H. erectus hypodigm is quantitatively meager and still poorly characterized for the extent of its endostructural variation. We used micro-focus X-ray tomography techniques of virtual imaging coupled with geometric morphometrics for comparatively investigating the endostructural conformation (tissue proportions, enamel thickness distribution, enamel-dentine junction morphology, pulp cavity shape) of the four specimens stored in Uppsala, all previously reported for their outer features. The results suggest the existence of time-related differences between continental and insular Southeast Asian dental assemblages, the Middle Pleistocene Chinese teeth apparently retaining an inner signature closer to the likely primitive condition represented by the Early Pleistocene remains from Java, while the Indonesian stock evolved toward tooth structural simplification.

Synchrotron X-ray imaging of a dichasium cupule of Castanopsis from Eocene Baltic amber.

PREMISE OF THE STUDY: The Eocene Baltic amber deposit represents the largest accumulation of fossil resin worldwide, and hundreds of thousands of entrapped arthropods have been recovered. Although Baltic amber preserves delicate plant structures in high fidelity, angiosperms of the "Baltic amber forest" remain poorly studied. We describe a pistillate partial inflorescence of Castanopsis (Fagaceae), expanding the knowledge of Fagaceae diversity from Baltic amber. METHODS: The amber specimen was investigated using light microscopy and synchrotron-radiation-based X-ray micro-computed tomography (SRµCT). KEY RESULTS: The partial inflorescence is a cymule, consisting of an involucre of scales that surround all four pistillate flowers, indicating a dichasium cupule. Subtending bracts are basally covered with peltate trichomes. Flowers possess an urecolate perianth of six nearly free lobes, 12 staminodia hidden by the perianth, and a tri-locular ovary that is convex-triangular in cross section. The exceptional three-dimensional preservation suggests that the fossil belongs to the extant East Asian genus Castanopsis. The amber inclusion represents the first record of Castanopsis from Baltic amber and the first pistillate inflorescence of Fagaceae from Eurasia. CONCLUSIONS: The partial female inflorescence reported here provides an important addition to acorns of Castanopsis described from middle Eocene strata of Europe. Furthermore, the intercontinental distribution of Castanopsis in the Eocene is confirmed. The amber fossil also broadens the picture of the Baltic amber source area, indicating oligotrophic, sandy, bog-like habitats. Finally, this study underscores the great benefit of SRµCT as a powerful tool to investigate plant inclusions from amber in a nondestructive way.

The effects of cracks on the quantification of the cancellous bone fabric tensor in fossil and archaeological specimens: a simulation study.

Cancellous bone is very sensitive to its prevailing mechanical environment, and study of its architecture has previously aided interpretations of locomotor biomechanics in extinct animals or archaeological populations. However, quantification of architectural features may be compromised by poor preservation in fossil and archaeological specimens, such as post mortem cracking or fracturing. In this study, the effects of post mortem cracks on the quantification of cancellous bone fabric were investigated through the simulation of cracks in otherwise undamaged modern bone samples. The effect on both scalar (degree of fabric anisotropy, fabric elongation index) and vector (principal fabric directions) variables was assessed through comparing the results of architectural analyses of cracked vs. non-cracked samples. Error was found to decrease as the relative size of the crack decreased, and as the orientation of the crack approached the orientation of the primary fabric direction. However, even in the best-case scenario simulated, error remained substantial, with at least 18% of simulations showing a > 10% error when scalar variables were considered, and at least 6.7% of simulations showing a > 10° error when vector variables were considered. As a 10% (scalar) or 10° (vector) difference is probably too large for reliable interpretation of a fossil or archaeological specimen, these results suggest that cracks should be avoided if possible when analysing cancellous bone architecture in such specimens.

Quantifying the impact of µCT-scanning of human fossil teeth on ESR age results.

Fossil human teeth are nowadays systematically CT-scanned by palaeoanthropologists prior to any further analysis. It has been recently demonstrated that this noninvasive technique has, in most cases, virtually no influence on ancient DNA preservation. However, it may have nevertheless an impact on other techniques, like Electron Spin Resonance (ESR) dating, by artificially ageing the apparent age of the sample. To evaluate this impact, we µCT-scanned several modern enamel fragments following the standard analytical procedures employed by the Dental Anthropology Group at CENIEH, Spain, and then performed ESR dose reconstruction for each of them. The results of our experiment demonstrate that the systematic high-resolution µCT-scanning of fossil hominin remains introduces a nonnegligible X-ray dose into the tooth enamel, equivalent to 15-30 Gy depending on the parameters used. This dose may be multiplied by a factor of ∼8 if no metallic filter is used. However, this dose estimate cannot be universally extrapolated to any µCT-scan experiment but has instead to be specifically assessed for each device and set of parameters employed. The impact on the ESR age results is directly dependent on the magnitude of the geological dose measured in fossil enamel but could potentially lead to an age overestimation up to 40% in case of Late Pleistocene samples, if not taken into consideration.

Absorption and Phase Contrast X-Ray Imaging in Paleontology Using Laboratory and Synchrotron Sources.

X-ray micro-computed tomography (µCT) is commonly used for imaging of samples in biomedical or materials science research. Owing to the ability to visualize a sample in a nondestructive way, X-ray µCT is perfectly suited to inspect fossilized specimens, which are mostly unique or rare. In certain regions of the world where important sedimentation events occurred in the Precambrian geological time, several fossilized animals are studied to understand questions related to their origin, environment, and life evolution. This article demonstrates the advantages of applying absorption and phase-contrast CT on the enigmatic fossil Corumbella werneri, one of the oldest known animals capable of building hard parts, originally discovered in Corumbá (Brazil). Different tomographic setups were tested to visualize the fossilized inner structures: a commercial laboratory-based µCT device, two synchrotron-based imaging setups using conventional absorption and propagation-based phase contrast, and a commercial X-ray microscope with a lens-coupled detector system, dedicated for radiography and tomography. Based on our results we discuss the strengths and weaknesses of the different imaging setups for paleontological studies.

Cranial anatomy of the Duchesnean primate Rooneyia viejaensis: new insights from high resolution computed tomography.

Rooneyia viejaensis is a North American Eocene primate of uncertain phylogenetic affinities. Although the external cranial anatomy of Rooneyia is well studied, various authors have suggested that Rooneyia is a stem haplorhine, stem strepsirrhine, stem tarsiiform, or stem anthropoid. Here we describe the internal cranial anatomy of the Rooneyia holotype based on micro-computed tomography and discuss the phylogenetic implications of this anatomy. Precise measurements of the natural endocast filling the braincase of the Rooneyia holotype reveal that the genus had a relative brain size comparable to some living callitrichines and strepsirrhines. Rooneyia was thus probably more encephalized than any other known omomyiform, adapiform, or plesiadapiform. Relative olfactory bulb size in Rooneyia was most comparable to some living strepsirrhines and the stem anthropoid Parapithecus. The nasal fossa of Rooneyia resembled that of living strepsirrhines in retaining an obliquely oriented nasolacrimal canal, four ethmoturbinals, and an olfactory recess separated from the nasopharyngeal meatus by a transverse lamina. The ear region of Rooneyia is characterized by large and complete canals for both the stapedial and promontory branches of the internal carotid artery. Rooneyia also retains a patent parotic fissure and thus had an extrabullar origin of the stapedius muscle. In most of these respects, Rooneyia exhibits the condition that is presumed to be primitive for crown primates and lacks a number of key crown haplorhine synapomorphies (e.g., a dorso-ventrally oriented nasolacrimal canal, loss of the olfactory recess, loss of ethmoturbinals 3-4, loss or extreme reduction of the stapedial canal due to involution of the stapedial artery). These data are consistent with the hypothesis that Rooneyia is an advanced stem primate or a basal crown primate but are inconsistent with prior suggestions that Rooneyia is a crown haplorhine.

The late Early Pleistocene human dental remains from Uadi Aalad and Mulhuli-Amo (Buia), Eritrean Danakil: macromorphology and microstructure.

Fieldwork performed during the last 15 years in various Early Pleistocene East African sites has significantly enlarged the fossil record of Homo erectus sensu lato (s.l.). Additional evidence comes from the Danakil Depression of Eritrea, where over 200 late Early to early Middle Pleistocene sites have been identified within a ∼1000 m-thick sedimentary succession outcropping in the Dandiero Rift Basin, near Buia. Along with an adult cranium (UA 31), which displays a blend of H. erectus-like and derived morpho-architectural features and three pelvic remains, two isolated permanent incisors (UA 222 and UA 369) have also been recovered from the 1 Ma (millions of years ago) Homo-bearing outcrop of Uadi Aalad. Since 2010, our surveys have expanded to the nearby (4.7 km) site of Mulhuli-Amo (MA). This is a fossiliferous area that has been preliminarily surveyed because of its exceptional concentration of Acheulean stone tools. So far, the site has yielded 10 human remains, including the unworn crown of a lower permanent molar (MA 93). Using diverse analytical tools (including high resolution µCT and µMRI), we analysed the external and internal macromorphology and microstructure of the three specimens, and whenever possible compared the results with similar evidence from early Homo, H. erectus s.l., H. antecessor, H. heidelbergensis (from North Africa), Neanderthals and modern humans. We also assessed the UA 369 lower incisor from Uadi Aalad for root completion timing and showed that it compares well with data for root apex closure in modern human populations.

Enamel thickness variation of deciduous first and second upper molars in modern humans and Neanderthals.

Enamel thickness and dental tissue proportions have been recognized as effective taxonomic discriminators between Neanderthal and modern humans teeth. However, most of the research on this topic focused on permanent teeth, and little information is available for the deciduous dentition. Moreover, although worn teeth are more frequently found than unworn teeth, published data for worn teeth are scarce and methods for the assessment of their enamel thickness need to be developed. Here, we addressed this issue by studying the 2D average enamel thickness (AET) and 2D relative enamel thickness (RET) of Neanderthal and modern humans unworn to moderately worn upper first deciduous molars (dm(1)s) and upper second deciduous molars (dm(2)s). In particular, we used 3D µCT data to investigate the mesial section for dm(1)s and both mesial and buccal sections for dm(2)s. Our results confirmed previous findings of an Neanderthal derived condition of thin enamel, and thinner enamel in dm(1)s than dm(2)s in both Neanderthal and modern humans. We demonstrated that the Neanderthal 2D RET indices are significantly lower than those of modern humans at similar wear stages in both dm(1)s and dm(2)s (p < 0.05). The discriminant analysis showed that using 2D RET from dm(1) and dm(2) sections at different wear stages up to 93% of the individuals are correctly classified. Moreover, we showed that the dm(2) buccal sections, although non-conventionally used, might have an advantage on mesial sections since they distinguish as well as mesial sections but tend to be less worn. Therefore, the 2D analysis of enamel thickness is suggested as a means for taxonomic discrimination between modern humans and Neanderthal unworn to moderately worn upper deciduous molars.

Combining radiographic and histological data for dental development to compare growth in the past and the present.

BACKGROUND: Being able to estimate the age at death of fossil hominins enables meaningful comparisons of both dental and general growth, past and present. AIM: The aim of this study was to use data for modern permanent canine formation derived from separate histological and radiographic studies to estimate the age at death of an early African Homo erectus specimen (KNM-WT 15 000) with a developing permanent maxillary canine. METHODS: Ground sections of 18 sexed modern human canines were used to reconstruct growth in tooth height along the enamel-dentine junction (EDJ) and onwards into root formation along the cement-dentine junction (CDJ). Daily rates of enamel and dentine formation were used to put a time scale to cumulative fractions of tooth height. RESULTS: Age estimates for KNM-WT 15 000 averaged 7.89-8.8 years of age (range = 6.6-10.3 years) and were close to previous histological estimates for this individual (7.6-8.8 years). CONCLUSIONS: Stages of dental development in KNM-WT 15 000 were easily accommodated within this age distribution of a modern sample. However, body mass and stature estimates for KNM-WT 15 000 fell well beyond those reported for a modern sample of 438 Sudanese children aged between 7.0-10 years.

Accelerating segmentation of fossil CT scans through Deep Learning.

Recent developments in Deep Learning have opened the possibility for automated segmentation of large and highly detailed CT scan datasets of fossil material. However, previous methodologies have required large amounts of training data to reliably extract complex skeletal structures. Here we present a method for automated Deep Learning segmentation to obtain high-fidelity 3D models of fossils digitally extracted from the surrounding rock, training the model with less than 1%-2% of the total CT dataset. This workflow has the capacity to revolutionise the use of Deep Learning to significantly reduce the processing time of such data and boost the availability of segmented CT-scanned fossil material for future research outputs. Our final Unet segmentation model achieved a validation Dice similarity of 0.96.

Reassessing trauma in a Late Neolithic cranium from Megalitho da Capella (Figueira da Foz, Portugal).

The Megalitho da Capella (Figueira da Foz, Coimbra, Portugal) is one of at least 21 dolmens in a megalithic complex explored by António dos Santos Rocha between 1880 and 1909. Among the human remains from Megalitho da Capella is an incomplete and fragmented cranium. Santos Rocha interpreted a groove on the parietal bone as an incision of traumatic origin with signs of remodeling that was suggestive of prolonged survival after an intentional intervention. This study provides a new examination of the groove using microcomputed tomographic (microCT) imaging, microscopy, and macroscopic observations of the groove in addition to the direct dating the skeletal remains. Results indicate that the human remains are dated to the Late Neolithic and that the "incision" is a normal anatomical variant corresponding to impressions from vascular tissue and temporal projections of the squamosal. We conclude that studies of bone surface modifications should consider normal anatomical variants (e.g., sulci, grooves, and furrows) when reporting results. Paleoimaging, microscopy, and comparative observations can assist in the identification bone modifications versus anatomical variants.

A conserved tooth resorption mechanism in modern and fossil snakes.

Whether snakes evolved their elongated, limbless bodies or their specialized skulls and teeth first is a central question in squamate evolution. Identifying features shared between extant and fossil snakes is therefore key to unraveling the early evolution of this iconic reptile group. One promising candidate is their unusual mode of tooth replacement, whereby teeth are replaced without signs of external tooth resorption. We reveal through histological analysis that the lack of resorption pits in snakes is due to the unusual action of odontoclasts, which resorb dentine from within the pulp of the tooth. Internal tooth resorption is widespread in extant snakes, differs from replacement in other reptiles, and is even detectable via non-destructive µCT scanning, providing a method for identifying fossil snakes. We then detected internal tooth resorption in the fossil snake Yurlunggur, and one of the oldest snake fossils, Portugalophis, suggesting that it is one of the earliest innovations in Pan-Serpentes, likely preceding limb loss.

A new Early Cretaceous lizard in Myanmar amber with exceptionally preserved integument.

We here report on a well-preserved juvenile lizard specimen in Albian amber (ca. 110 mya) from the Hkamti site (Myanmar). This new taxon is represented by an articulated skull and the anterior portion of the trunk, including the pectoral girdle and forelimbs. The scleral ossicles and eyelid are also visible, and the specimen exhibits pristine detail of the integument (of both head and body). In a combined molecular and morphological analysis, it was consistently recovered as a scincoid lizard (Scinciformata), as sister to Tepexisaurus + Xantusiidae. However, the phylogenetic position of the new taxon should be interpreted with caution as the holotype is an immature individual. We explored the possibility of miscoding ontogenetically variable characters by running alternative analyses in which these characters were scored as missing data for our taxon. With the exception of one tree, in which it was sister to Amphisbaenia, the specimen was recovered as a Pan-xantusiid. Moreover, we cannot rule out the possibility that it represents a separate lineage of uncertain phylogenetic position, as it is the case for many Jurassic and Cretaceous taxa. Nonetheless, this fossil offers a rare opportunity to glimpse the external appearance of one group of lizards during the Early Cretaceous.

Neuroanatomy of the nodosaurid Struthiosaurus austriacus (Dinosauria: Thyreophora) supports potential ecological differentiations within Ankylosauria.

Nodosauridae is a group of thyreophoran dinosaurs characterized by a collar of prominent osteoderms. In comparison to its sister group, the often club-tailed ankylosaurids, a different lifestyle of nodosaurids could be assumed based on their neuroanatomy and weaponry, e.g., regarding applied defensive strategies. The holotype of the nodosaurid Struthiosaurus austriacus consists of a single partial braincase from the Late Cretaceous of Austria. Since neuroanatomy is considered to be associated with ecological tendencies, we created digital models of the braincase based on micro-CT data. The cranial endocast of S. austriacus generally resembles those of its relatives. A network of vascular canals surrounding the brain cavity further supports special thermoregulatory adaptations within Ankylosauria. The horizontal orientation of the lateral semicircular canal independently confirms previous appraisals of head posture for S. austriacus and, hence, strengthens the usage of the LSC as proxy for habitual head posture in fossil tetrapods. The short anterior and angular lateral semicircular canals, combined with the relatively shortest dinosaurian cochlear duct known so far and the lack of a floccular recess suggest a rather inert lifestyle without the necessity of sophisticated senses for equilibrium and hearing in S. austriacus. These observations agree with an animal that adapted to a comparatively inactive lifestyle with limited social interactions.

The neuroanatomy of Zulmasuchus querejazus (Crocodylomorpha, Sebecidae) and its implications for the paleoecology of sebecosuchians.

The endocranial structures of the sebecid crocodylomorph Zulmasuchus querejazus (MHNC 6672) from the Lower Paleocene of Bolivia are described in this article. Using computed tomography scanning, the cranial endocast, associated nerves and arteries, endosseous labyrinths, and cranial pneumatization are reconstructed and compared with those of extant and fossil crocodylomorphs, representative of different ecomorphological adaptations. Z. querejazus exhibits an unusual flexure of the brain, pericerebral spines, semicircular canals with a narrow diameter, as well as enlarged pharyngotympanic sinuses. First, those structures allow to estimate the alert head posture and hearing capabilities of Zulmasuchus. Then, functional comparisons are proposed between this purportedly terrestrial taxon, semi-aquatic, and aquatic forms (extant crocodylians, thalattosuchians, and dyrosaurids). The narrow diameter of the semicircular canals but expanded morphology of the endosseous labyrinths and the enlarged pneumatization of the skull compared to other forms indeed tend to indicate a terrestrial lifestyle for Zulmasuchus. Our results highlight the need to gather new data, especially from altirostral forms in order to further our understanding of the evolution of endocranial structures in crocodylomorphs with different ecomorphological adaptations.