The Late Neogene vertebrate fossil record from Yushe Basin presents multiple, superposed assemblages from a single area, spanning roughly the interval of 6–2 Ma. Both large and small mammals show peak species richness in the middle Pliocene but indicate relative faunal stability throughout the Pliocene. Large mammals show turnover, especially extinction, around 5 and 2.5 Ma. Small mammals indicate change (over half of the species and several genera), as well as turnover at the species level, between 4 and 3.4 Ma. The loosely controlled dating of these events does not disprove hypothetical correlation with events in North America and with global climatic shifts. Elements that lack Yushe antecedents, some being long-distance dispersers, appear throughout the section, but with little effect on the resident assemblage. First records of well-documented immigrants (from North America, Europe, Africa, southern Asia, or high latitudes) generally do not coincide with ecomorph extinctions. Early Pliocene exchange between Asia and North America appears to have been balanced in both directions and involved a small proportion of the fauna. Immigration probably was opportunistic and contributed to faunal enrichment. We interpret the Yushe Pliocene mammalian assemblages as representing a fauna that was stable from ca. 5 to 2.5 Ma and changed mainly by additions and congeneric species substitutions.

Methods currently used to estimate taxonomic extinction probabilities from fossil data generally assume that the probability of encountering a specimen in a particular stratum, given that the taxon was extant in the time period and location represented by the stratum, either equals 1.0 or else is a constant for all strata. Methods used to estimate taxonomic diversity (number of taxa) and speciation rate generally assume that encounter probabilities equal 1.0. We suspect that these assumptions are often false. Capture-recapture models were historically developed for estimation in the face of variable and unknown sampling probabilities. These models can thus be used to estimate parameters of interest from paleobiological data when encounter probabilities are unknown and variable over time. These models also permit estimation of sampling variances, and goodness-of-fit tests are available for assessing the fit of data to most models. Here we describe capture-recapture models which should be useful in paleobiological analyses and discuss the assumptions which underlie them. We illustrate these models with examples and discuss aspects of study design. We conclude that these models should prove useful in paleobiological analyses.

Studies in the past 20 years have often interpreted size fluctuations in fossil mammal remains as a response to climatic change, in accord with Bergmann's rule. However, such paleoecological inference requires careful consideration of changes in community composition that could cause ecological character displacement or release. Recent size gradients of mammals should be screened for the possibility of character displacement if fossil size gradients are to be used as a “paleothermometer” for past climate. The use of teeth in paleontological studies as a measure of body size presents a further complication; for several carnivore guilds, it appears that competitive pressures act most strongly on tooth size. Teeth may therefore inaccurately estimate body size, even if body size accurately indicates climatic conditions. In the fossil record different species exhibit different size patterns under the same conditions of climatic change, and the same species may show diametrically opposite size fluctuations under similar conditions of climatic change, in different regions.

The morphologic radiation of Early Jurassic ammonites following the near extinction at the end of the Triassic is analyzed from 436 species of 156 genera that form a representative sample of morphs occurring worldwide in the first three stages of the Jurassic (Hettangian, Sinemurian, Pliensbachian: 36 subzones, 24 m.y.). Morphologic diversity is analyzed independently of taxonomy by processing 18 shape parameters using multivariate analysis and clustering techniques. The morphospace thus defined indicates that morphs fall readily into two groups made up of four and five adjacent morpho-subsets. The temporal pattern of morphospace occupation in the 36 Lower Jurassic subzones displays diversification, depletion (sometimes total), and displacement of successive parts of the morphospace, reflecting a complex history in which morphologic radiation appears to be more than a process of diffusion. The history of the morphologic evolution is tentatively related to sea-level changes and there is a suggestion that morphologic diversity increases during second-order transgressive periods.

Principal components analysis of Upper Carboniferous (Pennsylvanian) ammonoids (all 117 genera), using 21 variables to measure shell geometry, sculpture and suture complexity, shows that following a sharp decline (∼30%) in generic diversity after the mid-Carboniferous boundary, seven morphotypes persisted throughout the Pennsylvanian (ca. 30 m.y.). Six of these were polyphyletically adopted at different times, while the seventh was monopolized by the prolecanitids, a group whose evolution accelerated during the Pennsylvanian and later gave rise to Mesozoic ammonoids. Innovations in suture geometry distinguished at least 17 of 39 (44%) Pennsylvanian ammonoid families. Average suture complexity increased almost threefold; this was achieved by various methods (lobe serration, insertion of umbilical elements, prong subdivision, lobe trifurcation, and secondary bifurcation), which were recurrent and crossed morphotype boundaries. The Pennsylvanian record supports suggestions that Paleozoic ammonoids were confined to a certain suite of basic shell geometries, showing preference for a limited number of sites in the spectrum of available morphospace. However, these morphic constraints did not, with one possible exception (the prolecanitids), control the emergence of increasing sutural complexity during the Pennsylvanian, which occurred among different lineages in all seven morphotypes.

Cutan, a resistant non-hydrolyzable aliphatic biopolymer, was first reported in the cuticle of Agave americana and has generally been considered ubiquitous in leaf cuticles along with the structural biopolyester cutin. Because leaves and cuticles in the fossil record almost always have an aliphatic composition, it was argued that selective preservation of cutan played an important role in leaf preservation. However, the analysis of leaves using chemical degradation techniques involving hydrolysis to test for the presence of cutan reveals that it is absent in 16 of 19 taxa (angiosperm and gymnosperm), including many previously reported to contain cutan on the basis of pyrolysis data. Cutan is clearly much less widespread in leaves than previously thought, and its presence or absence does not exert any major bias on the preservation of leaves in the fossil record. In the absence of cutan, other constituents—cutin, plant waxes, and internal plant lipids—are incorporated into the geomacromolecule and contribute to the formation of a resistant aliphatic polymer by in situ polymerization during diagenesis.

New evidence from fossil plants at the Middle Miocene fossil quarry near Fort Ternan, Kenya, together with that from paleosols, allow reconstruction of a mosaic of early successional woodland (on Dhero paleosols), grassy woodland (on Chogo clay eroded phase and ferruginized nodule variant paleosols) and wooded grassland (on type Chogo and Onuria clay paleosols). This grassy open vegetation was on a high plateau of phonolite at the foot of a carbonatite-nephelinite stratovolcano, which probably supported dry Afromontane forest, alpine meadows, and marsh. This earliest savanna-mosaic vegetation yet documented from Africa, was probably recruited from dry lateritic soils elsewhere in Africa during climatic drying and cooling some 15 Ma. These early grassland ecosystems were very different from Early Miocene forest ecosystems of East Africa, but not altogether like modern grasslands either. Already present were grasses with dense growth and rich in silica bodies, and abundant antelope with moderately high crowned teeth and cursorial limb structure. These mammalian adaptations to grasslands, however, were not nearly so pronounced as they are in modern African grassland faunas, which include zebra and other Asiatic immigrants, as well as antelope. Grasses of the subfamily Chloridoideae and supertribe Panicanae were common in tropical Africa by Middle Miocene time, if not much earlier, but there is not yet evidence so far back in time for the grass supertribe Andropogonae which is now dominant in seasonally arid, overgrazed, and burned African grasslands.

The post-Paleozoic radiation of echinoids entailed a rapid diversification not only of adult morphology, but also of larval morphology. The timing, order, and phylogenetic distribution of evolutionary transformations in echinopluteus larvae are reconstructed here under maximum parsimony assumptions from a large neontological data base. Many echinoid larval apomorphies apparently evolved within the Paleozoic stem lineage and were subsequently retained during much of the crown-group radiation. This suite of apomorphies includes most (and perhaps all) of the skeletal elements and some features of soft anatomy such as vibratile lobes. Other features apparently arose or were modified during the post-Paleozoic radiation. These include skeletal features such as arm-rod structure and length, and soft structures such as epaulettes and skeletal muscles. Transformational hypotheses of this kind can be supported or rejected with further neontological data, and many can potentially be tested from fossil evidence. Many post-Paleozoic transformations in echinopluteus structure may be adaptive. For example, increases in arm length and flattening of arm ectoderm may increase feeding rate and efficiency, and both types of transformation have occurred several times within the crown group. Relational hypotheses of this nature can be tested through comparative functional studies in extant echinoplutei. Parallel evolutionary losses of feeding in echinoplutei are accompanied by loss or modification of characteristic structures. This suggests that developmental constraints do not fully explain the conservation of these structures in planktotrophic echinoplutei. Comparisons of larval and adult morphology over congruent time intervals demonstrate that the origin of many orders was accompanied by a suite of synapomorphies in larval morphology that was subsequently conserved. Many details of echinopluteus morphology are therefore of taxonomic significance. Intraordinal patterns of larval diversity, however, vary considerably. That larval morphology has diversified independently of adult morphology indicates that mosaic evolution has occurred within the life cycle and suggests that echinoid larvae and adults can and do respond to selection independently. Taken together, these findings underscore the complex ways in which complex life cycles can evolve.

If the dinosaurs Protoceratops grangeri and Hypselosaurus sp. grew at rates predicted for their body size from extant reptiles, their expected ages at reproductive maturity would be about 20 and 62 yr respectively. This calculation assumes that dinosaurs grew at ectothermic rates which are about an order of magnitude slower than those of endothermic vertebrates of the same body size. Such delayed reproductive maturity may have set a premium on selection for high juvenile survivorship that is reflected in the relatively large eggs of these dinosaurs and in their only moderately large clutch sizes compared to modern reptiles.

Synapsids dominated the terrestrial realm between the late Pennsylvanian and the Triassic. Their early evolution includes some of the first amniotes to evolve large size, herbivory, and macro-predators. However, little research has focused on the changes in diversity occurring during this early phase in their evolutionary history, with more effort concentrating on later events such the Permo-Triassic extinction. Here we assess synapsid diversity, at both the species and genus levels, between the Carboniferous (Moscovian) and the Middle Permian (Capitanian). A raw, taxic diversity (richness) estimate is generated, and we use two separate methods to correct for sampling biases in this curve. To remove the effect of anthropogenic sampling bias, we apply a recently published modification of the residual diversity method, and then generate a supertree, using matrix representation with parsimony to infer ghost lineages and obtain a phylogenetic diversity estimate. The general diversity pattern reflects the initial diversification of synapsids in the late Pennsylvanian and early Cisuralian, which was followed by an extinction event during the Sakmarian. Diversity recovered during the Artinskian and Kungurian, coinciding with the radiation of Caseidae, although other families begin to decline. A second extinction event occurred across the Kungurian/Roadian boundary, in which Edaphosauridae and Ophiacodontidae died out although Caseidae and Therapsida diversified. The sampling-corrected curves reveal further extinction during the Roadian, although therapsids were again unaffected. Pelycosaurian-grade synapsids survived during the Wordian and Capitanian, but were a minor part of an otherwise therapsid-dominated fauna. Evidence of significant anthropogenic sampling bias calls into question previous diversity studies that have not employed sampling correction.

Three closely related species of the irregular echinoid Oligopygus succeed one another in the late Eocene deposits of Florida. This apparent lineage, where each species is similar but larger than the preceding species, offers an excellent opportunity to examine relationships between heterochrony and environmental change. Bivariate and multivariate techniques illustrate patterns of simple and complex allometry and indicate that simple size increase related to changes in the timing of maturation account for most of the morphological differences among species. Those differences that are not the by-products of size increase are due to heterochronic changes dissociated from the otherwise global (i.e., whole organism) hypermorphosis and were probably needed to increase the relative food intake of the larger forms. Unlike the vast majority of allometric studies, which show constant growth ratios, the ontogenies analyzed here often exhibit curvilinear trajectories. Thus, heterochronic events are seen as systematic alterations of already changing growth ratios. It is suggested that these heterochronic changes provided quick, efficient responses to selective pressures on a plurality of characters and behaviors. As the Florida carbonate environment became more stable, responses associated with K-type life history strategies were favored, resulting in “size selection.” Thus, the morphological differentia among these species may not have resulted from selection directed at those traits, but were either simple sequelae of size increase or of changes which occurred to permit the size increase.

The variation in time-averaging between different types of marine skeletal accumulations within a depositional system is not well understood. Here we provide quantitative data on the magnitude of time-averaging and the age structure of the sub-fossil record of two species with divergent physical and ecological characteristics, the brachiopod Bouchardia rosea and the bivalve Semele casali. Material was collected from two sites on a mixed carbonate-siliciclastic shelf off the coast of Brazil where both species are dominant components of the local fauna.

Individual shells (n = 178) were dated using amino acid racemization (aspartic acid) calibrated with 24 AMS radiocarbon dates. Shell ages range from modern to 8118 years b.p. for brachiopods, and modern to 4437 years for bivalves. Significant differences in the shape and central tendency of age-frequency distributions are apparent between each sample. Such differences in time-averaging magnitude confirm the assumption that taphonomic processes are subject to stochastic variation at all spatial and temporal scales. Despite these differences, each sample is temporally incomplete at centennial resolution and three of the four samples have similar right-skewed age-frequency distributions. Simulations of temporal completeness indicate that samples of both species from the shallow site are consistent with a more strongly right-skewed and less-complete age-frequency distribution than those from the deep site.

We conclude that intrinsic characteristics of each species exert less control on the time-averaging signature of these samples than do extrinsic factors such as variation in rates of sedimentation and taphonomic destruction. This suggests that brachiopod-dominated and bivalve-dominated shell accumulations may be more similar in temporal resolution than previously thought, and that the temporal resolution of multi-taxic shell accumulations may depend more on site-to-site differences than on the intrinsic properties of the constituent organisms.

The fundamental goal of biochronology is ordering taxonomic first and last appearance events. The most useful biochronologic data are of the form “the first appearance event of one taxon predates the last appearance event of a second taxon” (FAE < LAE). FAE < LAE data sets are unusually reliable because they converge on a unique solution with greater sampling. The fact that the FAE of one taxon i < the LAE of another taxon j always can be inferred either if i is found lower than j in a stratigraphic section, or if i and j co-occur in at least one taxonomic list. Thus, FAE < LAE data accurately synthesize two disparate sources of information: routine biostratigraphic observations and taxonomic lists that may have no stratigraphic context. Appearance event ordination, the new method introduced here, is intended to summarize FAE < LAE data. The algorithm is founded on the following parsimony criterion: arrangements of FAEs and LAEs should always imply FAEi < LAEj when this is known, and otherwise imply LAEj < FAEi whenever possible. The technique differs from others related to correspondence analysis in its use of FAE < LAE data and explicit definition as a parsimony method. The algorithm is even more unique in that it uses different subsets of FAEi < LAEj statements at each iterative step, converging on separate sets of scores for the FAEs and LAEs. After arranging either the FAEs or the LAEs on the basis of their scores, the other set of scores can be discarded and the best arrangement of the remaining events can be inferred directly. An analysis of the Plio-Pleistocene mammalian record in the Lake Turkana region is used to illustrate the method. Biochronologic resolution on the order of 0.2-1.5 m.y. is achieved. The Turkana species lists by themselves demonstrate enough FAEi < LAEj relationships to resolve the basic biochronologic pattern, but stratigraphic information is still of great use.

Since David Raup's seminal 1976 work, paleontologists have been aware of the relationship between outcrop area and diversity. By incorporating lithologic data derived from Alexander Ronov and coworkers into our own data on areas of mapped outcrops from worldwide geologic maps, we are able to establish a quantitative connection between area of sedimentary rock exposure and diversity from the same general depositional environments. Significant power-law relations are observed at both global and continental scales of consideration. The addition of data on areas of habitable area estimated from paleogeographic maps does not substantially affect these correlations between outcrop area and diversity, indicating that the relation between outcrop area and diversity is primarily a function of sampling and not a common cause such as sea level. We observe a significant diversity-area effect, first noted by Jack Sepkoski in the marine realm. Unlike Sepkoski's, however, our diversity-area effect appears to play a substantial role in influencing diversity through time; a true global diversity signal appears to be contained in the rock record despite the impacts of variable sampling.

Greater outcrop area can serve to increase estimated diversity by increasing both the sample size and the range of habitats and biogeographic provinces sampled. After standardizing for pure sampling intensity by rarefying the number of taxon occurrences, outcrop area continues to explain a substantial portion of global marine diversity. This indicates that coverage, or sampling from multiple habitats and biogeographic provinces, is even more important than sampling intensity. If we remove the effect of outcrop area from our estimate of global biodiversity, we do not observe a net increase in diversity toward the present, lending support to other studies that have not supported a substantial, long-term global increase in biodiversity during the Phanerozoic.

Differences in the larval ecology of Ordovician trilobites directly influenced the outcome of the Ashgill extinction (latest Ordovician) and indirectly governed the pattern of evolution in post-Ordovician trilobites. Larval ecology also affected survivorship patterns within the Ordovician, particularly between the Llandeilo and the Caradoc stages. All taxa with pelagic adults became extinct by the end of the Ordovician. Similarly, trilobites with entirely planktonic larvae had all but disappeared by the end of the Ordovician. Although suffering a significant loss in diversity, taxa with benthic larvae provided the ancestral stock for the majority of post-Ordovician lineages. Trilobites with a two-stage protaspid period (single planktonic followed by benthic larvae) suffered least during the Ashgill extinction, giving rise to approximately 23% of the new genera appearing in the early Silurian.

Patterns of extinction/survivorship among trilobite taxa with different developmental strategies indicate that the so-called Ashgill extinction was most likely the result of a composite phenomenon, including environmental perturbations, ecosystem breakdown and biogeographic restriction, and was not the consequence of a single catastrophic event (e.g., bolide collision). Indeed, our results are consistent with extinction models which invoke periodic global cooling and sea level regression associated with glaciation. Taxa with planktonic larvae first suffered a marked decline in diversity between the Llandeilo and the Caradoc (end of Middle Ordovician), coincident with the onset of the Ordovician-Silurian glaciation. During this time interval, the paleogeographic ranges of most surviving genera with solely planktonic larvae were severely constricted to lower latitude paleobiogeographic provinces. During the Ashgill (Rawtheyan to Hirnantian), climatic and sea level fluctuations were most extreme because of continued and more extensive glaciation. At this time, when extinctions were particularly severe, there was also a significant effect upon the survivorship of taxa with benthic larvae.

Our results indicate that the proportion of the life cycle spent in the water column, dependent upon a planktonic food source, was a critical factor in the survivorship of trilobite taxa during Middle to Late Ordovician time. Consequently, differences in life history patterns predisposed individual taxa to survival or extinction.

Two kinds of adaptation aid infaunal bivalve mollusks in sustaining their life positions against potentially disruptive water movements: (1) ability to retard scour of surrounding sediment and (2) ability to reburrow rapidly if exhumed.

The shell of the venerid Anomalocardia brasiliana is ornamented with concentric ridges that are asymmetrical in cross-section; experiments show that these ridges aid the animal in burrowing by gripping the sediment during backward rotation of the shell. The shell of the less deeply burrowing venerid Chione cancellata also bears concentric ridges, but these are symmetrical and experiments show that they hinder burrowing; other experiments demonstrate that these ridges reduce scour of sand from around a partly exposed animal. The single cardiid species Trachycardium egmontianum possesses adaptations comparable to those of the two venerid species, in the form of spines of two varieties; experiments show that the flared anterior spines facilitate burrowing and the cupped posterior spines reduce scour.

Conspicuous ornamentation of the kinds considered here was rare throughout the Paleozoic. Its evolutionary deployment occurred primarily during the post-Paleozoic adaptive diversification of infaunal bivalves, which was triggered by the evolution of efficient burrowing mechanisms. The general premium on maintaining infaunal life positions was accentuated for bivalves after the Paleozoic by the origins of important modern predatory taxa.

Although there is extraordinary interest in the quantitative measurement of species diversity, published statements on the behavior of the components of species diversity are contradictory and lead to opposite conclusions. In this paper, we demonstrate that the confusion is due to two key oversights: (1) whether or not biological sampling is carried out within or between communities; and (2) determination of the statistical distribution underlying a biological community, which is crucial for the evaluation of all of the components of diversity measurement.

The problem of sampling “within” a population or community is basically distinct from the equivalent integration of structure and diversity measurement “between” differing multispecies populations. “Within-community sampling” is defined as a set of biological samples from a statistical population that has a particular statistical distribution or a constant value for the associated parameter(s). As the number of individuals increases along with the number of species, for a log series distribution, the diversity measures of Shannon's H, log series or Fisher's α, and Simpson's Index 1/λ remain constant while the evenness measures of Buzas-Gibson's E and Pielou's J decrease. For a log-normal distribution, J will remain constant while E decreases and α, 1/λ, and H increase. No single measure of evenness remains constant over all statistical distributions, so if constancy as a type of independence is required, the appropriate distribution must first be determined. Each species ensemble is mathematically fixed by the applicable statistical distribution.

In contrast, “between-community sampling” is defined as a set of biological samples from different statistical distributions and/or the same distribution with differing parametric values. If sampling is between communities and S increases while the number of individuals remains constant, then all the other measures considered here increase. The exception is the broken stick, for which E remains constant while H, J, α, and 1/λ increase.

Herein we propose and justify the use of the log-series distribution (with regression on the information decomposition equation) as a null model for determination of community structure and demonstrate that the community structure of a Miocene bed at Calvert Cliffs, Maryland, is a log series by use of this new unified methodology.

In phytogeographic data sets, the number of assemblages or floras from each interval may provide a test of the influence of sampling intensity on land-plant diversity. Using a data set of Silurian and Devonian compression-impression plant genera from Laurussia and the Acadian terrain, regression of five measures of land-plant diversity (total diversity, mean genus richness of floras, median assemblage diversity, most diverse assemblage, and standing diversity at interval boundaries) against the number assemblages or floras from thirteen intervals suggests that sampling bias influences all of the diversity measures to some extent, including within-habitat measures. The standing diversity of land plants at interval boundaries, the measure least influenced by sampling (r = 0.65, p = 0.05), increased steadily from the Middle Silurian to the late Givetian/early–middle Frasnian boundary, fell sharply in the early–middle Frasnian and remained low throughout the late Frasnian–middle Famennian. Standing diversity rose dramatically in the late Famennian and Strunian (latest Devonian): the Frasnian–Famennian extinction event may have affected land plants. The standing diversity of Silurian and Devonian microspore genera at interval boundaries mirrors that of compression-impression genera: neither record supports a land-plant diversity equilibrium during the Devonian.

Stage-level range data for 983 Jurassic and Cretaceous ammonite genera, distributed within 83 families, were analyzed by assigning absolute ages to stages or substages. We found ammonite genera to have a mean generic range of 7.3 Myr/ammonite genus. Using a similar methodology, mean generic range per family was also computed. The distribution of long-ranging genera (arbitrarily chosen as those ammonite genera ranging for 12 Myr or more) among families was found to be nonrandom. Instead, long-ranging genera were found to be concentrated in a few families, resulting in significant heterogeneity in the distribution of generic longevities within families (taxotely sensu Raup and Marshall 1980). Although some of the long-ranging genera were found to be morphologically simpler than shorter-ranging genera, others were equally or even more complex, indicating that longevity among ammonite genera is not merely a taxonomic artifact, dependent on degree of differentiable conch morphology. Those Cretaceous families composed of a large number of long-ranging genera were also among the leaders in mean species longevity per family, based on species-level range data for Cretaceous ammonites of the Great Valley Sequence of California. Many of the long-ranging genera and species possess a similar morphologic attribute: siphuncular tubes (connecting rings) of small diameter but high wall thickness.

Hierarchies in natural science are ranked and nested structures such that units at each rank include parts that are units at lower ranks. Hierarchies are able to render complexity tractable, by homogenizing units into collectives and by ordering collectives in ranks of increasing inclusiveness. Hierarchies contrast with positional structures, such as phylogenetic trees, for in trees all positions are occupied by the same sort of entity—there are no ranked collectives—and positions are specified by the order of appearance or precedence of the entities. In hierarchies, interactions within ranks are most important; in trees, sequences of events along branches are of primary concern. As a result hierarchies do, and trees do not, display emergent properties.

The value of the hierarchical structure can be lost when ranks are misspecified. A common error is the use of only a fraction of entities that actually occur in a rank, as when genes are considered as a rank below cells, disregarding the remaining cell contents and rendering the nature of cellular organization moot. Misspecification is also common when attributes or processes are used in ranks without indications of the physical entities to which they refer, thus losing track of the proper composition and ranking of the collectives.