Deep-sea benthic ostracod assemblages covering the last 2 Myr were investigated in Integrated Ocean Drilling Program Site U1426 (at 903 m water depth) in the southern Sea of Japan. Results show that (1) orbital-scale faunal variability has been influenced by eustatic sea-level fluctuations and oxygen variability and (2) secular-scale faunal transitions are likely associated with the mid-Brunhes event (MBE, ~0.43 Ma) and the onset of the Tsushima Warm Current (TWC, ~1.7 Ma). Krithe, Robertsonites, and Acanthocythereis are the three most abundant genera throughout the core, accounting for 78.5% of total specimens. Multiple-regression tree analysis indicated that the TWC, the MBE, and oxygen content are the significant controlling factors of ostracod dominance. Changes in assemblages exhibit decline and recovery patterns corresponding to orbital-scale cyclicity of sea-level changes. In the Sea of Japan marginal ocean setting, this cyclicity shows a close relationship with bottom-water oxygen variability since the onset of the TWC influx. The MBE amplified the influence of the TWC and oxygen variability to the deep-sea ecosystem through larger sea-level fluctuations. Acanthocythereis dunelmensis, a circumpolar species, dominates before the TWC onset. After the TWC onset and during the mid-Pleistocene transition (MPT, ~1.2–0.7 Ma) Krithe spp., known for their low-oxygen tolerance, substantially increase under moderate oxygen depletion. At the end of the MPT, Krithe dominance diminishes and is replaced by Robertsonites hanaii and Propontocypris spp. after the MBE. The post-MBE assemblage, characterized by R. hanaii, suggests a slightly warmer environment under the development of the TWC. In addition, the post-MBE high-amplitude climate system may have caused the increased abundance of active-swimming Propontocypris spp. due to their superior migration ability. Benthic ecosystems in marginal seas are sensitive and vulnerable to both short- and long-term climatic changes, and the MBE is suggested to be a global biotic event affecting benthic ecosystems substantially.

Evolving interactions between predators and prey constitute one of the major adaptive influences on marine animals during the Paleozoic. Crinoids and fish constitute a predator–prey system that may date back to at least the Silurian, as suggested by patterns of crinoid regeneration and spinosity in concert with changes in the predatory fauna. Here we present data on the frequency of breakage and regeneration in the spines of the Middle Devonian camerate Gennaeocrinus and late Paleozoic cladids, as well as an expanded survey of the prevalence of spinosity and infestation by platyceratid gastropods on crinoid genera during the Paleozoic. Spine regeneration frequency in the measured populations is comparable to arm regeneration frequencies from Mississippian Rhodocrinites and from modern deep-water crinoid populations. The prevalence of spinosity varies by taxon, time, and anatomy among Paleozoic crinoids; notably, spinosity in camerates increased from the Silurian through the Mississippian and decreased sharply during the Pennsylvanian, whereas spines were uncommon in cladids until their Late Mississippian diversification. Among camerates, tegmen spinosity is positively correlated with the presence of infesting platyceratid gastropods. These results allow us to evaluate several hypotheses for the effects of predation on morphological differences between early, middle, and late Paleozoic crinoid faunas. Our data corroborate the hypothesis that predators targeted epibionts on camerate crinoids and anal sacs on advanced cladids and suggest that the replacement of shearing predators by crushing predators after the Hangenberg extinction affected the locations of spines in Mississippian camerates.

Under stress, corals and foraminifera may eject or consume their algal symbionts (“bleach”), which can increase mortality. How bleaching relates to species viability over warming events is of great interest given current global warming. We use size-specific isotope analyses and abundance counts to examine photosymbiosis and population dynamics of planktonic foraminifera across the Paleocene–Eocene thermal maximum (PETM, ~56 Ma), the most severe Cenozoic global warming event. We find variable responses of photosymbiotic associations across localities and species. In the NE Atlantic (DSDP Site 401) PETM, photosymbiotic clades (acarininids and morozovellids) exhibit collapsed size-δ13C gradients indicative of reduced photosymbiosis, as also observed in Central Pacific (ODP Site 1209) and Southern Ocean (ODP Site 690) acarininids. In contrast, we find no significant loss of size-δ13C gradients on the New Jersey shelf (Millville) or in Central Pacific morozovellids. Unlike modern bleaching-induced mass mortality, populations of photosymbiont-bearing planktonic foraminifera increased in relative abundance during the PETM. Multigenerational adaptive responses, including flexibility in photosymbiont associations and excursion taxon evolution, may have allowed some photosymbiotic foraminifera to thrive. We conclude that deconvolving the effects of biology on isotope composition on a site-by-site basis is vital for environmental reconstructions.

The mode of locomotion of any swimming animal is constrained by its size, architecture, and phylogenetic history. Considering these factors and the range of locomotory systems used by extant zooplankton, the range of possible modes of locomotion for graptoloids can be effectively limited. Three assumptions have been made: (1) graptoloids did not use a mode of locomotion unknown among modern organisms; (2) all graptoloids employed essentially the same mode of locomotion except, possibly, in their early growth stages; and (3) graptoloids did not rely entirely on passive buoyancy—no extant zooplankton groups in the size range of the graptoloids do. Structures that increase buoyancy or drag are often found in actively swimming zooplankton. They enhance feeding efficiency and reduce sinking rates during nonswimming periods.

The modes of locomotion utilized by extant zooplankton groups are ciliary propulsion, elongate body undulation, jet propulsion, rowing with skeletonized appendages, and rowing or undulation with muscular appendages. Of these, all but the last can be rejected for the graptoloids on the basis of scale or architecture. It is concluded that graptoloids probably used a rowing or undulatory motion with muscular appendages for swimming. Using a pterobranch model for the graptoloid zooids, the lophophore is considered an unlikely propulsive structure because the design requirements would conflict with those of a ciliarly suspension-feeding organ. Winglike, lateral extensions of the muscular cephalic shield, the same structure used for creeping locomotion in the benthic pterobranchs, is regarded as the most likely propulsive organ, analogous to the pteropod swimming wings.

We document a positive and strong correlation between speciation and extinction rates in the Paleozoic zooplankton graptoloid clade, between 481 and 419 Ma. This correlation has a magnitude of ~0.35–0.45 and manifests at a temporal resolution of <50 kyr and, for part of our data set, <25 kyr. It cannot be explained as an artifact of the method used to measure rates, sampling bias, bias resulting from construction of the time series, autocorrelation, underestimation of species durations, or undetected phyletic evolution. Correlations are approximately equal during the Ordovician and Silurian, despite the very different speciation and extinction regimes prevailing during these two periods, and correlation is strongest in the shortest-lived cohorts of species.

We infer that this correlation reflects approximately synchronous coupling of speciation and extinction in the graptoloids on timescales of a few tens of thousands of years. Almost half of graptoloid species in our data set have durations of <0.5 Myr, and previous studies have demonstrated that, during times of background extinction, short-lived species were selectively targeted by extinction. These observations may be consistent with the model of ephemeral speciation, whereby new species are inferred to form constantly and at high rate, but most of them disappear rapidly through extinction or reabsorption into the ancestral lineage. Diversity dependence with a lag of ~1 Myr, also documented elsewhere, may reflect a subsequent and relatively slow, competitive dynamic that governed those species that dispersed beyond their originating water mass and escaped the ephemeral species filter.

The geometry of the simpler types of graptolite stipes can be quantified by assuming them to consist of stacked cylinders representing the thecal tubes. It can be shown that specification of any three characters, for example, thecal inclination, thecal spacing, and stipe width, effectively defines the others (thecal overlap, thecal length and width, thecal “density”); hence the parameters commonly used in the definition of species are not independent. Variation within and between species can be represented by three-character plots. The effects of altering the apertural angle from 90° on such characters as thecal spacing can also be represented geometrically. If thecae are considered as cones rather than cylinders, it follows that as stipe width increases, thecal curvature will describe a sine curve if the thecae are to remain in contact; this observation is matched on real graptolites. Thecal curvature beyond 90° to the dorsal wall is generally impossible without thecae detaching from their neighbors to produce thecal isolation. Growth of thecae along a stipe can be represented graphically. Computer fits to growth curves for five dichograptids show that they can be closely described by an exponential decrease in growth increments along the stipe, and that this model is more accurate than two possible alternatives.

Most evolutionary innovations—power-enhancing phenotypes previously absent in a lineage—have arisen multiple times within major clades. This repetition permits a comparative approach to ask how, where, when, in which clades, and under which circumstances adaptive innovations are acquired and secondarily lost. I use new and literature-based data on the phylogeny, functional morphology, and fossil record of gastropods to explore the acquisition and loss of the siphonal canal and its variations in gastropods. The siphonal indentation, canal, notch, or tube at the front end of the shell is associated in living gastropods with organs that detect chemical signals directionally and at a distance in an anteriorly restricted inhalant stream of water.

Conservative estimates indicate that the siphonate condition arose 23 times and was secondarily lost 17 times. Four siphonate clades have undergone prodigious diversification. All siphonate gastropods have a shell whose axis of coiling lies at a low angle above the plane of the aperture (retroaxial condition). In early gastropods, the siphonal canal was short and more or less confined to the apertural plane. Later (mainly Cretaceous and Cenozoic) variations include a dorsally deflected canal, a long canal, and a closed canal. The closed siphonal canal, in which the edges join to form a tube, arose 15 times, all in the adult stages of caenogastropods with determinate growth.

Gastropods in which the siphonate condition arose were mobile, bottom-dwelling, microphagous animals. Active predaceous habits became associated with the siphonate condition in the Mesozoic and Cenozoic Purpurinidae-Latrogastropoda clade. Loss of the siphonate condition is associated with nonmarine habits, miniaturization, and especially with a sedentary or slow-moving mode of life.

The siphonate condition arose seven times each during the early to middle Paleozoic, the late Paleozoic, and the early to middle Mesozoic, and only once each during the Late Cretaceous and Cenozoic. Well-adapted incumbents prevented most post-Jurassic clades from evolving a siphonal indentation and its associated organs. Dorsally deflected, long, and closed canals are known only from Cretaceous and Cenozoic marine gastropods, and represent improvements in sensation and passive armor.

In a discussion of contrasting ecologies of clades that gained and lost the siphonate condition, I argue that macroevolutionary trends in the comings and goings of innovations and clades must incorporate ecological and functional data. Acquisitions of energy-intensive, complex innovations that yield greater power have a greater effect on ecosystems, communities, and their resident clades than do reversals, which generally reflect energy savings.

The field of sclerochronology has long been known to paleobiologists. Yet, despite the central role of growth rate, age, and body size in questions related to macroevolution and evolutionary ecology, these types of studies and the data they produce have received only episodic attention from paleobiologists since the field's inception in the 1960s. It is time to reconsider their potential. Not only can sclerochronological data help to address long-standing questions in paleobiology, but they can also bring to light new questions that would otherwise have been impossible to address. For example, growth rate and life-span data, the very data afforded by chronological growth increments, are essential to answer questions related not only to heterochrony and hence evolutionary mechanisms, but also to body size and organism energetics across the Phanerozoic. While numerous fossil organisms have accretionary skeletons, bivalves offer perhaps one of the most tangible and intriguing pathways forward, because they exhibit clear, typically annual, growth increments and they include some of the longest-lived, non-colonial animals on the planet. In addition to their longevity, modern bivalves also show a latitudinal gradient of increasing life span and decreasing growth rate with latitude that might be related to the latitudinal diversity gradient. Is this a recently developed phenomenon or has it characterized much of the group's history? When and how did extreme longevity evolve in the Bivalvia? What insights can the growth increments of fossil bivalves provide about hypotheses for energetics through time? In spite of the relative ease with which the tools of sclerochronology can be applied to these questions, paleobiologists have been slow to adopt sclerochronological approaches. Here, we lay out an argument and the methods for a path forward in paleobiology that uses sclerochronology to answer some of our most pressing questions.

We know that the fossil record is incomplete. But how incomplete? Here we very coarsely estimate the completeness of the mammalian record in the Miocene, assuming that the duration of a mammalian species is about 1 Myr and the species diversity has stayed constant and is structurally comparable to the taxonomic diversity today. The overall completeness under these assumptions appears to be around 4%, but there are large differences across taxonomic groups. We find that the fossil record of proboscideans and perissodactyls as we know it for the Miocene must be close to complete, while we might know less than 15% of the species of artiodactyl or carnivore fossil species and only about 1% of primate species of the Miocene. The record of small mammals appears much less complete than that of large mammals.

Pterobranchs are the closest living relatives of graptolites. Their skeleton is constructed from the same material, and in a homologous manner. Growth rates of the pterobranch Cephalodiscus gracilis are described for the first time and, along with rhabdopleuran growth rates, they are used to estimate the amount of time invested by a graptolite colony in growing its rhabdosome. This is a measure of minimum age. The significance of age calculations is shown for individuals and large communities of graptoloids. Large individuals can be shown to be much older than the time it would have taken them to settle through seawater and so it is shown that graptoloids moved up, as well as down, through the water column. Life tables constructed for biserial graptoloids from the Utica shale in Quebec, Canada, suggest that these graptoloids died from constant environmental stress. Graptoloid length can thus be a function of environment and should only cautiously be considered to be of taxonomic significance.

The time separating the first appearances of species from their divergences from related taxa affects assessments of macroevolutionary hypotheses about rates of anatomical or ecological change. Branch durations necessarily posit stratigraphic gaps in sampling within a clade over which we have failed to sample predecessors (ancestors) and over which there are no divergences leading to sampled relatives (sister taxa). The former reflects only sampling rates, whereas the latter reflects sampling, origination, and extinction rates. Because all three rates vary over time, the probability of a branch duration of any particular length will differ depending on when in the Phanerozoic that branch duration spans. Here, I present a birth–death-sampling model allowing interval-to-interval variation in diversification and sampling rates. Increasing either origination or sampling rates increases the probability of finding sister taxa that diverge both during and before intervals of high sampling/origination. Conversely, elevated extinction reduces the probability of divergences from sampled sister taxa before and during intervals of elevated extinction. In the case of total extinction, a Signor-Lipps will reduce expected sister taxa leading up to the extinction, with the possible effect stretching back many millions of years when sampling is low. Simulations indicate that this approach provides reasonable estimates of branch duration probabilities under a variety of circumstances. Because current probability models for describing morphological evolution are less advanced than methods for inferring diversification and sampling rates, branch duration priors allowing for time-varying diversification could be a potent tool for phylogenetic inference with fossil data.

Deriving ecological and evolutionary descriptions of, and implications from, faunal assemblage patterns is commonly addressed by observation and a variety of exploratory techniques (scaling and clustering), along with qualitative evaluations of species occurrences and relative abundances. We argue that interpretations of faunal patterns, especially those documented by the fossil record, should be based upon the composition and structure of entire communities to provide strong conclusions and replicable results.

As an example, we use benthic foraminiferal data at high resolution (1–2 cm, corresponding to 300–1400 yr) over a section corresponding to about 20 kyr across the beginning of the Paleocene–Eocene thermal maximum (PETM). The PETM was an episode of rapid global warming about 55.5 Ma, associated with ocean acidification and lowered open oceanic productivity and deoxygenation and marked by severe turnover in benthic foraminiferal assemblages. Here we provide a stand-alone approach applicable to any dynamic faunal system, perturbation detection analysis (PDA), to recognize and identify community disruption evidenced as either positive growth or negative decline, and we use this methodical approach to obtain new information on foraminiferal communities before, during, and after the initiation of the PETM.

We conclude that the late Paleocene benthic foraminiferal community (FCOM1) was in a growth stage of positive increasing diversity, suggestive of favorable environmental conditions. This stage continued through the initial changes at the onset of the PETM, when disruption through environmental stress led to this community's termination. A second community (FCOM2) formed with declining diversity and high variability, showing a lack of adaptation to changing conditions. Knowledge of total assemblage status under both adverse and advantageous conditions is necessary, but not recognized by methods that rely upon analysis of single samples only: individual samples cannot be used to recognize disruptive changes in a community's structure, but these are easily identified using PDA.

Whether the evolutionary dynamics of one group of organisms influence that of another group of organisms over the vast timescale of the geological record is a difficult question to tackle. This is not least because multiple factors can influence or mask the effects of potential driving forces on evolutionary dynamics of the focal group. Here, we show how an approach amenable to causality inference for time series, linear stochastic differential equations (SDEs), can be used in a multivariate fashion to shed light on driving forces of diversification dynamics across the Phanerozoic. Using a new, enhanced stepwise search algorithm, we searched through hundreds of models to converge on a model that best describes the dynamic relationships that drove brachiopod and bivalve diversification rates. Using this multivariate framework, we characterized a slow process (half-life of c. 42 Myr) that drove brachiopod extinction. This slow process has yet to be identified from the geological record. Using our new framework for analyzing multiple linear SDEs, we also corroborate our previous findings that bivalve extinction drove brachiopod origination in the sense that brachiopods tended to diversify at a greater rate when bivalves were removed from the system. It is also very likely that bivalves “self-regulate” in the sense that bivalve extinctions also paved the way for higher bivalve origination rates. Multivariate linear SDEs as we presented them here are likely useful for studying other dynamic systems whose signatures are preserved in the paleontological record.

Placodontia were a group of marine reptiles that lived in shallow nearshore environments during the Triassic. Based on tooth morphology it has been inferred that they were durophagous, but tooth morphology differs among species: placodontoid placodonts have teeth described as hemispherical, and the teeth of more highly nested taxa within the cyamodontoid placodonts have been described as flat. In contrast, the sister taxon to the placodonts, Palatodonta bleekeri, like many other marine reptiles, has tall pointed teeth for eating soft-bodied prey. The goals of this paper are to quantify these different tooth morphologies and compare tooth shape among taxa and with a functionally “optimal” tooth. To quantify tooth morphology we measured the radius of curvature (RoC) of the occlusal surface by fitting spheres to 3D surface scans or computed microtomographic scans. Large RoCs correspond to flatter teeth, while teeth with smaller RoCs are pointier; positive RoCs have convex occlusal surfaces, and a negative RoC indicates that the occlusal surface of the tooth is concave. We found the placodontoid taxa have teeth with smaller RoCs than more highly nested taxa, and palatine teeth tend to be flatter and closer to the optimal morphology than maxillary teeth. Within one well-nested clade, the placochelyids, the rearmost palatine teeth have a more complex morphology than the predicted optimal tooth, with an overall concave occlusal surface with a small, medial cusp. These findings are in keeping with the hypothesis that placodonts were specialized durophagous predators with teeth modified to break hard prey items while resisting tooth failure.

Evolutionary trends seemingly abound throughout the history of life. Perhaps the best-known example is Cope's rule, the tendency for lineages to increase in size over time. Other examples include hypothesized trends toward increasing complexity and fitness. What kinds of mechanisms cause such large-scale trends—trends occurring in higher taxa over geological time spans—and how can we effectively visualize them?

The study of evolution has increasingly incorporated considerations of history, scale, and hierarchy, in terms of both the origin of variation and the sorting of that variation. Although the macroevolutionary exploration of developmental genetics has just begun, considerable progress has been made in understanding the origin of evolutionary novelty in terms of the potential for coordinated morphological change and the potential for imposing uneven probabilities on different evolutionary directions. Global or whole-organism heterochrony, local heterochrony (affecting single structures, regions, or organ systems) and heterotopies (changes in the location of developmental events), and epigenetic mechanisms (which help to integrate the developing parts of an organism into a functional whole) together contribute to profound nonlinearities between genetic and morphologic change, by permitting the generation and accommodation of evolutionary novelties without pervasive, coordinated genetic changes; the limits of these developmental processes are poorly understood, however. The discordance across hierarchical levels in the production of evolutionary novelties through time, and among latitudes and environments, is an intriguing paleontological pattern whose explanation is controversial, in part because separating effects of genetics and ecology has proven difficult. At finer scales, species in the fossil record tend to be static over geologic time, although this stasis—to which there are gradualistic exceptions—generally appears to be underlain by extensive, nondirectional change rather than absolute invariance. Only a few studies have met the necessary protocols for the analysis of evolutionary tempo and mode at the species level, and so the distribution of evolutionary patterns among clades, environments, and modes of life remains poorly understood. Sorting among taxa is widely accepted in principle as an evolutionary mechanism, but detailed analyses are scarce; if geographic range or population density can be treated as traits above the organismic level, then the paleontological and mac̀roecological literature abounds in potential raw material for such analyses. Even if taxon sorting operates on traits that are not emergent at the species level, the differential speciation and extinction rates can shape large-scale evolutionary patterns in ways that are not simple extrapolations from short-term evolution at the organismal level. Changes in origination and extinction rates can evidently be mediated by interactions with other clades, although such interactions need to be studied in a geographically explicit fashion before the relative roles of biotic and physical factors can be assessed. Incumbency effects are important at many scales, with the most dramatic manifestation being the postextinction diversifications that follow the removal of incumbents. However, mass extinctions are evolutionarily important not only for the removal of dominant taxa, which can occur according to rules that differ from those operating during times of lower extinction intensity, but also for the dramatic diversifications that follow upon the removal or depletion of incumbents. Mass extinctions do not entirely reset the evolutionary clock, so survivors can exhibit unbroken evolutionary continuity, trends that suffer setbacks but then resume, or failure to participate in the recovery.

Lipids found associated with skeletons represent an important avenue of study in molecular paleontology, because the chemical nature of these compounds means they are often biogenically specific and can survive in the geologic record over millions of years. Though it is clear that these skeletal compounds originate from the mineralizing organism, our understanding of the distributions and nutritional sources of lipids among invertebrates is still limited, requiring that baseline studies of modern taxa be completed to evaluate the potential of skeletal lipids in paleoecological studies.

In this study, skeletal lipids from nine modern invertebrate taxa (five mollusks, a brachiopod, an echinoid, a coral, and a barnacle) were extracted and analyzed. Though the major classes of lipids found in the skeletons are remarkably consistent, the sterol profiles from these organisms contain both dietary and environmental information. The skeletons of filter feeders generally have two to three times the variety of sterols as compared with carnivores and grazers. In addition, specific steroidal contributions from several plant and algal groups (including dinosterol, 22-dehydrocholesterol, and β- and γ-sitosterol) can be identified. The limited nature and distribution of sterols in the carnivore skeleton implies that both sterol-recycling and some degree of molecular selectivity may be occurring in this taxon. Taxa living in nearshore shallow marine habitats have significant sterol contributions from higher plants, while deepwater organisms have relatively little. Since the geologically stable form of sterols often retains the three-dimensional structure necessary to recognize the biological precursor, these compounds may be used for determining the ecology of fossil invertebrates.

Cameral water in the shell of the cephalopod Nautilus physically supports each septum while it is being formed; it also provides a reservoir of liquid ballast which is extracted to balance the increase in weight in seawater due to shell and tissue growth. It is not used as an aid to vertical movement. In adults, the sole function of cameral water is ballast in order to maintain Nautilus' slight weight in seawater.

Climate changes are multivariate in nature, and disentangling the proximal drivers of biotic responses to paleoclimate events requires time series of multiple environmental proxies. We reconstruct a multivariate time series of local environmental change for the early Miocene Newport Member of the Astoria Formation (20.26–18 Ma), using proxies for temperature (δ18O), productivity (δ13C), organic carbon flux (Δδ13C), oxygenation (δ15N), and sedimentary grain size (% mud). Our data suggest increases in productivity and declines in oxygenation on the Oregon shelf during this interval of global warming. We evaluate the association of individual environmental factors, and combinations of factors, with changes in faunal composition observed in benthic foraminiferal and molluscan communities collected from the exact same sediments as the environmental data. The δ15N values are the most parsimonious correlates with major changes in foraminiferal composition, whereas molluscan composition is most closely related to δ13C values, suggesting that different components of the environment are influencing each group. When the proxies that have the best supported relationships with the faunal gradients are removed from the analyses to simulate the absence of those proxy data, significant relationships between the faunal gradients and the remaining environmental proxies can still be found. This suggests that environmental drivers can be incorrectly attributed to faunal changes when key proxy data are missing. Paleoecological studies of biotic response that test multiple environmental drivers for multiple taxonomic groups are powerful tools for identifying the ecological consequences of past warming events and the regional drivers of ecological changes.