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.

Fossil bivalve shells are well-suited for landmark/semilandmark morphometric analysis because they preserve both traces of the internal anatomy and the whole shell outline. Utilizing landmarks and semilandmarks, we have characterized internal and external shape variation in a monophyletic clade of Cenozoic New Zealand and Australian crassatellid bivalves, to test the contiguity in morphospace of species-level taxa and to quantitatively examine the “Concept of Independent Entities” of Yonge (1953). Thirteen species from two genera (Spissatella Finlay 1926 and Eucrassatella Iredale 1924) are investigated. Spissatella n. sp. C is confirmed as forming a contiguous group separate to S. trailli and S. clifdenensis. Shell outline and internal anatomy are found to covary in shape, refuting the “Concept of Independent Entities” in the study group.

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.

Presented here is a coupled model of the nonmarine fossil record, based on a geometric model of deposition, a random-branching model of evolution, and an ecological model based on an elevation gradient. This model provides testable predictions about the stratigraphy and fossil occurrences in coastal nonmarine settings under three scenarios of sea-level change. A slow relative rise in sea level causes a declining ratio of channel to floodplain deposits, plus changes in community composition that reflect an upward increase in elevation relative to sea level. A rapid relative rise in sea level drives increasing aggradation rates, decreases the ratio of channel to floodplain deposits, and triggers a shift from higher-elevation (more inland) to lower-elevation (more coastal) communities. A fall in sea level produces an unconformity, manifested by valleys separated by interfluves. The resumption of deposition following the sea-level fall causes an abrupt shift in community composition across the unconformity, reflecting the duration of the hiatus and the increased elevation relative to sea level. This produces a cluster of first and last occurrences at the unconformity, and it is the only sequence-stratigraphic source of such clusters in a nonmarine system, in contrast to the multiple mechanisms for generating these clusters in marine systems. A central prediction of these models is that the nonmarine fossil record preserves systematic changes in community composition that reflect elevation (or equivalently, distance from shore). Diagnosing these gradients in ancient systems is a promising avenue of future research.

The 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.

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?

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.

Hypotheses regarding the evolution of many clades are often generated in the absence of data from the fossil record and potential biases introduced by exclusion of paleontological data are frequently ignored. With regard to body size evolution, extinct taxa are frequently excluded because of the lack of body mass estimates—making identification of reliable clade specific body mass estimators crucial to evaluating trends on paleontological timescales. Herein, I identify optimal osteological dimensions for estimating body mass in extinct species of Pan-Alcidae (Aves, Charadriiformes) and utilize newly generated estimates of body mass to demonstrate that the combination of neontological and paleontological data produces results that conflict with hypotheses generated when extant species data are analyzed in isolation. The wing-propelled diving Pan-Alcidae are an ideal candidate for comparing estimates of body mass evolution based only on extant taxa with estimates generated including fossils because extinct species diversity (≥31 species) exceeds extant diversity, includes examples from every extant genera, and because phylogenetic hypotheses of pan-alcid relationships are not restricted to the 23 extant species. Phylogenetically contextualized estimation of body mass values for extinct pan-alcids facilitated evaluation of broad scale trends in the evolution of pan-alcid body mass and generated new data bearing on the maximum body mass threshold for aerial flight in wing-propelled divers. The range of body mass in Pan-Alcidae is found to exceed that of all other clades of Charadriiformes (shorebirds and allies) and intraclade body mass variability is recognized as a recurring theme in the evolution of the clade. Finally, comparisons of pan-alcid body mass range with penguins and the extinct †Plotopteridae elucidate potentially shared constraints among phylogenetically disparate yet ecologically similar clades of wing-propelled divers.

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.

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

True muscular articulations, as opposed to ligamentary ones, are reported here for the first time in the biserial arms of advanced inadunate crinoids (Poteriocrinina). The topography of biserial articular surfaces indicates clearly derivation from a uniserial muscular articulation with two muscle scars, a transverse ridge, and other structures considered typical of this articular mode. Biserial muscular articulations extend from the arm base to within a few brachials of the arm tip, although the articulations are more pronounced and better developed proximally. The inadunate facets are compared with those of the biserial arms of camerates, which are shown to be non-muscular and probably were capable of only limited movement. The arm movements of inadunate biserial arms are interpreted to have been ones where alternating muscle bundles on either side of the arm induced twisting motions of the arms so that a planar filtration fan mode of feeding was possible, in contrast to the parabolic feeding fan or other modes of feeding that were probably performed by other Paleozoic crinoids.

A priori choices in the detail and breadth of a study are important in addressing scientific hypotheses. In particular, choices in the number and type of characters can greatly influence the results in studies of morphological diversity. A new character suite was constructed to examine trends in the disparity of early Paleozoic crinoids. Character-based rarefaction analysis indicated that a small subset of these characters (~20% of the complete data set) could be used to capture most of the properties of the entire data set in analyses of crinoids as a whole, noncamerate crinoids, and to a lesser extent camerate crinoids. This pattern may be the result of the covariance between characters and the characterization of rare morphologies that are not represented in the primary axes in morphospace. Shifting emphasis on different body regions (oral system, calyx, periproct system, and pelma) also influenced estimates of relative disparity between subclasses of crinoids. Given these results, morphological studies should include a pilot analysis to better examine the amount and type of data needed to address specific scientific hypotheses.

Because the paleontologic concept of Coccolithophoridae species is restricted and far removed from the biologic concept, which itself is not yet satisfactorily established, calcareous nannofossil taxonomy remains in an unsatisfactory state. This situation is clearly reflected by various authors' widely different interpretations of the phylogenetic relationships among species in a given genus and among genera. Examples taken from the extant genus Helicosphaera suggest that because of parallel evolution, delineation of phylogenetic relationships among coccolith morphospecies using morphologic data alone are hazardous, as is delineation of phylogenetic relationships among closely related genera.

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

Principal component analysis has been used to test for similarities in ecology and life habit between modern and fossil birds; however, the two main portions of the hind limb—the foot and the long bone elements—have not been examined separately. We examine the potential links between morphology, ecology, and phylogeny through a synthesis of phylogenetic paleoecological methods and morphospace analysis. Both hind limb morphologies and species’ ecologies exhibit extreme phylogenetic clumping, although these patterns are at least partially explainable by a Brownian motion style of evolution. Some morphologies are strongly correlated with particular ecologies, while some ecologies are occupied by a variety of morphologies. Within the morphospace analyses, the length of the hallux (toe I) is the most defining characteristic of the entire hind limb. The foot and hind limb are represented on different axes when all measurements are considered in an analysis, suggesting that these structures undergo morphological change separately from each other. Early birds tend to cluster together, representing an unspecialized basal foot morphotype and a hind limb reliant on hip-driven, not knee-driven, locomotion. Direct links between morphology, ecology, and phylogeny are unclear and complicated and may be biased due to sample size (~60 species). This study should be treated as a preliminary analysis that further studies, especially those examining the vast diversity of modern birds, can build upon.

Models of functional ecospace diversification within life-habit frameworks (functional-trait spaces) are increasingly used across community ecology, functional ecology, and paleoecology. In general, these models can be represented by four basic processes, three that have driven causes and one that occurs through a passive process. The driven models include redundancy (caused by forms of functional canalization), partitioning (specialization), and expansion (divergent novelty), but they also share important dynamical similarities with the passive neutral model. In this second of two companion articles, Monte Carlo simulations of these models are used to illustrate their basic statistical dynamics across a range of data structures and implementations. Ecospace frameworks with greater numbers of characters (functional traits) and ordered (multistate) character types provide more distinct dynamics and greater ability to distinguish the models, but the general dynamics tend to be congruent across all implementations. Classification-tree methods are proposed as a powerful means to select among multiple candidate models when using multivariate data sets. Well-preserved Late Ordovician (type Cincinnatian) samples from the Kope and Waynesville formations are used to illustrate how these models can be inferred in empirical applications. Initial simulations overestimate the ecological disparity of actual assemblages, confirming that actual life habits are highly constrained. Modifications incorporating more realistic assumptions (such as weighting potential life habits according to actual frequencies and adding a parameter controlling the strength of each model’s rules) provide better correspondence to actual assemblages. Samples from both formations are best fit by partitioning (and to lesser extent redundancy) models, consistent with a role for local processes. When aggregated as an entire formation, the Kope Formation pool remains best fit by the partitioning model, whereas the entire Waynesville pool is better fit by the redundancy model, implying greater beta diversity within this unit. The ‘ecospace’ package is provided to implement the simulations and to calculate their dynamics using the R statistical language.

This paper aims at assessing the influence of the bone ornamentation and, specifically, the associated loss of bone mass on the mechanical response of the crocodylomorph osteoderms. To this end, we have performed three-dimensional (3D) modeling and a finite element analysis on a sample that includes both extant dry bones and well-preserved fossils tracing back to the Late Triassic. We simulated an external attack under various angles on the apical surface of each osteoderm and further repeated the simulation on an equivalent set of smoothed 3D-modeled osteoderms. The comparative results indicated that the presence of an apical sculpture has no significant influence on the von Mises stress distribution in the osteoderm volume, although it produces a slight increase in its numerical score. Moreover, performing parametric analyses, we showed that the Young's modulus of the osteoderm, which may vary depending on the bone porosity, the collagen fiber orientation, or the calcification density, has no impact on the von Mises stress distribution inside the osteoderm volume. As the crocodylomorph bone ornamentation is continuously remodeled by pit resorption and secondary bone deposition, we assume that the apical sculpture may be the outcome of a trade-off between the bone mechanical resistance and the involvement in physiological functions. These physiological functions are indeed based on the setup of a bone superficial vessel network and/or the recurrent release of mineral elements into the plasma: heat transfers during basking and respiratory acidosis buffering during prolonged apnea in neosuchians and teleosaurids; compensatory homeostasis in response to general calcium deficiencies. On a general morphological basis, the osteoderm geometric variability within our sample leads us to assess that the global osteoderm geometry (whether square or rectangular) does not influence the von Mises stress, whereas the presence of a dorsal keel would somewhat reduce the stress along the vertical axis.