The two major approaches to studying macroevolution in deep time are the fossil record and reconstructed relationships among extant taxa from molecular data. Results based on one approach sometimes conflict with those based on the other, with inconsistencies often attributed to inherent flaws of one (or the other) data source. Any contradiction between the molecular and fossil records represents a failure of our ability to understand the imperfections of our data, as both are limited reflections of the same evolutionary history. We therefore need to develop conceptual and mathematical models that jointly explain our observations in both records. Fortunately, the different limitations of each record provide an opportunity to test or calibrate the other, and new methodological developments leverage both records simultaneously. However, we must reckon with the distinct relationships between sampling and time in the fossil record and molecular phylogenies. These differences impact our recognition of baselines and the analytical incorporation of age estimate uncertainty.

Both molecular clocks and the first appearances of major groups in the fossil record suggest that most of the range of diatom morphologies observed today had evolved by the end of the Cretaceous Period. Despite this, a canonical reading of the Cenozoic fossil record suggests a dramatic rise in taxonomic diversity that can be interpreted as an explosion of morphological variety. We investigated this apparent discrepancy by using a discrete-character-based, empirical diatom morphospace, resolved by molecular phylogeny and by fossil occurrences through time. The morphospace shows little correspondence to phylogeny and little Cenozoic change in disparity as measured by mean pairwise distance. There is, however, an increase in the total volume of morphospace occupied. Although the increase in occupied volume through time ostensibly supports a conclusion of increasing morphological variety, sampling biases and other data suggest an underlying stationary pattern more consistent with molecular clock data.

Dorsal sails supported by hyperelongate neural spines of dorsal vertebrae were evolved by various tetrapods, but most work on their function has centered on the pelycosaur Dimetrodon, in which the sail has generally been interpreted as a thermoregulatory structure that would permit rapid warming in the morning and cooling during the hot midday. The pelycosaur Edaphosaurus differed from other sailed tetrapods in that the neural spines supporting the sail had laterally directed tubercles or cross-bars. Past interpretations of Edaphosaurus suggested that the cross-bars were embedded in a thick fat-storage structure or extended from a thin sail to enhance its utility for intraspecific display. However, wind tunnel modeling of air flow over a thin sail with laterally projecting cross-bars supports a thermoregulatory interpretation of the sail of Edaphosaurus. The cross-bars would produce a turbulent flow, which would increase the effectiveness of convective cooling. Measurements of heat flow in an instrumented model show that cross-bars increase heat loss from the sail. The cross-bars may have enabled Edaphosaurus to thermoregulate effectively with a smaller and lower dorsal sail than would have been required without them.

Although much natural historical evidence has been adduced in support of the occurrence of several mass extinctions during the Phanerozoic, unambiguous statistical confirmation of the mass extinction phenomenon has remained elusive. Using bootstrapping techniques that have not previously been applied to the study of mass extinction, we have amassed strong or very strong statistical evidence for mass extinctions (see text for definitions) during the Late Ordovician, Late Permian, and Late Cretaceous. Bootstrapping therefore verifies three of the mass extinction events that were proposed by Raup and Sepkoski (1982). A small amount of bootstrapping evidence is also presented for mass extinctions in the Induan (Triassic) and Coniacean (Cretaceous) Stages, but high overall turnover rates (including high origination) in the Induan and uncertain estimates of the temporal duration of the Coniacean force us to conclude that the evidence is not compelling.

We also present the results of more liberal X2 tests of the differences between expected and observed numbers of familial extinctions for stratigraphic stages. In addition to verifying the mass extinctions identified using bootstrapping, these analyses suggest that several stages that could not be verified as mass extinction stages using bootstrapping (including the last three in the Devonian, and the Norian Stage of the Triassic) should still be regarded as candidates for mass extinction. Further analysis will be required to test these stages in more detail.

The silicoflagellates are a class of enigmatic chrysophytes characterized by netlike skeletons composed of opaline silica. Other major groups of siliceous plankton—the diatoms and radiolarians—exhibit evidence of decreasing size or silicification over the Cenozoic. We investigated trends in the silicoflagellate fossil record by constructing a species-level database of diversity and morphological metrics. This new database reveals a proliferation of silicoflagellate species with spined skeletons along with an increase in the mean number of spines per species over the Cenozoic. Although there is little change in skeleton size or silicification among species with spines, those without spines are larger than species with spines and exhibit a decrease in size toward the present. Increased grazing pressure combined with declining surface silicate availability may have shifted the costs and benefits of silicification, causing divergent responses in skeletal morphology between these different morphological lineages of silicoflagellates over time. We postulate that diminishing Cenozoic surface silicic acid availability may have predisposed large spineless silicoflagellate species to extinction, whereas increased grazing pressure may have contributed to the extinction of all remaining spineless species within the edible size range of grazers.

Miniaturization has been defined as the evolution of extremely small adult size in a lineage. It does not simply imply the decrease of the body size but also involves structural modifications to maintain functional efficiency at a strongly reduced size. Miniaturization has been proposed as a key factor in the origin of several major tetrapod clades. Current hypotheses propose that the living amphibians (lissamphibians) originated within a clade of Paleozoic dwarfed dissorophoid temnospondyls. Morphological traits shared by these small dissorophoids have been interpreted as resulting from constraints imposed by the extreme size reduction, but these statements were based only on qualitative observations. Herein, we assess quantitatively morphological changes in the skull previously associated with miniaturization in the lissamphibian stem lineage by comparing evolutionary and ontogenetic allometries in dissorophoids. Our results show that these features are not comparable to the morphological consequences of extreme size reduction as documented in extant miniature amphibians, but instead they resemble immature conditions of larger temnospondyls. We conclude that the truncation of the ancestral ontogeny, and not constraints related to miniaturization, might have been the factor that played a major role in the morphological evolution of small dissorophoids. Based on our results, we discuss the putative role of miniaturization in the origin of lissamphibians within Dissorophoidea.

Throughout their 250 Myr history, archosaurian reptiles have exhibited a wide array of body sizes, shapes, and locomotor habits, especially in regard to terrestriality. These features make Archosauria a useful clade with which to study the interplay between body size, shape, and locomotor behavior, and how this interplay may have influenced locomotor evolution. Here, digital volumetric models of 80 taxa are used to explore how mass properties and body proportions relate to each other and locomotor posture in archosaurs. One-way, nonparametric, multivariate analysis of variance, based on the results of principal components analysis, shows that bipedal and quadrupedal archosaurs are largely distinguished from each other on the basis of just four anatomical parameters (p < 0.001): mass, center of mass position, and relative forelimb and hindlimb lengths. This facilitates the development of a quantitative predictive framework that can help assess gross locomotor posture in understudied or controversial taxa, such as the crocodile-line Batrachotomus (predicted quadruped) and Postosuchus (predicted biped). Compared with quadrupedal archosaurs, bipedal species tend to have relatively longer hindlimbs and a more caudally positioned whole-body center of mass, and collectively exhibit greater variance in forelimb lengths. These patterns are interpreted to reflect differing biomechanical constraints acting on the archosaurian Bauplan in bipedal versus quadrupedal groups, which may have shaped the evolutionary histories of their respective members.

Patterns preserved in the fossil record are of the highest importance in addressing questions about long-term evolutionary processes, yet both the description of pattern and its translation into process can be difficult. With respect to gradual phyletic change, we know that randomly generated sequences may exhibit characteristics of a “trend” apparent patterns, therefore, must be interpreted with caution. Furthermore, even when the claim of a gradual trend can be statistically justified, interpretation of the underlying mechanisms may be challenging. Given that we can observe populations changing rapidly over tens or hundreds of years, it is now more difficult to explain instances of geologically gradual (as opposed to punctuated) change.

Here we describe morphologic change in two bivalve lineages from the late Miocene Lake Pannon. We evaluate change according to the model-based methods of Hunt. Both lineages exhibit size increases and shape changes over an interval of nearly 4 million years. Size and two shape variables in the conjungens lineage are best fit by a model of directional evolution; remaining shape variables mostly conform to unbiased random walks. Body-size evolution in the diprosopum lineage is also significantly directional but all shape variables are best fit by the unbiased random walk model; the small number of sampling intervals available for this lineage (n = 6) makes determination of the actual pattern more difficult. Model-fitting results indicate that the parallel trajectories of increasing log shell height over time in the two lineages can be accounted for by an underlying trend shared by both lineages, suggesting that the size increases may be a shared response to the same cause. The pace of phenotypic change, measured as Lynch's Δ, is slower than the neutral expectation for all size and shape traits.

Our examples illustrate well the paradox of gradualism; the sequences exhibit significant directional morphological evolution, but rates of change as measured over the long-term are apparently too slow for directional selection or even drift to be the cause. Viewing long-term phenotypic evolution in terms of populations tracking peaks on adaptive landscapes is useful in this context. Such a view allows for intervals of directional selection (during times of peak movement–resulting in the overall trends we can detect) interspersed with intervals of stasis (during times of peak stability–resulting in overall changes that appear to proceed more slowly than the neutral expectation). The paradox of gradualism thus reduces to (1) peak movements and their drivers, which are not restricted in rate as are population-genetic drivers, and (2) the maintenance of stasis, on which no consensus exists.

We can identify no environmental parameter in the central European Neogene that exhibits consistent change across the interval of gradual morphologic change. It may be that in Lake Pannon the long-term persistence of generally ameliorating conditions (plentiful resources and habitat space, few predators or competitors) resulted in geologically slow but consistent peak shifts, which in turn facilitated size increase and shape change in these lineages.

Periodicity has recently been reported in the extinction rates of fossil marine families since the Permian. The analysis used appears particularly sensitive to parameter estimation techniques, particularly in the definition of mass extinctions. It also fails to incorporate autocorrelation in the fossil record into its null hypothesis and rests on an inappropriate a posteriori comparison to the null hypothesis. An alternative analysis, examining the time-lags between periods of high extinction rates, produces no evidence of a cycle.

We have devised a simple model for assessing the role of development in shaping the evolution of morphological disparity. Disparity of a clade at any given time is expressed in terms of the developmental dynamics that lead to the variety of adult morphotypes observed. We use assumed phenotypic manifestations of developmental processes, as they could be detected from allometric characterizations, to distinguish a few, nonexclusive types of evolutionary changes in ontogeny. On the basis of this formalization, we describe the diversification of hypothetical clades, using the standard curve of adult morphological disparity, the curve of juvenile disparity, and the curve of allometric disparity, the latter quantifying the diversification of clades in allometric space. Contrasts of these curves reflect the underlying developmental scheme that drives temporal changes in disparity. We then vary the parameters of the model to assess the expected signature of each metric under specific conditions: changes in the relative frequencies of the types of evolutionary developmental changes, changes in the transition magnitude attached to each of them, and effects of temporal variation in average adult size on disparity curves and patterns of morphospace occupation. Results emphasize the potential contribution of these proxies for developmental dynamics—juvenile morphological disparity, allometric disparity, and average adult size—in enriching the interpretation of standard disparity curves and the description of clade histories, with possible process-oriented inferences.

The concept of evolvability—the capacity of a population to produce and maintain evolutionarily relevant variation—has become increasingly prominent in evolutionary biology. Paleontology has a long history of investigating questions of evolvability, but paleontological thinking has tended to neglect recent discussions, because many tools used in the current evolvability literature are challenging to apply to the fossil record. The fundamental difficulty is how to disentangle whether the causes of evolutionary patterns arise from variational properties of traits or lineages rather than being due to selection and ecological success. Despite these obstacles, the fossil record offers unique and growing sources of data that capture evolutionary patterns of sustained duration and significance otherwise inaccessible to evolutionary biologists. Additionally, there exist a variety of strategic possibilities for combining prominent neontological approaches to evolvability with those from paleontology. We illustrate three of these possibilities with quantitative genetics, evolutionary developmental biology, and phylogenetic models of macroevolution. In conclusion, we provide a methodological schema that focuses on the conceptualization, measurement, and testing of hypotheses to motivate and provide guidance for future empirical and theoretical studies of evolvability in the fossil record.

The regeneration abilities of crinoids not only are important to understanding crinoid ecology, but also can serve as the basis for assessing the pressure exerted on crinoids by predators both in the Recent and in the geologic past. This is especially true of regenerating arms, because arm loss, and subsequent regeneration, is thought to result from interactions with predators, primarily fish. However, the commonly used regeneration-based proxy for predation pressure (proportion of individuals with regenerating arms) does not provide a measure of the rate at which those events occurred. Here we present a method for reconstructing the arm-loss rate per individual, a more direct proxy of predation pressure. This metric accounts for differences in arm length, arm number, and branching pattern, features highly variable among taxa, among environments, and through geologic time. Normalizing for those characters permits the transformation of observed proportions of regenerating arms to rates that can be compared across samples of morphologically distinct crinoids. Applying this method to a Recent crinoid (Cenometra bella) reveals that this shallow-water comatulid loses arms at a rate of about once every ten days. The same approach reveals that Mississippian shallow-water crinoids (Rhodocrinites kirbyi) experienced arm loss much less frequently, approximately once every 36 days, suggesting that predation pressure on crinoids today is greater than it was in the Mississippian.

The geometric regularity of oblique sculptures in pectinids and some other bivalves was examined both theoretically and empirically. Camptonectes microsculpture occurs exclusively on the external surface of foliated calcite, and is well characterized by an invariably orthogonal relation to growth increments and almost uniform density over the surface. It is genetically unrelated to radial and other sculpturing. According to our SEM observations, its divergent orientation seems to be controlled primarily by the growth of calcite laths. In contrast, the shagreen microsculpture of pectinids is characterized by a quincunx arrangement of scales on the diagonal network. Shagreen microsculpture can be regarded as a variant of diagonal sculpture together with the simple oblique, divaricate, V-shaped, and zigzag patterns that are widespread in other bivalves. The geometric regularity of these variations as well as their mutual relationship can be readily recognized by computer simulations. All of these diagonal sculptures may result from interference between radial and commarginal elements. The formation of diagonal sculptures seems to occur by the periodic activation of regularly arranged sculpture-producing cells on the mantle margin.

Reconstructing patterns of macroevolution has become a central endeavor in paleobiology, because it offers insight into evolutionary models shaping the history of life. As the most diverse and abundant animals since the Cambrian period, arthropods provide copious data to elucidate the emergence of body plans in metazoan lineages. However, information provided by fossils on the tempo and mode of this phenomenon has lacked a recent synthesis. Here, I investigate macroevolutionary patterns of morphological evolution in Euarthropoda using a combined extinct and extant dataset optimized for multivariate analyses. Overall ordination patterns between the main morphogroups are consistent with another, independently coded, extant-only dataset providing molecular and morphological rates of evolution. Based on a “deep split” phylogenetic framework, total-group Mandibulata and Arachnomorpha emerge as directional morphoanatomical lineages, with basal fossil morphogroups showing heterogeneously spread-out occupations of the morphospace. In addition to a more homogeneous morphological variation, new morphogroups arose by successive reductions of translation distances; this pattern was interrupted only by terrestrialization events and the origin of pancrustaceans. A displaced optimum type of model is proposed to explain the fast assembly of canalized body plans during the Cambrian, with basal fossil morphogroups fitting intermediate fitness peaks in a moving adaptive landscape. Given time constraints imposed by the paleontological evidence, and owing to the interplay between canalization and modularity, as well as a decoupling between molecular and morphological rates, the rise of euarthropods would support the view that the swiftness of the Cambrian explosion was mostly associated with the buildup of genetic regulatory networks.

The purpose of this paper is to explore the possibility and utility of estimating multivariate selection in fossil assemblages, using naticid gastropods as a case study. We used the presence or the absence of a naticid borehole as an index of survival with respect to drilling attacks, enabling us to estimate the multivariate selection gradient exerted by this predator on the shell length and shell thickness of two bivalve genera, Astarte and Spisula. We hypothesized that naticid selection pressure would favor the survival of large, thick-shelled bivalve prey throughout the Cenozoic.

Differential survival of prey was recorded over geologic time using processed bulk assemblages from the Miocene, Pliocene, and Pleistocene Epochs. Multivariate logistic regressions were performed by time period to determine if length and thickness were important factors affecting survival. The direction and magnitude of selection on length and thickness for the two genera ranged from zero (no selection) to large positive or negative values. Only two selection coefficients were significant after sequential Bonferroni corrections: thin-shelled Astarte survived substantially better than thick-shelled Astarte during the Pleistocene (βavggrad = −1.23) and large Spisula survived slightly better than small Spisula during the Miocene Epoch (βavggrad = 0.05).

This is the first study using fossils to calculate multivariate selection gradients. It suggests that naticids were not necessarily strong agents of selection on two traits previously thought to be important to survival of drilling attacks for two of their common prey species. We also show that multivariate selection gradient estimates differ from traditional predation intensity estimates but are superior for estimating the magnitude and direction of natural selection because they use differential mortality of different prey phenotypes rather than just absolute mortality from predation. This work is especially significant for research that involves estimating the relative importance of predation (naticid or otherwise) as an evolutionary force and will be useful for fossil studies where differential survival can be recorded.

To assess evolutionary processes in deep time, it is essential to understand the roles of development and environment, both recorded through the morphological variability of fossil assemblages. Thanks to their great abundance and the high temporal resolution of their fossil record, conodont elements are ideal to address this issue. In this paper, we present the first quantitative study of a Carnian–Norian (Late Triassic) assemblage of closely related P1 conodont elements. Using geometric morphometrics (landmarks, sliding landmarks, and elliptic Fourier analysis), we explore the main axes of phenotypic variation and relate them to classically used taxonomic characters. We show that some important taxonomic features follow laws of covariation, hence highlighting developmental constraints. Furthermore, the intraspecific variation within all considered species, either Carnian or Norian forms, is similarly restricted, emphasizing, for the first time in conodont P1 elements, a common line of least resistance to evolution, which means that similar intrinsic (developmental) factors were acting on these taxa and likely biased the evolutionary trajectories of all these taxa in a similar way. Because the evolution between Carnian and Norian forms is known to have followed a trajectory that is significantly different from the line of least resistance, strong extrinsic pressures, such as environmental disturbances, were probably at play around the Carnian/Norian boundary to counteract the effects of these intrinsic, developmental constraints.

The Guadalupian (middle Permian) extinction may have triggered substantial ecological restructuring in level-bottom communities, such as turnover in dominant brachiopod genera or a shift from abundant brachiopods to mollusks, despite comparatively minor taxonomic losses. However, ecological changes in relative abundance have been inferred from limited data; as a result, constraints on important shifts like the brachiopod-mollusk transition are imprecise. Here, I reevaluate the magnitude of ecological shifts during the Guadalupian–Lopingian (G-L) interval by supplementing previous census counts of silicified assemblages with counts from non-silicified assemblages and global occurrence data, both sourced from the Paleobiology Database. Brachiopod occurrences are consistent with more pronounced faunal composition changes from the Guadalupian to Lopingian than among stages within those intervals, but only in Iran and South China, and not in Pakistan or a Tethys-wide data set. In Iran and South China, Bray-Curtis dissimilarity values comparing occurrence frequencies between adjacent stages were elevated across the G-L transition, although other intervals exhibited similarly large shifts. However, genus occurrence frequencies were less strongly correlated or were anti-correlated across the G-L transition, suggesting moderate faunal turnover among dominant brachiopod genera. In contrast to previous inferences from silicified faunas, abundances of brachiopods, bivalves, and gastropods remained consistent from the Guadalupian to Lopingian in non-silicified local counts and global occurrences, implying that the brachiopod-mollusk shift did not occur until the end-Permian extinction. Ecological and taxonomic consequences were both minor in level-bottom settings, suggesting that severe environmental perturbations may not be necessary to explain biotic changes during the Guadalupian-Lopingian transition.

Psychological evidence suggests that the visual outline of an object is the most important character for discriminating differences in external morphology. External morphology is an important taxonomic character in describing living and fossil species, for example, the blastoid Pentremites. Comparison of different views of the same specimen utilizing Fourier series suggests that the skeleton of Pentremites commonly is not rotationally symmetrical and that the asymmetry is not associated with any specific ray. Analysis of a growth series indicates that the amplitudes of the second and third harmonics are significantly correlated with growth, which is demonstrated to be anisometric. Definable changes in the lateral outline can be attributed to changes in harmonic amplitudes and a wide range of morphological forms comparable to known taxa can be generated by systematically varying the amplitudes of the first four harmonics. The population used in this study probably represents Pentremites robustus Lyon and is from Bangor Limestone in the abandoned Moulton Quarry, Lawrence County, Alabama.

Improvements in the perceived completeness of the fossil record may be driven both by new discoveries and by reinterpretation of known fossils, but disentangling the relative effects of these processes can be difficult. Here, we propose a new methodology for evaluating historical trends in the perceived completeness of the fossil record, demonstrate its implementation using the freely available software ASCC (version 4.0.0), and present an example using crown-group birds (Aves). Dates of discovery and recognition for the oldest fossil representatives of 75 major lineages of birds were collected for the historical period ranging from 1910 to 2010. Using a comprehensive phylogeny, we calculated minimum implied stratigraphic gaps (MIG range) across these 75 lineages. Our results show that a reduction in global MIG values of 1.35 Ga (billion years) occurred over the past century in avian paleontology. A pronounced increase in the average rate of global MIG reduction is noted in the post-1970s interval (290.5 Myr per decade) compared to the pre-1970s interval (31.9 Myr per decade). Although the majority of the improvement in the fossil record of birds has come from new discoveries, substantial improvement (∼22.5%) has resulted from restudy and phylogenetic revision of previously described fossils over the last 40 years. With a minimum estimate indicating that at least 1.34 Gyr of gaps remain to be filled between the predicted and observed first appearances of major lineages of crown Aves, there is much progress to be made. However, a notable tapering off in the rate of global MIG reduction occurs between 1990 and 2010, suggesting we may be approaching an asymptote of oldest record discoveries for birds. Only future observations can determine whether this is a real pattern or a historical anomaly. Either way, barring the discovery of fossils that substantially push back the minimum age for the origin of crown-clade Aves, new discoveries cannot continue to reduce global MIG values at the average post-1970s rate over the long term.