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.

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.

Northern Appalachian Basin deposits and associated fossils have served as exemplars for ecological-evolutionary investigations, and as the reference interval for the concept of coordinated stasis. Here, we examine faunal and environmental changes within the uppermost Hamilton and lowermost Genesee Groups of the late Middle Devonian succession of New York State. Dramatic diversity loss, faunal migrations, and ecological restructuring recognized in these strata have been used previously to define the end of the Hamilton ecological-evolutionary subunit, and, furthermore, these strata and corresponding faunal changes represent the type region for the global Taghanic Biocrisis. We present and analyze a new, high-resolution data set of post-Taghanic Genesee fossil assemblages, in which we recognize 11 biofacies corresponding to an onshore-offshore (depth) gradient. The Genesee Fauna shows an unexpectedly high taxonomic similarity to nearshore biofacies of the pre-Taghanic Hamilton Fauna, related to the persistence of siliciclastic-dominated nearshore settings through the Taghanic Biocrisis, whereas the onset of anoxic/dysoxic conditions typified offshore portions of the environmental gradient. The “Nearshore Refugium Model” of Erwin offers a possible explanation for the persistence of taxa through the biocrisis in nearshore settings. This constriction was followed by subsequent expansion of these residual taxa to offshore environments in relatively similar associations, as increased Acadian orogenic activity and resultant delta progradation increased habitable space offshore by decreasing the extent of deeper-water, oxygen-poor settings. Although taxonomic similarity was high between the Hamilton and Genesee Faunas, biofacies structure differed primarily because of tectonically driven physical transformations to the basin and associated biotic turnover. Nevertheless, the combination of high taxonomic persistence of Hamilton nearshore taxa and the introduction of relatively few new taxa in the Genesee Fauna resulted in a taxonomic holdover that was much higher than observed in the original formulation of coordinated stasis.

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 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.

Understanding spatial variation in origination and extinction can help to unravel the mechanisms underlying macroevolutionary patterns. Although methods have been developed for estimating global origination and extinction rates from the fossil record, no framework exists for applying these methods to restricted spatial regions. Here, we test the efficacy of three metrics for regional analysis, using simulated fossil occurrences. These metrics are then applied to the marine invertebrate record of the Permian and Triassic to examine variation in extinction and origination rates across latitudes. Extinction and origination rates were generally uniform across latitudes for these time intervals, including during the Capitanian and Permian–Triassic mass extinctions. The small magnitude of this variation, combined with the possibility of its attribution to sampling bias, cautions against linking any observed differences to contrasting evolutionary dynamics. Our results indicate that origination and extinction levels were more variable across clades than across latitudes.

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.

The Cambrian information revolution describes how biotically driven increases in signals, sensory abilities, behavioral interactions, and landscape spatial complexity drove a rapid increase in animal cognition concurrent with the Cambrian radiation. Here, we compare cognitive complexity in Cambrian and post-Cambrian marine ecosystems, documenting changes in animal cognition after the initial Cambrian increase. In a comparison of Cambrian and post-Cambrian Lagerstätten, we find no strong trend in the proportion of genera possessing two types of macroscopic sense organs (eyes and chemoreceptive organs such as antennae, feelers, or nostrils). There is also no trend in general nervous system complexity. These results suggest that sophisticated information processing was already common in early Phanerozoic ecosystems, comparable with behavioral evidence from the trace fossil record. Most taxa capable of complex information processing in Cambrian ecosystems were panarthropods, whereas mollusks and chordates made up larger proportions afterward. In both the Cambrian and the present day, ecological occupation of diverse habitat tiers and feeding modes is possible with even simple nervous systems, but ecological lifestyles requiring rapid, regular movement are almost exclusively associated within brain-bearing taxa, suggesting a connection with fast information-processing abilities and bodily responses. The overall rise in cognitive sophistication in the Cambrian was likely a unique event in the history of life, although some lineages subsequently developed more elaborate sensory systems and/or larger brains.

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.

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.

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.

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.

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.

Clymeniid ammonoids appeared during the Late Devonian (Mid-Famennian) and quickly radiated before becoming extinct at the Devonian/Carboniferous boundary. Outwardly indistinguishable from other ammonoids, clymeniids are distinguished internally by their dorsal siphuncle, contrasted to a ventral siphuncle in almost all other ammonoids. Comparisons of a sample of Clymeniida (n = 22 genera), Goniatitida (n = 33), Prolecanitida (n = 12), and Anarcestida (n = 13) indicate that clymeniids fall within the range of other ammonoids in terms of shell geometry and suture complexity, but their siphuncles average two to three times larger and clymeniid shells are approximately 33% thicker than those of other ammonoids. Although a dorsal siphuncle would be about 50% smaller in surface area and volume than if located in a ventral position, the enlarged clymeniid siphuncle partially and, in some cases, fully compensated for this loss. Hydrostatic simulations of 15 clymeniid genera indicate that their thicker (therefore heavier) shells would have resulted in relatively short body chambers (≈280°) and high aperture orientations (≈90°). In static life-position, these orientations would have placed the dorsal clymeniid siphuncle at or near the bottom of the most recently formed chambers, seemingly an ideal location for draining liquid from the chamber. Migration of the siphuncle to the dorsal side of the shell occurs suddenly during early ontogeny (within the first two or three chambers), and mutation of homeotic gene expression is offered as a possible explanation for the sudden shift. A dorsal siphuncle may have resulted in selection for enlarged siphuncles, but this may have incurred loss of strength against hydrostatic pressure (thereby reducing depth limits) and thus rendered the clade more susceptible to the multiple eustatic and anoxic events that marked the end of the Devonian.

Biodiversity hotspots are increasingly recognized as areas of high taxonomic and functional diversity. These hotspots are dynamic and shift geographically over time in response to environmental change. To identify drivers of the origin, evolution, and persistence of diversity hotspots, we investigated the diversity patterns of reef-building corals (Scleractinia) in the Central Indo-Pacific, a marine biodiversity hotspot for the last 25 Myr. We used the scleractinian fossil record (based on literature and a newly acquired fossil collection) to examine the taxonomic and functional diversity of corals from the Eocene to Pliocene. Our data identify potential drivers of coral diversity through time (and space) in the Central Indo-Pacific by constraining the timing of taxonomic turnover events and correlating them with known environmental changes. Increases in taxonomic diversity, high origination rates, and changes in abundance of functional character states indicate that the origin of the Central Indo-Pacific hotspot occurred during the Oligocene, initially through proliferation of pre-existing taxa and then by origination of new taxa. In contrast to taxonomic diversity, overall functional diversity of Central Indo-Pacific reef-building corals remained constant from the Eocene to the Pliocene. Our results identify global sea level as a main driver of diversity increase that, together with local tectonics, regulates availability of suitable habitats. Moreover, marine biodiversity hotspots develop from both the accumulation of taxa from older biodiversity hotspots and origination of new taxa. Our study demonstrates the utility of a combined literature-based and new collection approach for gaining new insights into the timing, drivers, and development of tropical biodiversity hotspots.

The excellent fossil record of the past few million years, combined with the overwhelming similarity of the biota to extant species, provides an outstanding opportunity for understanding paleoecological and macroevolutionary patterns and processes within a rigorous biological framework. Unfortunately, this potential has not been fully exploited because of lack of well-sampled time series and adequate statistical analysis. Nevertheless, four basic patterns appear to be of general significance. First, a major pulse of extinction occurred 1–2 m.y. ago in many ocean basins, more or less coincident with the intensification of glaciation in the Northern Hemisphere. Rates of origination also increased greatly but were more variable in magnitude and timing. The fine-scale correlation of these evolutionary events with changes in climate is poorly understood. Similar events probably occurred on land but have not been tested adequately. Second, rates of origination and extinction in the oceans waned after the pulse of extinction, especially during the past 1 m.y. Thus, most marine species originated long before the Pleistocene under very different environmental circumstances, suggesting that they are “exapted” rather than adapted to their present ecological circumstances. The same may be true for many terrestrial groups, but not for the mammals or fresh-water fishes that have continued to undergo speciation throughout the Pleistocene. Third, community membership of late Pleistocene coral reef communities was more stable than expected by chance. These are the only paleoecological data adequate to test hypotheses of community stability, so that we do not know whether community structure involving other taxa or environments typically reflects more than the collective behavior of individual species distributions. Regardless, the strong evidence for nearly universal exaptation of ecological characteristics argues strongly against ideas of coevolution of species in communities. Finally, ecological communities were profoundly altered by human activities long before modern ecological studies began. Holocene paleontological, archeological, and historical data constitute the only ecological baseline for “pristine” ecological communities before significant human disturbance. Holocene records should be much more extensively used as a baseline for Recent ecological studies and for conservation and management.

Paleoecological studies enhance our understanding of biotic responses to climate change because they consider long timescales not accessible through observational and experimental studies. Using predatory drillholes produced on fossil bivalve shells by carnivorous gastropods, we provide an example of how climate change affected predator–prey interactions. We quantitatively examine temporal changes in fossil molluscan assemblages and predation patterns from the Pleistocene Japan Sea, which experienced drastic environmental changes in relation to glacial–interglacial climate cycles. We found significant changes in predation patterns associated with a decline in the abundance of warm-water molluscan species. Climate-mediated fluctuations in the eustatic sea level and resultant weakening of the Tsushima Warm Current caused a decline in a warm-water shell-drilling predator, which moderated the predation pressure and size relationship between the predators and the bivalve prey. Our results indicate that climate-mediated range shifts of species in present-day and future marine ecosystems can likewise increase altered predator–prey interactions.

Feeding behaviors may differ between past and current predators due to differences in the environments inhabited by these species at different times. We provide an example of this behavioral variability in spotted hyena (Crocuta crocuta), for which our analysis of a late Pleistocene micromammal assemblage indicates that hyenas preyed upon small rodents, a feeding habit that is rarely observed today among hyenas.

The Bois Roche cave site is situated at the edge of a low bluff overlooking the floodplain of a small stream in Cherves-Richemont (Charente, France). The deposits are dated by electron spin resonance (ESR) to about 69.7 ± 4.1 Ka. Excavations at the site recovered fossil bones and teeth of large and small mammals, together with hyena coprolites. Water screening of the sediments produced large accumulations of rodent remains with low taxonomic diversity. Small mammal bones were recovered from hyena coprolites as well. Descriptions of small mammal bone modification, both from the sediments and coprolites, are reported here. The analysis yielded a distinct taphonomic pattern representative of large carnivores (over 30 kg), which differs from any other modern or fossil predator-accumulated microfaunal assemblage taphonomically analyzed to date. To our knowledge, previous studies of hyena diet have not recorded high concentrations of a single-rodent prey species. We conclude that the low species diversity of this small mammal assemblage most likely relates to a local abundance of the prey species due to an outbreak in the rodent population, rather than from specialist predator behavior and hunting technique.