As of September 2019, the Florida Museum of Natural History (FLMNH) had a curated collection of 117,449 chondrichthyan specimens from Florida, spanning the Eocene through the Pleistocene. Herein, I evaluate the completeness of the chondrichthyan fossil record from Florida based on the FLMNH collection, while analyzing patterns in taxonomic and ecomorphological diversity. At least 70 chondrichthyan taxa were recognized, representing 10 orders, 26 families, and 42 genera; of which, 20 taxa represent first occurrences from Florida. A sample of 107,698 specimens was organized into 12 time bins to analyze taxonomic and ecomorphological diversity, with an expectation that diversity patterns would correspond with global climate events (e.g., the Eocene–Oligocene transition and the middle Miocene climatic optimum). However, diversity patterns were obscured by pervasive sampling bias, attributable to variable collection methods, research prioritizations, and regional lithologic controls. Sampling is particularly poor for smaller specimens and older geologic units (e.g., the Paleogene). Despite incomplete sampling of the Florida chondrichthyan fossil record, there was an apparent turnover along the Atlantic and Gulf Coastal Plains from a lamniform- to carcharhiniform-dominated chondrichthyan fauna that occurred during the Eocene. This turnover corresponded with the extinction of many lamniform taxa with grasping-dominated dentition types (e.g., Brachycarcharias, Jaekelotodus, and Macrorhizodus). Selachian taxa that survived the late Eocene extinctions were predominantly represented by cutting-dominant dentition types. As cutting aids in the dismemberment of prey, this may reflect a macroevolutionary trend toward active predation and scavenging on larger prey, such as marine mammals, teleost fish, and other sharks.

Conodonts were a highly diverse and abundant vertebrate group whose fossils are found in marine Paleozoic and Triassic strata around the world. They inhabited environments ranging from lagoons to open oceans and are represented by a wide variety of dental morphologies. Conodonts may have filled many different ecological niches and represent a significant proportion of nekton before the Devonian. Despite this, very little is known about trophic ecology of conodonts. While morphological diversity suggests a complex trophic structure within conodont communities, there is little evidence to support dietary niche partitioning among conodonts.

We tested the hypothesis that individual conodont taxa occupied different trophic niches, using Sr/Ca and Ba/Ca ratios preserved in the dental elements of assemblages from Silurian strata of Gotland, Sweden. Sr/Ca and Ba/Ca have been shown to vary in vertebrate skeletal tissues depending on trophic positioning, although biological and environmental conditions can affect these ratios. Environmental influences were minimized by examining entire conodont communities from a tropical epeiric sea and by measuring strontium isotope ratios using thermal ionization mass spectrometry in the most metropolitan taxon (Ozarkodina confluens). Composition of white matter, a tissue unique to conodonts, was also analyzed using microprobe analysis, revealing significantly lower Sr concentrations than in surrounding lamellar tissue, suggesting taxon-specific histology should be considered when analyzing conodonts for geochemical data. Excluding taxa with highly variable quantities of white matter, the results show that each taxon preserves different Sr/Ca and Ba/Ca ratios with limited overlap, indicating variation in trophic positioning.

Ilya Prigogine's trinomial concept is, he argued, applicable to many complex dissipative systems, from physics to biology and even to social systems. For Prigogine, this trinomial—functions, structure, fluctuations—was intended to capture the feedback-rich relations between upper and lower levels in these systems. The main novelty of his vision was his view of causation, in which the causal arrow runs downward from dissipative structures to their components or functions. Following this insight, some physicists and biophysicists are beginning to apply terms formerly used mainly in biology, such as evolution, adaptation, learning, and life-like behavior, to physical and chemical nonequilibrium systems. Here, instead, we apply Prigogine's view to biology, in particular to evolution, and especially the major transitions in evolution (MTE), arguing that at least the hierarchical transitions—the transitions in individuality—follow a trajectory anticipated by the trinomial. In this trajectory, formerly free-living organisms are transformed into “functions” within a larger organic “structure.” The Prigogine view also predicts that, consistent with available data, the increase in number of hierarchical levels in organisms should accelerate over time. Finally, it predicts that, on geological timescales, ecosystems and Gaia in particular will tend to “de-Darwinize” or “machinify” their component organisms.

Presented here is a coupled model of the nonmarine fossil record, based on a geometric model of deposition, a random-branching model of evolution, and an ecological model based on an elevation gradient. This model provides testable predictions about the stratigraphy and fossil occurrences in coastal nonmarine settings under three scenarios of sea-level change. A slow relative rise in sea level causes a declining ratio of channel to floodplain deposits, plus changes in community composition that reflect an upward increase in elevation relative to sea level. A rapid relative rise in sea level drives increasing aggradation rates, decreases the ratio of channel to floodplain deposits, and triggers a shift from higher-elevation (more inland) to lower-elevation (more coastal) communities. A fall in sea level produces an unconformity, manifested by valleys separated by interfluves. The resumption of deposition following the sea-level fall causes an abrupt shift in community composition across the unconformity, reflecting the duration of the hiatus and the increased elevation relative to sea level. This produces a cluster of first and last occurrences at the unconformity, and it is the only sequence-stratigraphic source of such clusters in a nonmarine system, in contrast to the multiple mechanisms for generating these clusters in marine systems. A central prediction of these models is that the nonmarine fossil record preserves systematic changes in community composition that reflect elevation (or equivalently, distance from shore). Diagnosing these gradients in ancient systems is a promising avenue of future research.

Predation has strongly shaped past and modern marine ecosystems, but the scale dependency of patterns in drilling predation, the most widely used proxy for predator–prey interactions in the fossil record, is a matter of debate. To assess the effects of spatial and taxonomic scale on temporal trends in the drilling frequencies (DFs), we analyzed Holocene molluscan assemblages of different benthic habitats and nutrient regimes from the northern Adriatic shelf in a sequence-stratigraphic context. Although it has been postulated that low predation pressures facilitated the development of high-biomass epifaunal communities in the eastern, relatively oligotrophic portion of the northern Adriatic shelf, DFs reaching up to 30%–40% in the studied assemblage show that drilling predation levels are comparable to those typical of late Cenozoic ecosystems. DFs tend to increase from the transgressive systems tract (TST) into the highstand systems tract (HST) at the local scale, reflecting an increase in water depth by 20–40 m and a shift from infralittoral to circalittoral habitats over the past 10,000 years. As transgressive deposits are thicker at shallower locations and highstand deposits are thicker at deeper locations, a regional increase in DFs from TST to HST is evident only when these differences are accounted for. The increase in DF toward the HST can be recognized at the level of total assemblages, classes, and few abundant and widespread families, but it disappears at the level of genera and species because of their specific environmental requirements, leading to uneven or patchy distribution in space and time.

The end-Permian mass extinction occurred alongside a large swath of environmental changes that are often invoked as extinction mechanisms, even when a direct link is lacking. One way to elucidate the cause(s) of a mass extinction is to investigate extinction selectivity, as it can reveal critical information on organismic traits as key determinants of extinction and survival. Here we show that machine learning algorithms, specifically gradient boosted decision trees, can be used to identify determinants of extinction as well as to predict extinction risk. To understand which factors led to the end-Permian mass extinction during an extreme global warming event, we quantified the ecological selectivity of marine extinctions in the well-studied South China region. We find that extinction selectivity varies between different groups of organisms and that a synergy of multiple environmental stressors best explains the overall end-Permian extinction selectivity pattern. Extinction risk was greater for genera that had a low species richness, narrow bathymetric ranges limited to deep-water habitats, a stationary mode of life, a siliceous skeleton, or, less critically, calcitic skeletons. These selective losses directly link the extinctions to the environmental effects of rapid injections of carbon dioxide into the ocean–atmosphere system, specifically the combined effects of expanded oxygen minimum zones, rapid warming, and potentially ocean acidification.

The timing of early animal evolution remains one of the biggest conundrums in biology. Molecular data suggest Porifera diverged from the metazoan lineage some 800 Ma to 650 Ma, which contrasts with the earliest widely accepted fossils of sponges at 535 Ma. However, the lack of criteria by which to recognize the earliest animals in the fossil record presents a challenge. The sponge body plan is unchanged since the early Cambrian, which makes a sponge-type animal a good candidate for the earliest fossils. Here we propose a method for identifying an organism as sponge grade by translating the sponge pump character into a quantifiable morphological trait. We show that the ratio between the two major components of the aquiferous system, the cross-sectional area of the osculum (OSA) and the surface area of the whole sponge (SA), is an effective metric of the pump character of extant sponges and that the slope of this ratio is distinct for three classes of Porifera: Demospongiae, Calcarea, and Hexactinellida. Furthermore, this metric is effective at distinguishing as sponges both extant taxa and fossils from two extremes of the Phanerozoic, the Cambrian and Paleogene. We tested this metric on the putative Ediacaran sponge Thectardis avalonensis from Mistaken Point, Newfoundland, and found Thectardis fits both with Cambrian sponges and with modern demosponges. These analyses show that the OSA/SA ratio is a reliable character by which to identify fossils as sponge grade, opening up exciting possibilities for classifying new fossils as sponges.

The fossil record is notoriously imperfect and biased in representation, hindering our ability to place fossil specimens into an evolutionary context. For groups with fossil records mostly consisting of disarticulated parts (e.g., vertebrates, echinoderms, plants), the limited morphological information preserved sparks concerns about whether fossils retain reliable evidence of phylogenetic relationships and lends uncertainty to analyses of diversification, paleobiogeography, and biostratigraphy in Earth's history. To address whether a fragmentary past can be trusted, we need to assess whether incompleteness affects the quality of phylogenetic information contained in fossil data. Herein, we characterize skeletal incompleteness bias in a large dataset (6585 specimens; 14,417 skeletal elements) of fossil squamates (lizards, snakes, amphisbaenians, and mosasaurs). We show that jaws + palatal bones, vertebrae, and ribs appear more frequently in the fossil record than other parts of the skeleton. This incomplete anatomical representation in the fossil record is biased against regions of the skeleton that contain the majority of morphological phylogenetic characters used to assess squamate evolutionary relationships. Despite this bias, parsimony- and model-based comparative analyses indicate that the most frequently occurring parts of the skeleton in the fossil record retain similar levels of phylogenetic signal as parts of the skeleton that are rarer. These results demonstrate that the biased squamate fossil record contains reliable phylogenetic information and support our ability to place incomplete fossils in the tree of life.

The Cambrian information revolution describes how biotically driven increases in signals, sensory abilities, behavioral interactions, and landscape spatial complexity drove a rapid increase in animal cognition concurrent with the Cambrian radiation. Here, we compare cognitive complexity in Cambrian and post-Cambrian marine ecosystems, documenting changes in animal cognition after the initial Cambrian increase. In a comparison of Cambrian and post-Cambrian Lagerstätten, we find no strong trend in the proportion of genera possessing two types of macroscopic sense organs (eyes and chemoreceptive organs such as antennae, feelers, or nostrils). There is also no trend in general nervous system complexity. These results suggest that sophisticated information processing was already common in early Phanerozoic ecosystems, comparable with behavioral evidence from the trace fossil record. Most taxa capable of complex information processing in Cambrian ecosystems were panarthropods, whereas mollusks and chordates made up larger proportions afterward. In both the Cambrian and the present day, ecological occupation of diverse habitat tiers and feeding modes is possible with even simple nervous systems, but ecological lifestyles requiring rapid, regular movement are almost exclusively associated within brain-bearing taxa, suggesting a connection with fast information-processing abilities and bodily responses. The overall rise in cognitive sophistication in the Cambrian was likely a unique event in the history of life, although some lineages subsequently developed more elaborate sensory systems and/or larger brains.

Relaxed clock models are fundamental in Bayesian clock dating, but a single distribution characterizing the clock variation is typically selected. Hence, I developed a new reversible-jump Markov chain Monte Carlo (rjMCMC) algorithm for drawing posterior samples between the independent lognormal (ILN) and independent gamma rates (IGR) clock models. The ability of the rjMCMC algorithm to infer the true model was verified through simulations. I then applied the algorithm to the Mesozoic bird data previously analyzed under the white noise (WN) clock model. In comparison, averaging over the ILN and IGR models provided more reliable estimates of the divergence times and evolutionary rates. The ILN model showed slightly better fit than the IGR model and much better fit than the autocorrelated lognormal (ALN) clock model. When the data were partitioned, different partitions showed heterogeneous model fit for ILN and IGR clocks. The implementation provides a general framework for selecting and averaging relaxed clock models in Bayesian dating analyses.

The concept of evolvability—the capacity of a population to produce and maintain evolutionarily relevant variation—has become increasingly prominent in evolutionary biology. Paleontology has a long history of investigating questions of evolvability, but paleontological thinking has tended to neglect recent discussions, because many tools used in the current evolvability literature are challenging to apply to the fossil record. The fundamental difficulty is how to disentangle whether the causes of evolutionary patterns arise from variational properties of traits or lineages rather than being due to selection and ecological success. Despite these obstacles, the fossil record offers unique and growing sources of data that capture evolutionary patterns of sustained duration and significance otherwise inaccessible to evolutionary biologists. Additionally, there exist a variety of strategic possibilities for combining prominent neontological approaches to evolvability with those from paleontology. We illustrate three of these possibilities with quantitative genetics, evolutionary developmental biology, and phylogenetic models of macroevolution. In conclusion, we provide a methodological schema that focuses on the conceptualization, measurement, and testing of hypotheses to motivate and provide guidance for future empirical and theoretical studies of evolvability in the fossil record.

The evolution of thermometabolism in pseudosuchians (Late Triassic to the present) remains a partly unsolved issue: extant taxa (crocodilians) are ectothermic, but the clade was inferred ancestrally endothermic. Here we inferred the thermometabolic regime of two neosuchian groups, Goniopholididae (Early Jurassic to Late Cretaceous) and Dyrosauridae (middle Cretaceous to late Eocene), close relatives of extant crocodilians, in order to elucidate the evolutionary pattern across Metasuchia (Early Jurassic to the present), a clade comprising Neosuchia (Early Jurassic to the present) and Notosuchia (Middle Jurassic until the late Miocene). We propose a new integrative approach combining geochemical analyses to infer body temperature from the stable oxygen isotope composition of tooth phosphate and paleohistology and phylogenetic comparative methods to infer resting metabolic rates and red blood cell dimensions. †Dyrosaurus and †Goniopholis share with extant crocodilians similar lifestyles, body forms, bone tissue organization, body temperatures, metabolic rates, and red blood cell dimensions. Consistently, we infer ectothermy for †Dyrosaurus and †Goniopholis with the parsimonious implication of neosuchians and metasuchians being primitively ectothermic.

The effects of overdispersion and zero inflation (e.g., poor model fits) can result in misinterpretation in studies using count data. These effects have not been evaluated in paleoecological studies of predation and are further complicated by preservational bias and time averaging. We develop a hierarchical Bayesian framework to account for uncertainty from overdispersion and zero inflation in estimates of specimen and predation trace counts. We demonstrate its application using published data on drilling predators and their prey in time-averaged death assemblages from the Great Barrier Reef, Australia.

Our results indicate that estimates of predation frequencies are underestimated when zero inflation is not considered, and this effect is likely compounded by removal of individuals and predation traces via preservational bias. Time averaging likely reduces zero inflation via accumulation of rare taxa and events; however, it increases the uncertainty in comparisons between assemblages by introducing variability in sampling effort. That is, there is an analytical cost with time-averaged count data, manifesting as broader confidence regions. Ecological inferences in paleoecology can be strengthened by accounting for the uncertainty inherent to paleoecological count data and the sampling processes by which they are generated.

Intraspecific aggression, or agonism, is a widespread intrasexual selective behavior important to understanding animal behavioral ecology and reproductive systems. Such behavior can be studied either by direct observation or inferred from wound/scar frequency in extant species but is difficult to document in extinct taxa, limiting understanding of its evolution. Among extant archosaurs, crocodylians display extensive intrasexual aggression, whereas birds show extreme visual/vocal intersexual display. The evolutionary origin of this behavioral divergence, and pattern in non-avian dinosaurs, is unknown. Here we document the morphology, frequency, and ontogeny of intraspecific facial bite lesions (324 lesions) in a large sample of tyrannosaurids (202 specimens, 528 elements) to infer patterns of intraspecific aggression in non-avian theropods. Facial scars are consistent in position and orientation across tyrannosaurid species, suggesting bites were inflicted due to repeated/postured behavior. Facial scars are absent in young tyrannosaurids, first appear in immature animals (~50% adult skull length), are present in ~60% of the adult-sized specimens, and show aggressor:victim size isometry. The ontogenetic distribution of bite scars suggests agonistic behavior is associated with the onset of sexual maturity, and scar presence in approximately half the specimens may relate to a sexual pattern. Considered in a phylogenetic context, intraspecific bite marks are consistent and widely distributed in fossil and extant crocodyliforms and non-maniraptoriform theropods, suggesting a potential plesiomorphic behavior in archosaurs. Their absence in maniraptoriform theropods, including birds, may reflect a transition from boney cranial ornamentation and crocodylian-like intrasexual aggression to avian-like intersexual display with the evolution of pennaceous feathers.

As practitioners of a historical science, paleontologists and geoscientists are well versed in the idea that the ability to understand and to anticipate the future relies upon our collective knowledge of the past. Despite this understanding, the fundamental role that the history of paleontology and the geosciences plays in shaping the structure and culture of our disciplines is seldom recognized and therefore not acted upon sufficiently. Here, we present a brief review of the history of paleontology and geology in Western countries, with a particular focus on North America since the 1800s. Western paleontology and geology are intertwined with systematic practices of exclusion, oppression, and erasure that arose from their direct participation in the extraction of geological and biological resources at the expense of Black, Indigenous, and People of Color (BIPOC). Our collective failure to acknowledge this history hinders our ability to address these issues meaningfully and systemically in present-day educational, academic, and professional settings. By discussing these issues and suggesting some ways forward, we intend to promote a deeper reflection upon our collective history and a broader conversation surrounding racism, colonialism, and exclusion within our scientific communities. Ultimately, it is necessary to listen to members of the communities most impacted by these issues to create actionable steps forward while holding ourselves accountable for the past.

We know that the fossil record is incomplete. But how incomplete? Here we very coarsely estimate the completeness of the mammalian record in the Miocene, assuming that the duration of a mammalian species is about 1 Myr and the species diversity has stayed constant and is structurally comparable to the taxonomic diversity today. The overall completeness under these assumptions appears to be around 4%, but there are large differences across taxonomic groups. We find that the fossil record of proboscideans and perissodactyls as we know it for the Miocene must be close to complete, while we might know less than 15% of the species of artiodactyl or carnivore fossil species and only about 1% of primate species of the Miocene. The record of small mammals appears much less complete than that of large mammals.

The Ordovician–Silurian (~485–419 Ma) was a time of considerable evolutionary upheaval, encompassing both great evolutionary diversification and one of the first major mass extinctions. The Ordovician diversification coincided with global climatic cooling and paleocontinental collision, the ecological impacts of which were mediated by region-specific processes including substrate changes, biotic invasions, and tectonic movements. From the Sandbian–Katian (~453 Ma) onward, an extensive carbonate shelf developed in the eastern Baltic paleobasin in response to a tectonic shift to tropical latitudes and an increase in the abundance of calcareous macroorganisms. We quantify the contributions of environmental differentiation and temporal turnover to regional diversity through the Ordovician and Silurian, using brachiopod occurrences from the more shallow-water facies belts of the eastern Baltic paleobasin, an epicontinental sea on the Baltica paleocontinent. The results are consistent with carbonate shelf development as a driver of Ordovician regional diversification, both by enhancing broadscale differentiation between shallow- and deep-marine environments and by generating heterogeneous carbonate environments that allowed increasing numbers of brachiopod genera to coexist. However, temporal turnover also contributed significantly to apparent regional diversity, particularly in the Middle–Late Ordovician.

Plant–insect associations have been a significant component of terrestrial ecology for more than 400 Myr. Exploring these interactions in the fossil record through novel perspectives provides a window into understanding evolutionary and ecological forces that shaped these interactions. For the past several decades, researchers have documented, described, and categorized fossil evidence of these interactions. Drawing on powerful tools from network science, we propose here a bipartite network representation of fossilized plants and their herbivore-induced leaf damage to understand late Paleozoic plant–insect interactions at the local community level. We focus on four assemblages from north-central Texas, but the methods used in this work are general and can be applied to any well-preserved fossil flora. Network analysis can address key questions in the evolution of insect herbivory that often would be difficult to summarize using standard herbivory metrics.

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.