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.

The end-Cretaceous (K/Pg) mass extinction event is the most recent and well-understood of the “big five” and triggered establishment of modern terrestrial ecosystem structure. Despite the depth of research into this event, our knowledge of upper Maastrichtian terrestrial deposits globally relies primarily on assemblage-level data limited to a few well-sampled formations in North America, the Hell Creek and Lance Formations. These assemblages disproportionally affect our interpretations of this important interval. Multiple investigations have quantified diversity patterns within these assemblages, but the potential effect of formation-level size-dependent taphonomic biases and their implications on extinction dynamics remains unexplored. Here, the relationship between taphonomy and body size of the Hell Creek Formation and Lance Formation dinosaurs and mammals are quantitatively analyzed. Small-bodied dinosaur taxa (<70 kg) are consistently less complete, unlikely to be articulated, and delayed in their description relative to their large-bodied counterparts. Family-level abundance (particularly skeletons) is strongly tied to body mass, and the relative abundance of juveniles of large-bodied taxa similarly is underrepresented. Mammals show similar but nonsignificant trends. The results are remarkably similar to those from the Campanian-aged Dinosaur Park Formation, suggesting a widespread strong taphonomic bias against the preservation of small taxa, which will result in their seemingly depauperate diversity within the assemblage. This taphonomically skewed view of diversity and abundance of small-bodied taxa amid our best late Maastrichtian samples has significant implications for understanding speciation and extinction dynamics (e.g., size-dependent extinction selectivity) across the K/Pg boundary.

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.

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.

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 taxonomic and ecologic composition of Earth's biota has shifted dramatically through geologic time, with some clades going extinct while others diversified. Here, we derive a metric that quantifies the change in biotic composition due to extinction or origination and show that it equals the product of extinction/origination magnitude and selectivity (variation in magnitude among groups). We also define metrics that describe the extent to which a recovery (1) reinforced or reversed the effects of extinction on biotic composition and (2) changed composition in ways uncorrelated with the extinction. To demonstrate the approach, we analyzed an updated compilation of stratigraphic ranges of marine animal genera. We show that mass extinctions were not more selective than background intervals at the phylum level; rather, they tended to drive greater taxonomic change due to their higher magnitudes. Mass extinctions did not represent a separate class of events with respect to either strength of selectivity or effect. Similar observations apply to origination during recoveries from mass extinctions, and on average, extinction and origination were similarly selective and drove similar amounts of biotic change. Elevated origination during recoveries drove bursts of compositional change that varied considerably in effect. In some cases, origination partially reversed the effects of extinction, returning the biota toward the pre-extinction composition; in others, it reinforced the effects of the extinction, magnifying biotic change. Recoveries were as important as extinction events in shaping the marine biota, and their selectivity deserves systematic study alongside that of extinction.

The typical pelecypod form, long thought to be primitively adaptive to burrowing, is likely to have been originally adaptive to a suspension feeding, epifaunal, possibly crawling mode of life. At small body size (< 1 cm), pelecypods possessing typical burrowing features can function as epifaunal crawlers. Pelecypods arose at small body sizes and are part of a molluscan evolutionary sequence in which relative size of the mantle cavity increased to accommodate a few large gills specialized for suspension feeding.

Acquisition of a bivalved shell by ancestral epifaunal suspension feeders may have offered protection from sediment clogging on soft bottoms, additional control over the direction, volume, and rate of water flow through the mantle cavity, more effective protection from predators, and better short-term control of the internal environment. Consideration of invertebrate groups analogous to the pelecypods (Branchiopoda, Cladocera, Ostracoda, Phyllocarida) support the view that the bivalve condition is primarily an adaptation for suspension feeding and predator avoidance in benthic environments.

The earliest known pelecypod, Fordilla troyensis Barrande, was not necessarily infaunal just because it had features similar to much larger, Recent burrowers. The size, shell morphology and environment of preservation of F. troyensis all suggest that it is reasonable to envision Cambrian pelecypods as epifaunal suspension feeders, possibly crawling on sedimentary bottoms. Moreover, the sudden Ordovician expansion of pelecypods and increase in individual size may be explained as a result of invasion of the infaunal adaptive zone.

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.

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.

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 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.

Body mass is an important organism-level variable in mammalian biology, correlated with physiology, life history, and ecology. To analyze the dynamics of body size evolution, increases and decreases in body mass were tallied for ancestor-descendant (AD) species pairs for 519 terrestrial caniform taxa. To account for uncertainty phylogeny, a bootstrapping routine shuffled hypothesized AD pairs, and average proportions of increases were binned as a function of ancestral body mass. A set of models relating the rate of body size increase were evaluated with the Akaike Information Criterion (AIC). AIC selected three models of the candidate set as equivalent in support by the observed body mass data. These three models propose body size increase for small AD pairs and body size decrease for large AD pairs, although they differ in their treatment of taxa at intermediate sizes.

These results demonstrate the presence of constraints bounding the caniform distribution at large and small body sizes, stabilizing the distribution through time, which stands in contrast to a broader mammalian pattern. At a finer phylogenetic scale, subclades within intermediate size classes display proportions that are significantly different from unbiased, with several clades previously cited as examples of “Cope's Rule” showing biased increases in size, and basal mustelids (badgers, and allied genera), Mephitidae (skunks), and Vulpini (“foxes”) exhibiting biased decreases. The caniform pattern is therefore the result of superimposed, clade-specific trajectories, demonstrating that the inferred dynamics of body size evolution and even the direction of trends in body size evolution within the Caniformia, and for mammals in general, depend on the hierarchical scale of the analysis.

Many apparent homeomorphs have been recognized among genera assigned to the Paleozoic stenolaemate bryozoan orders Trepostomata and Cryptostomata. Morphologies are evaluated to determine whether such homeomorphy should be expected, or is likely to have resulted from incomplete taxonomic analysis. Historical and constructional constraints prevalent in the phylum appear to provide ample opportunity for adaptive convergence, a conclusion supported by the occurrence of similar morphologies in distantly related post-Paleozoic bryozoans.

Cryptostomes are distinguished in part by the presence of restricted budding loci. Loci pattern is hypothesized to be the key innovation in the establishment of the clade and the pattern also is considered critical to the evolution of the relatively slender branches and short zooecia typical of cryptostomes.

Loci development does not provide a taxonomic panacea. This is because the hypothesis does not preclude convergent evolution of broadly similar restricted loci in Paleozoic non-cryptostome groups, although presumably the cryptostomes in general would have been best equipped to succeed under conditions favoring restricted loci.

Environmental conditions for the cryptostomes in general and changing life history strategies for rhabdomesoids in particular provide possible controlling factors for the evolution of these bryozoans.

Studying the deep-time origins of macroecological phenomena can help us to understand their long-term drivers. Given the considerable spatiotemporal bias of the terrestrial fossil record, it behooves us to understand how much biological information is lost. The aim of this study is to establish whether latitudinal diversity gradients are detectable in a biased terrestrial fossil record. I develop a simulated fossilization approach, weighting the probability of terrestrial mammal species appearing in the fossil record based on body size and geographic-range size; larger species with larger range sizes are more likely to enter the fossil record. I create simulated fossil localities from the modern North American mammal record. I vary the percentage of species successfully fossilized and estimate the magnitude of the latitudinal diversity gradient (slope of the richness gradient and degree of species turnover). I find that estimates of the latitudinal diversity gradient are sensitive to the loss of species with small body size and geographic-range sizes. In some cases, simulated fossil-record bias completely obliterates evidence of declining richness with latitude, a phenomenon that is not ameliorated by the application of nonparametric richness estimation. However, if the rate of preservation is medium (50% of species) to high (75% of species), the magnitude of the latitudinal diversity gradient can be reliably estimated. Similarly, changes in the diversity gradient estimates are largely explained by differences in the diversity–climate relationship among iterations, suggesting that these relationships may be measurable in the fossil record.

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.

Fusion occurred between pairs of conspecific colonies of Permian fenestrate bryozoans that were of approximately equal radius at time of contact. In contrast, no fusion occurred in pairs of conspecific colonies that were of unequal radius at time of contact. It is suggested that histologically compatible colonies developed from larvae that settled essentially simultaneously and that the larvae were siblings, lecithotrophic with low mobility, and of the same genotype (i.e., polyembryonic). Thus polyembryony appears to have existed as a reproductive “strategy” for at least 275 Myr, and its scarcity in modern taxa cannot be due to recentness of evolution.

The rise of durophagous predators during the Paleozoic represents an ecological constraint imposed on sessile marine fauna. In crinoids, it has been suggested that increasing predation pressure drove the spread of adaptations against predation. Damage to a crinoid's arms from nonlethal predation varies as a function of arm branching pattern. Here, using a metric for resilience to predation (“expected arm loss,” EAL), we test the hypothesis that the increase in predation led to more predation-resistant arm branching patterns (lower EAL) among Paleozoic crinoids. EAL was computed for 230 genera of Paleozoic crinoids and analyzed with respect to taxonomy and time. The results show significant variability among taxa. Camerates, especially monobathrids, display a pattern of increasingly convergent and predation-resistant arm morphologies from the Ordovician through the Devonian, with no significant change during the Mississippian. In contrast, the mean EAL among cladids follows no overall trend through the Paleozoic. Regenerating arms are known to be significantly more common in camerates than in other Paleozoic taxa; if regeneration is taken as a proxy for nonlethal interactions with durophagous predators, this indicates that nonlethal predation occurred more often among camerates throughout the Early and Middle Paleozoic. In addition, frequency of injury among camerates is inversely correlated with EAL and positively correlated with infestation by parasitic snails. From this we conclude that decreasing EAL signals a selective pressure in favor of resistance to grazing predation in camerates but not in other subclasses before the Mississippian, with an apparent relaxation in this constraint after the late Devonian extinctions.

Based on high-resolution palynological analysis of 680 samples from a core, short-term changes in plant diversity and floristic composition within the Paleogene greenhouse were detected in the lacustrine succession of a lower to middle Eocene maar lake at Messel (Federal State of Hesse, Germany). The microfloristic data show that taxonomic diversity increased rapidly within some decades during recolonization of a volcanically devastated area around the lake. With the establishment of a climax vegetation at the end of recolonization, the maximum in palynological diversity was reached within the crater area. During the following 640 Kyr the composition of the palynospectrum changed only gradually. However, different richness and evenness estimations show that alpha and gamma diversity decreased up to 35%, which can be related to the establishment of an equilibrium stage within the climax vegetation that led to the dominance of an assemblage of self-replacing species. Nevertheless, time-series analysis of alpha-diversity changes within the climax vegetation reveals that orbitally controlled climate change of Milankovitch and sub-Milankovitch order influenced the diversity of the vegetation, resulting in a rise of beta diversity. Based on the composition of the vegetation and comparison to modern analogues, our analysis proves that Eocene paratropical plant diversity increased during periods of slightly higher temperature and precipitation. Therefore, both composition and diversity of the vegetation was highly susceptible to minor-scale, short-term changes in climate, even during equable greenhouse conditions.

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.