Gaps in the fossil record can be identified in compilations of stratigraphic ranges of lower taxa classified within higher taxa. Statistical properties of such gaps suggest the following conclusions. First, the random sampling model most commonly used to correct for incompleteness in the record is inconsistent with the data. Second, the decline in taxonomic extinction rate during the Phanerozoic is not just an artifact of an increase in the completeness of the record.

An enigma of deep-sea biodiversity research is that the abyss with its low productivity and densities appears to have a biodiversity similar to that of shallower depths. This conceptualization of similarity is based mainly on per-sample estimates (point diversity, within-habitat, or α-diversity). Here, we use a measure of between-sample within-community diversity (β1H) to examine benthic foraminiferal diversity between 333 stations within 49 communties from New Zealand, the South Atlantic, the Gulf of Mexico, the Norwegian Sea, and the Arctic. The communities are grouped into two depth categories: 200–1500 m and >1500 m. β1H diversity exhibits no evidence of regional differences. Instead, higher values at shallower depths are observed worldwide. At depths of >1500 m the average β1H is zero, indicating stasis or no biodiversity gradient. The difference in β1H-diversity explains why, despite species richness often being greater per sample at deeper depths, the total number of species is greater at shallower depths. The greater number of communities and higher rate of evolution resulting in shorter species durations at shallower depths is also consistent with higher β1H values.

Taxonomic membership frequencies exhibit distributions in which groups with few numbers of subtaxa are much more common in a clade than those with more subtaxa. Here, a “broken plate” model is developed to describe such taxonomic memberships; some higher taxonomic group (the plate) is randomly subdivided into intermediate taxonomic units (plate fragments), whose sizes are dependent on the number of taxonomic subunits that they each contain. Theoretical distributions of membership frequencies produced by this model yield a superior fit to data from both modern and fossil groups, as illustrated by classifications for primarily fossil brachiopods and entirely modern mammals. The nature of these distributions is consistent with the contention that Linnaean membership frequencies result from the random partitioning of taxonomic/morphologic space. Moreover, numbers of taxa contained within hierarchically equivalent groups are unrelated, as are membership numbers at taxonomically higher and lower levels of consideration. Agreement between observed taxonomic memberships and those anticipated from the random partitioning of diversity as described by the “broken plate” model bears directly on a number of fundamental questions including the significance of extreme polytypy and inferred causes of adaptive radiation within many taxonomic groups.

One important and sometimes contentious challenge in paleobiology is discriminating between species, which is increasingly accomplished by comparing specimen shape. While lengths and proportions are needed to achieve this task, finer geometric information, such as concavity, convexity, and curvature, plays a crucial role in the undertaking. Nonetheless, standard morphometric methodologies such as landmark analysis are not able to capture in a quantitative way these features and other important fine-scale geometric notions.

Here we develop and implement state-of-the-art techniques from the emerging field of computational geometry to tackle this problem with the Mississippian blastoid Pentremites. We adapt a previously known computational framework to produce a measure of dissimilarity between shapes. More precisely, we compute “distances” between pairs of 3D surface scans of specimens by comparing a mix of global and fine-scale geometric measurements. This process uses the 3D scan of a specimen as a whole piece of data incorporating complete geometric information about the shape; as a result, scans used must accurately reflect the geometry of whole, undamaged, undeformed specimens. Using this information we are able to represent these data in clusters and ultimately reproduce and refine results obtained in previous work on species discrimination. Our methodology is landmark free, and therefore faster and less prone to human error than previous landmark-based methodologies.

Crinoids were relatively unaffected by the end-Devonian Hangenberg mass extinction event. Major clades of Devonian durophagous fishes suffered significant extinctions, however, and the dominant surviving clades were biting or nipping predators. In part as a response to the Hangenberg event, early Mississippian crinoids underwent an adaptive radiation, while fish clades with a shell-crushing durophagous strategy diversified. Durophagous predators are inferred to have been more effective predators on camerate crinoids; and it is hypothesized, following the predictions of escalation, that through the early Mississippian, camerate crinoids evolved more effective anti-predatory strategies in response. We test this hypothesis of escalation by examining the changes in spinosity and plate convexity among camerate crinoids throughout this interval. A new method was formulated to test for an increase in convexity of the tegmen plates. Traits in Agaricocrinus, Aorocrinus, and Dorycrinus (Family Coelocrinidae) were tested for congruence to the escalation hypothesis, and results were mixed. Convexity of tegmen plates in Agaricocrinus, spine length/calyx diameter in Aorocrinus, calyx size in Aorocrinus, central spine length in Dorycrinus, and spine width in Dorycrinus did not have size increase trends supporting escalation. Rather than an increase in convexity, the variance of convexity in Agaricocrinus tegmen plates narrowed, which could reflect an optimum. Alternatively, morphological change consistent with the escalation hypothesis occurred in calyx size of Agaricocrinus and in lateral spine length and calyx size in Dorycrinus. Furthermore, central and lateral spine length, parameters of the spine width, and size trends support escalation when Aorocrinus and Dorycrinus are treated as a lineage. Thus, inferred escalation acted on traits differently within a single lineage and was relevant for both speciation and the diversification of a new genus.

Recent progresses in our knowledge of mouse odontogenesis have enhanced rodent tooth morphology as a model for Evo-Devo studies. Deciphering the connection between macroevolution and microevolution, however, especially in the case of mammalian teeth, requires examples to illustrate how morphological differences among species, or higher taxa, can stem from population-level processes. In this paper we use paleontological material to study intraspecific variation of tooth morphology in the late Miocene species Progonomys clauzoni, over a short span of geological time in a restricted area. Progonomys is of particular interest as a stem genus of all murine rodents (Old World rats and mice). We use morphometrical and statistical methods to illustrate how change in the amplitude in variation at the population level through geological time is associated with the emergence of new characters. Some of these new characters, including functional ones, become fixed in parallel in distinct murine lineages. Nine million years ago, Progonomys clauzoni displayed variational properties of the developmental system shared by the Murinae, which can also explain some singular tooth characteristics that now are scattered among the diverse lineages. Further morphometric studies, however, are necessary to explain how the variety of cusp patterns observed in Progonomys clauzoni can be explained by developmental properties.

The trophic role assumed by an animal taxon in a community is best understood when the structure of the community is viewed in historical perspective (Whittaker 1977). In many environments it is not physical and behavioral limitations which guide a group's evolutionary potential, but the opportunity to exploit available adaptive zones, which, because of the nature of the fauna, were open (Hecht 1975, p. 248). [The term adaptive zone is used as defined by Van Valen (1971, p. 421) … “the niche of any taxon, especially a supraspecific one.” Van Valen distinguished adaptive zones from the “ways of life” of taxa. Adaptive zones are part of the environment and exist independently of taxa that exploit them.] It is often assumed or implied that a systematic group can, in its adaptive radiation, fill most of the available niches within a particular adaptive zone (Hecht 1975, p. 247). This type of “taxocene” analysis (Whittaker 1972, p. 218; Levandowsky and White 1977, p. 133), which promotes these views, has obvious shortcomings. It is now evident that mammals, for example, were unable to equally exploit and partition all available adaptive zones on every continent. The failure of carnivorous mammals to do this to a complete degree in Australia (see Hecht 1975, p. 247) and in South America (see Marshall 1977, p. 709) has some historical basis in the development of the stratification of the vertebrate fauna.

Estimating biodiversity and its variations through geologic time is a notoriously difficult task, due to several taphonomic and methodological effects that make the reconstructed signal potentially distinct from the unknown, original one. Through a simulation approach, we examine the effect of a major, surprisingly still understudied, source of potential disturbance: the effect of time discretization through biochronological construction, which generates spurious coexistences of taxa within discrete time intervals (i.e., biozones), and thus potentially makes continuous- and discrete-time biodiversity curves very different. Focusing on the taxonomic-richness dimension of biodiversity (including estimates of origination and extinction rates), our approach relies on generation of random continuous-time richness curves, which are then time-discretized to estimate the noise generated by this manipulation. A broad spectrum of data-set parameters (including average taxon longevity and biozone duration, total number of taxa, and simulated time interval) is evaluated through sensitivity analysis. We show that the deteriorating effect of time discretization on the richness signal depends highly on such parameters, most particularly on average biozone duration and taxonomic longevity because of their direct relationship with the number of false coexistences generated by time discretization. With several worst-case but realistic parameter combinations (e.g., when relatively short-lived taxa are analyzed in a long-ranging biozone framework), the original and time-discretized richness curves can ultimately show a very weak to zero correlation, making these two time series independent. Based on these simulation results, we propose a simple algorithm allowing the back-transformation of a discrete-time taxonomic-richness data set, as customarily constructed by paleontologists, into a continuous-time data set. We show that the reconstructed richness curve obtained this way fits the original signal much more closely, even when the parameter combination of the original data set is particularly adverse to an effective time-discretized reconstruction.

The inner ear of the two higher clades of modern cetaceans (Neoceti) is highly adapted for hearing infrasonic (mysticetes) or ultrasonic (odontocetes) frequencies. Within odontocetes, Platanistoidea comprises a single extant riverine representative, Platanista gangetica, and a diversity of mainly extinct marine species from the late Oligocene onward. Recent studies drawing on features including the disparate tympanoperiotic have not yet provided a consensus phylogenetic hypothesis for platanistoids. Further, cochlear morphology and evolutionary patterns have never been reported. Here, we describe for the first time the inner ear morphology of late Oligocene–early Miocene extinct marine platanistoids and their evolutionary patterns. We initially hypothesized that extinct marine platanistoids lacked a specialized inner ear like P. gangetica and thus, their morphology and inferred hearing abilities were more similar to those of pelagic odontocetes. Our results reveal there is no “typical” platanistoid cochlear type, as the group displays a disparate range of cochlear anatomies, but all are consistent with high-frequency hearing. Stem odontocete Prosqualodon australis and platanistoid Otekaikea huata present a tympanal recess in their cochlea, of yet uncertain function in the hearing mechanism in cetaceans. The more basal morphology of Aondelphis talen indicates it had lower high-frequency hearing than other platanistoids. Finally, Platanista has the most derived cochlear morphology, adding to evidence that it is an outlier within the group and consistent with a >9-Myr-long separation from its sister genus Zarhachis. The evolution of a singular sound production morphology within Platanistidae may have facilitated the survival of Platanista to the present day.

Stratigraphic range data are used to derive time scales on which taxonomic survivorship curves for genera and families are as nearly as possible independent of their times of origin. These time scales correct for temporal variations in overall extinction rates caused by major extinctions and the pull of the Recent. Survivorship curves for genera and families on their respective time scales are well fit by Pareto distributions differing only in their scale parameter.

Approximately 50,000–11,000 years ago many species around the world became extinct or were extirpated at a continental scale. The causes of the late Pleistocene extinctions have been extensively debated and continue to be poorly understood. Several extinction models have been proposed, including two nutritionally based extinction models: the coevolutionary disequilibrium and mosaic-nutrient models. These models draw upon the individualistic response of plant species to climate change to present a plausible scenario in which nutritional stress is considered one of the primary causes for the late Pleistocene extinctions.

In this study, we tested predictions of the coevolutionary disequilibrium and mosaic-nutrient extinction models through the study of dental wear and enamel hypoplasia of Equus and Bison from various North American localities. The analysis of the dental wear (microwear and mesowear) of the samples yielded results that are consistent with predictions established for the coevolutionary disequilibrium model, but not for the mosaic-nutrient model. These ungulate species show statistically different dental wear patterns (suggesting dietary resource partitioning) during preglacial and full-glacial time intervals, but not during the postglacial in accordance with predictions of the coevolutionary disequilibrium model. In addition to changes in diet, these ungulates, specifically the equid species, show increased levels of enamel hypoplasia during the postglacial, indicating higher levels of systemic stress, a result that is consistent with the models tested and with other climate-based extinction models. The extent to which the increase in systemic stress was detrimental to equid populations remains to be further investigated, but suggests that environmental changes during the late Pleistocene significantly impacted North American equids.

It was once thought that the endemic carnivorous mammals of South America, the metatherian sparassodonts, were driven extinct by North American carnivorans through competitive exclusion. However, sparassodonts went extinct before most groups of carnivorans entered South America; only the endemic Cyonasua-group procyonids (Cyonasua and Chapalmalania), which immigrated to South America nearly 4 million years earlier than other carnivorans, significantly overlapped with sparassodonts in time. In this study, we examine the functional morphology of the dentition of Cyonasua and Chapalmalania through quantitative analysis to determine the dietary habits of these taxa and the degree to which they may have ecologically overlapped sparassodonts and large predatory Neogene didelphimorphians. We find Cyonasua and Chapalmalania to be more carnivorous than extant procyonids, other than Bassariscus, in agreement with previous studies, but more omnivorous than most other carnivorans and all meat-eating South American metatherians, including sparassodonts. The extreme ecological dissimilarity between Cyonasua-group procyonids and members of the endemic South American predator guild may explain why procyonids were able to successfully establish themselves in South America several million years earlier than most other northern mammals (including all other carnivorans): they moved into a previously unoccupied ecological niche (large omnivore) and avoided direct competition with incumbent native species, a situation similar to that documented in historical cases of biological invasion. The omnivorous diets and climbing/swimming abilities of procyonids may have increased their chances for a successful over-water dispersal relative to other carnivorans, further favoring their successful establishment in South America.

Models for the areal distribution of marine animals may be formulated in such a way that their validity can be tested statistically. Five such models are described here: in each case the distributions of the individual taxa are made functions of depth of water, oceanicity, and substrate type.

The simplest model proposes that benthic species are substrate-dependent: it can be verified by a series of χ2 tests. Benthic species can also be seriated along an environmental gradient: this second model can be tested by using a Monte Carlo simulation procedure. The third model proposes that planktic species are to some degree stratified in the water column, and hence that their remains are distributed additively in the underlying sediments: tests on modern and sub-fossil data sets indicate that realistic versions of this model are probably valueless for most geological work. The final models are extensions of the additive model: they are used here to demonstrate the importance of selecting an appropriate model and, in particular, of knowing the mode of life of each species before the model is selected.

Death assemblages that occupy the upper tens of centimeters of sediment in shallow-marine settings are often subject to extensive mixing, thereby limiting their usefulness in assessing environmentally mediated compositional changes through time in the local biota. Here, we provide evidence that dense, Thalassia-rich seagrass beds preserve a stratigraphic record of biotic variation because their dense root–rhizome mats inhibit mixing. We sampled benthic mollusk assemblages at seven localities in Thalassia-rich beds around St. Croix, USVI, collecting three separate sediment intervals of ~13 cm each to a total depth of ~40 cm below the sediment–water interface, and found evidence that sedimentary intervals preserved compositional stratigraphy. Further, some localities displayed systematic, directional changes down-core. An examination of interval-to-interval changes in composition revealed that compositional variation was unique from locality to locality rather than reflecting coordinated, island-wide transitions. In general, however, relative abundances of epifaunal gastropods and small lucinid bivalves tended to decrease with depth below the sediment–water interface. Quantitative comparisons of life-to-death assemblages from each successive sedimentary interval demonstrated that the shallowest death assemblages were typically more similar to the life assemblages than were deeper assemblages, suggesting that deeper intervals provide records of earlier community states.

Constraint is a universal feature of morphological evolution. The vertebral column of synapsids (mammals and their close relatives) is a classic example of this phenotypic restriction, with greatly reduced variation in the number of vertebrae compared with the sauropsid lineage. Synapsids generally possess only three sacral vertebrae, which articulate with the ilium and play a key role in locomotion. Dicynodont anomodonts are the exception to this rule, possessing seven or more sacral vertebrae while reaching a range of body sizes rivaled among synapsids only by therian mammals. Here we explore the evolution of this unusual sacral morphology in dicynodonts by (1) hypothesizing homologies of the additional sacral vertebrae, (2) using ancestral state reconstruction and phylogenetic regressions (e.g., logistic regression, Poisson regression) to track the coevolution of sacral count and body size, and (3) proposing mechanisms by which additional sacral vertebrae were incorporated during dicynodont evolution. We find that sacral vertebral morphology covaries with sacral count in consistent ways across dicynodonts, implying that sacra with a given number of vertebrae are composed of homologous elements. There is a correlation between increased sacral count and larger body size, especially at the shift from four to five sacrals near the origin of Bidentalia. Based on position, morphology, and the consistent number of presacral vertebrae among dicynodonts, we hypothesize that the additional sacrals anterior to the plesiomorphic three are duplications of the first sacral, and that a single caudosacral was incorporated by a shift in the identity of the anteriormost caudal vertebra. Although changes in sacral count appear to be correlated with shifts in body size in dicynodonts, the evolution of general morphological conservativism in the synapsid sacrum remains to be further explored.

A submarine cave is a unique environment that is dark, food limited, semi-isolated from the outside, and sheltered from wave action. However, our knowledge of the long-term change in submarine-cave ecosystems remains limited. We document here the community-scale responses toward long-term change in a submarine cave, Daidokutsu in Okinawa in southern Japan. Using both metazoans (ostracods and bivalves) and protozoans (larger benthic foraminiferans) in two sediment cores obtained from the cave, we reconstruct the faunal and diversity changes of the past 7 Kyr. All taxonomic groups showed long-term, gradual linear change of faunal composition from predominantly open-water taxa to predominantly cave taxa, and ostracods showed short-term variability of species diversity. The long-term faunal trend probably reflects gradual isolation of the cave ecosystem due to coral reef development (i.e., development of the cave ceiling) during periods of the Holocene transgression and subsequent sea-level highstand. The short-term diversity changes show substantial similarity to centennial- to millennial-scale Holocene Asian monsoon variability. Ostracod species diversity peaks tend to correspond with periods of strong East Asian winter monsoons. The results indicate that limestone submarine-cave ecosystems, an important cryptic habitat, developed gradually during the Holocene and may be sensitive to rapid climate changes.

Farming is a behavior in which an organism promotes the growth and reproduction of other organisms in or on a substrate as a food source. A number of trace fossils have been suggested to record the occurrence of farming behavior. These include the deep-sea graphoglyptid trace fossils, proposed to be microbial farms on the seafloor, and terrestrial fossil social insect nests thought to represent fungicultural behavior. The presumed farming behavior of graphoglyptids is the basis of the ethological category agrichnia. Four criteria have been proposed as diagnostic of farming behavior, and these can be applied to both observed modern and proposed trace fossil examples of farming behavior. The evidence for farming behavior in the social insect trace record is strong but is much weaker in the case of graphoglyptids. The use of agrichnia as an ethological category should be limited to well-supported cases.

Intrinsic features of organisms, such as morphology or DNA sequences, and the stratigraphic occurrence of fossils provide distinct evidence of the phylogenetic history of life. Because there is only one true history, we expect the historical signals preserved by these data sets to be similar, and several metrics have been developed to measure the fit of phylogenetic hypotheses to the fossil record. However, a variety of biases affect these metrics, and it is unclear whether they can provide more than an estimate of whether one tree fits the fossil record better than another when used on their own. Here we explore two novel applications of stratigraphic fit metrics when they are used with a combination of phylogeny reconstruction methods that do and do not directly include stratigraphic occurrence data (e.g., cladistics and stratocladistics). In particular, we are interested in whether differences in the stratigraphic fit of cladistic and stratocladistic trees can be used to identify cases in which the stratocladistic results are likely to be more accurate, as well as whether such differences can be used to identify potential problems in the underlying data sets.

Using 550 simulated data sets that were analyzed with cladistics and stratocladistics, we found that the absolute difference in fit to stratigraphy between the results of the two methods was strongly correlated with the probability of character state transition and the accuracy of the stratocladistic results relative to the cladistic results. Completeness of the fossil record and number of taxa included in the analysis were more weakly correlated with stratigraphic fit, and the statistical significance of the differences in fit between the two sets of results did not show a meaningful relationship with improvements in accuracy or potential data problems. These results suggest that measuring the difference in stratigraphic fit between cladistic and stratocladistic trees might be useful for qualitatively estimating whether the addition of stratigraphic data benefited a phylogenetic analysis, and for identifying data sets with high average rates of character state change.