The record of the taxonomic evolution of North American ungulates is critical to our understanding of mammalian evolution and environmental change throughout the Cenozoic. The distribution of sampling in the ungulate fossil record over time and geographic space and the degree to which this biases the observed patterns of taxonomic evolution is poorly understood. To address these issues, I placed fossil collections and occurrences drawn from the Paleobiology Database into 2-Myr time intervals between 55 and 1 Ma. I determined the variation in numbers of fossil collections and occurrences, using three metrics to measure geographic variation: first, the area of the convex hull containing all collections in an interval, to determine the areal coverage of sampling; second, the mean pairwise geographic distance among collections as a measurement of the dispersion of collections within that area; and third, the interval-to-interval migration of the geographic centroid of all collections, to calculate changes in the geographic location of sampling. Each of these showed considerable variation over the Cenozoic, and both the area of the convex hull (ACH) encompassing all collections in an interval, and mean pairwise distance (MPWD) among them showed increasing trends over time.

To minimize the effect of variation in numbers of fossil samples over time, I used standard sample-standardization procedures. To minimize the effect of geographic variation in sampling over time, I standardized the area of sampling among intervals. I also employed both standardizations sequentially. Each standardization procedure had surprisingly little effect on observed patterns of taxonomic richness and rates. This indicates that, for North American ungulates, neither variation in number nor geographic distribution of fossil samples exerts an overwhelming influence on perceived macroevolutionary patterns. These results confirm the ungulate fossil record as a critical and faithful record for our understanding of Cenozoic environmental change and the mammalian evolutionary response.

The rise of durophagous predators during the Paleozoic represents an ecological constraint imposed on sessile marine fauna. In crinoids, it has been suggested that increasing predation pressure drove the spread of adaptations against predation. Damage to a crinoid's arms from nonlethal predation varies as a function of arm branching pattern. Here, using a metric for resilience to predation (“expected arm loss,” EAL), we test the hypothesis that the increase in predation led to more predation-resistant arm branching patterns (lower EAL) among Paleozoic crinoids. EAL was computed for 230 genera of Paleozoic crinoids and analyzed with respect to taxonomy and time. The results show significant variability among taxa. Camerates, especially monobathrids, display a pattern of increasingly convergent and predation-resistant arm morphologies from the Ordovician through the Devonian, with no significant change during the Mississippian. In contrast, the mean EAL among cladids follows no overall trend through the Paleozoic. Regenerating arms are known to be significantly more common in camerates than in other Paleozoic taxa; if regeneration is taken as a proxy for nonlethal interactions with durophagous predators, this indicates that nonlethal predation occurred more often among camerates throughout the Early and Middle Paleozoic. In addition, frequency of injury among camerates is inversely correlated with EAL and positively correlated with infestation by parasitic snails. From this we conclude that decreasing EAL signals a selective pressure in favor of resistance to grazing predation in camerates but not in other subclasses before the Mississippian, with an apparent relaxation in this constraint after the late Devonian extinctions.

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.

The set of environmental conditions under which a taxon can survive and maintain viable populations, known as the ecological niche, is a fundamental determinant of a taxon's distribution. Because of the central importance of ecological niches, they have been assumed to remain relatively stable during intervals of morphological stasis. However, the assumption of niche stability has rarely been tested directly with fossil data spanning multiple temporal intervals. Thus, the conditions under which this assumption is likely to be accurate are not well understood. In this study, we use ecological niche modeling (ENM) to reconstruct the ecological niche for 11 genera of marine benthos (crinoids, trilobites, molluscs, bryozoans, and corals) from the Type Cincinnatian Series (Late Ordovician, Katian Stage) across nine temporal intervals spanning approximately three million years. This interval includes both abiotic environmental change (gradual sea-level fall) and biotic change (rapid pulses of the Richmondian Invasion), thus allowing the relative effect of different environmental perturbations to be constrained. A previous symmetrical analysis of niche stability of brachiopod species recovered an increase in niche evolution following the Richmondian Invasion. Herein we test the generality of the brachiopod pattern within the community. Niche stability was evaluated in geographic space, ecological space, and niche parameter space. Niche stability varied through time; during the Pre-Invasion interval, taxa exhibited niche stability during gradual shallowing of sea level in the basin, whereas niche evolution became more common during the Richmondian Invasion. Taxa adjusted to the increased competition by altering aspects of their niche. Notably, surviving taxa contracted their niche into a subset of their previous niche parameters. This represents an adaptive response to increased competition for resources with the newly established invader taxa, and it was employed most successfully by generalist taxa. Patterns of niche evolution were congruent between clades, among feeding styles, and across taxonomic levels.

In the assessment of Phanerozoic marine global biodiversity, there has been longstanding interest in quantifying compositional similarities among sampling points as a function of their distances from one another (geodisparity). Previous research has demonstrated that faunal similarity between any two locations tends to decrease significantly as the great circle distance (GCD) between the locations increases, but the rate of decrease begins to stabilize at transoceanic distances. The accuracy of these assessments, and comparisons among different temporal intervals, may suffer, however, because of intervening landmasses that are not accounted for when distance is calibrated simply as GCD. Here, we present a new method for determining the shortest overwater distance (WD) between two marine locations, and we use the method to recalibrate for several Phanerozoic intervals previous measures of global geodisparity in the taxonomic compositions of marine biotas. WD was determined by using a cost-distance approach in ArcGIS, modified to work on a spherical, as opposed to a planar, surface. Results demonstrate two notable effects of using WD. First, mean compositional similarity between locations tends to decrease more continuously as a function of distance with WD than with GCD. Second, pairs of locations with WDs that are at least 50% greater than their GCDs tend to have lower compositional similarity to one another than those with more closely matching WDs and GCDs. These differences are expected as WD better represents the “true” distance between locations; they diminish at GCDs of 5000 km or more when clear, transoceanic paths between locations become more common. Despite these effects, using WD does not alter fundamental temporal trends in global geodisparity through the Phanerozoic observed in previous research, but it is likely to have more significant ramifications for more confined paleobiogeographic investigations.

We review and synthesize multiple biotic and abiotic proxies for marine nutrient and food availability, primary productivity, and food quality (stoichiometry) and propose what their relationships may have been to macroevolutionary processes, especially speciation. This review confirms earlier suggestions that there has been an overall increase in marine primary productivity over the Phanerozoic, but indicates that the increase has been irregular and that present levels may not be the peak. We integrate these indicators into a new estimate of relative primary productivity in the global ocean through the Phanerozoic. We then combine multiple, frequently conflicting ecological-evolutionary hypotheses into a general model for how primary production may affect speciation over geological time scales. This model, an elaboration and extension of the “speciation cycle” previously proposed by Grant and Grant, attempts to explain why an increase in food supply sometimes is associated with decreased diversity, and at other times with increased diversification. We propose some simple tests for the application of this model to the fossil record.

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.

With species found throughout both marine and fresh waters, the diatom order Thalassiosirales is one of the most phylogenetically and ecologically diverse lineages of planktonic diatoms. A clear understanding of the timescale of Thalassiosirales evolution would provide novel insights into the rates and patterns of species diversification associated with major habitat shifts, as well as provide valuable context for understanding the age and evolutionary history of the model species, Cyclotella nana (= Thalassiosira pseudonana). The freshwater fossil record for Thalassiosirales is extensive, well characterized, and generally supportive of a Miocene origin for the major freshwater lineages. The marine record is, by comparison, more sparse and in many cases, unverified. The discovery of freshwater thalassiosiroids in Eocene sediments pushed the freshwater fossil record considerably further back in time, highlighting an apparent gap of some 30 million years. An alternative interpretation is that the Miocene and Eocene reports represent competing hypotheses. In the absence of additional independent and decisive fossil data, I explored the relative plausibility of these two scenarios with Bayesian relaxed molecular clock methods under a range of fossil calibration schemes. Although I found no support for the Eocene fossil dates, the two major freshwater colonization events probably occurred much earlier than previously thought—as early as the Paleocene for Cyclotella, followed by an Eocene origin for the cyclostephanoid lineage. Much of the extant freshwater diversity in both lineages traces back to the Miocene, however, giving the impression of a single Miocene origin. Efforts to infer the timescale of Thalassiosirales evolution more accurately would benefit from a systematic reevaluation of the marine fossil record and formal integration of fossil species into existing phylogenetic hypotheses.

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.

Here I test the hypothesis that temporal variation in geographic range size within genera is affected by the expansion and contraction of their preferred environments. Using occurrence data from the Paleobiology Database, I identify genera that have a significant affinity for carbonate or terrigenous clastic depositional environments that transcends the Database's representation of these environments during the stratigraphic range of each genus. These affinity assignments are not a matter of arbitrarily subdividing a continuum in preference; rather, genera form distinct, nonrandom subsets with respect to environmental preference. I tabulate the stage-by-stage transitions in range size within individual genera and the stage-by-stage changes in the extent of each environment. Comparing the two shows that genera with a preference for a given environment are more likely to increase in geographic range, and to show a larger average increase in range, when that environment increases in areal extent, and likewise for decreases in geographic range and environmental area. Similar results obtain for genera with preferences for reefal and non-reef settings. Simulations and subsampling experiments suggest that these results are not artifacts of methodology or sampling bias. Nor are they confined to particular higher taxa. Genera with roughly equal preference for carbonates and clastics do not have substantially broader geographic ranges than those with a distinct affinity, suggesting that, at this scale of analysis, spatial extent of preferred environment outweighs breadth of environmental preference in governing geographic range. These results pertain to changes over actual geologic time within individual genera, not overall average ranges. Recent work has documented a regular expansion and contraction when absolute time is ignored and genera are superimposed to form a composite average. Environmental preference may contribute to this pattern, but its role appears to be minor, limited mainly to the initial expansion and final contraction of relatively short-lived genera.

An enigma of deep-sea biodiversity research is that the abyss with its low productivity and densities appears to have a biodiversity similar to that of shallower depths. This conceptualization of similarity is based mainly on per-sample estimates (point diversity, within-habitat, or α-diversity). Here, we use a measure of between-sample within-community diversity (β1H) to examine benthic foraminiferal diversity between 333 stations within 49 communties from New Zealand, the South Atlantic, the Gulf of Mexico, the Norwegian Sea, and the Arctic. The communities are grouped into two depth categories: 200–1500 m and >1500 m. β1H diversity exhibits no evidence of regional differences. Instead, higher values at shallower depths are observed worldwide. At depths of >1500 m the average β1H is zero, indicating stasis or no biodiversity gradient. The difference in β1H-diversity explains why, despite species richness often being greater per sample at deeper depths, the total number of species is greater at shallower depths. The greater number of communities and higher rate of evolution resulting in shorter species durations at shallower depths is also consistent with higher β1H values.

With a single complete mandible and 56 mandibular symphyseal fragments of various sizes, the Late Cretaceous Hungarian azhdarchid material has been considered one of the most extensive monospecific pterosaur assemblages in the world. Representing a broad size range, these elements have been thought to demonstrate a developmental series of Bakonydraco galaczi. As such, they were ideal to test whether absolute size and/or morphology reliably indicate relative ontogenetic stages in this pterosaur. Forty-five specimens were selected for multivariate morphometrics and classified into four size classes. After acquiring the morphometric data set, we thin-sectioned eight symphyses representing all size groups and classified them into relative ontogenetic stages based on qualitative microstructural inspection prior to quantitative histological analyses. Microstructural characters suggestive of developmental state were then quantified for intra- and interindividual uni- and multivariate analyses to test the correspondence among the results of qualitative and quantitative analyses. In contrast to our expectations, histological features identified the smallest specimen as an adult and not an early juvenile. The substantial size difference between this specimen and other adults, along with its distinct microanatomical and histological features, implies the presence of at least two pterosaur taxa in this symphysis assemblage. This hypothesis is further supported by multivariate morphometrics, which separate the smallest symphyses from all other specimens that form one continuous group. Although the latter group also shows considerable size variability in corresponding ontogenetic stages, this suggests developmental plasticity rather than the presence of even more taxa, and indicates that symphysis size and morphology are poor indicators of skeletal maturity in these animals. Hence, bone histology is an important independent test of the assessment of ontogenetic stage using size and morphology.

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.

Reconstructing the tree of life requires deciphering major evolutionary transformations and the functional capacities of fossils with “transitional” morphologies. Some of the most iconic, well-studied fossils with transitional features are theropod dinosaurs, whose skeletons and feathered forelimbs record the origin and evolution of bird flight. However, in spite of over a century of discussion, the functions of forelimb feathers during the evolution of flight remain enigmatic. Both aerodynamic and non-aerodynamic roles have been proposed, but few of the form-function relationships assumed by these scenarios have been tested. Here, we use the developing wings of a typical extant ground bird (Chukar Partridge) as possible analogues/homologues of historical wing forms to provide the first empirical evaluation of aerodynamic potential in flapping theropod “protowings.” Immature ground birds with underdeveloped, rudimentary wings generate useful aerodynamic forces for a variety of locomotor tasks. Feather development in these birds resembles feather evolution in theropod dinosaurs, and reveals a predictable relationship between wing morphology and aerodynamic performance that can be used to infer performance in extinct theropods. By spinning an ontogenetic series of spread-wing preparations on a rotating propeller apparatus across a range of flow conditions and measuring aerodynamic force, we explored how changes in wing size, feather structure, and angular velocity might have affected aerodynamic performance in dinosaurs choosing to flap their incipient wings. At slow angular velocities, wings produced aerodynamic forces similar in magnitude to those produced by immature birds during behaviors like wing-assisted incline running. At fast angular velocities, wings produced forces sufficient to support body weight during flight. These findings provide a quantitative, biologically relevant bracket for theropod performance and suggest that protowings could have provided useful aerodynamic function early in maniraptoran history, with improvements in aerodynamic performance attending the evolution of larger wings, more effective feather morphologies, and faster angular velocities.

Studies of the end-Permian mass extinction have suggested a variety of patterns from a single catastrophic event to multiple phases. But most of these analyses have been based on fossil distributions from single localities. Although single sections may simplify the interpretation of species diversity, they are susceptible to bias from stratigraphic incompleteness and facies control of preservation. Here we use a data set of 1450 species from 18 fossiliferous sections in different paleoenvironmental settings across South China and the northern peri-Gondwanan region, and integrate it with high-precision geochronologic data to evaluate the rapidity of the largest Phanerozoic mass extinction. To reduce the Signor-Lipps effect, we applied constrained optimization (CONOP) to search for an optimal sequence of first and last occurrence datums for all species and generate a composite biodiversity pattern based on multiple sections. This analysis indicates that an abrupt extinction of 62% of species took place within 200 Kyr. The onset of the sudden extinction is around 252.3 Ma, just below Bed 25 at the Meishan section. Taxon turnover and diversification rates suggest a deterioration of the living conditions nearly 1.2 Myr before the sudden extinction. The magnitude of the extinction was such that there was no immediate biotic recovery. Prior suggestions of highly variable, multi-phased extinction patterns reflect the impact of the Signor-Lipps effect and facies-dependent occurrences, and are not supported following appropriate statistical treatment of this larger data set.

Marine planktonic microfossils have provided some of the best examples of evolutionary rates and patterns on multi-million-year time scales, including many instances of gradual evolution. Lineage splitting as a result of speciation has also been claimed, but all such studies have used subjective visual species discrimination, and interpretation has often been complicated by relatively small sample sizes and oceanographic complexity at the study sites. Here we analyze measurements on a collection of 10,200 individual tests of the Eocene planktonic foraminifer Turborotalia in 51 stratigraphically ordered samples from a site within the oceanographically stable tropical North Pacific gyre. We use novel multivariate statistical clustering methods to test the hypothesis that a single evolutionary species was present from 45 Ma to its extinction ca. 34 Ma. After identification of a set of biologically relevant traits, the protocol we apply does not require a prior assignment of individuals to species. We find that for most of the record, contemporaneous specimens form one morphological cluster, which we interpret as an evolving species that shows quasi-continuous but non-directional gradual evolutionary change (anagenesis). However, in the upper Eocene from ca. 36 to ca. 34 Ma there are two clusters that persistently occupy distinct areas of morphospace, from which we infer that speciation (cladogenesis) must have occurred.

Within ancient ecosystems, it is generally difficult to determine the specific diets of species from higher trophic levels, which in turn hinders our understanding of trophic relationships and energy flow through these systems. To better understand the ecology of taxa at higher trophic levels, we used analysis of tooth enamel stable carbon isotope values to infer the dietary preferences of Canis edwardii and Smilodon gracilis from the Leisey Shell Pit 1A (LSP 1A) and Inglis 1A, two Pleistocene localities in Florida. The goals of the analyses were to (1) determine whether these carnivorans specialized in particular prey types or maintained a generalist diet; (2) ascertain whether carbon isotope values support what was previously suggested about the ecology of these species; and (3) establish what ecological details of ancient food webs can be discovered by carbon isotope analyses at higher trophic levels. Results show that the sampled carnivoran carbon isotope values are distributed among suspected prey isotope values, suggesting that varied prey were taken at the study localities. Prey compositions were modeled for each carnivoran species by using Stable Isotope Analysis in R (SIAR). The modeled diets indicate that each studied carnivoran had a generalist diet; however, there are differences in how these taxa achieved dietary generalization. At the glacial Inglis 1A locality, sampled individuals of C. edwardii and S. gracilis show similar isotope values and modeled dietary prey proportions, although both carnivorans do show a preference for grazing prey species. The similar isotopic values, and calculated prey proportions, observed between these species may imply greater interspecific competition for food. At the interglacial LSP 1A locality, C. edwardii shows values similar to those observed at Inglis 1A. In contrast, the data for S. gracilis shows a preference for consuming browsing prey species. Further, its restricted range of carbon isotope values suggests that S. gracilis may have concentrated its feeding within a particular habitat. Examination of stable carbon isotope values among species at higher trophic levels reveals that some intricacies of ancient food webs can be discerned.

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.