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.

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.

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.

The synergic relationship between physiology, ecology, and evolutionary process makes the body-size distribution (BSD) an essential component of the community ecology. Body size is highly susceptible to environmental change, and extreme upheavals, such as during a mass extinction event, could exert drastic changes on a taxon's BSD. It has been hypothesized that the Late Triassic mass extinction event (LTE) was triggered by intense global warming, linked to massive volcanic activity associated with the Central Atlantic Magmatic Province. We test the effects of the LTE on the BSD of fossil bivalve assemblages from three study sites spanning the Triassic/Jurassic boundary in the United Kingdom. Our results show that the effects of the LTE were rapid and synchronous across sites, and the BSDs of the bivalves record drastic changes associated with species turnover. No phylogenetic signal of size selectivity was recorded, although semi-infaunal species were apparently most susceptible to change. Each size class had the same likelihood of extinction during the LTE, which resulted in a platykurtic BSD with negative skew. The immediate postextinction assemblage exhibits a leptokurtic BSD, although with negative skew, wherein surviving species and newly appearing small-sized colonizers exhibit body sizes near the modal size. Recovery was relatively rapid (~100 kyr), and larger bivalves began to appear during the pre-Planorbis Zone, despite recurrent dysoxic/anoxic conditions. This study demonstrates how a mass extinction acts across the size spectrum in bivalves and shows how BSDs emerge from evolutionary and ecological processes.

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.

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 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 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.

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.