CARE-ing for Indigenous nonhuman genomic data - rethinking our approach.

Earlier this year, an international group of scientists published a paper in ScienceAdvances on the draft genome of the little bush moa (Anomalopteryx didiformis), one of about nine species of extinct flightless birds endemic to Aotearoa (New Zealand). The genome was sequenced from the ancient DNA of a "poorly provenanced" fossil bone acquired by the Royal Ontario Museum. It held important clues about the moa's evolutionary history and aspects of its biology.

A Cambrian spiny stem mollusk and the deep homology of lophotrochozoan scleritomes.

Mollusks encompass enormous disparity, including familiar clams and snails alongside less familiar aculiferans (chitons and vermiform aplacophorans) with complex multicomponent skeletons. Paleozoic fossils trace crown mollusks to forms exhibiting a combination of biomineralized shells and sclerites (e.g., scales, spines, and spicules). We describe a shell-less, Cambrian stem mollusk, Shishania aculeata gen. et sp. nov., with conical, hollow chitinous sclerites and a smooth girdle, broad foot, and mantle cavity. The sclerites have a microstructure of narrow canals consistent with the impressions of chaetal microvilli found in annelids and brachiopods. Shishania sclerites provide a morphological stepping stone between typical chaetae (chitinous bristles) and the external organic part of aculiferan sclerites that encloses a mineralized body. This discovery reinforces a common origin of lophotrochozoan chaetae and the biomineralized aculiferan sclerites, suggesting that the mollusk ancestor was densely covered with hollow chitinous chaetae.

Latitudinal gradients in the phylogenetic assembly of angiosperms in Asia during the Holocene.

Spatio-temporal assessment of phylogenetic diversity gradients during the Holocene (past 12,000 years) provides an opportunity for a deeper understanding of the dynamics of species co-occurrence patterns under environmental fluctuations. Using two robust metrics of phylogenetic dispersion (PD) and 99 fossil pollen sequences containing 6557 samples/assemblages, we analyse spatio-temporal variation in PD of angiosperms and its relationship with Holocene climate in central Asia. Overall, PD throughout the Holocene decreases linearly with increasing latitude, except for a rise in mean nearest taxon distance from ca. 25 to 35° N. This indicates that phylogenetically divergent taxa decrease progressively with increasing latitude, leaving more phylogenetically closely related taxa in the assemblages, thereby increasing phylogenetic relatedness among the co-occurring taxa. The latitudinal gradient of PD has not been consistent during the Holocene, and this temporal variation is concordant with the Holocene climate dynamics. In general, profound temporal changes in the latitudinal PD toward higher latitudes implies that the major environmental changes during the Holocene have driven considerable spatio-temporal changes in the phylogenetic assembly of high-latitude angiosperm assemblages. Our results suggest that environmental filtering and the tendency of taxa and lineages to retain ancestral ecological features and geographic distributions (phylogenetic niche conservatism) are the main mechanisms underlying the phylogenetic assembly of angiosperms along the climate-latitudinal gradient. Ongoing environmental changes may pose future profound phylogenetic changes in high-latitude plant assemblages, which are adapted to harsh environmental conditions, and therefore are phylogenetically less dispersed (more conservative or clustered).

Endocranial shape variation and allometry in Euarchontoglires.

While brain size in primates and their relatives within Euarchontoglires is well-studied, less research has examined brain shape, or the allometric trajectories that underlie the relationship between size and shape. Defining these patterns is key to understanding evolutionary trends. 3D geometric morphometric analyses of endocranial shape were performed on 140 species of extant euarchontoglirans using digital cranial endocasts. Principal component analyses on Procrustes shape variables show a clear phylogenetic pattern in endocranial shape, supported by an ANOVA which identified significant differences in shape among several groups (e.g., Platyrrhini, Strepsirrhini, Scandentia, Rodentia, and Lagomorpha). ANOVAs of shape and size also indicate that allometry has a small but significant impact on endocranial shape across Euarchontoglires, with homogeneity of slopes tests finding significant differences in the scaling relationship between shape and size among these same groups. While most of these clades possess a distinct endocranial morphotype, the highly derived platyrrhines display the strongest relationship between size and shape. Rodents show the most diversity in endocranial shape, potentially attributed to their comparatively weak relationship between shape and size. These results suggest fundamental differences in how shape and size covary among Euarchontoglires, which may have facilitated the adaptive radiations that characterize members of this group.

The latest shallow-sea isocrinids from the Miocene of Paratethys and implications to the Mesozoic marine revolution.

The predation-driven Mesozoic marine revolution (MMR) is believed to have induced a dramatic change in the bathymetric distribution of many shallow marine invertebrates since the late Mesozoic. For instance, stalked crinoids - isocrinids (Isocrinida) have undergone a striking decline in shallow-sea environments and today they are restricted to deep-sea settings (below 100 m depth). However, the timing and synchronicity of this shift are a matter of debate. A delayed onset of MMR and/or shifts to a retrograde, low-predation community structure during the Paleogene in the Southern Ocean were invoked. In particular, recent data from the Southern Hemisphere suggest that the environmental restriction of isocrinids to the deep-sea settings may have occurred at the end of the Eocene around Antarctica and Australia, and later in the early Miocene in New Zealand. Here, we report the anomalous occurrence of the isocrinids in shallow nearshore marine facies from the middle Miocene of Poland (Northern Hemisphere, Central Paratethys). Thus, globally, this is the youngest record of shallow-sea stalked crinoids. This finding suggests that some relict stalked crinoids may have been able to live in the shallow-water environments by the middle Miocene, and further confirms that the depth restriction of isocrinids to offshore environments was not synchronous on a global scale.

Unraveling sauropod diversity in the Portezuelo Formation of Patagonia through a comprehensive analysis of new and existing material.

The Portezuelo Formation preserves an outstanding record of the upper Turonian - lower Coniacian. Despite the discovery of a significant quantity of sauropod fossil material from the formation, only two species have been formally described to date: Malarguesaurus florenciae and Futalognkosaurus dukei. Here we present new sauropod material mostly composed of non-articulated caudal vertebrae (MCF-PVPH 916 and 917) that belong to two titanosauriforms on the basis of the following features: anterior caudal vertebrae with procoelous-opisthoplatyan articulations, transverse processes that reach the posterior articular face of the centrum and neural spines with a transverse width of around 50% of their anteroposterior length; anterior and middle caudal vertebrae with the neural arch restricted to the anterior half of the centrum; middle caudal centra with circular cross-section. Phylogenetic analysis recovers the new material in close relation to Malarguesaurus within a monophyletic clade at the base of Somphospondyli. This clade shares large pedicel height with a vertical anterior border on the middle caudal vertebrae, a vertical orientation of the neural spines on the distalmost middle caudal vertebrae and proximalmost posterior caudal vertebrae, and subequal relative lengths of the proximal ulnar condylar processes. The specimens presented here are distinct not only from Futalognkosaurus, but also from other indeterminate titanosaurian remains from the same formation. However, there are no significant differences between the specimen MCF-PVPH 917 and Malarguesaurus, but there are differences between the posterior caudal vertebrae of MCF-PVPH 916 and Malarguesaurus, so they could be considered different species. Whilst we err on the side of caution in not naming new taxa here, the two specimens significantly expand what we know about sauropods in the Turonian-Coniacian ecosystems of Patagonia, which will continue to do so as more material is discovered.

Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.

Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth's death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.

The Cambrian Odaraia alata and the colonization of nektonic suspension-feeding niches by early mandibulates.

The diversity of cephalic morphologies in mandibulates (myriapods and pancrustaceans) was key to their evolutionary success. A group of Cambrian bivalved arthropods called hymenocarines exhibit diagnostic mandibulate traits that illustrate this diversity, but many forms are still poorly known. These include the odaraiids, typified by Odaraia alata from the Burgess Shale (Wuliuan), characterized by its unique tubular carapace and rudder-like tail fan, and one of the largest Cambrian euarthropods at nearly 20 cm in length. Unfortunately, odaraiid cephalic anatomy has been largely unknown, limiting evolutionary scenarios and putting their mandibulate affinities into question. Here, we reinvestigate Odaraia based on new specimens from the Burgess Shale and describe exquisitely preserved mandibles with teeth and adjacent structures: a hypostome, maxillae and potential paragnaths. These structures can be homologized with those of Cambrian fuxianhuiids and extant mandibulates, and suggest that the ancestral mandibulate head could have had a limbless segment but retained its plasticity, allowing for limb re-expression within Pancrustacea. Furthermore, we show the presence of limbs with spinose endites which created a suspension-feeding structure. This discovery provides morphological evidence for suspension feeding among large Cambrian euarthropods and evinces the increasing exploitation of planktonic resources in Cambrian pelagic food webs.

Earliest evidence of human occupations and technological complexity above the 45th North parallel in Western Europe. The site of Lunery-Rosieres la-Terre-des-Sablons (France, 1.1 Ma).

The site of LuneryRosieres la-Terre-des-Sablons (Lunery, Cher, France) comprises early evidence of human occupation in mid-latitudes in Western Europe. It demonstrates hominin presence in the Loire River Basin during the Early Pleistocene at the transition between an interglacial stage and the beginning of the following glacial stage. Three archaeological levels sandwiched and associated with two diamicton levels deposited on the downcutting river floor indicate repeated temporary occupations. Lithic material yields evidence of simple and more complex core technologies on local Jurassic siliceous rocks and Oligocene millstone. Hominins availed of natural stone morphologies to produce flakes with limited preparation. Some cores show centripetal management and a partially prepared striking platform. The mean ESR age of 1175 ka ± 98 ka obtained on fluvial sediments overlying the archaeological levels could correspond to the transition between marine isotopic stages (MIS) 37 and 36, during the normal Cobb Mountain subchron, and in particular at the beginning of MIS 36. The Lunery site shows that hominins were capable of adapting to early glacial environmental conditions and adopting appropriate strategies for settling in mid-latitude zones. These areas cannot be considered as inhospitable at that time as Lunery lies at some distance from the forming ice cap.

Dart and the Taung juvenile: making sense of a century-old record of hominin evolution in Africa.

The announcement in 1925 by Raymond Dart of the discovery of the Taung juvenile's skull in a quarry in sub-Saharan Africa is deservedly a classic publication in the history of palaeoanthropology. Dart's paper-which designated Taung as the type specimen of the early hominin species Australopithecus africanus-provided the first fossil evidence supporting Charles Darwin's 1871 prediction that Africa was where the human lineage originated. The Taung juvenile's combination of ape and human characteristics eventually led to a paradigm shift in our understanding of human evolution. This contribution focuses on the milieu in which Dart's paper appeared (i.e. what was understood in 1925 about human evolution), the fossil evidence as set out by Dart, his interpretation of how a species represented by a fossilized juvenile's skull fitted within prevailing narratives about human evolution and the significance of the fossil being found in an environment inferred to be very different from that occupied by living apes. We also briefly review subsequent fossil finds that have corroborated the argument Dart made for having discovered evidence of a hitherto unknown close relative of humans, and summarize our current understanding of the earliest stages of human evolution and its environmental context.

Origins of mammalian vertebral function revealed through digital bending experiments.

Unravelling the functional steps that underlie major transitions in the fossil record is a significant challenge for biologists owing to the difficulties of interpreting functional capabilities of extinct organisms. New computational modelling approaches provide exciting avenues for testing function in the fossil record. Here, we conduct digital bending experiments to reconstruct vertebral function in non-mammalian synapsids, the extinct forerunners of mammals, to provide insights into the functional underpinnings of the synapsid-mammal transition. We estimate range of motion and stiffness of intervertebral joints in eight non-mammalian synapsid species alongside a comparative sample of extant tetrapods, including salamanders, reptiles and mammals. We show that several key aspects of mammalian vertebral function evolved outside crown Mammalia. Compared to early diverging non-mammalian synapsids, cynodonts stabilized the posterior trunk against lateroflexion, while evolving axial rotation in the anterior trunk. This was later accompanied by posterior sagittal bending in crown mammals, and perhaps even therians specifically. Our data also support the prior hypothesis that functional diversification of the mammalian trunk occurred via co-option of existing morphological regions in response to changing selective demands. Thus, multiple functional and evolutionary steps underlie the origin of remarkable complexity in the mammalian backbone.

Unveiling Challenging Microbial Fossil Biosignatures from Rio Tinto with Micro-to-Nanoscale Chemical and Ultrastructural Imaging.

Understanding the nature and preservation of microbial traces in extreme environments is crucial for reconstructing Earth's early biosphere and for the search for life on other planets or moons. At Rio Tinto, southwestern Spain, ferric oxide and sulfate deposits similar to those discovered at Meridiani Planum, Mars, entomb a diversity of fossilized organisms, despite chemical conditions commonly thought to be challenging for life and fossil preservation. Investigating this unique fossil microbiota can elucidate ancient extremophile communities and the preservation of biosignatures in acidic environments on Earth and, potentially, Mars. In this study, we use an innovative multiscale approach that combines the state-of-the-art synchrotron X-ray nanoimaging methods of ptychographic X-ray computed laminography and nano-X-ray fluorescence to reveal Rio Tinto's microfossils at subcellular resolution. The unprecedented nanoscale views of several different specimens within their geological and geochemical contexts reveal novel intricacies of preserved microbial communities. Different morphotypes, ecological interactions, and possible taxonomic affinities were inferred based on qualitative and quantitative 3D ultrastructural information, whereas diagenetic processes and metabolic affinities were inferred from complementary chemical information. Our integrated nano-to-microscale analytical approach revealed previously invisible microbial and mineral interactions, which complemented and filled a gap of spatial resolution in conventional methods. Ultimately, this study contributes to the challenge of deciphering the faint chemical and morphological biosignatures that can indicate life's presence on the early Earth and on distant worlds.

When is a handaxe a planned-axe? exploring morphological variability in the Acheulean.

The handaxe is an iconic stone tool form used to define and symbolise both the Acheulean and the wider Palaeolithic. There has long been debate around the extent of its morphological variability between sites, and the role that extrinsic factors (especially raw material, blank type, and the extent of resharpening) have played in driving this variability, but there has been a lack of high-resolution examinations of these factors in the same study. In this paper, we present a 2D geometric morphometric analysis of 1097 handaxes from across Africa, the Levant, and western Europe to examine the patterning of this variability and what it can tell us about hominin behaviour. We replicate the findings of previous studies, that handaxe shape varies significantly between sites and entire continental regions, but we find no evidence for raw material, blank type, or resharpening in determining this pattern. What we do find, however, is that markers of reduction trajectory vary substantially between sites, suggesting that handaxes were deployed differently according to hominin need at a given site. We argue this is reflective of a continuum of reduction strategies, from those focused on the maintenance of a sharp cutting edge (i.e. direct use in cutting activities), to those focused on maintaining tip shapes, and perhaps a corresponding production of flakes. Implications for hominin behavioural flexibility are discussed.

Diverse growth rates in Triassic archosaurs-insights from a small terrestrial Middle Triassic pseudosuchian.

The small pseudosuchian Benggwigwishingasuchus eremacarminis was found in Anisian (Middle Triassic) marine sediments. Neither the skeleton nor osteohistology or microanatomy shows any secondary aquatic adaptations, and a dominantly terrestrial lifestyle of this new taxon is evident. Bone tissue consists of a scaffold of parallel-fibered matrix, which is moderately vascularized by small, mainly longitudinal primary osteons. The innermost cortex is less densely vascularized and more highly organized. No parts of the cortex contain any woven bone. The cortex is regularly stratified by annual growth marks. Bone tissue and growth pattern indicate an adult individual that has had slow growth rates throughout its ontogeny. Tissue type, slow growth rate, and inferred low resting metabolic rate of Benggwigwishingasuchus are similar to that of crocodylomorphs but differ from that of Sillosuchus and Effigia, poposaurids to which Benggwigwishingasuchus is related based on phylogenetic analyses. However, according to current knowledge, growth rates in early archosaurs are more likely influenced by body size and environment than by phylogeny. Benggwigwishingasuchus is thus another example of unpredictable variability in growth rates within Triassic archosaurs.

Spatial organisation within the earliest evidence of post-built structures in Britain.

This paper explores tool-using activities undertaken in and around the earliest known evidence of post-built structures in Britain. Microwear results associated with at least three structures identified at the Early Mesolithic site of Star Carr, North Yorkshire, are examined as a means of identifying activity zones associated with the diverse stone tools used to process a variety of materials (e.g. wood, bone, antler, plant, hide, meat, fish). With 341 lithic artefacts analysed, this research represents the first microwear study focused on the post-built structures at Star Carr. A combination of spatial and microwear data has provided different scales of interpretation: from individual tool use to patterns of activity across the three structures. Different types of tool use observed have aided interpretations of possible activity areas where objects were produced and materials were processed. Zones of activity within one of the structures suggest that the working of some materials was more spatially restricted than others; even where there are high densities of flint deposition, spatial patterns in tool-using activity were observed. From this, it is interpreted that social norms and behaviours influenced the spatial organisation of different spaces. Our results demonstrate the importance of combining microwear analysis with GIS to explore function and variability in the use of Mesolithic structures-providing new insights into their role as social spaces.

Finds of Skulls of Juvenile Kurdalagonus maicopicus (Cetacea, Cetotheriidae) in the Upper Miocene of the Republic of Adygea.

Fragments of two skulls of young cetotheriid baleen whales were described from the Fortep'yanka 2 locality (Russia, Republic of Adygea, Maikop district, Fortep'yanka River valley, Upper Miocene, Upper Sarmatian, Blinovskaya Formation). The finds were attributed to Kurdalagonus maicopicus (Spasskii, 1951) based on the morphology of the posterior (mastoid) process of the petrosal bone, the structure of the posterior edge of the temporal fossa, and the S-like shape of the supraoccipital ridges. The skull proportions and the degree of suture closure made it possible to determine the individual age of the whales within a year. New finds significantly complement the data on the structure of the sutures of the lateral wall of the skull and age-related variability of cranial morphology in representatives of the genus Kurdalagonus.

Cretaceous and Paleocene fossils reveal an extinct higher clade within Cornales, the dogwood order.

PREMISE: Characterization and phylogenetic integration of fossil angiosperms with uncertain affinities is relatively limited, which may obscure the diversity of extinct higher taxa in the flowering plant tree of life. The order Cornales contains a diversity of extinct taxa with uncertain familial affinities that make it an ideal group for studying turnover in angiosperms. Here, we describe a new extinct genus of Cornales unassignable to an extant family and conduct a series of phylogenetic analyses to reconstruct relationships of fossils across the order. METHODS: Two permineralized endocarps were collected from the Cedar District Formation (Campanian, 82-80 Ma) of Sucia Island, State of Washington, United States. Fossils were sectioned with the cellulose acetate peel technique and incorporated into a morphological dataset. To assess the utility of this dataset to accurately place taxa in their respective clades, we used a series of phylogenetic pseudofossilization analyses. We then conducted a total-evidence analysis and a scaffold-based approach to determine relationships of fossils. RESULTS: Based on their unique combination of characters, the fossils represent a new genus, Fenestracarpa washingtonensis gen. nov. et sp. nov. Pseudofossilization analyses indicate that our morphological dataset can be used to accurately recover taxa at the major clade to family level, generally with moderate to high support. The total-evidence and scaffold-based analyses recovered Fenestracarpa and other fossil genera in an entirely extinct clade within Cornales. CONCLUSIONS: Our findings increase the reported diversity of extinct Cornales and indicate that the order's initial radiation likely included the divergence of an extinct higher clade that endured the end-Cretaceous Mass extinction but perished during the Cenozoic.

Estimates of late Early Cretaceous atmospheric CO2 from Mongolia based on stomatal and isotopic analysis of Pseudotorellia.

PREMISE: The Aptian-Albian (121.4-100.5 Ma) was a greenhouse period with global temperatures estimated as 10-15°C warmer than pre-industrial conditions, so it is surprising that the most reliable CO2 estimates from this time are <1400 ppm. This low CO2 during a warm period implies a very high Earth-system sensitivity in the range of 6 to 9°C per CO2 doubling between the Aptian-Albian and today. METHODS: We applied a well-vetted paleo-CO2 proxy based on leaf gas-exchange principles (Franks model) to two Pseudotorellia species from three stratigraphically similar samples at the Tevshiin Govi lignite mine in central Mongolia (~119.7-100.5 Ma). RESULTS: Our median estimated CO2 concentration from the three respective samples was 2132, 2405, and 2770 ppm. The primary reason for the high estimated CO2 but with relatively large uncertainties is the very low stomatal density in both species, where small variations propagate to large changes in estimated CO2. Indeed, we found that at least 15 leaves are required before the aggregate estimated CO2 approaches that of the full data set. CONCLUSIONS: Our three CO2 estimates all exceeded 2000 ppm, translating to an Earth-system sensitivity (~3-5°C/CO2 doubling) that is more in keeping with the current understanding of the long-term climate system. Because of our large sample size, the directly measured inputs did not contribute much to the overall uncertainty in estimated CO2; instead, the inferred inputs were responsible for most of the overall uncertainty and thus should be scrutinized for their value choices.

Intraspecific variation in the pterosaur Rhamphorhynchus muensteri-implications for flight and socio-sexual signaling.

Pterosaurs were the first powered flying vertebrates, with a fossil record that stretches back to about 230 million years before present. Most species are only known from one to three specimens, which are most often fragmentary. However, Rhamphorhynchus muensteri is known from numerous excellent specimens, including multiple specimens with soft tissue preservation. As such, Rhamphorhynchus muensteri is one of the only pterosaurs amenable to analysis for intraspecific variation. It has been previously predicted that elements directly involved in the flight apparatus, such as those of the forelimb, will be more highly constrained in their proportions than other parts of the skeleton. We investigated the degree of variation seen in elements and body parts of Rhamphorhynchus, which represents the best model system among pterosaurs for testing these expectations of intraspecific variation. We recover evidence for high levels of constraint throughout the appendicular and axial elements (head, neck, torso, tail, forelimbs, hindlimbs), suggesting that all were important for flight. We further find that tail variation increases among the largest specimens, suggesting reduced constraint and/or stronger sexual selection on the tail in more mature individuals.