Determining whether a species has gone extinct is a central problem in both paleobiology and conservation biology. Past literature has mostly employed equations that yield confidence intervals around the endpoints of temporal ranges. These frequentist methods calculate the chance of not having seen a species lately given that it is still alive (a conditional probability). However, any reasonable person would instead want to know the chance that a species is extinct given that it has not been seen (the posterior probability). Here, I present a simple Bayesian equation that estimates posteriors. It uninterestingly assumes that the sampling probability equals the frequency of sightings within the range. It interestingly sets the prior probability of going extinct during any one time interval (E) by assuming that extinction is an exponential decay process and there is a 50% chance a species has gone extinct by the end of its observed range. The range is first adjusted for undersampling by using a routine equation. Bayes' theorem is then used to compute the posterior for interval 1 (ε1), which becomes the prior for interval 2. The following posterior ε2 again incorporates E because extinction might have happened instead during interval 2. The posteriors are called “creeping-shadow-of-a-doubt values” to emphasize the uniquely iterative nature of the calculation. Simulations show that the method is highly accurate and precise given moderate to high sampling probabilities and otherwise conservative, robust to random variation in sampling, and able to detect extinction pulses after a short lag. Improving the method by having it consider clustering of sightings makes it highly resilient to trends in sampling. Example calculations involving recently extinct Costa Rican frogs and Maastrichtian ammonites show that the method helps to evaluate the status of critically endangered species and identify species likely to have gone extinct below some stratigraphic horizon.

The organic matrix components of a fossil ammonoid shell from the Upper Cretaceous, can be separated into sub-fractions which are generally comparable to those found in extant Nautilus, using ion exchange chromatography. This suggests that at least portions of these components are sufficiently well preserved to interact characteristically with the ion exchange resin. Amino acid compositions of these sub-fractions, however, do not resemble Nautilus organic matrix sub-fractions, indicating that considerable diagenetic alteration of this material has taken place.

Ptychopariid trilobites from the Marjumiid biomere of Laurentia underwent a statistically significant morphological diversification that is concordant with proposed adaptive radiations of trilobites in each of the Cambrian biomeres. An analysis of a subset consisting of the biomere's most characteristic taxa, the Asaphiscacea, Raymondinacea, and Marjumiacea, also illustrates this morphological diversification. In detail, the total data set and subset show a limited range of morphologies near the base of the biomere and a large increase in range in the upper portion of the biomere.

Regional assemblages from the Appalachians, Great Basin, and Texas were also studied to determine if they too show the larger-scale macroevolutionary patterns of trilobites from Laurentia as a whole. The regional assemblages illustrate similar, but not identical, morphological diversifications, which are also similar to the overall Laurentian pattern. Subsets of the characteristic taxa also show this diversification. These results suggest that regional assemblages can be used to investigate these larger-scale macroevolutionary patterns.

Causal mechanisms for the diversification patterns are not clear. Potential mechanisms include: (1) endemic evolution of new morphologies in Laurentia; (2) migration of new morphologies, including intra- and inter-continental migrations; and (3) environmental controls over the distribution of morphologies. Likely causes for the morphological diversification and its similarity among regions probably include aspects of all three mechanisms.

Taxon-age distributions were compiled for families of marine animals surviving or becoming extinct in each stage of the Phanerozoic. I demonstrate, through the use of a modified bootstrap analysis, that there is no difference between the longevity of families becoming extinct during times of background extinction and times of mass extinction. In both mass and background extinction intervals the mean age of families that become extinct is 2 standard deviations below the geometric mean taxon age of families available for extinction. Young families are more susceptible to extinction, perhaps as the result of lower species richness or of occupying a smaller geographic range. There is no tendency during mass extinctions toward loss of families with different taxon ages other than those that become extinct during background times. Thus, in terms of family survival, mass extinction appears to be an exaggeration of processes of background extinction.

Studies of extinction in the fossil record commonly involve comparisons of taxonomic extinction rates, often expressed as the percentage of taxa (e.g., families or genera) going extinct in a time interval. Such extinction rates may be influenced by factors that do not reflect the intrinsic severity of an extinction trigger. Two identical triggering events (e.g., bolide impacts, sea level changes, volcanic eruptions) could lead to different taxonomic extinction rates depending on factors specific to the time interval in which they occur, such as the susceptibility of the fauna or flora to extinction, the stability of food webs, the positions of the continents, and so on. Thus, it is possible for an extinction event with a higher taxonomic extinction rate to be caused by an intrinsically less severe trigger, compared to an event with a lower taxonomic extinction rate.

Here, we isolate the effects of taxonomic susceptibility on extinction rates. Specifically, we quantify the extent to which the taxonomic extinction rate in a substage is elevated or depressed by the vulnerability to extinction of classes extant in that substage. Using a logistic regression model, we estimate that the taxonomic susceptibility of marine fauna to extinction has generally declined through the Phanerozoic, and we adjust the observed extinction rate in each substage to estimate the intrinsic extinction severity more accurately. We find that mass extinctions do not generally occur during intervals of unusually high susceptibility, although susceptibility sometimes increases in post-extinction recovery intervals. Furthermore, the susceptibility of specific animal classes to extinction is generally similar in times of background and mass extinction, providing no evidence for differing regimes of extinction selectivity. Finally, we find an inverse correlation between extinction rate within substages and the evenness of diversity of major taxonomic groups, but further analyses indicate that low evenness itself does not cause high rates of extinction.

Radiodonts (stem Euarthropoda) were ecologically diverse, but species generally displayed limited functional specialization of appendages along the body axis compared with crown group euarthropods. This is puzzling, because such functional specialization is considered to have been an important driver of euarthropod ecological diversification. One way to circumvent this constraint could have been the functional specialization of different parts of the frontal appendages, known to have been ecologically important in radiodonts. This hypothesis has yet to be tested explicitly. Here we redescribe the poorly known mid-Cambrian hurdiid radiodont Stanleycaris hirpex from the Burgess Shale (Stephen Formation) and quantitatively assess functional specialization of the frontal appendages of stem euarthropods. The appendages of Stanleycaris are composed of 14 podomeres, variously differentiated by their possession of pectinate endites, mono- to trifurcate medial gnathites, and outer spines. The oral cone is tetraradially organized and can be uniquely distinguished from those of other hurdiids by the presence of 28 rather than 32 smooth tridentate plates. Our phylogenetic analysis finds Stanleycaris in a grade of hurdiids retaining plesiomorphic raptorial appendicular functionality alongside derived adaptations for sweep feeding and large, bilaterally opposed gnathites. We conclude that the latter performed a masticatory function, convergent with gnathal structures like mandibles in various panarthropods. Taken together, Stanleycaris and similar hurdiids provide an extreme example of the evolution of division of labor within the appendage of a stem euarthropod and suggest that this innovation may have facilitated the functional transition, from raptorial to sweep feeding, at the origin of the hurdiid clade.

The rapid and accurate taxonomic identification of fossils is of great significance in paleontology, biostratigraphy, and other fields. However, taxonomic identification is often labor-intensive and tedious, and the requisition of extensive prior knowledge about a taxonomic group also requires long-term training. Moreover, identification results are often inconsistent across researchers and communities. Accordingly, in this study, we used deep learning to support taxonomic identification. We used web crawlers to collect the Fossil Image Dataset (FID) via the Internet, obtaining 415,339 images belonging to 50 fossil clades. Then we trained three powerful convolutional neural networks on a high-performance workstation. The Inception-ResNet-v2 architecture achieved an average accuracy of 0.90 in the test dataset when transfer learning was applied. The clades of microfossils and vertebrate fossils exhibited the highest identification accuracies of 0.95 and 0.90, respectively. In contrast, clades of sponges, bryozoans, and trace fossils with various morphologies or with few samples in the dataset exhibited a performance below 0.80. Visual explanation methods further highlighted the discrepancies among different fossil clades and suggested similarities between the identifications made by machine classifiers and taxonomists. Collecting large paleontological datasets from various sources, such as the literature, digitization of dark data, citizen-science data, and public data from the Internet may further enhance deep learning methods and their adoption. Such developments will also possibly lead to image-based systematic taxonomy to be replaced by machine-aided classification in the future. Pioneering studies can include microfossils and some invertebrate fossils. To contribute to this development, we deployed our model on a server for public access at www.ai-fossil.com.

The Main Karoo Basin of South Africa contains a near-continuous sequence of continental deposition spanning ~80 Myr from the mid-Permian to the Early Jurassic. The terrestrial vertebrates of this sequence provide a high-resolution stratigraphic record of regional origination and extinction, especially for the mid–late Permian. Until now, data have only been surveyed at coarse stratigraphic resolution using methods that are biased by nonuniform sampling rates, limiting our understanding of the dynamics of diversification through this important time period. Here, we apply robust methods (gap-filler and modified gap-filler rates) for the inference of patterns of species richness, origination rates, and extinction rates to a subset of 1321 reliably-identified fossil occurrences resolved to approximately 50 m stratigraphic intervals. This data set provides an approximate time resolution of 0.3–0.6 Myr and shows that extinction rates increased considerably in the upper 100 m of the mid-Permian Abrahamskraal Formation, corresponding to the latest part of the Tapinocephalus Assemblage Zone (AZ). Origination rates were only weakly elevated in the same interval and were not sufficient to compensate for these extinctions. Subsampled species richness estimates for the lower part of the overlying Teekloof Formation (corresponding to the Pristerognathus and Tropidostoma AZs) are low, showing that species richness remained low for at least 1.5–3 million years after the main extinction pulse. A high unevenness of the taxon abundance–frequency distribution, which is classically associated with trophically unstable postextinction faunas, in fact developed shortly before the acme of elevated extinction rates due to the appearance and proliferation of the dicynodont Diictodon. Our findings provide strong support for a Capitanian (“end-Guadalupian”) extinction event among terrestrial vertebrates and suggest that further high-resolution quantitative studies may help resolve the lack of consensus among paleobiologists regarding this event.

An early Pliocene fossil locality in the Canadian High Arctic preserves the remains of the extinct beaver Dipoides sp. (Castoridae, Rodentia) in association with an assemblage of fossil beaver-cut wood. The wood assemblage presents a first opportunity to investigate woodcutting behavior and ecological performance in an extinct castorid genus. This study compares woodcutting in Dipoides sp. with that of the modern beaver, Castor canadensis, using evidence from small-diameter cut sticks (i.e., sticks transected by parallel series of cut marks) in combination with behavioral observations of Castor woodcutting. During woodcutting both Castor and Dipoides used their incisors unilaterally; the upper incisor was pressed against the stick while the corresponding lower incisor cut. Cut marks were relatively larger for Castor than Dipoides (scaled to incisor size). Compared with Dipoides, Castor more frequently used a cutting strategy that minimized the number of cuts needed to transect a stick (e.g., clipping as opposed to chip removal). Taken together, the behavioral evidence suggests that ecological cutting performance was lower for Dipoides than Castor.

Examination of organismal characteristics which promote survivorship through both background and mass extinctions may reveal general ecological principles potentially critical to modern conservation efforts. This study explores survivorship of brachiopods, a highly diverse and abundant Paleozoic clade, through the mid-Permian to mid-Triassic interval, which includes the greatest mass extinction in the history of metazoan life. This interval of time separates two of the major Phanerozoic evolutionary faunas. In this regard, survivorship across any one extinction during the interval would not have been relevant if the survivor went extinct shortly after the extinction event; surviving background extinction is as important as surviving a mass extinction. Similarly, taxa that survived but failed to rediversify also were not major elements of the Mesozoic evolutionary fauna. Thus, the analysis aims to analyze survivorship not just across a single extinction but across the entire mid-Permian to mid-Triassic; only survivors through the entire interval can be the ancestors of the Mesozoic clades.

Fewer brachiopod genera survived the interval than did brachiopod clades, suggesting that pseudoextinction or insufficient sampling could be a problem in analyzing these extinctions; thus, survivorship analysis should be conducted at the clade level. Nine characteristics were examined for generic representatives of 20 North American brachiopod clades, five of which survived both Permian extinctions and the subsequent earliest Triassic transitional interval. Characteristics include both those that operate on global scales and those that operate on the higher-resolution scales of individuals and populations.

Survivors were significantly smaller and occurred less frequently than victims. Mean diversity of communities in which survivors were present was significantly greater. The finding that rare taxa belonging to high-diversity communities were more likely to survive runs counter to traditional predictions. However, these results are consistent with recent studies suggesting that higher diversity within a trophic level may create a buffer, as surviving taxa quickly occupy the vacant niche space of the victims. As size, abundance, and community diversity are all statistically related, the small size of survivors may be an artifact of reduced biovolume per taxon in a diverse community.

No significant relationship exists between global-scale processes and survivorship of brachiopods through the mid-Permian to mid-Triassic. The results suggest that ecological processes can strongly influence global extinction patterns.

Numerous methods exist for estimating the true stratigraphic range of a fossil taxon based on the stratigraphic positions of its fossil occurrences. Many of these methods require the assumption of uniform fossil recovery potential—that fossils are equally likely to be found at any point within the taxon's true range. This assumption is unrealistic, because factors such as stratigraphic architecture, sampling effort, and the taxon's abundance and geographic range affect recovery potential. Other methods do not make this assumption, but they instead require a priori quantitative knowledge of recovery potential that may be difficult to obtain. We present a new Bayesian method, the Adaptive Beta method, for estimating the true stratigraphic range of a taxon that works for both uniform and non-uniform recovery potential. In contrast to existing methods, we explicitly estimate recovery potential from the positions of the occurrences themselves, so that a priori knowledge of recovery potential is not required. Using simulated datasets, we compare the performance of our method with existing methods. We show that the Adaptive Beta method performs well in that it achieves or nearly achieves nominal coverage probabilities and provides reasonable point estimates of the true extinction in a variety of situations. We demonstrate the method using a dataset of the Cambrian mollusc Anabarella.

Nautilus pompilius at Fiji lives abundantly to about 600 m depth while the shell implodes between 730–900 m when sunk in a cage. From this, and the average parameters of the septum, its tensile strength is calculated to 110–140 MPa. This is markedly higher than the latest value from direct tensile tests (78 MPa). In recent pressure tests by Saunders and Wehman with dry shells from the Philippines, implosion occurred at pressure equivalents to 310–680 m depth, without significant correlation with septal thickness. We attribute this excessive range and non-correlation to structural damage by postnecrotic processes. The recalculated tensile strength from their original data is 56–137 MPa; the higher values are compatible with our values for septal nacre of Nautilus and Spirula (c. 155 MPa). Septal curvature and thickness in orthocones thus remain useful guides to bathymetry.

In the past twenty years, both knowledge of fossil plants and ways of looking at the paleobotanical record have expanded significantly. Studies of Precambrian microfossils have provided insight on early photoautotrophs, while fundamental changes in perceptions of Silurian and Devonian plant remains have clarified our understanding of the colonization of land, as well as the subsequent evolution of complex stems, leaves, and the seed habit. A recurring question concerns the phylogenetic relationships of gymnosperms: is the gymnospermy found in various living and extinct taxa the result of evolutionary convergence or of common descent? Rapidly accumulating data on the reproductive and developmental biology of Paleozoic seed ferns is reopening debate on this issue. The mystery of angiosperm origins remains “abominable”, but the past two decades of research have seen convincing documentation of the initial radiation and rise to taxonomic and ecological dominance of the flowering plants.

While phylogenetic and systematic botany remain at the core of paleobotanical research, increased attention is being devoted to studies of ontogeny and reproductive biology, paleoecology, taphonomy, paleophytochemistry, paleoclimatology, and paleobiogeography. Studies of evolutionary rates and diversity are in their infancy, but initial results permit an optimistic appraisal of the contributions that paleobotanists can make to evolutionary paleontology.

Facets of the Silurian receptaculitid Ischadites barrandei are arranged in circlets about a nucleus. They form a set of spirals, originally eight in number, but increasing by the intercalation of new facets (initiating new spirals) in later circlets. We have simulated the surficial geometry of this alga by assuming, as much evidence indicates, that facets are limited in final size and that new spirals must therefore be intercalated in order to cover the surface with a fully tesselated pattern. We use only five parameters in our simulation: nature of the surface (radius of a sphere), tightness of the spirals (assumed to be logarithmic) and rate of increase in facet width (three parameters of an equation fitted to actual data). The program draws facets in circlets and intercalates new ones whenever the sum of facet diameters is at least a facet less than the circumference of the circlet. By holding all but one parameter constant, we can test the influence of single factors upon the pattern of intercalation. We compare these figures with actual patterns of intercalation for eight specimens. Variation in tightness of the spiral seems to affect the pattern most radically—tight spirals intercalate fewer facets because new circlets stay near the pole of the sphere. The morphology of intercalation supports the interpretation of Rietschel (1969, contra Nitecki, 1972 and Byrnes, 1968) that the nuclear circlets are the oldest part of the plant and that new circlets are generated at the opposite pole. Our simulation represents a basic pattern in nature, not a specific feature of receptaculitids. All structures that fill space with spirals and impose limits upon the size of individual units must add new spirals. Bryozoans subject to similar constraints but growing in a completely different way (peripheral growth in radial rows) display the same final pattern.

Ammonites have disparate adult morphologies indicative of diverse ecological niches, but ammonite hatchlings are small (~1 mm diameter), which raises questions about the similarity of egg incubation and hatchling life mode in ammonites. Modern Nautilus is sometimes used as a model organism for understanding ammonites, but despite their outward similarities, the groups are only distantly related. Trends in ammonite diversity and extinction vulnerability in the fossil record contrast starkly with those of nautilids, and embryonic shells from Late Cretaceous ammonites are two orders of magnitude smaller than nautilid embryonic shells. To investigate possible environmental changes experienced by ammonite hatchlings, we used secondary ion mass spectrometry to analyze the oxygen and carbon isotope composition of the embryonic shells and early postembryonic whorls of five juveniles of Hoploscaphites comprimus obtained from a single concretion in the Fox Hills Formation of South Dakota. Co-occurring bivalves and diagenetic calcite were also analyzed to provide a benthic baseline for comparison. The oxygen isotope ratios of embryonic shells are more like those of benthic bivalves, suggesting that ammonite eggs were laid on the bottom. Ammonite shell immediately after hatching has more negative δ18O, suggesting movement to more shallow water that is potentially warmer and/or fresher. After approximately one whorl of postembryonic growth, the values of δ18O become more positive in three of the five individuals, suggesting that these animals transitioned to a more demersal mode of life. Two other individuals transition to even lower δ18O values that could suggest movement to nearshore brackish water. These data suggest that ammonites, like many modern coleoids, may have spawned at different times of the year. Because scaphites were one of the short-term Cretaceous–Paleogene extinction survivors, it is possible that this characteristic allowed them to develop a broader geographic range and, consequently, a greater resistance to extinction.

As paleontological studies are generally distorted by gaps and biases in the fossil record, it is important to assess its completeness. Here we address the fossil record of Parareptilia, a Permian–Triassic amniote clade, applying two measures of specimen completeness: the skeletal completeness metric (SCM) and the character completeness metric (CCM). The SCM quantifies how much of the skeletal material of a taxon is preserved, whereas the CCM measures the amount of phylogenetic information available. The latter was implemented using two different approaches. In this study, we compare three completeness metrics. Two CCM implementations show a strong correlation with each other, but only the second implementation of the CCM correlates significantly with the SCM, possibly due to character selection in phylogenetic data sets. There is no correlation between diversity of parareptiles and their completeness, implying that the observed fluctuations in diversity are not driven by the completeness of the fossils. The mean completeness of parareptiles through time is consistently high compared with previously studied tetrapod clades, suggesting that most parareptile taxa are based on reasonably complete specimens. Clade-specific differences reveal no link between body size and completeness. However, the analyses confirm the impact of ecology, with aquatic mesosaurids being better preserved than terrestrial taxa.

Shotwell's method of paleoecological reconstruction attempts to define community membership of mammals represented within paleontological assemblages. Analysis of the measure of community membership upon which the method is based (relative skeletal completeness) shows this measure to be a function of sample size. A method for controlling for the effects of sample size upon measures of relative skeletal completeness is needed. A method is suggested which employs ratios of numbers of individuals to numbers of specimens, and a specific correction of Shotwell's method is proposed.

Among the various forms developed by marine colonial filter feeders, erect colonial fans have evolved in representatives of several phyla. Branches are relatively narrow, evenly spaced from one another, proliferate by bifurcation, and in most colonies continue from their point of origin to the distal margin of the colony. Their narrowness and uniform placement is apparently related to filling an area with multiple tentacle bells of similar size. The major architectural problem for such a colonial suspension feeder seems to be construction of a sheet composed of narrow branches such that water may be filtered as it flows through the sheet, between branches.

The simplest form of the filtration sheets is a uniformly expanding wedge, in which new branches originate at regular intervals from the point of origin of the wedge. Variation in rate of addition of new branches results in more complex forms, such as paraboloids, flaring fans, spirals, and highly folded sheets.

Survival of North American shelf trilobite families during a mass extinction across the upper boundary of the Upper Cambrian Sunwaptan Stage (=“Ptychaspid Biomere”) cannot be predicted from patterns of turnover among their component species: on the shelf, stratigraphic ranges of species belonging to surviving families do not differ significantly from those of eliminated families. Thus, the sorting of families during the extinctions cannot be explained by simple upward causation from the individual level. However, families that ranged from shelf to slope environments before the extinctions (most of which are pandemic) fared significantly better than those confined to shelf settings (which tend to be endemic to North America), indicating that family survival was influenced by geographic and environmental distribution, a property emergent above the individual level. One factor implicated in clade survival during normal background times, high species richness, did not influence the outcome of mass extinction. The results affirm the importance of a hierarchical approach to the interpretation of macroevolutionary patterns and provide some support to the suggestion that sorting processes operating during mass extinctions differ from those of background times.

Understanding the evolution of a Bauplan starts with discriminating phylogenetic signal from adaptation and the latter from exaptation in the observed biodiversity. Whether traits have predated, accompanied, or followed evolution of particular functions is the basic inference to establish the type of explanations required to determine morphological evolution. To accomplish this, we focus in a particular group of vertebrates, the anurans. Frogs and toads have a unique Bauplan among vertebrates, with a set of postcranial features that have been considered adaptations to jumping locomotion since their evolutionary origin. This interpretation is frequently stated but rarely tested in scientific literature. We test this assumption reconstructing the locomotor capabilities of the earliest known salientian, Triadobatrachus massinoti. This extinct taxon exhibits a mosaic of features that have traditionally been considered as representing an intermediate stage in the evolution of the anuran Bauplan, some of which were also linked to jumping skills. We considered T. massinoti in an explicit evolutionary framework by means of multivariate analyses and comparative phylogenetic methods. We used length measurements of major limb bones of 188 extant limbed amphibians (frogs and salamanders) and lizards as a morphological proxy of observed locomotor behavior. Our findings show that limb data correlate with locomotion, regardless of phylogenetic relatedness, and indicate that salamander-like lateral undulatory movements were the main mode of locomotion of T. massinoti. These results contrast with recent hypotheses and indicate that derived postcranial features that T. massinoti shared with anurans might have been later co-opted as exaptations in jumping frogs.