The Rhynchonellida is a major group of brachiopods that survived the “big five” mass extinctions and flourished after the Permian/Triassic (P/Tr) crisis. However, phylogenetic and character evolution in the Rhynchonellida across the P/Tr transition is poorly understood. In view of the widespread homoplasy across this order, we employ a tip-dated Bayesian analysis to reconstruct phylogenetic relationships for late Permian–Triassic rhynchonellides. The same data were also analyzed using three other methods: undated Bayesian, equal-weighting, and implied-weighting parsimony. Compared with trees generated by other methods, those constructed by tip-dating best account for the homoplasy in this group and are closer to previous assumptions on the evolution of this order. Based on the analyses of multiple trees, the major increase in lineage richness occurred in the Early and early Middle Triassic. Also, richness in the Anisian almost reached the highest level seen in the Triassic. According to fossil records, a pronounced reduction in shell size and in the development of ornamentation occurred after the P/Tr extinction, which is largely due to the loss of large and highly sculptured genera and the diversification of small-sized and weakly ornamented genera. Ancestral-state estimation of shell size and development of ornamentation, coupled with comparisons of other characters, indicate that the Early–Middle Triassic mature “small-sized taxa” may have characters displayed by juveniles of their ancestors. This suggests that for these genera, paedomorphosis was possibly a strategy to survive and diversify in the harsh environment after the P/Tr extinction.

Neogene and Pleistocene African suids displayed convergent evolutionary trends in the third molar (M3) morphology, with increasingly elongated and higher crowns through time. While these features can prevent premature loss of masticatory functionality and potentially increase long-term reproductive success, changes in dental occlusal traits such as enamel complexity and thickness can also improve chewing efficiency and increase short-term energetic return. While both long-term and short-term benefits can contribute to the thriving of a lineage, the selective pressures associated with each category can be different. To examine how crown elongation correlates with these functional occlusal traits, we selected M3s of Kolpochoerus, Notochoerus, and Metridiochoerus from Kenya and South Africa, dated between 3.0 Ma and 0.4 Ma. To account for dental wear, we used micro-computed tomography imaging of unworn/slightly worn M3s to simulate wear progression within each tooth. We compared morphometric representatives of occlusal enamel complexity and thickness among the specimens following their respective wear trajectories. We found that M3 elongation correlates with higher occlusal complexity and thinner enamel in Notochoerus and Metridiochoerus lineages through time. In Kolpochoerus, enamel complexity and thickness were generally maintained through time, despite M3 elongation. The differences in M3 morphometric trends suggest that Kolpochoerus likely experienced a different set of selective pressures on functional occlusal traits compared with Notochoerus and Metridiochoerus. The shared evolutionary trends of M3 specialization among Notochoerus and Metridiochoerus suggest similar selective pressures on their chewing efficiency and the possibility of a dietary niche overlap in more xeric habitats.

Classic similarity indices measure community resemblance in terms of incidence (the number of shared species) and abundance (the extent to which the shared species are an equivalently large component of the ecosystem). Here we describe a general method for increasing the amount of information contained in the output of these indices and describe a new “soft” ecological similarity measure (here called “soft Chao-Jaccard similarity”). The new measure quantifies community resemblance in terms of shared species, while accounting for intraspecific variation in abundance and morphology between samples. We demonstrate how our proposed measure can reconstruct short ecological gradients using random samples of taxa, recognizing patterns that are completely missed by classic measures of similarity. To demonstrate the utility of our new index, we reconstruct a morphological gradient driven by river flow velocity using random samples drawn from simulated and real-world data. Results suggest that the new index can be used to recognize complex short ecological gradients in settings where only information about specimens is available. We include open-source R code for calculating the proposed index.

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.

Pollen malformations have been proposed as a paleoenvironmental stress proxy. However, the frequency and variability of pollen malformations under near-optimal conditions and environmental stress, as well as their developmental origins, remain unclear. To bridge these gaps, we compared pollen malformation frequencies and assemblages of 14 extant conifer genera of Pinaceae and Podocarpaceae producing saccate (winged) grains grown under near-optimal conditions. These baseline pollen yields were compared with those produced by Pinus mugo ‘Columnaris’ cultured under an abiotic stress—three experimentally heightened ultraviolet-B radiation (UV-B) regimes proposed for the end-Permian crisis. We additionally reviewed previous cytological literature of abnormal microsporogenesis in conifers. Under near-optimal conditions, malformations comprise <3% of pollen yields in 12 out of 13 bisaccate genera and >10% of yields in the naturally trisaccate Dacrycarpus dacrydioides. We detected no phylogenetic pattern in malformation assemblages of the baseline comparisons. UV-B–irradiated P. mugo produced significantly higher malformation frequencies and different assemblage compositions when compared with baseline bisaccate lineages. We propose that pollen malformations originate during the meiotic and tetrad stages of microsporogenesis and present a framework for the ontogeny of different malformation types seen in the fossil record. Malformations comprising >3% of bisaccate pollen yields can be used as a paleoenvironmental stress proxy, but rare, naturally trisaccate lineages are not suitable for such assessments. Furthermore, heightened UV-B not only increases pollen malformation production, but also alters the types of abnormalities trees produce. Different environmental stresses may therefore leave behind distinct fingerprints in the fossil record.

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.

Studies in extant populations have shown that plasticity in developmental trajectories can contribute to the origin of novel traits and species divergence via the expression of previously cryptic variation in response to environmental change. Finding evidence for plasticity-led evolution in the fossil record remains challenging due to the poor preservation of developmental stages in many organisms. Planktic foraminifera are ideally suited for addressing this knowledge gap, because adult organisms in species in which development has been studied retain information about all the ontogenetic stages they have undergone. Here we map changes in the developmental trajectories of 68 specimens in the Globorotalia plesiotumida–tumida lineage of planktic foraminifera from the late Miocene until Recent using high-resolution computer tomography techniques. Our unique dataset shows that the transition from the ancestral G. plesiotumida to the descendant G. tumida is preceded by an increased variability in total cumulative volume—an important indicator of reproductive success in this taxon. We also find that the transition interval is marked by a distinct shift in developmental trajectory, which supports a rapid lineage division rather than gradual change. We suggest that high levels of plasticity—particularly in the early stages of development—have contributed to divergence in the ancestral morphology when subjected to a global cooling trend in the late Miocene. The large variation in developmental trajectories that we uncover within our samples emphasizes the need for high-throughput approaches in studies of ontogenetic change 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.

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.

The evolution of different spore size classes, or heterospory, is a fundamental reproductive innovation in land plants. The appearance of heterospory is particularly notable during the Devonian, when most known origins of the trait occur. Here we provide a perspective on the evolution of heterospory during this time interval, particularly from the late Early Devonian through the Middle Devonian (Emsian to Givetian Stages; 408–383 Ma), which shows an unusually high concentration of heterospory origins. We use theoretical considerations and compilations of fossil and extant spore sizes to suggest that the basic features of most heterosporous lineages, large spores and gametophytes that mature within the spore wall, are difficult to evolve in combination, because large spores disperse poorly but small spores cannot support a functional gametophyte developing within their walls; evolving spores between 100 and 200 microns in diameter appears to represent a particularly important barrier for the evolution of heterospory. We then discuss why this barrier may have been lower in the Devonian, noting that the appearance and spread of heterospory is coincident with the emergence of peat-accumulating wetland habitats. We suggest that more widespread wetland habitats would have generally lowered barriers to the evolution of heterospory by reducing dispersal limitation in larger spores. Ultimately, we suggest that the initial evolution of heterospory may be explained by major changes in sedimentology, thought to have been driven by plant evolution itself, that increased the diversity of terrestrial depositional environments and led to a greater number of habitats where large spores could be successful.

With 14 species recorded, the Miocene La Venta bat fauna is the most diverse bat paleocommunity in South America. It includes the oldest plant-visiting bat in the New World and some of the earliest representatives of the extant families Phyllostomidae, Thyropteridae, and Noctilionidae. La Venta's Notonycteris magdalenensis is an extinct member of the subfamily Phyllostominae, a group of modern Neotropical animalivorous bats, and is commonly included in studies of the evolution of Neotropical bats, but aspects of its biology remain unclear. In this study, we used multivariate dental topography analysis (DTA) to reconstruct the diet of N. magdalenensis by quantitatively comparing measures of molar complexity with those of 25 modern noctilionoid species representing all major dietary habits in bats. We found clear differences in molar complexity between dietary guilds, indicating that DTA is potentially an informative tool to study bat ecomorphology. Our results suggest N. magdalenensis was probably an omnivore or insectivore, rather than a carnivore like its modern relatives Chrotopterus auritus and Vampyrum spectrum. Also, we reconstructed the body mass of N. magdalenensis to be ~95 g, larger than most insectivorous bats, but smaller than the largest carnivorous bat (V. spectrum). Our results confirm that N. magdalenensis was not a specialized carnivore. It remains to be demonstrated that the specialized carnivory ecological niche was occupied by the same lineage of phyllostomines from at least the middle Miocene. Combining our diet and body-mass reconstructions, we suggest that N. magdalenensis exhibits morphological pre-adaptations crucial for the evolution of specialized carnivory.

Because teeth are the most easily preserved part of the vertebrate skeleton and are particularly morphologically variable in mammals, studies of fossil mammals rely heavily on dental morphology. Dental morphology is used both for systematics and phylogeny as well as for inferences about paleoecology, diet in particular. We analyze the influence of evolutionary history on our ability to reconstruct diet from dental morphology in the mammalian order Carnivora, and we find that much of our understanding of diet in carnivorans is dependent on the phylogenetic constraints on diet in this clade. Substantial error in estimating diet from dental morphology is present regardless of the morphological data used to make the inference, although more extensive morphological datasets are more accurate in predicting diet than more limited character sets. Unfortunately, including phylogeny in making dietary inferences actually decreases the accuracy of these predictions, showing that dietary predictions from morphology are substantially dependent on the evolutionary constraints on carnivore diet and tooth shape. The “evolutionary ratchet” that drives lineages of carnivorans to evolve greater degrees of hypercarnivory through time actually plays a role in allowing dietary inference from tooth shape, but consequently requires caution in interpreting dietary inference from the teeth fossil carnivores. These difficulties are another reminder of the differences in evolutionary tempo and mode between morphology and ecology.

Paleobiological and paleoecological interpretations rely on constraining the temporal resolution of the fossil record. The taphonomic clock, that is, a correlation between the alteration of skeletal material and its age, is an approach for quantifying time-averaging scales. We test the taphonomic clock hypothesis for marine demersal and pelagic fish otoliths from a 10–40 m depth transect on the Mediterranean siliciclastic Israeli shelf by radiocarbon dating and taphonomic scoring. Otolith ages span the last ~8000 yr, with considerable variation in median and range along the transect. Severely altered otoliths, contrary to pristine otoliths, are likely to be older than 1000 yr. For pelagic fish otoliths, at 30 m depth, taphonomic degradation correlates positively with postmortem age. In contrast, no correlation occurs for demersal fishes at 10 and 30 m depth, mostly because of the paucity of very young pristine (<150 yr) otoliths, possibly due to a drop in production over the last few centuries. Contrary to molluscan and brachiopod shells, young otoliths at these depths are little affected and do not show a broad spectrum of taphonomic damage, because those that derive from predation are excreted in calcium- and phosphate-rich feces forming an insoluble crystallic matrix that increases their preservation potential. At 40 m depth, all dated otoliths are very young but rather damaged because of locally chemically aggressive sediments, thus showing no correlation between taphonomic grade and postmortem age. Our results show that local conditions and the target species population dynamics must be considered when testing the taphonomic clock hypothesis.

Camelids (Camelidae) were a diverse and widely distributed group in South America during the Pleistocene. According to the fossil record, three species inhabited southern Brazil in the recent past: Hemiauchenia paradoxa, Lama guanicoe, and Vicugna vicugna. The analysis of carbon and oxygen stable isotope ratios in bioapatite provides insight into the paleobiology of nonliving animals and the environment they used to inhabit. We applied this tool to investigate the diet of camelids from two geological localities in southern Brazil: Touro Passo and Santa Vitória Formations (H. paradoxa, n = 7; L. guanicoe, n = 6; V. vicugna, n = 4). Carbon stable isotopes from enamel, dentin, and bone indicated that H. paradoxa and L. guanicoe had diets comprising mostly C3 grasses, but the latter showed a broader diet due to one individual with a mixed diet, whereas V. vicugna had a mixed C3–C4 diet. These different foraging behaviors may have minimized interspecific competition and favored niche partitioning and the coexistence of related species. Combined oxygen and carbon isotope data showed a consistent diet according to climate, probably due to the greater availability in glacial periods of cool-season grasses, which mainly use the C3 photosynthetic pathway. Given their adaptations to grazing, the climate amelioration, followed by the loss of grasslands, likely had a great impact on camelid populations, leading to their extinction in southern Brazil. These results, therefore, contribute to the understanding of the dynamics of paleocommunities in this region.

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.