Palaeontological Database Research Articles

Ordovician of the Eastern Baltic palaeobasin and the Tornquist Sea margin of Baltica

Abstract This paper summarizes recent knowledge on the palaeontology, biostratigraphy, correlation, sea-level and climate history and isotopic geochemistry of the Ordovician rocks in the western and central parts of the East European Craton, in the area extending from the southern margin of the Fennoscandian Shield to the western margin of the Ukrainian Shield. The regional chronostratigraphic standard is briefly summarized and its correlation to the global standard of the Ordovician is addressed. A two-part correlation chart of 10 areas with unique local Ordovician successions is aligned with the most recent international correlation standard of the Ordovician System and presented against the regular timescale. An updated summary of the evolution of the marine assemblages is provided, the principal gaps in the existing extremely rich palaeontological database are identified and the main bioevents are discussed.

A status report on a section-based stratigraphic and palaeontological database – the Geobiodiversity Database

Abstract. Big data are significant for quantitative analysis and contribute to data-driven scientific research and discoveries. Here a brief introduction is given to the Geobiodiversity Database (GBDB), a comprehensive stratigraphic and palaeontological database, and its data. The GBDB includes abundant geological records from China and has supported a series of scientific studies on the Paleozoic palaeogeography and tectonic and biodiversity evolution of China. The data that the GBDB has including those that are newly collected are described in detail; the statistical results and structure of the data are given. A comparison between the GBDB; the largest palaeobiological database, the Paleobiology Database (PBDB); and the geological rock database Macrostrat is drawn. The GBDB and other databases are complementary in palaeontological and stratigraphic research. The GBDB will continually provide users access to detailed palaeontological and stratigraphic data based on publications. Non-structured data of palaeontology and stratigraphy will also be included in the GBDB, and they will be organically correlated with the existing data of the GBDB, making the GBDB more widely used for both researchers and anyone who is interested in fossils and strata. The GBDB fossil and stratum dataset (Xu, 2020) is freely downloadable from https://doi.org/10.5281/zenodo.4245604.

IchnoDB: structure and importance of an ichnology database

The design of a relational database for ichnological data is presented to illustrate and address deficiencies in present-day palaeontological databases. Currently, palaeontology databases apply concepts and terminology derived from the study of body fossils to trace fossil records. We suggest that fundamental differences between body and trace fossils make this practice inappropriate. These differences stem from the fact that trace fossils represent the behaviour of the tracemaker, and not the phylogenetic affinities of an organism. This database, referred to as IchnoDB, has been tested by the authors throughout the design process to ensure that recommended alterations to current palaeontology databases made herein are functional. In describing the design and logic that underpins an ichnology database, it is our desire to see established palaeontological databases incorporate ichnology specific fields into their structure. This would support and encourage future research, involving the use of large ichnological datasets.

CoordinateCleaner: Standardized cleaning of occurrence records from biological collection databases

Abstract Species occurrence records from online databases are an indispensable resource in ecological, biogeographical and palaeontological research. However, issues with data quality, especially incorrect geo‐referencing or dating, can diminish their usefulness. Manual cleaning is time‐consuming, error prone, difficult to reproduce and limited to known geographical areas and taxonomic groups, making it impractical for datasets with thousands or millions of records. Here, we present CoordinateCleaner, an r‐package to scan datasets of species occurrence records for geo‐referencing and dating imprecisions and data entry errors in a standardized and reproducible way. CoordinateCleaner is tailored to problems common in biological and palaeontological databases and can handle datasets with millions of records. The software includes (a) functions to flag potentially problematic coordinate records based on geographical gazetteers, (b) a global database of 9,691 geo‐referenced biodiversity institutions to identify records that are likely from horticulture or captivity, (c) novel algorithms to identify datasets with rasterized data, conversion errors and strong decimal rounding and (d) spatio‐temporal tests for fossils. We describe the individual functions available in CoordinateCleaner and demonstrate them on more than 90 million occurrences of flowering plants from the Global Biodiversity Information Facility (GBIF) and 19,000 fossil occurrences from the Palaeobiology Database (PBDB). We find that in GBIF more than 3.4 million records (3.7%) are potentially problematic and that 179 of the tested contributing datasets (18.5%) might be biased by rasterized coordinates. In PBDB, 1205 records (6.3%) are potentially problematic. All cleaning functions and the biodiversity institution database are open‐source and available within the CoordinateCleaner r‐package.

The fossil record of the sixth extinction.

Comparing the magnitude of the current biodiversity crisis with those in the fossil record is difficult without an understanding of differential preservation. Integrating data from palaeontological databases with information on IUCN status, ecology and life history characteristics of contemporary mammals, we demonstrate that only a small and biased fraction of threatened species (<9%) have a fossil record, compared with 20% of non-threatened species. We find strong taphonomic biases related to body size and geographic range. Modern species with a fossil record tend to be large and widespread and were described in the 19(th) century. The expected magnitude of the current extinction based only on species with a fossil record is about half of that of one based on all modern species; values for genera are similar. The record of ancient extinctions may be similarly biased, with many species having originated and gone extinct without leaving a tangible record.

High dependence of Ordovician ocean surface circulation on atmospheric CO2 levels

Life on Earth radiated dramatically during the Ordovician Period (485–444Ma) at all taxonomic levels during an evolutionary episode known as the ‘Great Ordovician Biodiversification Event’. Abundant scientific literature has documented the pattern of biodiversification for numerous organism groups. However, fully understanding this event also requires detailed knowledge about the spatial distribution of the organisms. The full potential of the palaeobiodiversity patterns remains under-explored due to the lack of knowledge about past ocean circulation. Surface circulation significantly conditions the dispersal of organisms, in creating preferential ocean migration pathways or, in contrast, by isolating specific regions and thus establishing major physical barriers. These uncertainties persist because neither direct observational data, nor proxy data independent from the fossil record, are available to reconstruct the ocean surface circulation. Here we present new maps of Ordovician ocean surface circulation based on simulations using the general circulation model FOAM. This is a coupled ocean-atmosphere general circulation model and represents a methodological improvement over previously published work. In addition, we use the most up-to-date palaeogeographical reconstructions to increase compatibility with recent palaeontological databases. In providing clear, synthetic maps of ocean surface circulation in addition to raw model outputs, we aim to facilitate data-model comparison, to assist in interpretation of palaeontological datasets, and to promote renewed discussion about Ordovician biogeography. Finally, we investigate the sensitivity of the circulation pattern to the atmospheric CO2 content, which remains poorly constrained in the Ordovician, potentially ranging from more than 15 times the preindustrial atmospheric CO2 level (PAL) to ~5 PAL. Maps are systematically constructed for a high (16 PAL), medium (8 PAL) and low (4 PAL) CO2 value. We show that the circulation pattern is much more sensitive to CO2 than previously suggested.

Collateral mammal diversity loss associated with late Quaternary megafaunal extinctions and implications for the future

Abstract Using data from two palaeontological databases, MIOMAP and FAUNMAP (now linked as NEOMAP), we explore how late Quaternary species loss compared in large and small mammals by determining palaeospecies-area relationships (PSARs) at 19 temporal intervals ranging from c. 30 million to 500 years ago in 10 different biogeographical provinces in the USA. We found that mammalian diversity of both large and small mammals remained relatively stable from 30 million years ago up until both crashed near the Pleistocene–Holocene transition. The diversity crash had two components: the well-known megafaunal extinction that amounted to c. 21% of the pre-crash species, and collateral biodiversity loss due to biogeographical range reductions. Collateral loss resulted in large mammal diversity regionally falling an additional 6–31% above extinction loss, and small mammal diversity falling 16–51%, even though very few small mammals suffered extinction. These results imply that collateral losses due to biogeographical range adjustments may effectively double the regional diversity loss during an extinction event, substantially magnifying the ecological ramifications of the extinctions themselves. This is of interest in forecasting future ecological impacts of mammal extinctions, given that c. 8% of USA mammal species, and 22% of mammal species worldwide, are now considered ‘Threatened’ by the IUCN.

Easily-accessible digital palaeontological databases-a new perspective for the storage of palaeontological information

Easily-accessible digital palaeontological databases-a new perspective for the storage of palaeontological informationTechniques that allow to render diverse types of palaeontological data as publicly available internet resources are described. In order to develop an easily accessible digital palaeontological database, three steps should be followed: (1) digitization of the studied specimens, (2) acquisition of morphometric data, and (3) contribution of the data to open and searchable geoinformatic (palaeontological) databases. Digital data should be submitted to internet databases that allow a user to fetch various types of information from dispersed sources (semantic web services).

Palaeontological databases for palaeobiogeography, palaeoecology and biodiversity: a question of scale

Abstract Computerized databases provide an essential tool for investigating large-scale spatial and temporal palaeontological problems. Although advances in both software and hardware have made the logistics of building a database much easier, fundamental problems remain concerning the representation and qualification of the data. Data from the fossil record are highly heterogeneous. Databases must be designed to account for variations in scale (grain, resolution), inconsistency in the data, and potential errors (inaccuracy). These issues vary with the scope of the study (extent), the biological group, and the nature and scale-dependence of supplementary, non-biological datasets (e.g. climate and ocean parameters). With the application of desktop geographic information systems (GIS) to global Earth systems science, and the ability to efficiently integrate and query large, diverse datasets, the need to ensure robust qualification of data, especially scale, has become all the more essential. This chapter examines some of the issues involved, defines terminology and offers pragmatic solutions.

Species richness and abundance patterns of Tethyan Cretaceous rudist bivalves (Mollusca: Hippuritacea) in the central-eastern Mediterranean and Middle East, analysed from a palaeontological database

Data about the stratigraphical and regional distribution of Cretaceous rudist bivalves in the central-eastern Mediterranean and Middle East from the Barremian to the Maastrichtian have been compiled in a taxonomic databank system. The investigated region comprises northern, central and southern regions of the Cretaceous Tethys. The regionally different quality of taxonomic data is critically discussed. Both species richness and abundance (number of species records) peak in the Early Aptian, Late Cenomanian and Early Campanian. Temporal patterns in species richness are examined in relation to evolutionary innovations of the group. Crises in species richness and abundance during the Early and mid-Cretaceous were coeval with oceanic anoxia associated with platform drowning. Also, regional emergence affected large parts of the Apulian Plate and other central Tethyan carbonate platforms during the mid-Cretaceous period of globally high sea level, so that these crises can be attributed to regional environmental perturbations, induced by either oceanic anoxia or tectonic movements. The Cenomanian–Turonian transition marks an important faunal turnover, as indicated by the demise of taxonomic groups which are characterised by recumbent ecological morphotypes and predominantly aragonitic shells. During the Turonian, they were replaced by associations dominated by largely calcitic Radiolitidae and Hippuritidae, among which elevator morphotypes dominated. The stratigraphy of many post-Turonian deposits in the studied region is too imprecise for a detailed analysis of Late Cretaceous distributional patterns, and the demise of rudists during the Maastrichtian in particular. The regional pattern of species richness and abundance is similar throughout most of the investigated region. A notable exception is the broad north-eastern African shelf from Libya to Lebanon, where rudists were almost completely absent after the Coniacian. This coincided with shallow-water phosphorite and black-shale formation on the extended shelf of this region, indicating the upwelling of nutrient-rich waters and stagnant conditions. During this time (Campanian–Maastrichtian), species-rich associations thrived along the north-eastern Afro-Arabian margin, now exposed in south-eastern Turkey, Iran, the United Arab Emirates (UAE) and Oman. This region forms the single distinct faunal province during the Cretaceous in the studied region, as indicated by an endemism of 40% at the genus level. The low species richness and abundance of Hippuritidae on Turonian–Maastrichtian central Tethyan carbonate platforms, when compared with regions having mixed calcareous–siliciclastic sedimentation, is interpreted to argue against a widespread photosymbiosis in the group. Several aspects of this study highlight the importance of regional tectonic and oceanographic controls of distributional, and perhaps also evolutionary, patterns of rudist bivalves. Their delineation still suffers from the regionally different quality of stratigraphical and taxonomic data.

Numerical palaeobiology: computer-based modelling and analysis of fossils and their distributions

Quantitative and Morphometric Methods in Taxonomy (D. Harper & A. Owen). Phylogenetic Systematics and Palaeontology (S. Carlson). Computer-based Serial Section Reconstruction (M. Herbert). Statistical and Imaging Methods Applied to Deformed Fossils (N. Hughes). Computer Models of Fossil Morphology (A. Swan). Quantitative Biostratigraphy (H. Armstrong). The Quantitative Description of Biotic Change Using Palaeontological Databases (K. Johnson & T. McCormick). The History of Life: Large Databases in Palaeontology (M. Benton). Community Analysis (W. Etter). Multivariate Techniques in Palynofacies Analysis (J. Smith). Quantitative Approaches to the Resolution of Taxonomic Problems in Invertebrate Ichnology (P. Orr). A New Approach to Seriation (P. Ryan, et al.). Indexes.

Self-similarity of extinction statistics in the fossil record

The dynamical processes underlying evolution over geological timescales remain unclear1,2. Analyses of time series of the fossil record have highlighted the possible signature of periodicity in mass extinctions3,4, perhaps owing to external influences such as meteorite impacts. More recently the fluctuations in the evolutionary record have been proposed to result from intrinsic nonlinear dynamics for which self-organized criticality provides an appropriate theoretical framework5,6,7. A consequence of this controversial8 conjecture is that the fluctuations should be self-similar, exhibiting scaling behaviour like that seen in other biological9 and socioeconomic10,11 systems. The self-similar character is described by a 1/f power spectrum P(f), which measures the contributions of each frequency f to the overall time series. If self-similarity is present, then P(f) ≈ f− β with 0 < β <2. This idea has not been sufficiently tested, however, owing to a lack of adequate data. Here we explore the statistical fluctuation structure of several time series obtained from available palaeontological data bases, particularly the new ‘Fossil Record 2’18. We find that these data indeed show self-similar fluctuations characterized by a 1/f spectrum. These findings support the idea that a nonlinear response of the biosphere to perturbations provides the main mechanism for the distribution of extinction events.

The evolution and global migration of the Aceraceae

This article shows how a large palaeontological database (the Plant Fossil Record version 2.2, available on the Internet) can be used to draw evolutionary and migratory pathways. 2946 published records of the family Aceraceae have been found as leaf, fruit and seed, wood or pollen fossils, and their geographical and stratigraphical distributions are presented here in different graphical forms. Manipulation and analysis of the data have produced palaeo-geographic maps of these distributions, curves of the number of records in five global regions over the last 100 million years, and cladograms of taxa and their geography. The results give objective evidence which shows that early members of the family became well established on upland slopes of the north Pacific rim during the Palaeogene. Some of these early species migrated eastwards across Greenland to Europe before the North Atlantic opened to the Arctic. Later and larger migrations started in the Oligocene, from Asia westwards to central Europe, bringing a diversification in species both there and in the regions of origin.