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.

Comprising Holostei and Teleostei, the ~32,000 species of neopterygian fishes are anatomically disparate and represent the dominant group of aquatic vertebrates today. However, the pattern by which teleosts rose to represent almost all of this diversity, while their holostean sister-group dwindled to eight extant species and two broad morphologies, is poorly constrained. A geometric morphometric approach was taken to generate a morphospace from more than 400 fossil taxa, representing almost all articulated neopterygian taxa known from the first 150 million years—roughly 60%—of their history (Triassic‒Early Cretaceous). Patterns of morphospace occupancy and disparity are examined to: (1) assess evidence for a phenotypically “dominant” holostean phase; (2) evaluate whether expansions in teleost phenotypic variety are predominantly abrupt or gradual, including assessment of whether early apomorphy-defined teleosts are as morphologically conservative as typically assumed; and (3) compare diversification in crown and stem teleosts. The systematic affinities of dapediiforms and pycnodontiforms, two extinct neopterygian clades of uncertain phylogenetic placement, significantly impact patterns of morphological diversification. For instance, alternative placements dictate whether or not holosteans possessed statistically higher disparity than teleosts in the Late Triassic and Jurassic. Despite this ambiguity, all scenarios agree that holosteans do not exhibit a decline in disparity during the Early Triassic‒Early Cretaceous interval, but instead maintain their Toarcian‒Callovian variety until the end of the Early Cretaceous without substantial further expansions. After a conservative Induan‒Carnian phase, teleosts colonize (and persistently occupy) novel regions of morphospace in a predominantly gradual manner until the Hauterivian, after which expansions are rare. Furthermore, apomorphy-defined teleosts possess greater phenotypic variety than typically assumed. Comparison of crown and stem teleost partial disparity indicates that, despite a statistically significant increase in crown teleost disparity between the Late Jurassic and earliest Cretaceous, stem teleosts remained important long-term contributors to overall teleost disparity during this time.

Studying the deep-time origins of macroecological phenomena can help us to understand their long-term drivers. Given the considerable spatiotemporal bias of the terrestrial fossil record, it behooves us to understand how much biological information is lost. The aim of this study is to establish whether latitudinal diversity gradients are detectable in a biased terrestrial fossil record. I develop a simulated fossilization approach, weighting the probability of terrestrial mammal species appearing in the fossil record based on body size and geographic-range size; larger species with larger range sizes are more likely to enter the fossil record. I create simulated fossil localities from the modern North American mammal record. I vary the percentage of species successfully fossilized and estimate the magnitude of the latitudinal diversity gradient (slope of the richness gradient and degree of species turnover). I find that estimates of the latitudinal diversity gradient are sensitive to the loss of species with small body size and geographic-range sizes. In some cases, simulated fossil-record bias completely obliterates evidence of declining richness with latitude, a phenomenon that is not ameliorated by the application of nonparametric richness estimation. However, if the rate of preservation is medium (50% of species) to high (75% of species), the magnitude of the latitudinal diversity gradient can be reliably estimated. Similarly, changes in the diversity gradient estimates are largely explained by differences in the diversity–climate relationship among iterations, suggesting that these relationships may be measurable in the fossil record.

Body mass is an important organism-level variable in mammalian biology, correlated with physiology, life history, and ecology. To analyze the dynamics of body size evolution, increases and decreases in body mass were tallied for ancestor-descendant (AD) species pairs for 519 terrestrial caniform taxa. To account for uncertainty phylogeny, a bootstrapping routine shuffled hypothesized AD pairs, and average proportions of increases were binned as a function of ancestral body mass. A set of models relating the rate of body size increase were evaluated with the Akaike Information Criterion (AIC). AIC selected three models of the candidate set as equivalent in support by the observed body mass data. These three models propose body size increase for small AD pairs and body size decrease for large AD pairs, although they differ in their treatment of taxa at intermediate sizes.

These results demonstrate the presence of constraints bounding the caniform distribution at large and small body sizes, stabilizing the distribution through time, which stands in contrast to a broader mammalian pattern. At a finer phylogenetic scale, subclades within intermediate size classes display proportions that are significantly different from unbiased, with several clades previously cited as examples of “Cope's Rule” showing biased increases in size, and basal mustelids (badgers, and allied genera), Mephitidae (skunks), and Vulpini (“foxes”) exhibiting biased decreases. The caniform pattern is therefore the result of superimposed, clade-specific trajectories, demonstrating that the inferred dynamics of body size evolution and even the direction of trends in body size evolution within the Caniformia, and for mammals in general, depend on the hierarchical scale of the analysis.

Evolutionary inferences from fossil data often require accurately reconstructing differences in richness and morphological disparity between fossil sites across space and time. Biases such as sampling and rock availability are commonly accounted for in large-scale studies; however, preservation bias is usually dealt with only in smaller, more focused studies. Birds represent a diverse, but taphonomically fragile, group commonly used to infer environmental conditions in recent (Pleistocene and later) fossil assemblages, and their relative scarcity in the fossil record has led to controversy over the timing of their radiation. Here, I use simulations to show how even weak taphonomic biases can distort estimates of richness, and render variance sensitive to sample size. I then apply an ecology-based filtering model to recent bird assemblages to quantify the distortion induced by taphonomy. Certain deposit types, such as caves, show less evidence of taphonomic distortion than others, such as fluvial and lacustrine deposits. Archaeological middens unsurprisingly show some of the strongest evidence for taphonomic bias, and they should be avoided when reconstructing Pleistocene and early Holocene environments. Further, these results support previously suggested methods for detecting fossil assemblages that are relatively faithfully preserved (e.g., presence of difficult-to-preserve taxa), and I use these results to recommend that future large-scale studies include facies diversity along with metrics such as rock volume, or compare only sites with similar taphonomic histories.

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.

Carbon and nitrogen stable isotopic compositions of fossil materials from Lake Messel (47 Ma) in Germany are used to investigate Eocene ecosystem dynamics. Autolithified soft tissues of terrestrial and aquatic vertebrate organisms, as well as plant compression fossils, contain organic material (20–50 wt% C, 1–6 wt% N), which appears to retain precursor compositions. Stable isotopic compositions (δ13C and δ15N) of Messel fossils are similar to those reported for components in modern lacustrine ecosystems. These data show trophically sensible enrichments relative to food sources, reflect multiple feeding strategies for each organism (e.g., omnivory, planctivory, piscivory), and differentiate between benthic and pelagic organic carbon sources. These chemical data broadly confirm existing Messel food web models based on coprolite and gut content analyses. δ13C values for the lacustrine shale range from −30.3 to −26.3‰, pointing to mixed terrestrial and aquatic origins for primary producers in the food web. δ13C values for primary consumers such as insects overlap with those for primary producers but are comparatively enriched in 15N. Secondary and higher consumers (fish, crocodiles, and frogs) are associated with even more positive δ15N values and show a more constrained range of δ13C values. Omnivory appears widespread in both low and high trophic level consumers. Hence, the stable isotopic compositions of Messel fossils are complex and overlap, and must be combined with paleontological investigations in order to be conclusive. This study represents the first comprehensive isotopic reconstruction, featuring tens of components, of an ecosystem of Eocene age. A thorough understanding of trophic structure in Eocene Lake Messel contributes to the global databank of ecological history.

A computer model of background and mass extinctions in a taxonomic hierarchy has been used to study the effects of different extinction patterns in a search for clues as to the causes of actual extinction events. Model taxa at four levels were built up from speciation events in adaptive space according to rules of origination which seem plausible biologically. The frequency distribution of species among the three higher taxonomic levels in the model is similar to that in living marine taxa which have good fossil records. Three mass extinction patterns were imposed on the model after species diversity had attained equilibrium (i.e., when speciation = background extinction): random; bloc (contiguous niches were cleared); and clade (all members of selected higher taxa were removed). Effects on the taxonomic profile varied with pattern. Four of the five historical mass extinctions resemble the effects of the random pattern. End-Permian families were harder hit than those in the random model, but this may be a result of an extremely high species extinction level. It is concluded that the effect of extinctions on the taxonomic hierarchy provides a tool to help in understanding extinction causes.

The founders of North American vertebrate paleontology, F. V. Hayden, Joseph Leidy, E. D. Cope, O. C. Marsh, and their colleagues, collected and described the first suites of fossil mammals obtained from the rich Tertiary successions of the western United States. Among them were remains of fossil horses, and subsequent study of these resulted in an interpretation that supported the concept of Darwinian gradualism as the major mode of evolution. The fossil record of horses also contributed importantly to the demise of orthogenesis as an evolutionary pattern, and to the evaluation of evolutionary rates and long-term evolutionary trends in a major phyletic group of organisms.

During land plant evolution, a change in stelar architecture, i.e., in the geometric arrangement of the water-conducting tissue inside the plant axis, can be observed. In the most primitive stele type, the protostele, the vascular tissue is organized as a simple central strand. Further evolutionary changes led to more peripherally arranged vascular tissues. In the siphonostele, for example, the vascular tissue forms a hollow cylinder filled with pith. A functional explanation of this early stelar evolution is provided in the present paper. Using a numerical simulation approach, we analyze the water transport properties of various protostelic and siphonostelic model axes. The results indicate that several geometric parameters are relevant for understanding the water transport properties of various stele types and for explaining the early stelar evolution: the parenchymatic path lengths (i.e., the distance between the xylem surface and the transpiring plant surface), the ratio of xylem surface over transpiring surface, and the ratio of cross-sectional area of xylem to cross-sectional area of the parenchyma outside of the xylem. As a whole, the evolution of early stele types may be viewed as a size-related multi-criteria optimization process in which the xylem volume as well as the fluid pressure gradients in the parenchyma and in the xylem are minimized. For slender plant axes, a protostele appears to be the optimal stelar architecture. In wider plant axes, however, other stelar architectures (such as a siphonostele) prove to be more efficient than a protostele.

For mammals today, mountains are diverse ecosystems globally, yet the strong relationship between species richness and topographic complexity is not a persistent feature of the fossil record. Based on fossil-occurrence data, diversity and diversification rates in the intermontane western North America varied through time, increasing significantly during an interval of global warming and regional intensification of tectonic activity from 18 to 14 Ma. However, our ability to infer origination and extinction rates reliably from the fossil record is affected by variation in preservation history. To investigate the influence of preservation on estimates of diversification rates, I simulated fossil records under four alternative diversification hypotheses and six preservation scenarios. Diversification hypotheses included tectonically controlled speciation pulses, while preservation scenarios were based on common trends (e.g., increasing rock record toward the present) or derived from fossil occurrences and the continental rock record. For each scenario, I estimated origination, extinction, and diversification rates using three standard methods—per capita, three-timer, and capture–mark–recapture (CMR) metrics—and evaluated the ability of the simulated fossil records to accurately recover the underlying diversification dynamics. Despite variable and low preservation probabilities, simulated fossil records retained the signal of true rates in several of the scenarios. The three metrics did not exhibit similar behavior under each preservation scenario: while three-timer and CMR metrics produced more accurate rate estimates, per capita rates tended to better reproduce true shifts in origination rates. All metrics suffered from spurious peaks in origination and extinction rates when highly volatile preservation impacted the simulated record. Results from these simulations indicate that elevated diversification rates in relation to tectonic activity during the middle Miocene are likely to be evident in the fossil record, even if preservation in the North American fossil record was variable. Input from the past is necessary to evaluate the ultimate mechanisms underlying speciation and extinction dynamics.

High levels of biodiversity and endemism in ancient lakes have motivated research on evolutionary processes in these systems. Drill-core records from Lake Titicaca (Bolivia, Peru), an ancient lake in the high-elevation Altiplano, record the history of climate, landscape dynamics, and diatom evolution. That record was used to examine the patterns and drivers of morphological evolution of an endemic species complex of diatoms in the lake, the Cyclostephanos andinus complex. In an attempt to delineate species within the complex based on morphology, no discernible evidence was found for species separation based on an ordination analysis of multiple characters, but multiple populations were detected based on the distribution of valve size in individual samples. Likelihood modeling of phyletic evolution showed that size evolved through punctuated change. Correlation of size trends with environmental variables indicates that C. andinus size responded to regional environmental change driven by global processes that influenced Lake Titicaca by affecting lake level and thermal stratification.

Most geometric morphometric studies are underpinned by sets of photographs of specimens. The camera lens distorts the images it takes, and the extent of the distortion will depend on factors such as the make and model of the lens and camera and user-controlled variation such as the zoom of the lens. Any study that uses populations of geometric data digitized from photographs will have shape variation introduced into the data set simply by the photographic process. We illustrate the nature and magnitude of this error using a 30-specimen data set of Recent New Zealand Mactridae (Mollusca: Bivalvia), using only a single camera and camera lens with four different photographic setups. We then illustrate the use of retrodeformation in Adobe Photoshop and test the magnitude of the variation in the data set using multivariate Procrustes analysis of variance. The effect of photographic method on the variance in the data set is significant, systematic, and predictable and, if not accounted for, could lead to misleading results, suggest clustering of specimens in ordinations that has no biological basis, or induce artificial oversplitting of taxa. Recommendations to minimize and quantify distortion include: (1) that studies avoid mixing data sets from different cameras, lenses, or photographic setups; (2) that studies avoid placing specimens or scale bars near the edges of the photographs; (3) that the same camera settings are maintained (as much as practical) for every image in a data set; (4) that care is taken when using full-frame cameras; and (5) that a reference grid is used to correct for or quantify distortion.

George Gaylord Simpson was one of the first paleontologists to apply survivorship analysis to the study of fossil taxa. His finding that the survivorship curve for extant bivalve genera plotted above that for extinct genera led him to conclude that bivalve genera are drawn from at least two distinct distributions of longevities, and formed the fundamental basis for his influential concepts of horotelic and bradytelic evolutionary rates. Survivorship curves presented in this paper show the same pattern of disjunct survivorship in genera from the Treatise on Invertebrate Paleontology and in families from Sepkoski's compendium.

Some of the observed differences between survivorship curves are artificial, occurring because long-lived genera and families are more likely to survive to the Recent than short-lived genera and families. The living fauna thus contains a disproportionate number of long-lived genera and families, and the survivorship curve for the living fauna is expected to lie above that for the extinct fauna for this reason alone—even if all longevities are drawn from the same distribution. Recognition of this bias led Raup (1975) to question the significance of the survivorship patterns presented by Van Valen (1973), and Stanley's (1984) acceptance of Raup's argument led him to dismiss the survivorship pattern discovered by Simpson. But statistical analysis using bootstrapping shows that this bias accounts for only a small proportion of the difference between survivorship curves. Other biases considered, such as “pull of the Recent,” “asymmetrical range truncation,” and erroneous concatenation of stratigraphic ranges, do not account for the pattern either. Although still other biases, as yet unknown, cannot definitively be ruled out, it appears that the longevities of extinct and living bivalve taxa are meaningfully different, and that the fundamental causes are biological.

The Neogene species Petaloconchus sculpturatus presents a contradiction in terms, for it grows whorl “packages” of nearly perfect regularity, but ranks within the most geometrically irregular family of uncoiled gastropods, the Vermetidae. We perform a first biometric study of vermetids (only possible because sufficient regularity of growth permits us to number and identify whorls) to specify and characterize the factors on both sides of this “exquisite tension” between promotion and prevention of recoiling. Promoting factors include the older phyletic heritage of preserved dextral coiling, and the more immediate vermetid (or specifically petaloconchid) features of growth toward open spaces (where regular coiling might proceed in an unimpeded fashion); radular excision of discordant feeding tubes with shaping of the resulting scar so that growth may proceed in conformity with previous whorls; and locking of subsequent whorls upon a keel formed by longitudinal bead-rows of the previous whorl. Preventing factors include prominent phyletic heritage of all vermetids—maximal early irregularity enjoined by discordance between larval and subsequent growth (with teleoconch wrapping itself around the protoconch), thus precluding an ordered substrate to act as a foundation for regular whorl “packages” of intermediary growth—and a set of features specific to this lineage and acting as geometric constraints. In this category, we particularly document the exceedingly low rate of whorl expansion and the consequently wide umbilical space that produces a shell akin to winding a cylindrical coil of narrow-diameter rope around the periphery of a wide circular platform. This complex combination of promoting and preventing factors produces a shell that is tantalizingly close to fully regular, but cannot truly reattain this previous phyletic state—thus providing a fine example of Dollo's Law at the centenary of his formation of irreversibility.

Polycystine radiolarians axe the most widely distributed (geographically and geologically) of the well-preserved microzooplankton. To correctly interpret the tempo and mode of radiolarian microevolution, speciation and macroevolution, the zoogeography and ecological niches of extant, and paleozoogeography and paleoecological niches of extinct subspecies, species and higher taxa of the studied lineages should be carefully considered. Such studies of the Stichocorys and Lamprocyrtis lineages suggest that allopatric speciation as peripheral isolates is important. Sympatric speciation is also a possible mode of evolution in these lineages. Hybridization may play a role in the evolution of one subspecies and one species. Allopatrically evolved subspecies and species require some time to inhabit their maximum geographical range after evolving in an isolated and peripheral part of that “environment,” whereas the supposedly sympatrically evolved forms do not. Cooling trends and water mass reorganization may be related to the speciation events. Similar, but much less controlled, studies on a macroevolutionary scale (evolution above the species level, essentially the “family” level) suggest that there have been about half a dozen periods of major adaptive breakthroughs resulting in quantum, or macro, evolution. Global coolings and the initiations of “new” cold-water spheres and related water masses appear to have allowed these macroevolutionary steps during the Ordovician, Devonian-Carboniferous, Permian, and early Neogene. Ecological pressure from diatoms and planktonic foraminiferans appears to have been related to macroevolutionary events bounding the Cretaceous-Tertiary transition.

We describe statistical methods to formulate and validate statements about survival rates given a small number of individuals. These methods allow one to estimate the age-specific survival rate and assess its uncertainty, to assess whether the survival rates during some age range differ from the survival rates during another age range, and to assess whether the survivorship curve has a particular shape. We illustrate these methods by applying them to a sample of 22 Albertosaurus sarcophagus individuals. We show that this sample is too small to provide any confidence in the claim that this species had a “convex” survivorship curve arising from age-specific survival rates that decreased monotonically with age. However, we show that a sample of 50 to 100 individuals has reasonable statistical power to support such a claim. There is evidence for the much weaker claim that average survival rates for ages 2 to 15 were higher than survival rates for later ages. Finally, we describe one way to account for size-dependent fossilization rates and show that a plausible positively-size-dependent fossilization rate results in a substantially non-convex survivorship curve for A. sarcophagus.

The morphological and ecological diversity of lemurs and lorisiformes once rivaled that of the rest of the primate order. Here, we assemble a dataset of 3D models representing the second mandibular molars of a wide range of extant and fossil strepsirrhines encompassing this diversity. We use these models to distill quantitative descriptors of tooth form and then analyze these data using new analytical methods. We employ a recently developed dental topography metric (ariaDNE), which is less sensitive to details of random error in 3D model quality than previously used metrics (e.g., DNE); Bayesian multinomial modeling with metrics designed to measure overfitting risk; and a tooth segmentation algorithm that allows the shapes of disaggregated tooth surface features to be quantified using dental topography metrics. This approach is successful at reclassifying extant strepsirrhine primates to known dietary ecology and indicates that the averaging of morphological information across the tooth surface does not interfere with the ability of dental topography metrics to predict dietary adaptation. When the most informative combination of dental topography metrics is applied to extinct species, many subfossil lemurs and the most basal fossil strepsirrhines are predicted to have been primarily frugivorous or gummivorous. This supports an ecological contraction among the extant lemurs and the importance of frugivory in the origins of crown Strepsirrhini, potentially to avoid competition with more insectivorous and folivorous members of Paleogene Afro-Arabian primate faunas.

Identifying biological traits that promote evolutionary success is fundamental for understanding biodiversity dynamics and for assessing the evolutionary response of organisms to global change. We tested the hypothesis that image-forming eyes have contributed to the diversification of taxa in the geological past. Using fossil occurrences in the Paleobiology Database, we analyzed the diversity and evolutionary rates of more than 17,000 Phanerozoic genera of marine invertebrates living on or above the shallow-water seafloor according to their visual capabilities. Analysis of the complete data set shows a peak in the proportional diversity of sighted genera early in the Phanerozoic, and their continuance at a relatively low and stable level after the Ordovician. As an explanation of this pattern we suggest that selection pressure to develop eyes rose in the Cambrian, and that behavioral constraints had a balancing effect thereafter. In contrast to the pooled data, a clade-level study of those subgroups that contain both sighted and blind genera revealed that—in trilobites, all epifaunal bivalves, pectinoid bivalves, gastropods, and echinoderms—sighted genera diversified more strongly than blind genera. This difference is controlled by significantly raised extinction rates of blind genera. These more finely resolved patterns support the hypothesis that good vision is a key trait that promoted preferential diversification.

Simulations are playing an increasingly important role in paleobiology. When designing a simulation study, many decisions have to be made and common challenges will be encountered along the way. Here, we outline seven rules for executing a good simulation study. We cover topics including the choice of study question, the empirical data used as a basis for the study, statistical and methodological concerns, how to validate the study, and how to ensure it can be reproduced and extended by others. We hope that these rules and the accompanying examples will guide paleobiologists when using simulation tools to address fundamental questions about the evolution of life.