The two major approaches to studying macroevolution in deep time are the fossil record and reconstructed relationships among extant taxa from molecular data. Results based on one approach sometimes conflict with those based on the other, with inconsistencies often attributed to inherent flaws of one (or the other) data source. Any contradiction between the molecular and fossil records represents a failure of our ability to understand the imperfections of our data, as both are limited reflections of the same evolutionary history. We therefore need to develop conceptual and mathematical models that jointly explain our observations in both records. Fortunately, the different limitations of each record provide an opportunity to test or calibrate the other, and new methodological developments leverage both records simultaneously. However, we must reckon with the distinct relationships between sampling and time in the fossil record and molecular phylogenies. These differences impact our recognition of baselines and the analytical incorporation of age estimate uncertainty.

Estimating the effects and timing of anthropogenic impacts on the composition of macrobenthic communities is challenging, because early twentieth-century surveys are sparse and the corresponding intervals in sedimentary sequences are mixed by bioturbation. Here, to assess the effects of eutrophication on macrobenthic communities in the northern Adriatic Sea, we account for mixing with dating of the bivalve Corbula gibba at two stations with high accumulation (Po prodelta) and one station with moderate accumulation (Isonzo prodelta). We find that, first, pervasively bioturbated muds typical of highstand conditions deposited in the early twentieth century were replaced by muds with relicts of flood layers and high content of total organic carbon (TOC) deposited in the late twentieth century at the Po prodelta. The twentieth century shelly muds at the Isonzo prodelta are amalgamated but also show an upward increase in TOC. Second, dating of C. gibba shells shows that the shift from the early to the late twentieth century is characterized by a decrease in stratigraphic disorder and by an increase in temporal resolution of assemblages from ~25–50 years to ~10–20 years in both regions. This shift reflects a decline in the depth of the fully mixed layer from more than 20 cm to a few centimeters. Third, the increase in abundance of the opportunistic species C. gibba and the loss of formerly abundant, hypoxia-sensitive species coincided with the decline in bioturbation, higher preservation of organic matter, and higher frequency of seasonal hypoxia in both regions. This depositional and ecosystem regime shift occurred in ca. a.d. 1950. Therefore, the effects of enhanced food supply on macrobenthic communities were overwhelmed by oxygen depletion, even when hypoxic conditions were limited to few weeks per year in the northern Adriatic Sea. Preservation of trends in molluscan abundance and flood events in cores was enhanced by higher frequency of hypoxia that reduced bioturbation in the late twentieth century.

Mass extinctions affect the history of life by decimating existing diversity and ecological structure and creating new evolutionary and ecological pathways. Both the loss of diversity during these events and the rebound in diversity following extinction had a profound effect on Phanerozoic evolutionary trends. Phylogenetic trees can be used to robustly assess the evolutionary implications of extinction and origination.

We examine both extinction and origination during the Late Ordovician mass extinction. This mass extinction was the second largest in terms of taxonomic loss but did not appear to radically alter Paleozoic marine assemblages. We focus on the brachiopod order Strophomenida, whose evolutionary relationships have been recently revised, to explore the disconnect between the processes that drive taxonomic loss and those that restructure ecological communities.

A possible explanation for this disconnect is if extinction and origination were random with respect to morphology. We define morphospace using principal coordinates analysis (PCO) of character data from 61 Ordovician–Devonian taxa and their 45 ancestral nodes, defined by a most parsimonious reconstruction in Mesquite. A bootstrap of the centroid of PCO values indicates that genera were randomly removed from morphospace by the Late Ordovician mass extinction, and new Silurian genera were clustered within a smaller previously unoccupied region of morphospace. Diversification remained morphologically constrained throughout the Silurian and into the Devonian. This suggests that the recovery from the Late Ordovician mass extinction resulted in a long-term shift in strophomenide evolution. More broadly, recovery intervals may hold clues to understanding the evolutionary impact of mass extinctions.

Understanding temporal patterns in biodiversity is an enduring question in paleontology. Compared with studies of taxonomic diversity, long-term perspectives on ecological diversity are rare, particularly in terrestrial systems. Yet ecological diversity is critical for the maintenance of biodiversity, especially during times of major perturbations. Here, we explore the ecological diversity of Cretaceous herbivorous dinosaurs leading up to the K-Pg extinction, using dental and jaw morphological disparity as a proxy. We test the hypothesis that a decline in ecological diversity could have facilitated their rapid extinction 66 Ma. We apply three disparity metrics that together capture different aspects of morphospace occupation and show how this approach is key to understanding patterns of morphological evolution. We find no evidence of declining disparity in herbivorous dinosaurs as a whole—suggesting that dinosaur ecological diversity remained high during the last 10 Myr of their existence. Clades show different disparity trends through the Cretaceous, but none except sauropods exhibits a long-term decline. Herbivorous dinosaurs show two disparity peaks characterized by different processes; in the Early Cretaceous by expansion in morphospace and in the Campanian by morphospace packing. These trends were only revealed by using a combination of disparity metrics, demonstrating how this approach can offer novel insights into macroevolutionary processes underlying patterns of disparity and ecological diversity.

A large sample of postembryonic specimens of Dalmanitina proaeva elfrida and D. socialis from the Upper Ordovician (Sandbian to Katian) Prague Basin allows for the first reasonably complete ontogenetic sequence of Dalmanitoidea (Phacopina). The material provides an abundance of morphological information, including well-preserved marginal spines in protaspides and meraspides, and hypostome external surfaces throughout. The development of D. proaeva elfrida is unusual due to variability in timing of the first trunk articulation. This broadens our developmental understanding of Phacopina, a diverse group of phacopid trilobites, and also allows us to study the evolution of their specializations in exoskeletal molting behavior. Adult phacopines, unlike most other trilobites, had fused facial sutures. This means that rather than molting through the sutural gape mode, characterized by opening of the facial sutures and separation of the librigenae, they disarticulated the entire cephalon in Salter’s mode of molting. For other phacopine clades (Phacopoidea) the transition to Salter’s mode occurs during the meraspid period or at the onset of holaspis, and its developmental timing is intraspecifically fixed. However, owing to the large sample size, we can see that facial suture fusion likely occurred later in Dalmanitina, usually during the holaspid period, and was intraspecifically variable with holaspides of varying sizes showing unfused sutures. Further, D. proaeva elfrida specimens showed an initial librigenal–rostral plate fusion event, where the librigenae began as separate entities but appear fused with the rostral plate as one structure (the “lower cephalic unit”) from M1, and are discarded as such during molting. Dalmanitoidea is considered to represent the first phacopine divergence, occurring earliest in the fossil record. This material therefore provides insight into how linked morphologies and behaviors evolved, potentially suggesting the timing of facial suture fusion in Phacopina moved earlier during development and became more intraspecifically fixed over geological time.

Conodont fossils are highly valuable for Paleozoic biostratigraphy and for interpreting evolutionary change, but identifying and describing conodont morphologies, and characterizing gradual shape variation remain challenging. We used geometric morphometric (GM) analysis to conduct the first landmark-based morphometric analysis of the biostratigraphically useful conodont genus Neognathodus. Our objective is to assess whether previously defined morphotype groups are reliably distinct from one another. As such, we reevaluate patterns of morphologic change in Neognathodus P1elements, perform maximum-likelihood tests of evolutionary modes, and construct novel, GM-based biozonations through a Desmoinesian (Middle Pennsylvanian) section in the Illinois Basin. Our GM results record the entire spectrum of shape variability among Neognathodus morphotypes, thus alleviating the problem of documenting and classifying gradual morphologic transitions between morphotypes. Statistically distinct GM groups support previously established classifications of N. bassleri, N. bothrops, and N. roundyi. Statistically indistinct pairs of GM groups do not support literature designations of N. medadultimus and N. medexultimus, and N. dilatus and N. metanodosus, and we synonymize each pair. Maximum-likelihood tests of evolutionary modes provide the first statistical assessment of Neognathodus evolutionary models in the Desmoinesian. The most likely evolutionary models are an unbiased random walk or a general random walk. We name four distinct biozones through the Desmoinesian using GM results, and these align with previous biozonation structure based on the Neognathodus Index (NI), illustrating that Neognathodus-based biostratigraphic correlations would not change between GM or NI methods. The structural similarity between both biozonations showcases that determining GM-based biozones is not redundant, as this comparison validates using landmark-based GM work to construct viable biozonations for subsequent stratigraphic correlations. Although this study is limited to the Illinois Basin, our quantitative methodology can be applied broadly to test taxonomic designations of additional genera, interpret statistically robust evolutionary patterns, and construct valid biozones for this significant chordate group.

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.

Based on high-resolution palynological analysis of 680 samples from a core, short-term changes in plant diversity and floristic composition within the Paleogene greenhouse were detected in the lacustrine succession of a lower to middle Eocene maar lake at Messel (Federal State of Hesse, Germany). The microfloristic data show that taxonomic diversity increased rapidly within some decades during recolonization of a volcanically devastated area around the lake. With the establishment of a climax vegetation at the end of recolonization, the maximum in palynological diversity was reached within the crater area. During the following 640 Kyr the composition of the palynospectrum changed only gradually. However, different richness and evenness estimations show that alpha and gamma diversity decreased up to 35%, which can be related to the establishment of an equilibrium stage within the climax vegetation that led to the dominance of an assemblage of self-replacing species. Nevertheless, time-series analysis of alpha-diversity changes within the climax vegetation reveals that orbitally controlled climate change of Milankovitch and sub-Milankovitch order influenced the diversity of the vegetation, resulting in a rise of beta diversity. Based on the composition of the vegetation and comparison to modern analogues, our analysis proves that Eocene paratropical plant diversity increased during periods of slightly higher temperature and precipitation. Therefore, both composition and diversity of the vegetation was highly susceptible to minor-scale, short-term changes in climate, even during equable greenhouse conditions.

Energy availability influences natural selection on the ontogenetic histories of organisms. However, it remains unclear whether physiological controls on size remain constant throughout ontogeny or instead shift as organisms grow larger. Benthic foraminifera provide an opportunity to quantify and interpret the physicochemical controls on both initial (proloculus) and adult volumes across broad environmental gradients using first principles of cell physiology. Here, we measured proloculus and adult test dimensions of 129 modern rotaliid species from published images of holotype specimens, using holotype size to represent the maximum size of all species’ occurrences across the North American continental margin. We merged size data with mean annual temperature, dissolved oxygen concentration, particulate organic carbon flux, and seawater calcite saturation for 718 unique localities to quantify the relationship between physicochemical variables and among-species adult/proloculus size ratios. We find that correlation of community mean adult/proloculus size ratios with environmental parameters reflects covariation of adult test volume with environmental conditions. Among-species proloculus sizes do not covary identifiably with environmental conditions, consistent with the expectation that environmental constraints on organism size impose stronger selective pressures on adult forms due to lower surface area-to-volume ratios at larger sizes. Among-species adult/proloculus size ratios of foraminifera occurring in resource-limited environments are constrained by the limiting resource in addition to temperature. Identified limiting resources are food in oligotrophic waters and oxygen in oxygen minimum zones. Because among-species variations in adult/proloculus size ratios from the North American continental margin are primarily driven by the local environment’s influence on adult sizes, the evolution of foraminiferal sizes over the Phanerozoic may have been strongly influenced by changing oceanographic conditions. Furthermore, lack of correspondence between among-species proloculus sizes and environmental conditions suggests that offspring sizes in foraminifera are rarely limited by physiological constraints and are more susceptible to selection related to other aspects of fitness.

Naturally time-averaged accumulations of skeletal remains—death assemblages—provide reliable, albeit temporally coarse, information on the species composition and structure of communities in diverse settings, and their mismatch with local living communities usually signals recent human-driven ecological change. Here, we present the first test of live–dead mismatch as an indicator of human stress using ostracodes. On three islands along a gradient of human population density in the Bahamas, we compared the similarity of living and death assemblages in 10 lakes with relatively low levels of human stress to live–dead similarity in 11 physically comparable lakes subject to industrial, agricultural, or other human activities currently or in the past. We find that live–dead agreement in pristine lakes is consistently excellent, boding well for using death assemblages in modern-day and paleolimnological biodiversity assessments. In most comparison of physically similar paired lakes, sample-level live–dead mismatch in both taxonomic composition and species’ rank abundance is on average significantly greater in the stressed lakes; live–dead agreement is not lower in all samples from stressed lakes, but is more variable. When samples are pooled for lake-level and island-level comparisons, stressed lakes still yield lower live–dead agreement, but the significance of the difference with pristine lakes decreases—species that occur dead-only (or alive-only) in one sample are likely to occur alive (or dead) in other samples. Interisland differences in live–dead agreement are congruent with, but not significantly correlated with, differences in human population density. This situation arises from heterogeneity in the timing and magnitudes of stresses and in the extent of poststress recovery. Live–dead mismatch in ostracode assemblages thus may be a reliable indicator of human impact at the sample level with the potential to be a widely applicable tool for identifying impacted habitats and, perhaps, monitoring the progress of their recovery.

Life span bias potentially alters species abundance in death assemblages through the overrepresentation of short-lived organisms compared with their long-lived counterparts. Although previous work found that life span bias did not contribute significantly to live–dead discordance in bivalve assemblages, life span bias better explained discordance in two groups: longer-lived bivalve species and species with known life spans. More studies using local, rather than global, species-wide life spans and mortality rates would help to determine the prevalence of life span bias, especially for long-lived species with known life spans. Here, we conducted a field study at two sites in North Carolina to assess potential life span bias between Mercenaria mercenaria and Chione elevata, two long-lived bivalve species that can be aged directly. We compared the ability of directly measured local life spans with that of regional and global life spans to predict live–dead discordance between these two species. The shorter-lived species (C. elevata) was overrepresented in the death assemblage compared with its live abundance, and local life span data largely predicted the amount of live–dead discordance; local life spans predicted 43% to 88% of discordance. Furthermore, the global maximum life span for M. mercenaria resulted in substantial overpredictions of discordance (1.4 to 1.6 times the observed live–dead discordance). The results of this study suggest that life span bias should be considered as a factor affecting proportional abundances of species in death assemblages and that using life span estimates appropriate to the study locality improves predictions of discordance based on life span compared with using global life span estimates.