Many modern paleobiological analyses are conducted at the generic level, a practice predicated on the validity of genera as meaningful proxies for species. Uncritical application of genera in such analyses, however, has led—perhaps inadvertently—to the unjustified reification of genera in an evolutionary context. While the utility of genera as proxies for species in evolutionary studies should be evaluated as an empirical issue, in practice it is increasingly assumed (rather than demonstrated) that genera are suitable proxies for species. This is problematic on both ontological and epistemological grounds. Genera are arbitrarily circumscribed, non-equivalent, often paraphyletic, and sometimes polyphyletic collections of species. They are useful tools for communication but have no theoretical or biological reality of their own and, whether monophyletic or not, cannot themselves operate in the evolutionary process. Attributes considered important for understanding macroevolution—e.g., geographic ranges, niche breadths, and taxon durations—are frequently variable among species within genera and will be inflated at the generic level, especially in species-rich genera. Consequently, the meaning(s) of results attained at the generic level may not “trickle down” in any obvious way that elucidates our understanding of evolution at the species level. Ideally, then, evolutionary studies that are actually about species should be pursued using species-level data rather than proxy data tabulated using genera. Where genera are used, greater critical attention should be focused on the degree to which attributes tabulated at the generic level reflect biological properties and processes at the species level.

Chitin occurs in a variety of invertebrates, especially in arthropod cuticles, but is rarely reported in the fossil record. Although it has been detected in fossils as old as Middle Cambrian and Silurian, the majority of records come from much younger, Cenozoic deposits. In this paper, we report the preservation of chitin in Early Jurassic neritimorph gastropod egg capsules deposited in bivalve shells from prodelta-deltafront and nearshore paleoenvironments of the Holy Cross Mountains, Poland. We used a number of analytical methods to confirm the presence of chitin preserved in these ancient fossils. This is the first record of chitin preservation in Mesozoic deposits that, interestingly, do not follow the conventional Konservat-Lagerstätten manner of preserving soft-bodied and non-biomineralized organisms. We believe that deltaic settings characterized by episodic, high input of fluvial deposits, oligohaline conditions, and oxygen-poor microenvironment within the sediment—as well as early cementation of sediment infilling the shells—were crucial for chitin preservation. The preservation of chitin in such recalcitrant structures as egg capsules and deposits that formed outside conventional Konservat-Lagerstätten conditions renders it likely similar deposits may yield promise for discoveries of similar biological macromolecules.

Accurate interpretation of origination and extinction of fossil species is crucial to answering a variety of questions in paleontology. Fossil datums, the observed age of first or last occurrences, are subject to sampling error as a result of preservation and low abundances near range endpoints. This sampling error can cause local range offset, an age difference between the observed first or last occurrence of a species and its true origination or extinction. Here, we develop and test a new technique, the Probable Datum Method (PDM), that can be used to assess the extent of local range offset for nannofossil species. The PDM estimates the original abundance of a taxon and its probable true age of first or last occurrence. The PDM uses a model in which original abundance is related to count abundance through preservation and the counting process. This model is empirically parameterized, including an experimental determination of false positive and error rates of a nannofossil count. The model is simulated then inverted to estimate likely original abundance and true datum age from count abundance data. We first test the PDM in a positive control experiment with known parameter values. This experiment shows that the PDM is robust and returns known values accurately. Next we apply the method to the origination of nannoplankton after the Cretaceous/Paleogene boundary to test whether first occurrences were synchronous between widely spaced locations. The PDM results suggest that observed diachrony of K/Pg originations cannot be explained by the effects of local range offset; rather, in some cases they indicate truly diachronous first occurrences between localities. Although the technique was developed to analyze nannoplankton ranges, the statistical nature of the PDM, its experimentally derived parameters, and its parsimonious nature should make it applicable to many micropaleontological studies that interpret patterns of origination and extinction.

Comparisons between modern death assemblages and their source communities have demonstrated fidelity to species diversity across a variety of environments and taxonomic groups. However, differential species preservation and collection (including body-size bias) in both modern and fossil death assemblages may still skew the representation of other important ecological characteristics. Here, we move beyond live-dead taxonomic fidelity and focus on the recovery of functional ecology (how species interact with their ecosystem) at the community level for a diverse non-volant mammal community (87 species; Amboseli, Kenya). We use published literature to characterize species, using four functional traits and their associated categorical attributes (i) dietary mode (11 attributes; e.g., browser, grazer), (ii) preferred feeding habitat (16 attributes; e.g., grassland, woodland), (iii) preferred sheltering habitat (17 attributes; e.g., grassland, underground cavity), and (iv) activity time (7 attributes; e.g., diurnal, nocturnal, nocturnally dominated crepuscular). For each functional ecological trait we compare the death assemblage's recovered richness and abundance structure of constituent functional attributes with those of the source community, using Jaccard similarity, Spearman's rho, and the Probability of Interspecific Encounter (evenness). We use Monte Carlo simulations to evaluate whether these empirical comparisons are significantly different from expectations calculated from randomized sampling of species from the source community. Results indicate that although the Amboseli death assemblage is significantly overrepresented by large-bodied species relative to the Amboseli source community, it captures many functional dimensions of the ecosystem within expectations of a randomized collection of species. Additional resampling simulations and logistic regressions further illustrate that the size bias inherent to the Amboseli death assemblage is not a major driver of deviations between the functional ecological properties of the death assemblage and its source community. Finally, the Amboseli death assemblage also enhances our understanding of the mammal community by adding nine species and two functional attributes previously unknown from the ecosystem.

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 pelvic structure in non-avian archosaurs plays a key role in understanding the evolution of terrestrial locomotor patterns because the pelvis contains major attachment sites for proximal hind limb musculature. In order to investigate patterns of pelvic evolution in archosaurs, this study compiled three pelvic indices, as well as femoral head orientation, for 92 archosaur taxa. With the metrics and a reconstructed supertree, we examined the correlated evolution of the pelvis and femur, the correlation among pelvic components, and temporal trends in the evolution of the pelvis. The result shows that archosaurs with medially directed femoral heads have more cranially shifted iliac centroids and more posteriorly rotated pubes than taxa with anteromedially directed femoral heads. The craniad shift of the iliac centroid might be correlated to the posterior rotation of pubis. The pelvic structures of pterosaurs, ornithischians, sauropods, and avetheropods occupy a different morphospace from basal archosaurs, pseudosuchians, basal dinosauromorphs, basal theropods, and basal sauropodomorphs in having more cranially expanded ilia, more posteriorly rotated pubes, and medially deflected femoral heads. This may imply that pterosaurs and those derived dinosaurs independently underwent similar shifts in thigh muscles and locomotion. The evolutionary model fitting supports the early-burst model for iliac and pubic metrics in more inclusive archosaur clades, indicating that larger changes of archosaur pelves occurred in early times of the clade's history.

Within a ∼60-Myr interval in the Late Triassic to Early Jurassic, a major mass extinction took place at the end of Triassic, and several biotic and environmental events of lesser magnitude have been recognized. Climate warming, ocean acidification, and a biocalcification crisis figure prominently in scenarios for the end-Triassic event and have been also suggested for the early Toarcian. Radiolarians, as the most abundant silica-secreting marine microfossils of the time, provide a control group against marine calcareous taxa in testing selectivity and responses to changing environmental parameters. We analyzed the origination and extinction rates of radiolarians, using data from the Paleobiology Database and employing sampling standardization, the recently developed gap-filler equations and an improved stratigraphic resolution at the substage level. The major end-Triassic event is well-supported by a late Rhaetian peak in extinction rates. Because calcifying and siliceous organisms appear similarly affected, we consider global warming a more likely proximate trigger of the extinctions than ocean acidification. The previously reported smaller events of radiolarian turnover fail to register above background levels in our analyses. The apparent early Norian extinction peak is not significant compared to the long-term trajectory, and is probably a sampling artifact. The Toarcian Oceanic Anoxic Event, previously also thought to have caused a significant radiolarian turnover, did not significantly affect the group. Radiolarian diversity history appears unique and complexly forced, as its trajectory parallels major calcareous fossil groups at some events and deviates at others.

Crura, the calcareous support structures of the lophophore in rhynchonellide brachiopods, have historically been used to justify higher-level rhynchonellide classification and reveal major evolutionary lineages within rhynchonellides. Seventeen crural types have been described and categorized into four groups based on variation in overall structure and cross-sectional shape, but not evaluated in a quantitative or comprehensive manner. Heterochrony has been hypothesized to play a role in the evolutionary transitions among some types, but the structural, developmental, and phylogenetic context for testing these hypotheses has not yet been established. In this study, we use three-dimensional geometric morphometric techniques to quantify morphological disparity among all six crural morphs in Recent adult rhynchonellides, with the goal of delineating more objective criteria for identifying and comparing crural morphs, ultimately to test hypotheses explaining morphological transformations in ontogeny and phylogeny. We imaged the crura of seven Recent rhynchonellide species, using X-ray computed microtomography. We used landmarks and semi-landmarks to define the dimensions and curvature of the crura and the surrounding hinge area. Procrustes-standardized landmark coordinates were analyzed using a principal component analysis to test the discreteness of the individual crural morphs and named groups of morphs, and to identify features that vary most among the crural configurations.

Our results demonstrate that microCT imaging techniques provide novel ways to investigate the morphology of small features that may be otherwise impossible to quantify using more conventional imaging techniques. Although we predicted overlap among crural morphs in the 3-D shape space, the principal component analyses suggest that five of the six crural morphs differ distinctly from one another. Some but not all previously designated crural groups appear to exhibit morphological cohesion. This study establishes a quantitative morphological foundation necessary to begin an investigation of the phylogenetic significance of ontogenetic changes in crura, which will allow hypotheses of heterochrony to be tested.

Even though Neogene outcrops along the temperate Pacific coast of South America harbor a rich marine vertebrate fossil record, no studies have examined the diversification patterns of these taxa. Here, we analyze diversification trends based on the stratigraphic ranges of 86 genera of marine vertebrates, including sharks, rays, chimaeras, marine mammals, and seabirds. The richness of genera shows a hump-shaped trend, with maximum values around the late Miocene, driven by a large pulse of origination during mid-Miocene and higher extinction rates during the Pliocene. Trends varied markedly among taxa and departed largely from expectations based on global diversification patterns. Moreover, these trends cannot be explained solely as a sampling artifact derived from sampling intensity (i.e., number of occurrences) or sedimentary rock availably (i.e., number of geologic maps). A large fraction of genera (42%) went globally extinct by the late Pliocene–Pleistocene, and the extinction was highly selective according to different ecological and life-history traits. An analysis using “randomForest” showed that taxonomic structure and the geographic midpoint of distribution could explain up to 83% of extinction of genera. The extinction was taxonomically clumped (i.e., disproportionally high in Cetacea and very low in Carcharhiniformes) and concentrated in the northern area of the temperate Pacific coast of South America. Our results suggest that the particular paleogeographic, paleoclimatic, and paleoceanographic events that took place during the Neogene along the temperate Pacific coast of South America had a significant effect on the structure of marine biodiversity.

Determining which biological traits affect taxonomic durations is critical for explaining macroevolutionary patterns. Two approaches are commonly used to investigate the associations between traits and durations and/or extinction and origination rates: analyses of taxonomic occurrence patterns in the fossil record and comparative phylogenetic analyses, predominantly of extant taxa. By capitalizing upon the empirical record of past extinctions, paleontological data avoid some of the limitations of existing methods for inferring extinction and origination rates from molecular phylogenies. However, most paleontological studies of extinction selectivity have ignored phylogenetic relationships because there is a dearth of phylogenetic hypotheses for diverse non-vertebrate higher taxa in the fossil record. This omission inflates the degrees of freedom in statistical analyses and leaves open the possibility that observed associations are indirect, reflecting shared evolutionary history rather than the direct influence of particular traits on durations. Here we investigate global patterns of extinction selectivity in Devonian terebratulide brachiopods and compare the results of taxonomic vs. phylogenetic approaches. Regression models that assume independence among taxa provide support for a positive association between geographic range size and genus duration but do not indicate an association between body size and genus duration. Brownian motion models of trait evolution identify significant similarities in body size, range size, and duration among closely related terebratulide genera. We use phylogenetic regression to account for shared evolutionary history and find support for a significant positive association between range size and duration among terebratulides that is also phylogenetically structured. The estimated range size–duration relationship is moderately weaker in the phylogenetic analysis due to the down-weighting of closely related genera that were both broadly distributed and long lived; however, this change in slope is not statistically significant. These results provide evidence for the phylogenetic conservatism of organismal and emergent traits, yet also the general phylogenetic independence of the relationship between range size and duration.