A model is developed to explore the potential responses of paleocommunities to disruptions of primary production during times of mass extinction and ecological crisis. Disruptions of primary production are expected to generate bottom-up cascades of secondary extinction, and these are predictable given species richnesses, functional diversity, and trophic link distributions. If, however, consumers are permitted to compensate for the loss of trophic resources by increasing the intensities of their remaining biotic interactions, top-down driven catastrophic increases of secondary extinction emerge from the model. Both bottom-up and top-down effects are themselves controlled by the geometry of the food webs. The general Phanerozoic trends of increasing taxonomic and ecological diversities, as well as the varying strengths of biotic interactions, have led to food webs of increasing complexity. The frequency of catastrophic secondary extinction increases as food web complexity increases, but increased complexity also serves to dampen the magnitude of the secondary extinctions. When intraguild competitive interactions are included in the model, competitively inferior taxa are observed to possess greater probabilities of survival if the guilds are embedded in simple subnetworks of the overall food web. The result is the emergence of postextinction guilds dominated by those inferior taxa. These results are congruent with empirical observations of “disaster taxa” dominance after some mass extinction events, and provide a mechanism for the reorganization of ecosystems that is observed after those events. The model makes the testable prediction that dominance by disaster taxa, however, should be observed only when bottom-up disruptions have caused ecosystems to collapse catastrophically.

Previous observations about the stable nature of coral-rich assemblages from the Middle Devonian Hamilton Group have led some researchers to invoke the primacy of ecological controls in maintaining biofacies structure through time. However, few analyses have examined the degree to which recurring biofacies vary quantitatively, and none have assessed lateral variability as a benchmark for testing the significance of temporal variability. Thus, the extent to which Hamilton biofacies persist and the mechanism(s) responsible for their hypothesized stability remain contentious. In this study, recurring coral-rich biofacies were evaluated from two stratigraphic horizons within the Middle Devonian Appalachian Basin to examine (1) the extent to which species assemblages persisted within the basin through space and time, and (2) whether ecological interactions may be a plausible mechanism for generating the degree of stasis observed in this case.

Variations in species composition and abundance were examined across multiple spatial scales within both sampled coral-rich horizons. This permitted the establishment of a baseline against which temporal differences in biofacies composition and structure could be evaluated. Although successive coral-rich horizons remained taxonomically stable, their dominance structures changed significantly through the 1.5 Myr study interval. Moreover, additional comparisons among older Hamilton coral-rich horizons corroborate our primary results. These findings support a model in which species respond individually to fluctuations in the physical environment, as indicated by the fluidity of their relative abundances geographically and temporally.

The centric diatom Stephanodiscus yellowstonensis Theriot and Stoermer is endemic to Yellowstone Lake, where it can be an important component of the summer phytoplankton assemblage. Its close relative, Stephanodiscus niagarae Ehrenberg, is abundant in nearby lakes and regional reservoirs. We used the stratigraphic record of Yellowstone Lake to investigate the evolution of S. niagarae to S. yellowstonensis and to describe the limnologic and climatic conditions associated with its evolution. A dramatic morphological shift took place between about 13.7 and 10.0 Ka, but morphology remained stable from 10 Ka to the present. Coincident with morphological change in the S. niagarae/S. yellowstonensis complex were changes in the diatom species assemblage, biogenic silica concentrations, sediment lithology, and regional vegetation. These changes suggest an environment that experienced progressive warming following the retreat of continental glaciers. We could not identify a specific selective factor driving evolution. Nevertheless, nonrandom morphological evolution strongly associated with continuous environmental change suggests that directional selection is a reasonable hypothesis to account for evolution of S. yellowstonensis. Protists are presumed to evolve gradually after speciation events because of large population size, high dispersal capacity, and low reproductive barriers. However, published diatom examples and the evolution of S. yellowstonensis suggest that it is premature to generalize about rates of evolution in protists, or at least to include diatoms in this generalization.

Persistent fossil taxa contravene paradigms of evolution: pervasive morphological change and taxic turnover. Comparative studies of taxic duration have often been approached from biogeographic, climatic, and ecological perspectives, with a focus on process. Here I use a morphological approach to study the pattern of longevity of a large family of marine living and fossil podocopid ostracodes, Trachyleberididae sensu lato. I test if geologically longer-lived genera are collectively morphologically more deviant from a group mean than their shorter-lived relatives by using both discrete morphological data and outline data. I discovered that long-lived genera are in general not significantly more or less morphologically deviant from the average morphology than their shorter-lived relatives. However, I found that contemporaneous subsets of long-lived trachyleberidids are often at least marginally significantly more deviant in discrete morphology than shorter-lived ones, especially in external morphology. No significant patterns of association between morphological deviation and durations in other subdivisions of the data emerged (i.e., whole data set, birth cohorts, groups of morphological characters, and outline data using both Fourier analysis and eigenshape analysis). This is in contrast to a previous finding that long-lived genera of crinoids within orders are often morphologically less deviant than their shorter-lived relatives than expected by chance.

The species-characteristic combination of morphological characters that depend on an environmental gradient can be used to determine the frequency distribution of the species along the gradient. All functional characters of a phylogenetically closely related species group demonstrate overlapping intervals along an environmental gradient. The gradual change in character composition along the gradient is called a morphocoenocline. Based on transfer functions, a morphocoenocline can be used for gradient values estimation (proxies) in the historical or geological past, similar to a coenocline based on species (democoenocline).

Transforming the empirical frequency distributions of characters and character states along the gradient to probability distributions enables calculating a probability density function of any subset of characters of the morphocoenocline. Because a species is distinguished by a specific combination of characters that are functionally related to the gradient, the distribution of this species along the gradient can be estimated using the probability density functions of combined characters. Assuming “functional uniformitarianism” this estimation can be extended into the geologic past for all fossil species, as long as their functional characters are homologous or analogous to those found among Recent forms. When a morphocoenocline is based on a compound environmental gradient, such as depth, which represents a combination of single environmental factors, the gradient estimation reflects only a specific combination of single factors.

A morphocoenocline for test characters of symbiont-bearing benthic foraminifera from the West Pacific was established for water depth. This compound environmental gradient represents tropical open sea conditions at a slope where the water is highly transparent (low inorganic nutrients and sediment input). Depth distributions based on probability density functions were compared with empirical distributions to prove the accuracy of this method, and were used to estimate the depth distribution of other living species that had not been included in the determination of the morphocoenocline because they live in other regions. The method was also applied to fossil species that are closely related to Recent forms (Nummulites, Assilina from the Eocene) and to fossil species that are more distantly related to the living species (Orbitoides from the Upper Cretaceous).

The purpose of this paper is to explore the possibility and utility of estimating multivariate selection in fossil assemblages, using naticid gastropods as a case study. We used the presence or the absence of a naticid borehole as an index of survival with respect to drilling attacks, enabling us to estimate the multivariate selection gradient exerted by this predator on the shell length and shell thickness of two bivalve genera, Astarte and Spisula. We hypothesized that naticid selection pressure would favor the survival of large, thick-shelled bivalve prey throughout the Cenozoic.

Differential survival of prey was recorded over geologic time using processed bulk assemblages from the Miocene, Pliocene, and Pleistocene Epochs. Multivariate logistic regressions were performed by time period to determine if length and thickness were important factors affecting survival. The direction and magnitude of selection on length and thickness for the two genera ranged from zero (no selection) to large positive or negative values. Only two selection coefficients were significant after sequential Bonferroni corrections: thin-shelled Astarte survived substantially better than thick-shelled Astarte during the Pleistocene (β_avggrad = −1.23) and large Spisula survived slightly better than small Spisula during the Miocene Epoch (β_avggrad = 0.05).

This is the first study using fossils to calculate multivariate selection gradients. It suggests that naticids were not necessarily strong agents of selection on two traits previously thought to be important to survival of drilling attacks for two of their common prey species. We also show that multivariate selection gradient estimates differ from traditional predation intensity estimates but are superior for estimating the magnitude and direction of natural selection because they use differential mortality of different prey phenotypes rather than just absolute mortality from predation. This work is especially significant for research that involves estimating the relative importance of predation (naticid or otherwise) as an evolutionary force and will be useful for fossil studies where differential survival can be recorded.

A neurological method for assessment of nasal cavity homologies in extant archosaurs is extended to lambeosaurine hadrosaurids (Dinosauria: Ornithischia) to test functional hypotheses associated with their hypertrophied nasal passages and highly derived cranial crests. The olfactory system and associated cranial nerve pathways that have consistent relationships to soft tissue divisions of the nasal cavity are reconstructed in lambeosaurines on the basis of new paleoneurological data and a comparative phylogenetic approach. The new model of the lambeosaurine olfactory system and nasal cavity shows that a significant portion of nasal cavity proper was located outside the crest cavities and that the primary olfactory region was located rostromedial to the orbits.

All available data indicate that the evolutionary hypertrophy of the nasal cavity occurred predominantly within the non-olfactory nasal vestibule, and that crest development was not causally associated with olfaction. The high level of interspecific and ontogenetic variation in crest shape and nasal vestibule development in lambeosaurine dinosaurs is most consistent with proposed behavioral functions, notably acoustic resonance for intraspecific communication. Despite significant modification to the nasal cavity within Archosauria and its extreme hypertrophy and supraorbital development in Lambeosaurinae, the neural olfactory system and the olfactory region of the nasal cavity proper retain their plesiomorphic positions and associations, suggesting that this system is highly conserved in vertebrate evolution.

Understanding the extent to which the reported fossil record reflects biological history, rather than preservational artifacts or other biasing factors, remains one of the central issues in the interpretation of the history of life on Earth. The development of large interactive paleontological databases, such as the Paleobiology Database (PBDB), allows detailed analyses of the patterns of occurrence, both regionally and globally, of taxa in the fossil record and makes possible testing hypotheses of the controls of the patterns. An analysis of data from the PBDB shows that most genera in the fossil record are rare, whereas a relatively small percentage of taxa account for a disproportionate share of the total occurrences. These ubiquitous taxa tend to be speciose and have long stratigraphic ranges. These patterns of occurrence might represent a true biological signal; it is also possible that they reflect taphonomic processes or are the result of taxonomic practice. In particular, common taxa may be taxonomic wastebaskets, i.e., residual and polyphyletic groups resulting from inadequate systematic attention and/or from taphonomic biases resulting in inadequate specimens being preferentially placed in particular genera. A conceptual model for the development of taxonomic wastebaskets suggests that these taxa should be speciose, widely distributed, common, and old (in terms of year of first description), and that they should be the nominate forms for higher taxa. Our analyses suggest that many of the common taxa in the PBDB are consistent with two or more of these expectations and are thus good candidates for being wastebaskets. These taxa are, however, only a small percentage of total genera. A more detailed examination of one group, early gastropods, indicates that possible wastebaskets still are present in a group that has received much recent systematic work. Given that likely wastebasket taxa are a small fraction of all genera, they probably have little effect on overall temporal patterns of generic richness. Their impact on other types of metrics, such as turnover rates or metrics of community diversity or biogeographic similarity, however, might be quite important.

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.