Polar deciduous forests were an important biome during much of the Mesozoic and Paleogene, occupying upwards of 40% of the total land surface. Little is known about their physiological ecology, however, because these types of forests do not exist for study today. Furthermore, the role of high atmospheric CO2 levels in modulating the physiological response of ancient polar forests is poorly known. Here we report detailed measurements of whole-tree net carbon uptake over a full annual cycle for five tree species whose close ancestors were components of Cretaceous and Paleogene polar forests. Measurements were made on both evergreen and deciduous species after two years growth in a simulated Mesozoic polar (69°N) environment at either ambient (400 ppmv) or elevated (800 ppmv) levels of CO2. The deciduous species exhibited a significant pulse in carbon uptake during the late summer and early autumn (August to mid-October) that enabled them to achieve annual carbon budgets similar to those of evergreen trees, despite incurring higher carbon losses through annual leaf shedding. Area-based photosynthetic rates dropped progressively in all species during the polar summer (June to mid-July), resulting in decreases in whole-tree carbon uptake late in the polar summer. The high-CO2-grown trees were more strongly affected by this polar summer depression than the low-CO2-grown trees. Our results indicate that, from a carbon balance perspective, deciduous taxa have no clear advantage over evergreens. Moreover, the seasonal patterns reported here suggest that at latitudes poleward of 69°, evergreens will be even more strongly favored. The consideration of factors not directly related to carbon budgeting is probably therefore required to fully understand the adaptive significance of the deciduous leaf habit in ancient polar forests.

The Mesozoic–Cenozoic transition is generally seen as a pivotal time in the evolution of benthic marine assemblages but the details of the timing and drivers of these changes are poorly known. The Atlantic and Gulf Coastal Plains of the United States contain assemblages preserved as original aragonitic and calcitic material in unconsolidated sediments. This makes coastal plain assemblages ideally suited to paleoecological analyses. Data derived from bulk samples of the Coffee Formation (lower/middle Campanian: Mississippi) as well as published faunal lists from comparable samples of the Severn (Maastrichtian: Maryland), Providence (Maastrichtian: Georgia and Alabama), Stone City (Eocene: Texas), and Gosport (Eocene: Alabama) Formations are used to assess changes in taxonomic diversity and ecomorphological group (life habit and trophic group) composition through this time interval.

These analyses find a significant decrease in rarefied-sample species richness from the Campanian through the Eocene, but no change in evenness. With the notable exception of the Stone City Formation, increases in carnivore (neogastropod) richness and abundance occur before the Campanian. Epifaunal suspension-feeding species are a smaller proportion of the sample richness in Eocene samples than in Cretaceous samples. Decreased relative epifaunal suspension-feeder biomass but unchanged relative numbers of epifaunal suspension-feeder individuals suggests a relative decrease in epifaunal suspension-feeder size. Infaunal suspension feeders increase in richness and abundance through the interval. The proportion of drilled bivalves and gastropods does not change through the interval. Changes found in the structure of local shallow-shelf benthic assemblages from the Campanian through the Eocene are generally small relative to the variability between samples. Formation-level variation between assemblages is high relative to the magnitude of the temporal signal, emphasizing the need for investigators to include multiple formations per interval in tests of temporal trends.

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.

Stephen Jay Gould made impressive contributions to macroevolutionary theory; one of the topics in this area that particularly interested him was how to define and recognize species selection. Here we explore how and why Gould's ideas on concepts related to species selection evolved over 30 years, from the punctuated equilibria paper of 1972 to his “Structure of Evolutionary Theory” magnum opus published in 2002. Throughout his career his ideas on species selection shifted between three phases. Initially, Gould favored a definition of species selection that was more descriptive. Later, he came to distinguish between species sorting, which he called species selection in the broad sense, and true species selection, which is tied to the concept of species-level aptations. Finally, he came to view species selection in a broader, more inclusive way, effectively merging the two earlier viewpoints. His ideas on species selection changed over the years because he was trying to square his views on complex concepts like adaptation, natural selection, emergence, and the independence of macroevolutionary theory. Gould's thoughts on species selection not only help to define the history of debate on the concept but also help set a course for the future.

Marsupial mammals are characterized by a pattern of dental replacement thought to be unique. The apparent primitive therian pattern is two functional generations of teeth at the incisor, canine, and premolar loci, and a series of molar teeth, which by definition are never replaced. In marsupials, the incisor, canine, and first and second premolar positions possess only a single functional generation. Recently this pattern of dental development has been hypothesized to be a synapomorphy of metatherians, and has been used to diagnose taxa in the fossil record. Further, the suppression of the first generation of teeth has been linked to the marsupial mode of reproduction, through the mechanical suppression of odontogenesis during the period of fixation of marsupials, and has been used to reconstruct the mode of reproduction of fossil organisms. Here we show that dental development occurs throughout the period of fixation; therefore, the hypothesis that odontogenesis is mechanically suppressed during this period is refuted. Further, we present comparative data on dental replacement in eutherians and demonstrate that suppression of tooth replacement is fairly common in diverse groups of placental mammals. We conclude that reproductive mode is neither a necessary nor a sufficient explanation for the loss of tooth replacement in marsupials. We explore possible alternative explanations for the loss of replacement in therians, but we argue that no single hypothesis is adequate to explain the full range of observed patterns.

Neutral theory in ecology is based on the symmetry assumption that ecologically similar species in a community can be treated as demographically equivalent on a per capita basis—equivalent in birth and death rates, in rates of dispersal, and even in the probability of speciating. Although only a first approximation, the symmetry assumption allows the development of a quantitative neutral theory of relative species abundance and dynamic null hypotheses for the assembly of communities in ecological time and for phylogeny and phylogeography in evolutionary time. Although Steve Gould was not a neutralist, he made use of ideas of symmetry and of null models in his science, both of which are fundamental to neutral theory in ecology. Here I give a brief overview of the current status of neural theory in ecology and phylogeny and, where relevant, connect these newer ideas to Gould's work. In particular, I focus on modes of speciation under neutrality, particularly peripheral isolate speciation, and their implications for relative species abundance and species life spans. Gould was one of the pioneers in the study of neutral models of phylogeny, but the modern theory suggests that at least some of the conclusions from these early neutral models were premature. Modern neutral theory is a remarkably rich source of new ideas to test in ecology and paleobiology, the potential of which has only begun to be realized.

Relative abundance data are of primary importance in paleoecology, but it is not always obvious how they should be interpreted. Because relative abundance is expressed as a proportion of the total sample, change in the abundance of one group necessarily changes the relative abundance of all groups in the sample. There are two possible interpretations for a trend in the relative abundance of a taxon: an “active” scenario in which the trend reflects change in the population density of the group itself, or a “passive” scenario in which the change is driven by population changes in other taxa. To discriminate between these scenarios it is necessary to collect absolute abundance data (abundance expressed as a function of sample area or volume).

We examine both absolute and relative abundance trends through a major paleoecological transition: the shift from trilobite-dominated to brachiopod-dominated paleocommunities in shallow marine carbonates spanning the Lower/Middle Ordovician boundary in western Utah and eastern Nevada. We sampled 61 carbonate mudstone and wackestone beds from the upper Ibex Series (Lower Ordovician) and lower Whiterock Series (Middle Ordovician) at three sections that span the boundary. All samples come from the shallow subtidal Bathyurid trilobite biofacies. Samples were broken into small pieces, and all skeletal fragments >2 mm were identified to the finest possible taxonomic level. Consistent with previous work on this interval, the relative abundance of trilobites declines sharply across the boundary, while the relative abundance of brachiopods increases. Absolute abundance data indicate that the decline in trilobite abundance is genuine and not an artifact of normalization. The trend is not easily explained by sampling bias, facies distribution, taphonomic regime, or sedimentation style.

The dramatic shift in abundance contrasts with relatively minor changes in relative genus richness across the boundary. This is partly ascribable to differences in the relative abundance structure of trilobite faunas. Though comparable numbers of trilobite and brachiopod genera occur above and below the boundary, the trilobite fauna from the upper Ibex Series has lower evenness then the lower Whiterock Series fauna. Hence sampled trilobite richness is high in the lower Whiterock despite the small number of specimens. This highlights the importance of collecting abundance data. Although these data suggest that in at least some cases richness and abundance patterns are not closely coupled, more robust richness data are necessary to confirm this conclusion.

Although direct predator-prey interactions are unobservable in the fossil record, predation has been used to explain many evolutionary trends. Evidence of predation supporting such hypotheses is often presented as isolated instances of preserved sublethal damage, and less commonly, as the frequency of such injuries. For instance, numerous morphological and ecological trends and innovations observed in Phanerozoic crinoids have been causally linked to predation, and whereas the high frequency of arm regeneration in living crinoids is generally assumed to represent intense predation, attempts to assess regeneration frequency and patterns in paleontological samples are few. Can the frequency of fossil injuries be assessed to test hypothesized predation-driven trends, or are such data unavailable?

To address this question, we analyzed regeneration in crinoids from the lower Mississippian (Kinderhookian) Maynes Creek Formation near Le Grand, Iowa, a locality renowned for the preservation of thousands of crinoids in tangled masses of crowns, stalks, and holdfasts. Nine percent of the specimens that we examined contained at least one regenerating arm; however, whereas some species lacked evidence of regeneration, others preserved up to 27% arm regeneration. Furthermore, we observed specimens with all arms regenerating, multiple adjacent arms regenerating from the same place along the arm, and a specimen with a damaged and regenerated primaxil and anal sac.

The highest regeneration frequency was observed in the most abundant species, Rhodocrinites kirbyi, a significantly higher value than expected under a model of no taxonomic selectivity (binomial: p < 0.05). Furthermore, bootstrapped simulations of the probable number of regenerated individuals suggest that the number of regenerated arms observed in our sample is two to three times less than what existed in the living population. Rhodocrinites kirbyi constituted over 40% of the individuals in the Le Grand crinoid fauna and had the longest stalk of the studied species. In addition, regeneration in R. kirbyi is size related, with individuals above median dorsal cup height (7 mm) displaying nearly 50% regeneration, and smaller individuals only 2% (a statistically significant difference; χ2 test: p < 0.001). The regeneration patterns in R. kirbyi are consistent with predatory attacks that target the most apparent prey. Moreover, this study suggests that predation is the most likely explanation for the regeneration patterns observed in Le Grand crinoids, and that the fossil record potentially provides a valuable, yet overlooked, data source for testing hypotheses pertinent to the role of predation in the evolution of Phanerozoic marine life.

All interpretable trace fossils from the Ediacarian–Cambrian transition strata of northern Siberia, Ukraine, and elsewhere represent shelters of infaunal animals feeding from the sediment surface. There is a gradation of forms ranging from (1) makers of horizontal galleries in soft sand with bilobed lower surface and proboscis extended to the surface, through (2) linear or zigzag series of short, widely U-shaped burrows in firm clay with bilobed or three-lobed lower surface, to (3) series of cylindrical chambers dug completely inside the sediment but opening to its surface. At the same time, protective skeleton originated in animals living above the sediment surface. Apparently, the diversification of predators in the earliest Cambrian forced other animals to invest energy either in digging or in a protective armor (“the Verdun Syndrome”). True mud-eaters appeared later, as documented by the late Tommotian horizontal spreite structures from central Siberia. Most, if not all, of those infaunal traces of activity were produced probably by relatives of priapulid worms. It appears that body cavities and segmentation in the Metazoa (diverse already in the Ediacarian) evolved independently of, and prior to, hydraulic burrowing.

A large, morphologically heterogeneous population of acanthomorphic acritarchs from the early Neoproterozoic Wynniatt Formation, Victoria Island, northwestern Canada, is ascribed to two form-genera, Tappania and Germinosphaera, but just a single natural taxon, Tappania. Analysis of Tappania morphology shows it to have been an actively growing, benthic, multicellular organism capable of substantial differentiation. Most notably, its septate, branching, filamentous processes were capable of secondary fusion, a synapomorphy of the “higher fungi.” Combined with phylogenetic, taphonomic and functional morphologic evidence, such “hyphal fusion” identifies Tappania reliably, if not conclusively, as a fungus, probably a sister group to the “higher fungi,” but more derived than the zygomycetes.

The presence of Tappania in the Mesoproterozoic Roper Group of Australia extends the record of putative fungi to 1430 Ma. Along with other Proterozoic acritarchs exhibiting fungus-like characteristics (e.g., Trachyhystrichosphaera, Shuiyousphaeridium, Dictyosphaera, Foliomorpha), there is a case to be made for an extended and relatively diverse record of Proterozoic fungi.

The fossil record displays remarkable stasis in many species over long time periods, yet studies of extant populations often reveal rapid phenotypic evolution and genetic differentiation among populations. Recent advances in our understanding of the fossil record and in population genetics and evolutionary ecology point to the complex geographic structure of species being fundamental to resolution of how taxa can commonly exhibit both short-term evolutionary dynamics and long-term stasis.

A simple principle predicts a tendency, or vector, toward increasing organismal complexity in the history of life: As the parts of an organism accumulate variations in evolution, they should tend to become more different from each other. In other words, the variance among the parts, or what I call the “internal variance” of the organism, will tend to increase spontaneously. Internal variance is complexity, I argue, albeit complexity in a purely structural sense, divorced from any notion of function. If the principle is correct, this tendency should exist in all lineages, and the resulting trend (if there is one) will be driven, or more precisely, driven by constraint (as opposed to selection). The existence of a trend is uncertain, because the internal-variance principle predicts only that the range of options offered up to selection will be increasingly complex, on average. And it is unclear whether selection will enhance this vector, act neutrally, or oppose it, perhaps negating it. The vector might also be negated if variations producing certain kinds of developmental truncations are especially common in evolution.

Constraint-driven trends—or what I call large-scale trends of the fourth kind—have been in bad odor in evolutionary studies since the Modern Synthesis. Indeed, one such trend, orthogenesis, is famous for having been discredited. In Stephen Jay Gould's last book, The Structure of Evolutionary Thought, he tried to rehabilitate this category (although not orthogenesis), showing how constraint-driven trends could be produced by processes well within the mainstream of contemporary evolutionary theory. The internal-variance principle contributes to Gould's project by adding another candidate trend to this category.

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.