We use two approaches to test hypotheses regarding function in a group of extinct mammals (Family Mesotheriidae, Order Notoungulata) that lack any close extant relatives: a principle-derived paradigm method and empirically derived analog method. Metric and discrete morphological traits of mesotheriid postcranial elements are found to be consistent with the morphology predicted by a modified version of Hildebrand's paradigm for scratch diggers. Ratios of in-force to out-force lever arms based on skeletal elements indicate that the mesotheriids examined had limbs modified for high out-forces (i.e., they were “low geared”), consistent with the digging hypothesis. Other mesotheriid characters, such as cleft ungual phalanges, a curved olecranon, and a highly modified pelvis (with extra vertebrae incorporated into the sacrum and fusion between the ischium and the axial skeleton) are regarded as being functionally significant for digging and also occur in a variety of extant diggers. Analog methods indicate that mesotheriids share numerous traits common to a variety of extant diggers. Principal component analyses of postcranial elements indicate that mesotheriids consistently share morphometric space with larger extant fossorial mammals: aardvark, anteaters, wombats, and badger. Likewise, discriminant function analyses categorized mesotheriids as fossorial, though imperfectly analogous to the extant diggers analyzed. Thus, both theory-driven and empirically derived methods of estimating function in these extinct taxa support a digging hypothesis for the mesotheriids examined. Adaptations for digging in both the forelimb and sacropelvic functional complexes of mesotheriids provide independent support for the fossorial hypothesis.

This study examines the morphology and function of hindlimb plumage in Archaeopteryx lithographica. Feathers cover the legs of the Berlin specimen, extending from the cranial surface of the tibia and the caudal margins of both tibia and femur. These feathers exhibit features of flight feathers rather than contour feathers, including vane asymmetry, curved shafts, and a self-stabilizing overlap pattern. Many of these features facilitate lift generation in the wings and tail of birds, suggesting that the hindlimbs acted as airfoils. A new reconstruction of Archaeopteryx is presented, in which the hindlimbs form approximately 12% of total airfoil area. Depending upon their orientation, the hindlimbs could have reduced stall speed by up to 6% and turning radius by up to 12%. Presence of the “four-winged” planform in both Archaeopteryx and basal Dromaeosauridae indicates that their common ancestor used fore- and hindlimbs to generate lift. This finding suggests that arboreal parachuting and gliding preceded the evolution of avian flight.

New mid-Cretaceous stable isotope (δ18O and δ13C) records of multiple planktonic foraminiferal species and coexisting coccoliths from Blake Nose (western North Atlantic) document a major depth-ecology reorganization of planktonic foraminifera. Across the Albian/Cenomanian boundary, deep-dwelling Praeglobotruncana stephani and Rotalipora globotruncanoides adapted to living at a shallower depth, while, at the same time, the population of surface-dwelling Paracostellagerina libyca declined. Subsequently, the opportunistic species Hedbergella delrioensis shifted to a deep environment, and the deep-dwelling forms Rotalipora montsalvensis and Rotalipora reicheli first appeared. The primary paleoenvironmental cause of the observed changes in planktonic adaptive strategies is uncertain, yet their coincidence with an earliest Cenomanian cooling trend reported elsewhere implicates the importance of reduced upper-ocean stratification. Although there has been an implicit assumption that the species-specific depth habitats of fossil planktonic foraminifera were invariant through time, planktonic paleoecology is a potential variable. Accordingly, the possibility of evolutionary changes in planktonic foraminiferal depth ecology should be a primary consideration (along with other environmental parameters) in paleoceanographic interpretations of foraminiferal stable isotope data.

Some statistical methods are described for the detection and estimation of variability in the rate of evolution, from biometrical data on single characters in fossil lineages. The methods were applied to some published examples of protistan and mammalian lineages, extending between 0.8 and 6.4 Myr in duration. Of six cases examined, only one failed to show evidence for significant variation in the rate of evolution, and only four deviated significantly from a random walk pattern, despite significant net evolutionary change in all cases but one.

Two communities dominated by deposit-feeding bivalves are recognized in Quisset Harbor, Massachusetts. Interference with life position and sediment preconditioning restrict the distribution of some species. The Eel Grass Community, dominated by Nucula proxima, comprises primarily non-siphonate forms which live in fecal-pellet rich, high-water-content, oxygenated sediment. The sediment texture results from active burrowing. This soft, mobile sediment readily clogs the siphons of siphonate bivalves. The Channel Community, dominated by Yoldia limatula, comprises primarily siphonate forms which live in partly compacted, low-water-content muds. Each community is characterized by abundant surface, shallow, and deep feeding species. Competition for food has generated this distinct stratification in feeding depth of the dominant species with each community.

Similar competitive relationships, affecting both species occurrence and trophic stratification, are apparent in three Silurian age deposit-feeding bivalve communities from the McAdam Brook Formation of Nova Scotia. A community dominated by four non-siphonate species inhabited soupy, high-water-content muds. A community dominated by three siphonate species lived in cohesive muds. A mixed community, dominated by four species, two non-siphonate and two siphonate species (the most abundant of which are present, but not as the most abundant forms, in the other communities), characterized the mid-way point of the ecotone between the other two communities.

These deposit-feeding bivalve dominated communities have similar structural patterns although separated by 400 million years and despite environmental differences and evolutionary changes. Both response to physical factors, such as sediment character, and interspecific competition impose and maintain this type of community structure.

The subfamily Equinae in the Great Plains region of North America underwent a dramatic radiation and subsequent decline as climate changed from warm and humid in the middle Miocene to cooler and more arid conditions during the late Miocene. Here we use ecological niche modeling (ENM), specifically the GARP (Genetic Algorithm using Rule-set Prediction) modeling system, to reconstruct the geographic distribution of individual species during two time slices from the middle Miocene through early Pliocene. This method combines known species occurrence points with environmental parameters inferred from sedimentological variables to model each species' fundamental niche. The geographic range of each species is then predicted to occupy the geographic area within the study region wherever the set of environmental parameters that constrain the fundamental niche occurs. We analyze changes in the predicted distributions of individual species between time slices in relation to Miocene/Pliocene climate change. Specifically, we examine and compare distribution patterns for two time slices that span the period from the mid-Miocene (Barstovian) Climatic Optimum into the early Pliocene (Blancan) to determine whether habitat fragmentation led to speciation within the clade and whether species survival was related to geographic range size. Patchy geographic distributions were more common in the middle Miocene when speciation rates were high. During the late Miocene, when speciation rates were lower, continuous geographic ranges were more common. Equid species tracked their preferred habitat within the Great Plains region as well as regionally throughout North America. Species with larger predicted ranges preferentially survived the initial cooling event better than species with small geographic ranges. As climate continued to deteriorate in the late Miocene, however, range size became irrelevant to survival, and extinction rates increased for species of all range sizes. This is the first use of ENM and GARP in the continental fossil record. This powerful quantitative biogeographic method offers great promise for studies of other taxa and geologic intervals.

Geographic range size is one of the few traits that promoted survivorship during both mass and background extinctions, but the exact reason (or reasons) why a large geographic range confers extinction resistance remains unclear. Proposed explanations have focused on the roles of dispersal ability, climate tolerance, global abundance, and widespread ranges in predicting taxon longevities. This study uses biogeographic data for late Paleozoic brachiopod genera to test the relative contribution of these traits to genus longevities, using simple but accurate proxy measurements. The results demonstrate a strong positive relationship between genus longevity and geographic range size, which is robust to several potential errors. Further, latitudinal range, which predominantly reflects climate tolerance, was no more important than longitudinal range, which predominantly reflects dispersal ability, in predicting genus longevities. Rather, longevities were an outcome of the total number of occurrences, which estimates global abundance, and the advantages of widespread distribution, regardless of which particular traits were responsible for generating the total geographic range. The advantages of a large geographic range were apparent during both background and mass extinctions of late Paleozoic time. Although not statistically significant, there was a tendency for the greatest selectivity to occur in intervals with the lowest extinction rates. The correlation of genus longevity and geographic range size had a profound consequence for the secular pattern of global brachiopod diversity: because the diversity of genera with small geographic ranges was more volatile owing to their correspondingly shorter longevities, global diversity and mean geographic range size paralleled each other almost exactly. Given that the correlation between taxon longevity and geographic range size has also been demonstrated for other taxonomic groups and at other time intervals, these results suggest that global diversity curves compiled from taxonomic databases dominantly reflect changes in the diversity of genera with small geographic ranges.

We review and synthesize multiple biotic and abiotic proxies for marine nutrient and food availability, primary productivity, and food quality (stoichiometry) and propose what their relationships may have been to macroevolutionary processes, especially speciation. This review confirms earlier suggestions that there has been an overall increase in marine primary productivity over the Phanerozoic, but indicates that the increase has been irregular and that present levels may not be the peak. We integrate these indicators into a new estimate of relative primary productivity in the global ocean through the Phanerozoic. We then combine multiple, frequently conflicting ecological-evolutionary hypotheses into a general model for how primary production may affect speciation over geological time scales. This model, an elaboration and extension of the “speciation cycle” previously proposed by Grant and Grant, attempts to explain why an increase in food supply sometimes is associated with decreased diversity, and at other times with increased diversification. We propose some simple tests for the application of this model to the fossil record.

Ecological niche modeling (ENM) is a quantitative approach to predict species’ abiotic requirements. It is a correlative technique, requiring geographically explicit information on species occurrences and the suites of environmental conditions experienced at each occurrence point. The output of these models is a set of environmental suitability rules that can be projected geographically and through time to test biogeographic, ecologic, and evolutionary hypotheses. Although developed by biologists and used extensively in the modern, ENM is in its early stages of application to the deep-time fossil record (hence PaleoENM). In part its limited use in the fossil record thus far reflects the methodological challenge of constructing paleoenvironmental layers needed for PaleoENM analysis, whereas in the modern these layers are available from large public databases (e.g., WorldClim). This paper provides a contextual and methodological framework for appropriately applying PaleoENM, including best practices for developing species occurrence and paleoenvironmental data sets for PaleoENM analyses.

Species arise and establish themselves over the geologic time scale. This process is manifested as a change in the relative frequency of occurrences of a given species in the global pool of species. Our main goal here is to model this rise and the eventual decline of microfossil species using a mixed-effects model where groups each have a characteristic occurrence trajectory (main effects) and each species belonging to those groups is allowed to deviate from the given group trajectory (random effects). Our model can be described as a “hat” with logistic forms in the periods of increase and decline. Using the estimated timings of rises and falls, we find that the lengths of the periods of rise are about as long as the lengths of the periods when species are above 50% of their estimated maximal occurrences. These latter periods are here termed periods of dominance, which are in turn about the same length as the species' periods of fall. The peak rates of the rises of microfossils are in general faster than their peak rates of falls. These quantified observations may have broad macroevolutionary and macroecological implications. Further, we hypothesize that species that have experienced and survived high levels of environmental volatility (specifically, periods of greater than average variation in temperature and productivity) during their formative periods should have longer periods of dominance. This is because subsequent environmental variations should not drive them to decline with ease. We find that higher estimated environmental volatility early in the life of a species positively correlates with lengths of periods of dominance, given that a species survives the initial stress of the environmental fluctuations. However, we find no evidence that the steepness of the rise of a species is affected by environmental volatility in the early phases of its life.

It is now widely recognized that a large number of Cretaceous planktic foraminiferal species are commonly found associated with fully Danian faunas in many K/T boundary sections and deep-sea cores. This “Cretaceous” fauna has traditionally been regarded as representing the reworking of older Cretaceous sediments into younger strata, though recent isotopic data from some species indicates that, at least in these instances, the reworking hypothesis is false. To further test this reworking hypothesis the biogeography of this “Cretaceous” fauna is compared to the underlying uppermost Maastrichtian biogeography and to the biogeography of lowermost Danian planktic foraminiferal faunas. Results show that there is no regular decline in species richness, extinction, or faunal co-occurrence values for this “Cretaceous” fauna at progressively higher (=younger) Danian stratigraphic horizons. Moreover, there is no compelling association between the stratigraphic persistence of this “Cretaceous” fauna and shallow depositional settings. Instead, this fauna is characterized by: (1) a close (and predictive) association between “Cretaceous” and indigenous Danian species richness values throughout the lower Danian, (2) a close numerical and geographic correspondence between Danian speciation and the disappearance of “Cretaceous” species from the Danian fossil record, and (3) a pronounced similarity between changes in the general biogeographic structures of the “Cretaceous” and associated Danian faunas throughout the study interval. These data suggest that the K/T planktic foraminiferal extinction event exhibited a marked geographic structure with low and middle latitude faunas experiencing differentially high extinction rates in the lowermost Danian zones P0 and P1a and high latitude survivor faunas persisting more or less unchanged into the overlying zone, P1b and P1c. Taken together, these results challenge the traditional concept of an instantaneous uppermost Cretaceous planktic foraminiferal mass extinction and its proposed causal connection to bolide impact.

A survey was undertaken of the developmental types of the neogastropod families Volutidae, Fasciolariidae, Nassariidae, Mitridae, Buccinidae and Olividae in the Palaeocene and Eocene series of the Gulf of Mexico. Although the families were dominated by planktotrophic development in the Paleocene, most show a general increase in numbers of species with nonplanktotrophic development through the Eocene. Present day environmental correlations with larval development do not adequately explain the observed shift in developmental types in the Early Tertiary. It is proposed that higher speciation rates for nonplanktotrophs and a unidirectional trend in developmental change may account for the progressive increase of nonplanktotrophic development.

This paper presents a method for constraining the age of a clade with the ages of the earliest fossil specimens in that clade's outgroups. Given a sufficiently deep, robust, well-resolved, and stratigraphically consistent cladogram, this method can yield useful age constraints even in the absence of specific information about the fossil preservation and recovery rates of individual taxa. The algorithm is applied to simulated data sets to demonstrate that this method can yield robust constraints of clade ages if there are sufficient fossil outgroups available and if there is a finite chance that additional outgroups may be discovered in the future. Finally, the technique is applied to actual fossil data to explore the origin of modern placental mammals. Using data from recently published cladograms, this method indicates that if all Mesozoic eutherians are regarded as outgroups of Placentalia, then the last common ancestor of modern placental mammals and their Cenozoic allies lived between 65 and 88–98 million years ago, depending on the assumed cladogram and the number of outgroups included in the analysis.

Extinctions at the top of the Sunwaptan Stage (=“Ptychaspid Biomere”) near the Cambrian-Ordovician boundary eliminated about half of North American trilobite families. The families that extend from the shelf into the upper slope show significantly higher survival than those confined to the shelf. Biofacies and lithofacies distribution patterns indicate that the extinctions cannot be attributed to a shelfwide physical environmental perturbation, such as a fall in water temperature or the spread of anoxic waters. We develop a simple biogeographic model which suggests that diversity of a faunal province is influenced profoundly by changes in the number of component biofacies. This model is tested with an analysis of biofacies distribution patterns across the upper boundary of the Sunwaptan Stage. The extinctions correspond closely to lithofacies shifts in the outer shelf that indicate the initiation of major paleogeographic changes, possibly in response to a sea-level rise. The effects of these changes cascade across the entire shelf by the shoreward migration of off-shelf and shelf-margin taxa. Biofacies become reduced in number through telescoping and their environmental ranges expand during the extinction interval, suggesting an increase in the proportion of eurytopic taxa. Selective survival of wide-ranging eurytopes may have influenced the dynamics of faunal replacement by lowering speciation rates of shelf taxa. Consequently, the proportion of shelf endemics will decline and biofacies will be dominated by immigrant taxa. There are sufficient similarities in extinction patterns across the upper boundary of the Sunwaptan Stage and those at other Upper Cambrian stage boundaries to suggest that the biogeographic model developed here may have broader application.

Traditional wisdom of the evolution of lungs in fishes is that lungs arose when gill ventilation was hindered by an aquatic habitat that was low in oxygen. This scenario has been buttressed primarily by a proposed correlation between extant air-breathing fishes and hypoxic habitats, as well as by the fact that early vertebrate fossils were found in sediments believed to indicate a semi-arid environment. There are problems with this scenario, yet it retains a dominant influence on how the evolution of aerial respiration is viewed. This paper presents a new hypothesis for lung evolution that is more consistent with the fossil record and physiology of extant animals than the traditional scenario; I propose that lungs evolved to supply the heart with oxygen. The primitive vertebrate heart was spongy in architecture and devoid of coronary support, obtaining oxygen from luminal blood. By supplying oxygen to this tissue, lungs may have been important in ancient fishes for sustaining activity, regardless of environment. Furthermore, this function for lungs may have influenced cardiovascular adaptations of tetrapods because their divided cardiovascular system isolates the right side of the heart from pulmonary oxygen. I propose that three innovations compensate for this isolation: In extant amphibians oxygen-rich blood from cutaneous and buccal respiration enters the right side of the heart; in chelonians and lepidosaurs the intracardiac shunt washes oxygen-rich blood into the right side of the heart; in mammals, birds, and perhaps in crocodilians, support of the heart by coronary vasculature eliminates this problem.

The concept of coordinated stasis, manifest as a pattern of long intervals of concurrent taxonomic and ecologic persistence separated by comparatively abrupt periods of biotic change, has been challenged in recent studies that claim a lack of prolonged persistence of taxa and associations. A key problem has been the difficulty of distinguishing faunal change owing to localized, short-term environmental fluctuation or patchiness from that indicating regionally pervasive, long-term evolutionary or ecological change. Here, we use an extensive database from the Middle Devonian Hamilton Group of the Appalachian Basin to test for taxonomic and ecologic persistence within this ecological-evolutionary subunit, a succession of purported relative stability. Replicate samples collected from many localities and stratigraphic horizons over a wide geographic area allow us to address the effects of small-scale environmental variation and localized faunal patchiness while exploring basin-scale variation in faunal composition within and between the formations of the Hamilton Group.

Observed stratigraphic distributions of fossils are consistent with a scenario in which all taxa are present from bottom to top of the Hamilton Group, and absences result only from sampling failure. Although small-scale variation in faunal composition indeed does occur, there is no more variation among formations than occurs within them. Assemblages from different formations, whether they are defined by taxonomic or ecologic composition, are statistically indistinguishable according to several independent metrics, including ANOSIM and a maximum likelihood estimation that evaluates stratigraphic turnover using Bayesian “Information Criterion.” Simulated data sets indicate that test results are most consistent with species-level extinction of 2.6% per Myr within the Hamilton Group, far lower than the Givetian rate of 11.5% per Myr generic extinction derived from a global database. Such faunal persistence over the ~5.5 Myr encompassed by this unit is consistent with the pattern of coordinated stasis. Earlier studies showing greater amounts of temporal turnover in Hamilton Group faunas are likely influenced by their smaller geographic scale of analysis, suggesting that regional studies done elsewhere may yield similar results.

We present a morphometric analysis of water transport cells within a physiologically explicit three-dimensional space. Previous work has shown that cell length, diameter, and pit resistance govern the hydraulic resistance of individual conducting cells; thus, we use these three parameters as axes for our morphospace. We compare living and extinct plants within this space to investigate how patterns of plant conductivity have changed over evolutionary time. Extinct coniferophytes fall within the range of living conifers, despite differences in tracheid-level anatomy. Living cycads, Ginkgo biloba, the Miocene fossil Ginkgo beckii, and extinct cycadeoids overlap with both conifers and vesselless angiosperms. Three Paleozoic seed plants, however, occur in a portion of the morphospace that no living seed plant occupies. Lyginopteris, Callistophyton, and, especially, Medullosa evolved tracheids with high conductivities similar to those of some vessel-bearing angiosperms. Such fossils indicate that extinct seed plants evolved a structural and functional diversity of xylem architectures broader, in some ways, than the range observable in living seed plants.

Systematics and paleontology have had a long conceptual relationship, united by the common goal of reconstructing the history of life. Yet, with few exceptions, paleontologists have had little input into formulating systematic theory and methodology. The reasons for this apparently relate to two conceptual-philosophical traditions of post-Darwinian paleontology: (1) the widespread adoption of a species concept in which taxa are viewed as nondiscrete, arbitrarily designated segments of evolutionary continua, and (2) the belief that phylogenetic reconstruction is primarily an empirical matter of tracing evolutionary change through the stratigraphic record.

Available systematic evidence supports the hypothesis that species are real, discrete units in space and time and that, unless they are postulated to be directly ancestral to another species, they can be defined by the possession of one or more evolutionary novelties (derived characters). Species beginnings are delineated by speciation (vicariance) events and their terminations by subsequent speciation events or by extinctions.

Natural groups are composed of taxa that have shared a common genealogical history. Cladistic analysis is a method to construct and test hypotheses of monophyly and thereby define natural groups. Cladistic hypotheses are necessary to investigate many of the major questions within contemporary paleobiology. Virtually no studies of evolutionary rates, patterns of taxonomic diversity, modes of taxic evolution, and patterns of morphological diversification can be undertaken without reference to cladistic hypotheses about the composition of natural groups.

Because paleobiology is historical in its content, paleontologists are greatly limited in their ability to use paleontological data to investigate questions about the evolutionary process. According to current evolutionary theory, the concepts of adaptation and natural selection relate to genetic and ecological processes that take place within local populations (microevolution). If so, then data relevant to examining these phenomena are likely to be lacking in paleontological samples. Consequently, explanations of paleontological pattern that include process-related concepts such as adaptation and natural selection are axiomatic in their logical structure and thus cannot be falsified or critically evaluated by that paleontological pattern.

The end-Permian mass extinction is commonly portrayed not only as a massive biodiversity crisis but also as the time when marine benthic faunas changed from the Paleozoic Fauna, dominated by rhynchonelliform brachiopod taxa, to the Modern Fauna, dominated by gastropod and bivalve taxa. After the end-Permian mass extinction, scenarios involving the Mesozoic Marine Revolution portray a steady increase in numerical dominance by these benthic molluscs as largely due to the evolutionary effects of an “arms race.” We report here a new global paleoecological database from study of shell beds that shows a dramatic geologically sudden earliest Triassic takeover by bivalves as numerical dominants in level-bottom benthic marine communities, which continued through the Early Triassic. Three bivalve genera were responsible for this switch, none of which has any particular morphological features to distinguish it from many typical Paleozoic bivalve genera. The numerical success of these Early Triassic bivalves cannot be attributed to any of the well-known morphological evolutionary innovations of post-Paleozoic bivalves that characterize the Mesozoic Marine Revolution. Rather, their ability to mount this takeover most likely was due to the large extinction of rhynchonelliform brachiopods during the end-Permian mass extinction and aided by their environmental distribution and physiological characteristics that enabled them to thrive during periods of oceanic and atmospheric stress during the Permian/Triassic transition.

Ecological ordination can reveal gradients in the species composition of fossil assemblages that can be correlated with paleoenvironmental gradients. Ordinations of simulated data sets suggest that nonmetric multidimensional scaling (NMDS) generally produces less distorted results than detrended correspondence analysis (DCA). We ordinated 113 brachiopod-dominated samples from the Frasnian (Late Devonian) Brallier, Scherr, and lower Foreknobs Formations of southwest Virginia, which represent a range of siliciclastic marine paleoenvironments. A clear environmental signal in the ordination results was obscured by (apparently) opportunistic species that occurred at high abundance in multiple environments; samples dominated by these species aggregated in ordination space regardless of paleoenvironmental provenance. After the opportunist-dominated samples were removed, NMDS revealed a gradient in species composition that was highly correlated with substrate (grain size); a second, orthogonal gradient likely reflects variation in disturbance intensity or frequency within grain-size regimes. Additional environmental or ecological factors, such as oxygenation, may also be related to the gradients. These two gradients, plus the environmental factors that controlled the occurrence of opportunistic species, explain much of the variation in assemblage composition in the fauna. In general, the composition of fossil assemblages is probably influenced by multiple paleoecological and paleoenvironmental factors, but many of these can be decomposed and analyzed.