Fossil Occurrence Data Research Articles

The Effect of Fossil Sampling on the Estimation of Divergence Times with the Fossilized Birth-Death Process.

Timescales are of fundamental importance to evolutionary biology as they facilitate hypothesis tests of historical evolutionary processes. Through the incorporation of fossil occurrence data, the fossilized birth-death (FBD) process provides a framework for estimating divergence times using more paleontological data than traditional node calibration approaches have allowed. The inclusion of more data can refine evolutionary timescale estimates, but for many taxonomic groups it is computationally infeasible to include all available fossil occurrence data. Here, we utilize both empirical data and a simulation framework to identify approaches to subsampling fossil occurrence data that result in the most accurate estimates of divergence times. To achieve this we assess the performance of the FBD-Skyline model when implementing multiple approaches to incorporating subsampled fossil occurrence data. Our results demonstrate that it is necessary to account for all available fossil occurrence data to achieve the most accurate estimates of clade age. We show that this can be achieved if an empirical Bayes approach, accounting for fossil sampling through time, is applied to the FBD process. Random subsampling of occurrence data can lead to estimates of clade age that are incompatible with fossil evidence if no control over the affinities of fossil occurrences is enforced. Our results call into question the accuracy of previous divergence time studies incorporating the FBD process that have used only a subsample of all available fossil occurrence data.

Cascading trend of Early Paleozoic marine radiations paused by Late Ordovician extinctions.

The greatest relative changes in marine biodiversity accumulation occurred during the Early Paleozoic. The precision of temporal constraints on these changes is crude, hampering our understanding of their timing, duration, and links to causal mechanisms. We match fossil occurrence data to their lithostratigraphical ranges in the Paleobiology Database and correlate this inferred taxon range to a constructed set of biostratigraphically defined high-resolution time slices. In addition, we apply capture-recapture modeling approaches to calculate a biodiversity curve that also considers taphonomy and sampling biases with four times better resolution of previous estimates. Our method reveals a stepwise biodiversity increase with distinct Cambrian and Ordovician radiation events that are clearly separated by a 50-million-year-long period of slow biodiversity accumulation. The Ordovician Radiation is confined to a 15-million-year phase after which the Late Ordovician extinctions lowered generic richness and further delayed a biodiversity rebound by at least 35 million years. Based on a first-differences approach on potential abiotic drivers controlling richness, we find an overall correlation with oxygen levels, with temperature also exhibiting a coordinated trend once equatorial sea surface temperatures fell to present-day levels during the Middle Ordovician Darriwilian Age. Contrary to the traditional view of the Late Ordovician extinctions, our study suggests a protracted crisis interval linked to intense volcanism during the middle Late Ordovician Katian Age. As richness levels did not return to prior levels during the Silurian-a time of continental amalgamation-we further argue that plate tectonics exerted an overarching control on biodiversity accumulation.

FossilSim: An r package for simulating fossil occurrence data under mechanistic models of preservation and recovery

Abstract Key features of the fossil record that present challenges for integrating palaeontological and phylogenetic datasets include (i) non‐uniform fossil recovery, (ii) stratigraphic age uncertainty and (iii) inconsistencies in the definition of species origination and taxonomy. We present an r package FossilSim that can be used to simulate and visualise fossil data for phylogenetic analysis under a range of flexible models. The package includes interval‐, environment‐ and lineage‐dependent models of fossil recovery that can be combined with models of stratigraphic age uncertainty and species evolution. The package input and output can be used in combination with the wide range of existing phylogenetic and palaeontological r packages. We also provide functions for converting between FossilSim and paleotree objects. Simulated datasets provide enormous potential to assess the performance of phylogenetic methods and to explore the impact of using fossil occurrence databases on parameter estimation in macroevolution.

The stability of coastal benthic biogeography over the last 10 million years

AbstractAimWe demarcate marine benthic global bioregions based on fossil and recent occurrence data. Our main goal is to compare past and present biogeography and to extract major abiotic drivers of biogeographical patterns. We specifically test the hypothesis that global biogeography has changed markedly after the climatic fluctuations of the past 10 Myr.LocationWorldwide.Time periodRecent; late Miocene–Pleistocene interval.Major taxa studiedBenthic taxa with a rich fossil record: Bivalvia, Brachiopoda, Bryozoa, Gastropoda, Echinodermata, Decapoda and reef corals.MethodsWe use occurrence data from the Ocean Biogeographic Information System (OBIS) and the Paleobiology Database to construct compositional networks and outline objective marine bioregions of benthic marine invertebrates using the “infomap” community detection algorithm. We assess the association of modern bioregions with a variety of environmental parameters by applying multivariate statistical analyses, such as principal components analysis, random forests and multiple logistic regressions.ResultsRecent first‐order bioregions for the coastal ocean are, in general, consistent across all taxa. Seawater temperature surpasses nutrients, primary production and salinity as a predictor of modern bioregion distributions. Despite substantial climatic variations, late Cenozoic biogeographical patterns recorded in fossils are very similar to modern ones.Main conclusionsBiogeographical boundaries within oceans are strongly controlled by temperature gradients, but open oceanic and continental barriers determine the global biogeographical structure. The joint structure of a landmass distribution, deep ocean basins and the latitudinal temperature gradient defines bioregionalization of the benthic marine habitat, which did not change substantially over the past 10 Myr.

Detecting diversification rates in relation to preservation and tectonic history from simulated fossil records

AbstractFor mammals today, mountains are diverse ecosystems globally, yet the strong relationship between species richness and topographic complexity is not a persistent feature of the fossil record. Based on fossil-occurrence data, diversity and diversification rates in the intermontane western North America varied through time, increasing significantly during an interval of global warming and regional intensification of tectonic activity from 18 to 14 Ma. However, our ability to infer origination and extinction rates reliably from the fossil record is affected by variation in preservation history. To investigate the influence of preservation on estimates of diversification rates, I simulated fossil records under four alternative diversification hypotheses and six preservation scenarios. Diversification hypotheses included tectonically controlled speciation pulses, while preservation scenarios were based on common trends (e.g., increasing rock record toward the present) or derived from fossil occurrences and the continental rock record. For each scenario, I estimated origination, extinction, and diversification rates using three standard methods—per capita, three-timer, and capture–mark–recapture (CMR) metrics—and evaluated the ability of the simulated fossil records to accurately recover the underlying diversification dynamics. Despite variable and low preservation probabilities, simulated fossil records retained the signal of true rates in several of the scenarios. The three metrics did not exhibit similar behavior under each preservation scenario: while three-timer and CMR metrics produced more accurate rate estimates, per capita rates tended to better reproduce true shifts in origination rates. All metrics suffered from spurious peaks in origination and extinction rates when highly volatile preservation impacted the simulated record. Results from these simulations indicate that elevated diversification rates in relation to tectonic activity during the middle Miocene are likely to be evident in the fossil record, even if preservation in the North American fossil record was variable. Input from the past is necessary to evaluate the ultimate mechanisms underlying speciation and extinction dynamics.

Morphological and histological evidence for the oldest known softshell turtles from Japan

ABSTRACT Herein we report morphologically and histologically diagnostic trionychid specimens from the Barremian–Aptian (129.4–113.0 Ma) of Japan. One specimen (FPDM-V9487) is an associated skeleton that consists of a scapula, a humerus, an ischium, and hypoplastra. The limb and girdle bones are similar in morphology to those of modern trionychids. The hypoplastron also resembles that of modern trionychids; however, it is distinctive in that it completely lacks callosities. The other three new specimens are fragmentary costals that show a reduction in the shell bones and an absence of scute sulci. Two of the newly reported costals and FPDM-V0127 were examined histologically. Bone fiber bundles organized in a plywood-like structure, which is unique to trionychids, were identified. Fossil occurrence data indicate that morphologically and histologically typical trionychids already inhabited the coastal region of Asia (e.g., western Japan) as early as the Aptian. In contrast, the Hauterivian–Aptian stem trionychid Kappachelys okurai from Japan does not show a plywood-like shell microstructure, suggesting that K. okurai could be the earliest-branching taxon of known stem trionychids or a carettochelyid. Our paleobiogeographic compilation suggests that the spread of wetlands in the Northern Hemisphere and the high global temperature during the middle Cretaceous (Aptian–Turonian, 125.0–89.8 Ma) might have contributed to the dispersal of trionychids from Asia, allowing for the establishment of this modern freshwater reptilian fauna. Citation for this article: Nakajima, Y., I. G. Danilov, R. Hirayama, T. Sonoda, and T. M. Scheyer. 2017. Morphological and histological evidence for the oldest known softshell turtles from Japan. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2017.1278606.

Sea level regulated tetrapod diversity dynamics through the Jurassic/Cretaceous interval.

Reconstructing deep time trends in biodiversity remains a central goal for palaeobiologists, but our understanding of the magnitude and tempo of extinctions and radiations is confounded by uneven sampling of the fossil record. In particular, the Jurassic/Cretaceous (J/K) boundary, 145 million years ago, remains poorly understood, despite an apparent minor extinction and the radiation of numerous important clades. Here we apply a rigorous subsampling approach to a comprehensive tetrapod fossil occurrence data set to assess the group's macroevolutionary dynamics through the J/K transition. Although much of the signal is exclusively European, almost every higher tetrapod group was affected by a substantial decline across the boundary, culminating in the extinction of several important clades and the ecological release and radiation of numerous modern tetrapod groups. Variation in eustatic sea level was the primary driver of these patterns, controlling biodiversity through availability of shallow marine environments and via allopatric speciation on land.

The Paleobiology Database application programming interface

AbstractThe Paleobiology Database (PBDB; https://paleobiodb.org) consists of geographically and temporally explicit, taxonomically identified fossil occurrence data. The taxonomy utilized by the PBDB is not static, but is instead dynamically generated using an algorithm applied to separately managed taxonomic authority and opinion data. The PBDB owes its existence to many individuals, some of whom have entered more than 1.26 million fossil occurrences and over 570,000 taxonomic opinions, and some of whom have developed and maintained supporting infrastructure and analysis tools. Here, we provide an overview of the data model currently used by the PBDB and then briefly describe how this model is exposed via an Application Programming Interface (API). Our objective is to outline how PBDB data can now be accessed within individual scientific workflows, used to develop independently managed educational and scientific applications, and accessed to forge dynamic, near real-time connections to other data resources.

A simple way to improve multivariate analyses of paleoecological data sets

AbstractMultivariate methods such as cluster analysis and ordination are basic to paleoecology, but the messy nature of fossil occurrence data often makes it difficult to recover clear patterns. A recently described faunal similarity index based on the Forbes coefficient improves results when its complement is employed as a distance metric. This index involves adding terms to the Forbes equation and ignoring one of the counts it employs (that of species found in neither of the samples under consideration). Analyses of simulated data matrices demonstrate its advantages. These matrices include large and small samples from two partially overlapping species pools. In a cluster analysis, the widely used Dice coefficient and the Euclidean distance metric both create groupings that reflect sample size, the Simpson index suggests large differences that do not exist, and the corrected Forbes index creates groupings based strictly on true faunal overlap. In a principal coordinates analysis (PCoA) the Forbes index almost removes the sample-size signal but other approaches create a second axis strongly dominated by sample size. Meanwhile, species lists of late Pleistocene mammals from the United States capture biogeographic signals that standard ordination methods do recover, but the adjusted Forbes coefficient spaces the points out more sensibly. Finally, when biome-scale lists for living mammals are added to the data set and extinct species are removed, correspondence analysis misleadingly separates out the biome lists, and PCoA based on the Dice coefficient places them to the edge of the cloud of fossil assemblage data points. PCoA based on the Forbes index places them in more reasonable positions. Thus, only the adjusted Forbes index is able to recover true biological patterns. These results suggest that the index may be useful in analyzing not only paleontological data sets but any data set that includes species lists having highly variable lengths.

Paleo-Antarctic rainforest into the modern Old World tropics: the rich past and threatened future of the "southern wet forest survivors".

• Have Gondwanan rainforest floral associations survived? Where do they occur today? Have they survived continuously in particular locations? How significant is their living floristic signal? We revisit these classic questions in light of significant recent increases in relevant paleobotanical data.• We traced the extinction and persistence of lineages and associations through the past across four now separated regions-Australia, New Zealand, Patagonia, and Antarctica-using fossil occurrence data from 63 well-dated Gondwanan rainforest sites and 396 constituent taxa. Fossil sites were allocated to four age groups: Cretaceous, Paleocene-Eocene, Neogene plus Oligocene, and Pleistocene. We compared the modern and ancient distributions of lineages represented in the fossil record to see if dissimilarity increased with time. We quantified similarity-dissimilarity of composition and taxonomic structure among fossil assemblages, and between fossil and modern assemblages.• Strong similarities between ancient Patagonia and Australia confirmed shared Gondwanan rainforest history, but more of the lineages persisted in Australia. Samples of ancient Australia grouped with the extant floras of Australia, New Guinea, New Caledonia, Fiji, and Mt. Kinabalu. Decreasing similarity through time among the regional floras of Antarctica, Patagonia, New Zealand, and southern Australia reflects multiple extinction events.• Gondwanan rainforest lineages contribute significantly to modern rainforest community assembly and often co-occur in widely separated assemblages far from their early fossil records. Understanding how and where lineages from ancient Gondwanan assemblages co-occur today has implications for the conservation of global rainforest vegetation, including in the Old World tropics.

PyRate: a new program to estimate speciation and extinction rates from incomplete fossil data

Summary Despite the advancement of phylogenetic methods to estimate speciation and extinction rates, their power can be limited under variable rates, in particular for clades with high extinction rates and small number of extant species. Fossil data can provide a powerful alternative source of information to investigate diversification processes. Here, we present PyRate, a computer program to estimate speciation and extinction rates and their temporal dynamics from fossil occurrence data. The rates are inferred in a Bayesian framework and are comparable to those estimated from phylogenetic trees. We describe how PyRate can be used to explore different models of diversification. In addition to the diversification rates, it provides estimates of the parameters of the preservation process (fossilization and sampling) and the times of speciation and extinction of each species in the data set. Moreover, we develop a new birth–death model to correlate the variation of speciation/extinction rates with changes of a continuous trait. Finally, we demonstrate the use of Bayes factors for model selection and show how the posterior estimates of a PyRate analysis can be used to generate calibration densities for Bayesian molecular clock analysis. PyRate is an open‐source command‐line Python program available at http://sourceforge.net/projects/pyrate/.

Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data

The temporal dynamics of species diversity are shaped by variations in the rates of speciation and extinction, and there is a long history of inferring these rates using first and last appearances of taxa in the fossil record. Understanding diversity dynamics critically depends on unbiased estimates of the unobserved times of speciation and extinction for all lineages, but the inference of these parameters is challenging due to the complex nature of the available data. Here, we present a new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record. The rates are allowed to vary through time independently of each other, and the probability of preservation and sampling is explicitly incorporated in the model to estimate the true lifespan of each lineage. We implement a Bayesian algorithm to assess the presence of rate shifts by exploring alternative diversification models. Tests on a range of simulated data sets reveal the accuracy and robustness of our approach against violations of the underlying assumptions and various degrees of data incompleteness. Finally, we demonstrate the application of our method with the diversification of the mammal family Rhinocerotidae and reveal a complex history of repeated and independent temporal shifts of both speciation and extinction rates, leading to the expansion and subsequent decline of the group. The estimated parameters of the birth-death process implemented here are directly comparable with those obtained from dated molecular phylogenies. Thus, our model represents a step towards integrating phylogenetic and fossil information to infer macroevolutionary processes.

The environmental structure of trilobite morphological disparity

Despite the mounting evidence that taxonomic diversity dynamics are patterned environmentally and that taxonomic diversity and morphological disparity are decoupled both temporally and spatially in many clades, very little work has been done to assess whether disparity is also influenced by environment. Here I investigate whether trilobite disparity shows environmental patterning through time. I used the method developed by Simpson and Harnik (2009) for estimating latitudinal, substrate, and bathymetric affinities from fossil occurrence data, downloaded from the Paleobiology Database. This method has the advantages that the biological null hypothesis is explicitly separated from the expectation due to sampling, and that the posterior probability can be used to infer degree of preference for one habitat compared to another. To measure morphology, I used a data set of outlines of the trilobite cranidium from Foote (1993). Many of the species in this data set are not represented in the Paleobiology Database in sufficient numbers to assess species-level affinity for these taxa, but species-level affinity could be estimated with high fidelity by using genus-level affinities. Results show that cranidial morphological diversity was structured by environmental preferences of the taxa but the structure was complex and changed through time. In particular, there was little differentiation in morphospace around latitudinal, substrate, or bathymetric affinity during the Cambrian. In contrast, both diversification and expansion into previously unoccupied areas of morphospace during the Ordovician were dominated by tropical, deeper-water taxa.

Is Rapoport's rule a recent phenomenon? A deep time perspective on potential causal mechanisms

Macroecology strives to identify ecological patterns on broad spatial and temporal scales. One such pattern, Rapoport's rule, describes the tendency of species' latitudinal ranges to increase with increasing latitude. Several mechanisms have been proposed to explain this rule. Some invoke climate, either through glaciation driving differential extinction of northern species or through increased seasonal variability at higher latitudes causing higher thermal tolerances and subsequently larger ranges. Alternatively, continental tapering or higher interspecific competition at lower latitudes may be responsible. Assessing the incidence of Rapoport's rule through deep time can help to distinguish between competing explanations. Using fossil occurrence data from the Palaeobiology Database, we test these hypotheses by evaluating mammalian compliance with the rule throughout the Caenozoic of North America. Adherence to Rapoport's rule primarily coincides with periods of intense cooling and increased seasonality, suggesting that extinctions caused by changing climate may have played an important role in erecting the latitudinal gradients in range sizes seen today.

Contrasting patterns and connections of rock and biotic diversity in the marine and non-marine fossil records of North America

Macrostratigraphy uses packages of continuous sedimentation that are bound by hiatuses of non-deposition, erosion, or alternations between environments/lithologies to characterize spatiotemporal patterns of sedimentation. Previous work has linked the macrostratigraphy of marine shelf environments to many different macroevolutionary patterns in the marine animal fossil record. Here we use an improved macrostratigraphic database for North America, combined with fossil occurrence data in the Paleobiology Database, to show that macroevolutionary and macrostratigraphic patterns are correlated more strongly in marine environments than in non-marine environments. We also test the hypothesis that the temporal distribution of lithological diversity (measured as evenness, similar to ecological evenness based on the number of lithostratigraphic units with a given lithologic type within each time interval) has a relationship to genus-level taxonomic diversity in both the marine and non-marine realms. Uneven sampling of lithologies and their corresponding depositional environments can bias our perception of taxonomic diversity by causing taxa from poorly sampled environments to be underrepresented in the fossil record. Our results show a negative correlation between lithologic evenness and marine vertebrate generic richness — less even sampling of lithologies corresponds to a higher observed taxonomic richness, and no correlation with lithologic evenness and non-marine diversity measures. This suggests a difference in the relationship between biologic and sedimentary processes at work in the marine and non-marine realms, and possibly differences in the magnitude of the bias imposed by the rock record on the underlying biologic patterns.

A field-based analysis of the accuracy of niche models applied to the fossil record

The use of ecological niche modeling (ENM) to estimate the geographic ranges of species is widely employed with modern fauna and is becoming more widespread in paleontology. Herein, field validation is utilized to assess the predictive accuracy of ENM methods for Paleozoic brachiopod species. This study represents the first field validation analysis of ENM methods in the fossil record. Previously published species distributions models for 8 Late Ordovician brachiopod species from the Cincinnati, Ohio region (United States) developed using GARP (Genetic Algorithm using Rule-set Prediction) were assessed for accuracy by comparing species occurrence data from a newly available set of 18 localities with the original species distribution models. Based on this data, the statistical significance of the original model set was assessed; 18 of the 22 original models were demonstrated to be statistically significant, based on field validation. Of the 140 individual species occurrences assessed, 60.8% were accurately predicted, 9.2% exhibited over prediction, and 30% exhibited under prediction. Accurate results were more common for species modeled from the greatest number of species occurrence points. The least accurate species models developed were for eurytopic species or those for which taxonomic affinities are unclear. Results indicate that with ample outcrop, well-defined stratigraphy, and sufficient fossil occurrence data, ENM methods could be successfully applied to many intervals in Earth history.

Stratigraphic distribution of marine fossils in North America

The stratigraphic distribution of fossils reflects a combination of physical and biological factors. Although many studies have addressed the distribution of fossils at a basin scale and within sedimentary sequences spanning 10 4 –10 6 yr, little is known about the distribution of fossils within longer duration sedimentary successions covering broad geographic regions. Here we combine a North American macrostratigraphic database with fossil occurrence data from the Paleobiology Database to quantify the stratigraphic distribution of fossils within hiatus-bound marine sedimentary rock packages that have a mean duration of 10 7 yr. We find that fossil collections and marine genera are, when averaged over all Phanerozoic sedimentary rock packages, more abundant than expected in the top 40% of package durations, and less common than expected in the bottom ∼25%. Generic first and last appearance datums (FADs and LADs) in North America are not randomly distributed among fossil collections. Instead, LADs are more common than expected in the top ∼20% of package durations, whereas FADs are more uniformly distributed. This result is not consistent with an unconformity-related sampling bias, but is indicative of greater congruence in the temporal scales over which genus extinction and regression occur than genus initiation and transgression. These results support the hypothesis that macroevolution, particularly genus extinction, and large-scale patterns of sedimentation share a common set of forcing mechanisms that are related to the formation and destruction of shallow-marine habitats.

Macrostratigraphy and macroevolution in marine environments: testing the common-cause hypothesis

Abstract Quantitative patterns in the sedimentary rock record predict many different macroevolutionary patterns in the fossil record, but the reasons for this predictability remain uncertain. There are two competing, but non-mutually exclusive, hypotheses: (1) similarities reflect a sampling bias imposed by variable and incomplete sampling of fossils, and (2) similarities reflect environmental perturbations that influence both the patterns of sedimentation and macroevolution (i.e., common-cause). Macrostratigraphy, which is based on the quantitative analysis of hiatus-bound rock packages, permits variation in the rock record to be expressed in terms of rock quantity and, more importantly, spatiotemporal continuity. In combination with spatially-explicit fossil occurrence data in the Paleobiology Database, it is now possible to more rigorously test alternative hypotheses for similarities in the rock and fossil records and to start distinguishing between geologically-controlled sampling bias and the common-cause hypothesis. Here we summarize results from measuring the intersection of Macrostrat and the Paleobiology Database. Our results suggest that patterns in the fossil record are not dominated by large-scale stratigraphic biases. Instead, they suggest that linkages between multiple Earth systems are driving both spatiotemporal patterns of sedimentation and macroevolution.

Marine benthic invertebrates from the Upper Jurassic of northern Ethiopia and their biogeographic affinities

We present the first modern description of corals, brachiopods and bivalves from the Antalo Limestone in the Mekele Outlier of northern Ethiopia. This fauna is largely of Oxfordian age and lived in shallow subtidal environments and in small patch reefs. In combining our new data with fossil occurrence data from the Paleobiology Database, we conducted multidimensional scaling analyses to assess biogeographic patterns and the delineation of the Ethiopian Province for the Callovian to Kimmeridgian stages. Results suggest that an Ethiopian Province is indeed evident for our focal groups, but this is more confined than traditionally assumed. The so defined Ethiopian Province includes Tunisia, the Levant, Arabia and much of East Africa, but excludes Tanzania and India. The special status of India and Tanzania is perhaps due to latitudinal gradients in faunal composition.

THE PALEOECOLOGICAL SIGNIFICANCE OF OPPORTUNISTIC SPECIES

Opportunistic species are not resource-limited. With favorable events they can increase rapidly in numbers. Such species populations are typically very unstable and may become extinct very quickly. In contrast, equilibrium species populations are resource-limited and maintain stable population levels. The identification of explosive opportunists in the fossil record is an important means of recognizing animal communities which were primarily controlled by the physical, and not the biotic, environment. In young environments of high physiological stress where animal communities are physically controlled, most species are opportunistic. In old and biologically accommodated communities opportunists are relatively rare. Explosive opportunists can be recognized by means of distributional, relative abundance and fossil occurrence data.