Mohammed Yaqoob Ansari, Mohammed Ishaq Ansari, Mohammed Yusuf Ansari
et al.
Understanding ancient organisms and their interactions with paleoenvironments through the study of body fossils is a central tenet of paleontology. Advances in digital image capture now allow for efficient and accurate documentation, curation, and interrogation of fossil forms and structures in two and three dimensions, extending from microfossils to larger specimens. Despite these developments, key fossil image processing and analysis tasks, such as segmentation and classification, still require significant user intervention, which can be labor-intensive and subject to human bias. Recent advances in deep learning offer the potential to automate fossil image analysis, improving throughput and limiting operator bias. Despite the emergence of deep learning within paleontology in the last decade, challenges such as the scarcity of diverse, high quality image datasets and the complexity of fossil morphology necessitate further advancement which will be aided by the adoption of concepts from other scientific domains. Here, we comprehensively review state-of-the-art deep learning based methodologies applied to fossil analysis, grouping the studies based on the fossil type and nature of the task. Furthermore, we analyze existing literature to tabulate dataset information, neural network architecture type, and key results, and provide textual summaries. Finally, we discuss novel techniques for fossil data augmentation and fossil image enhancements, which can be combined with advanced neural network architectures, such as diffusion models, generative hybrid networks, transformers, and graph neural networks, to improve body fossil image analysis.
Ann-Kathrin Schuetz, Alexander Migala, Adam Boesky
et al.
The first detection of gravitational waves, recognized by the 2017 Nobel Prize in Physics, has opened up a new research field: gravitational-wave paleontology. When massive stars evolve into black holes and collide, they create gravitational waves that propagate through space and time. These gravitational-waves, now detectable on Earth, act as fossils tracing the histories of the massive stars that created them. Estimating physics parameters of these massive stars from detected gravitational-waves is a parameter estimation task, with the primary difficulty being the extreme rarity of collisions in simulated binary black holes. This rarity forces researchers to choose between prohibitively expensive simulations or accepting substantial statistical variance. In this work, we present RESOLVE, a rare event surrogate model that leverages polynomial chaos expansion (PCE) and Bayesian MCMC to emulate this rare formation efficiency. Our experimental results demonstrate that RESOLVE is the only surrogate model that achieves proper statistical coverage, while effectively learning the underlying distribution of each physics parameter. We construct a likelihood function incorporating both the emulated formation efficiency and LIGO's gravitational wave observations, which we then minimize to produce community-standard credible intervals for each physics parameter. These results enable astronomers to gain deeper insights into how the universe transformed from simple gases into the complex chemical environment that eventually made life possible.
Triassic strata in the portion of the Central European Basin (CEB) that cover parts of conterminous Germany have yielded a long if discontinuous record of continental tetrapods spanning this period. The classic Germanic Triassic succession comprises two mostly terrestrial units, the Buntsandstein and Keuper groups, separated by the predominantly marine Muschelkalk Group (Fig. 1). Thus, it is not possible to trace lineages of terrestrial tetrapods continuously through the entire Triassic Period. Skeletal remains of Early and early Middle Triassic (Induan-early Anisian) reptiles are rare in the Buntsandstein Group and mainly known from the Upper Buntsandstein Subgroup. The Middle Triassic (Anisian-Ladinian) marine carbonates of the Muschelkalk Group have yielded a considerable diversity of sauropterygians together with a few ichthyopterygians, a possible thalattosaurian, and the long-necked tanysaurian archosauromorph Tanystropheus. The late Middle and Late Triassic continental deposits of the Keuper Group preserve a substantial record of the rapidly diversifying crocodile-line and bird-line archosaurs together with stem-forms of some tetrapod crown clades such as turtles and lepidosaurs. In recent years, many new discoveries have greatly increased our knowledge of reptiles from the Keuper Group, especially from the Ladinian-age Lower Keuper Subgroup. The latest Triassic (Rhaetian) is represented by bonebeds containing bones and teeth of marine and continental vertebrates including reptiles that were deposited before the Early Jurassic transgression completely inundated the CEB. This paper provides a detailed overview of the currently known taxa of reptiles from the Triassic of conterminous Germany and explores some more general aspects of this fossil record.
Paleontology has provided invaluable basic knowledge on the history of life on Earth. The discipline can also provide substantial knowledge to societal challenges such as climate change. The long-term perspective of climate change impacts on natural systems is both a unique selling point and a major obstacle to becoming more pertinent for policy-relevant bodies like the Intergovernmental Panel on Climate Change (IPCC). Repeated experiments on the impacts of climate change without anthropogenic disturbance facilitate the extraction of climate triggers in biodiversity changes. At the same time, the long timescales over which paleontological changes are usually assessed are beyond the scope of policymakers. Based on first-hand experience with the IPCC and a quantitative analysis of its cited literature, we argue that the differences in temporal scope are less of an issue than inappropriate framing and reporting of most paleontological publications. Accepting that some obstacles will remain, paleontology can quickly improve its relevance by targeting climate change impacts more directly and focusing on effect sizes and relevance for projections, particularly on higher-end climate change scenarios.
Abstract Ontogenetic change is a major source of phenotypic variation among members of a species and is often of greater magnitude than the anatomical differences that distinguish closely related species. Ontogeny has therefore become a problematic confounding variable in vertebrate paleontology, especially in study systems distant from extant crown clades, rendering taxonomic hypothesis testing (a fundamental process in evolutionary biology) rife with difficulty. Paleontologists have adopted quantitative methods to compensate for the perception that juvenile specimens lack diagnostic apomorphies seen in their adult conspecifics. Here, I critically evaluate these methods and the assumptions that guide their interpretation using a µCT dataset comprising growth series of American and Chinese alligator. I find that several widespread assumptions are scientifically unjustifiable, and that two popular methods – geometric morphometrics and cladistic analysis of ontogeny – have unacceptably high rates of type II error and present numerous procedural difficulties. However, I also identify a suite of ontogenetically invariant characters that differentiate the living species of Alligator throughout ontogeny. These characters overwhelmingly correspond to anatomical systems that develop prior to (and play a signaling role in) the development of the cranial skeleton itself, suggesting that their ontogenetic invariance is a consequence of the widely conserved vertebrate developmental program. These observations suggest that the architecture of the cranium is fixed early in embryonic development, and that ontogenetic remodeling does not alter the topological relationships of the cranial bones or the soft tissue structures they house. I propose a general model for future taxonomic hypothesis tests in the fossil record, in which the hypothesis that two specimens different ontogenetic stages of a single species can be falsified by the discovery of character differences that cannot be attributed plausibly to ontogenetic variation.
Wan-Qian Zhao, Zhan-Yong Guo, Zeng-Yuan Tian
et al.
High quality ancient DNA (aDNA) is essential for molecular paleontology. Due to DNA degradation and contamination by environmental DNA (eDNA), current research is limited to fossils less than 1 million years old. The study successfully extracted DNA from Lycoptera davidi fossils from the Early Cretaceous period, dating 120 million years ago. Using high-throughput sequencing, 1,258,901 DNA sequences were obtained. We established a rigorous protocol known as the mega screen method. Using this method, we identified 243 original in situ DNA (oriDNA) sequences, likely from the Lycoptera genome. These sequences have an average length of over 100 base pairs and show no signs of deamination. Additionally, 10 transposase coding sequences were discovered, shedding light on a unique self-renewal mechanism in the genome. This study provides valuable DNA data for understanding ancient fish evolution and advances paleontological research.
This groundbreaking research extracted DNA from petroleum using nanoparticle affinity bead technology, yielding 3,159,020 petroleum DNA (pDNA) sequences, primarily environmental DNA. While most original in situ DNA (oriDNA) was lost, ancient DNA (aDNA) from petroleum offers an important source of ecological and evolutionary information, surpassing traditional fossils. This study reveals that oil, mainly sourced from algae and lower aquatic plants, now serves as a new type of fossil, providing detailed insights into Earth's hidden history, including unclassified species and ancient events, revolutionizing petroleum geology and paleontology.
Paleontology, the study of past life, fundamentally relies on fossils to reconstruct ancient ecosystems and understand evolutionary dynamics. Trilobites, as an important group of extinct marine arthropods, offer valuable insights into Paleozoic environments through their well-preserved fossil records. Reconstructing trilobite behaviour from static fossils will set new standards for dynamic reconstructions in scientific research and education. Despite the potential, current computational methods for this purpose like text-to-video (T2V) face significant challenges, such as maintaining visual realism and consistency, which hinder their application in science contexts. To overcome these obstacles, we introduce an automatic T2V prompt learning method. Within this framework, prompts for a fine-tuned video generation model are generated by a large language model, which is trained using rewards that quantify the visual realism and smoothness of the generated video. The fine-tuning of the video generation model, along with the reward calculations make use of a collected dataset of 9,088 Eoredlichia intermedia fossil images, which provides a common representative of visual details of all class of trilobites. Qualitative and quantitative experiments show that our method can generate trilobite videos with significantly higher visual realism compared to powerful baselines, promising to boost both scientific understanding and public engagement.
Li Ning, Susannah C. R. Maidment, Li Daqing
et al.
Abstract Stegosaurs are a minor but iconic clade of ornithischian dinosaurs, yet due to a poor fossil record, their early evolution is poorly understood. Here, we describe a new stegosaur, Baiyinosaurus baojiensis, gen. et sp. nov. from the Middle Jurassic Wangjiashan Formation of the Pingchuan District, Baiyin City, Gansu Province, China. The frontal of Baiyinosaurus possesses a unique characteristic among Stegosauria: it is wider than long and contributes to both the medial and anterior margins of the supratemporal fenestra. The character combinations of dorsal vertebrae of Baiyinosaurus are also different to other stegosaurs: its neural arches are not greatly elongated, its parapophyses are well developed, and its neural spines are axially expanded in lateral. The features of the frontal and vertebrae of Baiyinosaurus are reminiscent of basally branching thyreophorans, indicating that Baiyinosaurus is transitional in morphology between early thyreophorans and early-diverging stegosaurs. Systematic analysis shows that Baiyinosaurus is an early-diverging stegosaur.
Abstract The geological and paleoenvironmental setting and the vertebrate taxonomy of the fossiliferous, Cenomanian-age deltaic sediments in eastern Morocco, generally referred to as the “Kem Kem beds”, are reviewed. These strata are recognized here as the Kem Kem Group, which is composed of the lower Gara Sbaa and upper Douira formations. Both formations have yielded a similar fossil vertebrate assemblage of predominantly isolated elements pertaining to cartilaginous and bony fishes, turtles, crocodyliforms, pterosaurs, and dinosaurs, as well as invertebrate, plant, and trace fossils. These fossils, now in collections around the world, are reviewed and tabulated. The Kem Kem vertebrate fauna is biased toward large-bodied carnivores including at least four large-bodied non-avian theropods (an abelisaurid, Spinosaurus, Carcharodontosaurus, and Deltadromeus), several large-bodied pterosaurs, and several large crocodyliforms. No comparable modern terrestrial ecosystem exists with similar bias toward large-bodied carnivores. The Kem Kem vertebrate assemblage, currently the best documented association just prior to the onset of the Cenomanian-Turonian marine transgression, captures the taxonomic diversity of a widespread northern African fauna better than any other contemporary assemblage from elsewhere in Africa.
Non-technical Summary Researchers often use large databases to conduct their studies; however, they do not always provide credit, through citations, to the people who produced the data in the databases. In the field of paleontology, researchers use a large database called the Paleobiology Database (PBDB) to study global patterns and processes over millions of years. These studies use data from the PBDB and typically receive a greater number of citations than the original data-producing papers. This creates a situation where the hard work of collecting the data is not credited and rewarded in a fair way, even though this work is equally important to the field of paleontology. By fixing this issue and giving proper credit to data-producing papers, paleontology itself can be strengthened by increasing the incentives for producing data and at the same time creating more high-quality data for everyone to use. Abstract Data compilations expand the scope of research; however, data citation practice lags behind advances in data use. It remains uncommon for data users to credit data producers in professionally meaningful ways. In paleontology, databases like the Paleobiology Database (PBDB) enable assessment of patterns and processes spanning millions of years, up to global scale. The status quo for data citation creates an imbalance wherein publications drawing data from the PBDB receive significantly more citations (median: 4.3 ± 3.5 citations/year) than the publications producing the data (1.4 ± 1.3 citations/year). By accounting for data reuse where citations were neglected, the projected citation rate for data-provisioning publications approached parity (4.2 ± 2.2 citations/year) and the impact factor of paleontological journals (n = 55) increased by an average of 13.4% (maximum increase = 57.8%) in 2019. Without rebalancing the distribution of scientific credit, emerging “big data” research in paleontology—and science in general—is at risk of undercutting itself through a systematic devaluation of the work that is foundational to the discipline.
Philipp J. Heckmeier, Jeannette Ruf, Charlotte Rochereau
et al.
Protein dynamics form a critical bridge between protein structure and function, yet the impact of evolution on ultrafast processes inside proteins remains enigmatic. This study delves deep into nanosecond-scale protein dynamics of a structurally and functionally conserved protein across species separated by almost a billion years, investigating ten homologs in complex with their ligand. By inducing a photo-triggered destabilization of the ligand inside the binding pocket, we resolved distinct kinetic footprints for each homolog via transient infrared spectroscopy . Strikingly, we found a cascade of rearrangements within the protein complex which manifest in three discrete time points of dynamic activity, conserved over hundreds of millions of years within a narrow window. Among these processes, one displays a subtle temporal shift correlating with evolutionary divergence, suggesting reduced selective pressure in the past. Our study not only uncovers the impact of evolution on molecular processes in a specific case, but has also the potential to initiate a novel field of scientific inquiry within molecular paleontology, where species are compared and classified based on the rapid pace of protein dynamic processes; a field which connects the shortest conceivable time scale in living matter (10^-9 s) with the largest ones (10^16 s).
Artiodactyls diversified during the Eocene and Oligocene in North America and Europe after their first Holarctic appearance at the beginning of the Eocene. However, the relationships among early artiodactyls, European endemic forms, and later derived suiforms, tylopods, and ruminants remain unclear. Early artiodactyls are relatively rare in Asia compared to those known from North America and Europe; thus, investigation of Eocene artiodactyls from Asia is important to resolve these issues. Here we report two new genera and three new species of small early artiodactyls from middle Eocene deposits of the Erlian Basin, Inner Mongolia, China. The new materials represent a morphologically gradational series from Asian Land Mammal Ages Irdinmanhan to Sharamurunian, characterized by a trend towards bilophodonty in the lower molars. Morphologic and phylogenetic analyses suggest that these new taxa have a close relationship with the enigmatic European Tapirulus, which currently consists of five species that range from the middle Eocene to the early Oligocene. The close relationship between the Erlian specimens and Tapirulus suggests possible faunal exchanges between Europe and Asia during the middle Eocene, a view that has been supported by other mammalian groups across the two continents. The evolution of bilophodonty in Tapirulidae and Raoellidae is probably attributable to convergence.
Abstract. As practitioners of a historical science, paleontologists and geoscientists are well versed in the idea that the ability to understand and to anticipate the future relies upon our collective knowledge of the past. Despite this understanding, the fundamental role that the history of paleontology and the geosciences plays in shaping the structure and culture of our disciplines is seldom recognized and therefore not acted upon sufficiently. Here, we present a brief review of the history of paleontology and geology in Western countries, with a particular focus on North America since the 1800s. Western paleontology and geology are intertwined with systematic practices of exclusion, oppression, and erasure that arose from their direct participation in the extraction of geological and biological resources at the expense of Black, Indigenous, and People of Color (BIPOC). Our collective failure to acknowledge this history hinders our ability to address these issues meaningfully and systemically in present-day educational, academic, and professional settings. By discussing these issues and suggesting some ways forward, we intend to promote a deeper reflection upon our collective history and a broader conversation surrounding racism, colonialism, and exclusion within our scientific communities. Ultimately, it is necessary to listen to members of the communities most impacted by these issues to create actionable steps forward while holding ourselves accountable for the past.
Aurora Cossairt, Michael Buehlmann, Eve Kovacs
et al.
We present a detailed study of fossil group candidates identified in "Last Journey", a gravity-only cosmological simulation covering a $(3.4\, h^{-1}\mathrm{Gpc})^3$ volume with a particle mass resolution of $m_p \approx 2.7 \times 10^9\, h^{-1}\mathrm{M}_\odot$. The simulation allows us to simultaneously capture a large number of group-scale halos and to resolve their internal structure. Historically, fossil groups have been characterized by high X-ray brightness and a large luminosity gap between the brightest and second brightest galaxy in the group. In order to identify candidate halos that host fossil groups, we use halo merger tree information to introduce two parameters: a luminous merger mass threshold ($M_\mathrm{LM}$) and a last luminous merger redshift cut-off ($z_\mathrm{LLM}$). The final parameter choices are informed by observational data and allow us to identify a plausible fossil group sample from the simulation. The candidate halos are characterized by reduced substructure and are therefore less likely to host bright galaxies beyond the brightest central galaxy. We carry out detailed studies of this sample, including analysis of halo properties and clustering. We find that our simple assumptions lead to fossil group candidates that form early, have higher concentrations, and are more relaxed compared to other halos in the same mass range.
Motivation for this comment Recently, the Society of Vertebrate Paleontology (SVP) has sent around a letter, dated 21st April, 2020 to more than 300 palaeontological journals, signed by the President, Vice President and a former President of the society (Rayfield et al. 2020). The signatories of this letter request significant changes to the common practices in palaeontology. With our present, multi-authored comment, we aim to argue why these suggestions will not lead to improvement of both practice and ethics of palaeontological research but, conversely, hamper its further development. Although we disagree with most contents of the SVP letter, we appreciate this initiative to discuss scientific practices and the underlying ethics. Here, we consider different aspects of the suggestions by Rayfield et al. (2020) in which we see weaknesses and dangers. It is our intent to compile views from many different fields of palaeontology, as our discipline is (and should remain) pluralistic. This contribution deals with the aspects concerning Myanmar amber. Reference is made to Haug et al. (2020a) for another comment on aspects concerning amateur palaeontologists/ citizen scientists/private collectors.
Abstract An unprecedented amount of evidence now illuminates the phylogeny of living mammals and birds on the Tree of Life. We use this tree to measure the phylogenetic value of data typically used in paleontology (bones and teeth) from six data sets derived from five published studies. We ask three interrelated questions: 1) Can these data adequately reconstruct known parts of the Tree of Life? 2) Is accuracy generally similar for studies using morphology, or do some morphological data sets perform better than others? 3) Does the loss of non-fossilizable data cause taxa to occur in misleadingly basal positions? Adding morphology to DNA data sets usually increases congruence of resulting topologies to the well-corroborated tree, but this varies among morphological data sets. Extant taxa with a high proportion of missing morphological characters can greatly reduce phylogenetic resolution when analyzed together with fossils. Attempts to ameliorate this by deleting extant taxa missing morphology are prone to decreased accuracy due to long-branch artifacts. We find no evidence that fossilization causes extinct taxa to incorrectly appear at or near topologically basal branches. Morphology comprises the evidence held in common by living taxa and fossils, and phylogenetic analysis of fossils greatly benefits from inclusion of molecular and morphological data sampled for living taxa, whatever methods are used for phylogeny estimation. [Concatenation; fossilization; morphology; parsimony; systematics; taphonomy; total-evidence.]