Amecystis Ulrich and Kirk is a rhombless rhombiferan cystoid exhibiting adaptation to an active mode of life in the bilaterally symmetrical, dorso-ventrally compressed theca and to an active mode of respiration suggested by the lack of pore rhombs and greatly enlarged periproct. Like other members of the Pleurocystitidae, Amecystis probably wriggled along the bottom, but may have adopted a temporarily sessile habit by pushing the distal stele into the substrate or by grasping. Evolution of the genus began in the Middle Ordovician, probably as a development from Pleurocystites. General trends in the stratigraphic succession of recognized morphospecies: A. raymondi Parsley, A. woodi n.sp., and A. laevis (Raymond) show a reduction in angularity of thecal outline and obsolescence of surface features on the thecal plates. The use of the periproct as a pumping organ in respiration is regarded as an advanced trend that was probably utilized by many rhomb-bearing cystoids as an accessory respiratory mode; alone, it proved to be an unsuccessful adaptation in Amecystis.

Graphoglyptids are biogenic structures commonly found in deep-sea flysch deposits and occasionally detected on the modern deep-sea floor. They extend principally horizontally and take a variety of geometric patterns, whose functional morphology remains an enigma in ichnology and paleoceanography. Based on published materials from 1850 to 2017 (79 ichnotaxa from 28 ichnogenera of graphoglyptids) and systematic observations of one of the largest deep-sea trace fossil collections in the world, this paper proposes that topological analysis is an important ingredient in the taxonomy and functional interpretation of graphoglyptids. Accordingly, graphoglyptids are classified into line, tree, and net forms by their key topological architecture, and are further attributed to 19 topological prototypes by detailed secondary topological features. Line graphoglyptids are single-connected structures with uniform tunnel width, representing primarily the feeding patterns of solitary animals. Tree graphoglyptids, the most diverse architectural group of graphoglyptids, are ascribed to 11 topological prototypes according to the connectivity features of burrow segments and the number and distributional pattern of the branching points. Net graphoglyptids are subdivided into three topological prototypes on the basis of the connectivity features and/or the regularity of the meshes. Multiconnected net forms are considered as a continuous morphological spectrum with different levels of complexity in the net formation. The various connected components in multiconnected tree and net graphoglyptids generally exhibit small and uniform tunnel diameter in a given structure (suggesting a tiny trace maker[s]). The whole structure shows relatively extensive linear or surface coverage and overall good preservation, indicating sustained processes of burrow construction. It is highly probable that certain multiconnected tree and net graphoglyptids represent some emergent patterns from self-organized collective behaviors of conspecific animals. Graphoglyptids thus provide us with a new perspective on the study of solitary and collective behaviors of macrobenthos in the deep-sea environment.

Sharks have a long and rich fossil record that consists predominantly of isolated teeth due to the poorly mineralized cartilaginous skeleton. Tiger sharks (Galeocerdo), which represent apex predators in modern oceans, have a known fossil record extending back into the early Eocene (ca. 56 Ma) and comprise 22 recognized extinct and one extant species to date. However, many of the fossil species remain dubious, resulting in a still unresolved evolutionary history of the tiger shark genus. Here, we present a revision of the fossil record of Galeocerdo by examining the morphological diversity and disparity of teeth in deep time. We use landmark-based geometric morphometrics to quantify tooth shapes and qualitative morphological characters for species discrimination. Employing this combined approach on fossil and extant tiger shark teeth, our results only support six species to represent valid taxa. Furthermore, the disparity analysis revealed that diversity and disparity are not implicitly correlated and that Galeocerdo retained a relatively high dental disparity since the Miocene despite its decrease from four to one species. With this study, we demonstrate that the combined approach of quantitative geometric morphometric techniques and qualitative morphological comparisons on isolated shark teeth provides a useful tool to distinguish between species with highly similar tooth morphologies.

The emergence of Phanerozoic global diversity as a central theme of investigation has resulted from a confluence of factors, including the assembly by several researchers of global taxonomic databases; the advent of computers, which permitted construction and analysis of global Phanerozoic diversity trajectories; and the recognition that Phanerozoic diversity trends are important bellwethers of the evolutionary processes that cause biotic transitions. Despite the enormous progress in the measurement and interpretation of Phanerozoic diversity over the past quarter century, much of which has been reported in Paleobiology, these studies have collectively generated at least as many new questions as they have answered—arguably the mark of an area of inquiry that continues to be vital. In this essay, I discuss several outstanding issues in the investigation of Phanerozoic diversity, ranging from the viability of literature-derived databases for investigating global diversity trends, to the biological significance of the myriad biotic transitions that have taken place throughout the Phanerozoic.

The emergence of shell forms in the growth of foraminifera is an essential problem in the morphogenesis of these microorganisms. We present a model of foraminiferal shells that applies a moving-reference system. Previous models have referred to fixed-reference axes and have neglected apertures. Our model focuses on real morphologic characteristics and follows stepwise natural biological processes. It introduces apertures based on minimization of the local communication path and applies three parameters, which are either predetermined or selected at random from given ranges. Expression of stochastic parameters mimics phenotypic variability of a shell. We also present a detailed description of the method with examples of simulated shells and the first step toward analyses of the theoretical morphospace. The morphospace is divided into certain regions (phases) separated by transitional planes (phase transitions). Further prospects for foraminiferal modeling, which should focus on more in-depth models based on realistic intracellular dynamics, are also presented.

Estimates of taxonomic richness and abundance are complicated by sampling biases. The failure to sample rare taxa is most often attributed to inadequate sampling and to removal during the process of sample-size standardization. Here I present two methods for unveiling rare diversity by integrating species presence/absence data from museum collections and the literature with quantitative estimates of species richness and abundance gathered from field-based bulk samples. Combining museum, literature, and field data can provide a more comprehensive estimate of taxonomic richness and abundance without substantial increase in current sampling effort. First, in a given bulk sample, the lowest proportional abundance value observed can be used to estimate the maximum abundance of rare species known to have occurred at the locality at least once but not recorded in the current sample. Second, a model-selection approach can be used, in which a set of relative abundance distribution models are fit to the bulk-sample abundance data and the parameter estimates for the best model used to calculate the abundance distribution for all species known from the locality. The Paleogene marine fossil record of the U.S. Gulf Coastal Plain is suitable for applying these methods, because (1) the molluscan fauna is well represented in museum collections and the literature, (2) the molluscan fauna has been taxonomically standardized, and (3) many classic localities remain accessible for standardized bulk sampling. I introduce these methods by applying them to a single locality and then, using the faunas of the Gosport, Moodys Branch, and Red Bluff Formations, I demonstrate how the model-fitting approach can be used to compare taxonomic richness among multiple localities. A substantial fraction of the molluscan richness known from each locality is not captured in bulk samples and much of this unobserved richness may be attributed to the rarity of species. The multiple-locality comparison suggests that the greatest Paleogene decline in standing richness occurred in the middle Eocene and that the recovery of richness following the Eocene-Oligocene extinction was quite rapid despite substantial loss of taxa. These analyses underscore the magnitude of veiled diversity in marine fossil assemblages and the potential of existing sources of data to unveil rare taxa, allowing them to be incorporated into quantitative diversity studies.

The final 10 Myr of the Paleozoic saw two of the biggest biological crises in Earth history: the middlePermian extinction (often termed the Guadalupian–Lopingian extinction [GLE]) that was followed 7–8 Myr later by Earth's most catastrophic loss of diversity, the Permian–Triassic mass extinction (PTME). These crises are not only manifest as sharp decreases in biodiversity and—particularly for the PTME—total ecosystem collapse, but they also drove major changes in biological morphological characteristics such as the Lilliput effect. The evolution of test size among different clades of foraminifera during these two extinction events has been less studied. We analyzed a global database of foraminiferal test size (volume) including 20,226 specimens in 464 genera, 98 families, and 9 suborders from 632 publications. Our analyses reveal significant reductions in foraminiferal mean test size across the Guadalupian/Lopingian boundary (GLB) and the Permian/Triassic boundary (PTB), from 8.89 to 7.60 log10 μm3 (lg μm3) and from 7.25 to 5.82 lg μm3, respectively. The decline in test size across the GLB is a function of preferential extinction of genera exhibiting gigantism such as fusulinoidean fusulinids. Other clades show little change in size across the GLB. In contrast, all Lopingian suborders in our analysis (Fusulinina, Lagenina, Miliolina, and Textulariina) experienced a significant decrease in test size across the PTB, mainly due to size-biased extinction and within-lineage change. The PTME was clearly a major catastrophe that affected many groups simultaneously, and the GLE was more selective, perhaps hinting at a subtler, less extreme driver than the later PTME.

Rancho La Brea is unquestionably the most famous fossil deposit in North America, and its fauna occupies a key position in vertebrate paleontology as the basis for the Rancholabrean Land Mammal Age. The 23 acres now known as Hancock Park yielded the bulk of fossil specimens from this locality. A minimum of 518 taxa have been identified to date including 79 algae (all but one of which are diatoms), 72 vascular plants, 9 nonmarine mollusks (13 taxa of marine mollusks were carried to the site by early Indians), 135 arthropods, 27 lower vertebrates, 138 birds, and 58 mammals. A detailed list of the biota, too lengthy for inclusion here, is available from the authors on request.

Consider a one-dimensional sequence (temporal or spatial) of samples from a many-species community. The sequence may exhibit no steady change, or gradual, steady change, or one or more abrupt, stepwise changes. The pattern is graphically displayed in a similarity matrix, whose elements are the pairwise similarities between every possible pair of samples.

Statistical study of the patterns of similarity matrices will be shown to be informative. A criterion, Q, is proposed for measuring the “disarray” of a similarity matrix; matrices constructed from “perfect” sequences, exhibiting uninterrupted steady change, have Q = 0. The probability distribution of Q in “random” similarity matrices (constructed from sequences in which the ordering is wholly haphazard) is examined.

Several applications are illustrated, using data on foraminiferal assemblages in marine sediment cores as examples. Use of the criterion permits the following: (1) Objective recognition of regions in which stratigraphy is especially well preserved. (2) Selection for study of cores in which the sequence of change is especially clear, and rejection of cores in which the natural sequence has been obscured by reworking. (3) Judgment as to whether, in sequences exhibiting stepwise changes, gradual change between the steps occurs as well. (4) Discrimination between species-sets that track gradual environmental change and sets that switch abruptly. (5) Objective choice of the best similarity index for measuring pairwise similarities in a given body of data.

Historical biogeographers are divided over the major process whereby extant species, or their ancestors, arrived in their present geographical locations. One faction promotes the idea of discrete “centers” of evolutionary radiation, from which species have been supplied to other areas by long-distance dispersal. A second faction advances the notion of widespread ancestral biotas, which have been fractionated into descendant biotas over time (vicariance). A seemingly endless polemic has elevated these rather simple alternatives to causes célèbres, and many workers have responded by dismissing virtually the entire vicariance literature (see Pielou 1981). We believe that the important distinction between vicariance and center-of-origin/long-distance-dispersal can be made clear to those interested in questions of paleobiogeography. In our opinion, the recent contribution by Briggs (1981) in this journal did not do so, and we now take the opportunity to try.

As The Blob, of Steve McQueen's greatest triumph, so amply demonstrated, the more you encompass the more formless you become. Orzack accuses me of construing the modern synthesis too narrowly in describing a version championed only by Mayr and Fisher—a pair of unlikely bedfellows, I would have thought. Yet his version is so broad that he wins his own argument by internal definition, thus rendering it meaningless. As “the basis of the modern synthesis,” Orzack cites “the great evolutionary idea” — “all evolution can be explained in principle by an examination of the properties of individuals and of populations.” But what else is there, except perhaps Schindewolf's supernovae and Teilhard's ever-watchful Jesus, drawing organic activity towards Omega. If the synthesis only excludes some fringing finalists and unrepentant Lamarckians, then we are all inevitably in it, and we might as well recast the term as a synonym for evolution itself.

The origin of the Neogene planktonic foraminifer Globorotalia (Globoconella) pliozea in the subtropical southwest Pacific has been attributed to its isolation resulting from intensification of the Subtropical Divergence (Tasman Front). Oxygen isotopic analyses suggest that, although the Subtropical Divergence may have played a role, the evolution of Gr. (G.) pliozea was facilitated by depth segregation of Gr. (G.) conomiozea morphotypes (low and high conical) during an interval of near-surface warming and increasing thermal gradient. Oxygen isotopic analyses suggest that low conical morphotypes of Gr. (G.) conomiozea inhabited greater depths than high conical morphotypes. Low conical forms of Gr. (G.) conomiozea are considered ancestral to the low conical species, Gr. (G.) pliozea. Oxygen isotopes indicate that Gr. (G.) pliozea inhabited greater depths than its ancestor, Gr. (G.) conomiozea.

These data are consistent with depth-parapatric and depth-allopatric models, but not with a sympatric model of speciation. In the allopatric model, reproduction at different water depths acts as a barrier between morphotypes. In the parapatric model, clinal variation along a depth gradient acts as a barrier between morphotypes living at the limits of the gradient. Depth segregation in both models results in genetic isolation and evolutionary divergence. Our data support a correlation between morphological evolution and habitat changes in the Globoconella clade, implying separation of populations as a driving force for morphological evolution.

Ecological segregation of morphotypes and species may be related to morphology (height of the conical angle), based on the data from Gr. (G.) conomiozea and Gr. (G.) pliozea. However, morphological differences alone do not necessarily produce depth differences. Large morphological differences between Gr. (G.) pliozea and closely related Gr. (G.) puncticulata did not result in isotopic and therefore depth differences between these species. These species coexisted at the same water depths for nearly 1 m.y. Thus, it is unlikely that the extinction of Gr. (G.) pliozea in the middle Pliocene resulted from competition with Gr. (G.) puncticulata, as previously suggested.

A population of shells of the Cretaceous oyster Agerostrea mesenterica was obtained from a single locality. The age at death for each shell could be determined, and the population was deemed to be essentially undisturbed and capable of providing a mortality record of the local population averaged over a span of time. We measured four morphometric characters which, on the basis of a functional morphologic model, could be expected to have adaptive value. The frequency distribution of each character was analyzed separately for the three year old and for the six year and older specimens in order to determine which individuals died young and which survived to old age. Ontogenetic effects were separated from those of differential mortality by independent means. The results indicated that there was (1) directed selection for maximum curvature, (2) centripetal selection for a plica number of about 8, and (3) a net centripetal effect on both arc length and plica height, composed of selection against largest values coupled with a possible selection against smaller values that cannot be separated from ontogenetic effects. Only the selection for maximum curvature and optimal plica number can be reconciled with the predictions of the model.

Lanternfishes currently represent one of the dominant groups of mesopelagic fishes in terms of abundance, biomass, and diversity. Their otolith record dominates pelagic sediments below 200 m in dredges, especially during the entire Neogene. Here we provide an analysis of their diversity and rise to dominance primarily based on their otolith record. The earliest unambiguous fossil myctophids are known based on otoliths from the late Paleocene and early Eocene. During their early evolutionary history, myctophids were likely not adapted to a high oceanic lifestyle but occurred over shelf and upper-slope regions, where they were locally abundant during the middle Eocene. A distinct upscaling in otolith size is observed in the early Oligocene, which also marks their earliest occurrence in bathyal sediments. We interpret this transition to be related to the change from a halothermal deep-ocean circulation to a thermohaline regime and the associated cooling of the deep ocean and rearrangement of nutrient and silica supply. The early Oligocene myctophid size acme shows a remarkable congruence with diatom abundance, the main food resource for the zooplankton and thus for myctophids and whales. The warmer late Oligocene to early middle Miocene period was characterized by an increase in disparity of myctophids but with a reduction in their otolith sizes. A second and persisting secular pulse in myctophid diversity (particularly within the genus Diaphus) and increase in size begins with the “biogenic bloom” in the late Miocene, paralleled with diatom abundance and mysticete gigantism.

The application of molecular genetics, in particular comparative genomics, to the field of evolutionary biology is paving the way to an enhanced “New Synthesis.” Apart from their power to establish and refine phylogenies, understanding such genomic processes as the dynamics of change in genomes, even in hypothetical RNA-based genomes and the in vitro evolution of RNA molecules, helps to clarify evolutionary principles that are otherwise hidden among the nested hierarchies of evolutionary units. To this end, I outline the course of hereditary material and examine several issues including disparity, causation, or bookkeeping of genes, adaptation, and exaptation, as well as evolutionary contingency at the genomic level–issues at the heart of some of Stephen Jay Gould's intellectual battlegrounds. Interestingly, where relevant, the genomic perspective is consistent with Gould's agenda. Extensive documentation makes it particularly clear that exaptation plays a role in evolutionary processes that is at least as significant as–and perhaps more significant than–that played by adaptation.

Macrofossils from woodrat (Neotoma) middens serve as an important proxy for reconstructing past vegetation in arid and semiarid regions of North America. The presence/absence of plant macrofossils in middens can provide valuable information on temporal and spatial patterns of plant migration and range boundaries. The primary aim of this study was to determine how local plant abundance, distance of plant populations from midden sites, and species population density on the landscape affect the probability of occurrence of macrofossils in middens. The study was designed with the primary intent of determining the reliability of middens in detecting scattered populations of Pinus ponderosa. We analyzed macrofossil assemblages from 42 modern woodrat middens from West Carrizo Canyon in southeastern Colorado, near the current eastern range margin of Pinus ponderosa. We compared midden contents with composition of the surrounding vegetation, measuring distance from the midden to the nearest individual of selected plant species, and the percent cover of each species within 30 m of the midden. We used this information to model the probability of species presence in a midden across a range of population densities on the landscape. Macrofossils of Juniperus spp., Quercus gambelii, and Opuntia spp. were consistently found in middens regardless of their local abundance in vegetation, although populations occurred within 30 m of all middens. Pinus edulis and P. ponderosa occurred in nearly all middens within 20–30 m of individual trees. P. ponderosa was rare in middens >20–30 m away from individual trees. Results of a simple simulation model suggest that middens become absolutely reliable indicators of P. ponderosa presence on the landscape only when average tree density exceeds 50 stems ha−1. Woodrats reliably collected macrofossils of Pinus edulis, P. ponderosa, Juniperus spp., Quercus gambelii, and Opuntia spp. when populations of these taxa occur within 20–30 m of a midden site. Woodrats did not collect P. ponderosa when the nearest individuals were more than 30 m away. Low-density populations of these and other species may be difficult to detect in fossil woodrat-midden series owing to reduced probability that individuals grow within foraging distance of the middens. Data from this and similar studies can be used to construct and parameterize a forward model of macrofossil representation in woodrat middens.

The highly elongated necks, and often tails, of sauropod dinosaurs were composed of concavo-convex vertebrae that provided stability without compromising mobility. Polarities of these concavo-convex joints in the neck and tail are anatomically opposite one another but mechanically equivalent. Opisthocoelous cervical vertebrae and procoelous caudal vertebrae have the convex articular face directed away from the body and the concave articular face directed toward the body. This “sauropod-type” polarity is hypothesized to be (1) more resistant to fracturing of the cotylar rim and (2) better stabilized against joint failure by rotation than the opposite polarity. We used physical models to test these two functional hypotheses. Photoelastic analysis of model centra loaded as cantilevers reveals that neither polarity better resists fracture of the cotylar rim; strain magnitude and localization are similar in both polarities. We assessed the rotational stability of concavo-convex joints using pairs of concavo-convex centra loaded near the joint. Sauropod-type joints withstood significantly greater weight before failure occurred, a pattern we interpret to be dependent on the position of the center of rotation, which is always within the convex part of the concavo-convex joint. In sauropod-type joints, the free centrum rotates about a center of rotation that lies within the more stable proximal centrum. In contrast, the opposite polarity results in a free centrum that rotates about an internal point; when the condyle rotates down and out of joint, the distal end rotates back toward the body, unopposed by ligamentous support. Sauropod-type joints remained stable with greater mobility, more mechanically advantageous tensile element insertions, and greater distal loads than the opposite polarity. The advantages conferred by this joint polarity would have facilitated the evolution of hyperelongated necks and tails by sauropods. Polarity of concavo-convex joints of the appendicular skeleton (e.g., hip, shoulder) is also consistent with the demands of rotational stability.

The most popular theoretical propositions are often those which spell the final doom to a notion that has already fallen into disrepute. This is as true today as it was when August Weismann (1892) published his seminal volume, Der Keimplasma, which far more than Cuvier's vituperative attacks, put the ideas of Lamarck to final rest.

The study of tracks is often regarded as a fringe subdiscipline outside the scientific mainstream. Papers dealing with footprints traditionally appear either in popular magazines like Natural History (Bird 1939, 1944; Brown 1938), or in very obscure publications (Sarjeant 1974). Usually it is only the spectacular discoveries, which are directly applicable to topical debates, that rouse much scientific interest. For example, the discovery of Pliocene hominid tracks (Leakey and Hay 1979) provided unequivocal evidence for the antiquity of bipedalism (cf., Napier 1967). Similarly the tracks of a running theropod allowed for direct estimates of the speed attained by dinosaurs (Farlow 1981), and the tracks of a herd of running theropods fueled debate about gregariousness and stampede behavior (Thulborn and Wade 1984).

Muscle moment arms are important determinants of muscle function; however, it is challenging to determine moment arms by inspecting bone specimens alone, as muscles have curvilinear paths that change as joints rotate. The goals of this study were to (1) develop a three-dimensional graphics-based model of the musculoskeletal system of the Cretaceous theropod dinosaur Tyrannosaurus rex that predicts muscle-tendon unit paths, lengths, and moment arms for a range of limb positions; (2) use the model to determine how the T. rex hindlimb muscle moment arms varied between crouched and upright poses; (3) compare the predicted moment arms with previous assessments of muscle function in dinosaurs; (4) evaluate how the magnitudes of these moment arms compare with those in other animals; and (5) integrate these findings with previous biomechanical studies to produce a revised appraisal of stance, gait, and speed in T. rex. The musculoskeletal model includes ten degrees of joint freedom (flexion/extension, ab/adduction, or medial/lateral rotation) and 33 main muscle groups crossing the hip, knee, ankle, and toe joints of each hindlimb. The model was developed by acquiring and processing bone geometric data, defining joint rotation axes, justifying muscle attachment sites, and specifying muscle-tendon geometry and paths. Flexor and extensor muscle moment arms about all of the main limb joints were estimated, and limb orientation was statically varied to characterize how the muscle moment arms changed. We used sensitivity analysis of uncertain parameters, such as muscle origin and insertion centroids, to deterimine how much our conclusions depend on the muscle reconstruction we adopted. This shows that a specific amount of error in the reconstruction (e.g., position of muscle origins) can have a greater, lesser, similar, or no effect on the moment arms, depending on complex interactions between components of the musculoskeletal geometry. We found that more upright poses would have improved mechanical advantage of the muscles considerably. Our analysis shows that previously assumed moment arm values were generally conservatively high. Our results for muscle moment arms are generally lower than the values predicted by scaling data from extant taxa, suggesting that T. rex did not have the allometrically large muscle moment arms that might be expected in a proficient runner. The information provided by the model is important for determining how T. rex stood and walked, and how the muscles of a 4000–7000 kg biped might have worked in comparison with extant bipeds such as birds and humans. Our model thus strengthens the conclusion that T. rex was not an exceptionally fast runner, and supports the inference that more upright (although not completely columnar) poses are more plausible for T. rex. These results confirm general principles about the relationship between size, limb orientation, and locomotor mechanics: exceptionally big animals have a more limited range of locomotor abilities and tend to adopt more upright poses that improve extensor muscle effective mechanical advantage. This model builds on previous phylogenetically based muscle reconstructions and so moves closer to a fully dynamic, three-dimensional model of stance, gait, and speed in T. rex.