A paradoxical relationship exists between the genetic and morphologic adaptive strategies of benthic marine invertebrates; morphologically variable species from unstable environments have been shown to possess less genetic variability than species with more constant phenotypes from stable habitats. The mode of growth of Ordovician bryozoans provides an insight into this paradox. These bryozoans exhibit morphologic gradients within zooidal subcolonies that change throughout colony development. Entire clusters of zooids begin and cease growth as a function of their spatial position with respect to neighboring clusters. A comparison of the within-colony and among-colony components of developmental and morphologic variability was made from populations inhabiting Ordovician environments of differing stability. In four stratigraphically persistent species, the level of developmental variability is homogeneous within species, but varies significantly across taxa. The two species with the highest levels of developmental variability (less canalized development) fit the concept of r-selected opportunistic species and are most abundant in communities of lowest diversity. The other two species have much lower levels of variability (more canalized development), fit the concept of K-selected equilibrium species, and are most abundant in the communities of highest diversity. Within-colony morphologic variability is also higher in the opportunistic rather than the equilibrium species, indicating that the higher morphologic variability observed in unstable environments is the product of within-genotype deregulation, and not the result of higher genetic polymorphism. The equilibrium species in stable environments have lower levels of morphologic deregulation and correspondingly greater variation among genotypes than within genotypes in fossil populations.

All evolution attributable to natural selection, at any level, is due to a causal covariance between fitness and phenotype. Over macroevolutionary time scales, species selection is one of many possible mechanisms for generating large-scale morphological trends. For species selection to sort morphology, a correlation between morphology and taxonomic diversification rate must be present. Other trend mechanisms (driven mechanisms, e.g., a bias in the direction of speciation) produce a systematic change in the mean phenotype over time. All mechanisms can co-occur. Here I demonstrate (1) an inverse correlation between diversification rate and calyx complexity that demonstrates the effect of species selection on morphology. Genera with simple calyces tend to increase in diversity, whereas genera with complex calyces have a net decrease in diversity; and (2) the presence of a driven trend mechanism in monobathrid crinoids where descendant genera tend to be simpler than their ancestors. The separate effects of these two classes of trend mechanisms can be combined by using the Price's Theorem, which partitions the contribution to the overall change in calyx complexity over time accurately among selection and driven mechanisms. Price's Theorem provides significant conceptual and methodological clarification of the contribution of multiple and interacting hierarchical mechanisms in generating large-scale trends.

Fragments of cheilostome and cyclostome bryozoans are the most common fossils in the mound structures commonly found in the Lower Danian limestones of southern Scandinavia. Sedimentological investigations and measurement of colony morphology combined with flume channel experiments indicate that: 1) The mounds were affected by unidirectional currents which created relatively high current velocities on the upstream flanks and summits, and low velocities on the downstream flanks and in the basins. 2) Colonies with slender stems and thin walls dominated in areas with low current velocities and those with thick stems and thick walls dominated in areas with high velocities. 3) The specific variability of the stem diameter was mainly controlled by the geometrical arrangement of the zooids. In general, species with a bilamellar arrangement of the zooids show high variability, whereas species with a radial arrangement show small variability. 4) Variation in the wall thickness is primarily related to the mode of growth of the individual zooids. In the ascophorans deposition was confined to the external surface of the stems. On the other hand, in the coilostegoid anascans the secondary skeletal material was deposited on all the internal surfaces of the zooids as well as on the external side of the cryptocyst. Cuticles do not seem to have been present in the secondary thickened part of the frontal wall of either the coilostegoid anascans or the ascophorans. 5) Calcareous material was deposited predominantly on the lower and older portions of the colony.

The fossil stickleback, Gasterosteus doryssus, is highly variable for pelvic girdle structure and the number of dorsal spines. Six “sampling pits” were dug at known stratigraphic positions within a continuous section which contains abundant G. doryssus, and the stratigraphic position of each specimen within each pit was determined. The deposit apparently is composed of annual layers (varves), allowing relatively precise conversion of stratigraphic distance to years. The temporal distribution of phenotypes is heterogeneous but can be grouped into two temporally contiguous, nonheterogeneous sets. However, absence of heterogeneity for pelvic phenotypes within the two groups of pits could be an artifact of small sample size. The number of sample pits was insufficient to determine whether the observed phenotypic heterogeneity among pits represents temporal trends. Differences also occurred between mean temporal distributions of stickleback phenotypes within one of the pits located within a nonheterogeneous set of pits. Thus, there is within-pit temporal heterogeneity that is unresolved by between-pit comparisons, although the sampling pits are separated by an average of only about thirty thousand years. Larger time intervals usually used in paleontology may seriously underestimate evolutionary rates because fine scale reversals of evolutionary trajectory are undetected. Temporal variation in G. doryssus provides a system in which most limitations of other fossil systems for measuring the rate of evolution can be circumvented. As in virtually all paleontological studies, spatial variation cannot be entirely eliminated as a potential cause of stratigraphic variation.

Radiodonts (stem Euarthropoda) were ecologically diverse, but species generally displayed limited functional specialization of appendages along the body axis compared with crown group euarthropods. This is puzzling, because such functional specialization is considered to have been an important driver of euarthropod ecological diversification. One way to circumvent this constraint could have been the functional specialization of different parts of the frontal appendages, known to have been ecologically important in radiodonts. This hypothesis has yet to be tested explicitly. Here we redescribe the poorly known mid-Cambrian hurdiid radiodont Stanleycaris hirpex from the Burgess Shale (Stephen Formation) and quantitatively assess functional specialization of the frontal appendages of stem euarthropods. The appendages of Stanleycaris are composed of 14 podomeres, variously differentiated by their possession of pectinate endites, mono- to trifurcate medial gnathites, and outer spines. The oral cone is tetraradially organized and can be uniquely distinguished from those of other hurdiids by the presence of 28 rather than 32 smooth tridentate plates. Our phylogenetic analysis finds Stanleycaris in a grade of hurdiids retaining plesiomorphic raptorial appendicular functionality alongside derived adaptations for sweep feeding and large, bilaterally opposed gnathites. We conclude that the latter performed a masticatory function, convergent with gnathal structures like mandibles in various panarthropods. Taken together, Stanleycaris and similar hurdiids provide an extreme example of the evolution of division of labor within the appendage of a stem euarthropod and suggest that this innovation may have facilitated the functional transition, from raptorial to sweep feeding, at the origin of the hurdiid clade.

We documented changes in the relative abundance of bivalve genera and functional groups in the southwest Caribbean over the past 11 Myr to determine their response to oceanographic changes associated with the closure of the Central American Seaway ca. 3.5 Ma. Quantitative bulk samples from 29 localities yielded 106,000 specimens in 145 genera. All genera were assigned to functional groups based on diet, relationship to the substrate, and mobility. Ordinations of assemblages based on quantitative data for functional groups demonstrated strong shifts in community structure, with a stark contrast between assemblages older than 5 Ma and those younger than 3.5 Ma. These changes are primarily due to an increase in the abundance of attached epifaunal bivalves (e.g., Chama, Arcopsis, and Barbatia) and a decrease in infaunal bivalves (e.g., Varicorbula and Caryocorbula). Taxa associated with seagrasses, including deposit-feeding and chemosymbiotic bivalves (e.g., Lucina), also increased in relative abundance compared to suspension feeders. The composition of bivalve assemblages is correlated with the carbonate content of sediments and the percentage of skeletal biomass that is coral. Our results strongly support the hypothesis that increases in the extent of coral reefs and Thalassia communities were important drivers of biologic turnover in Neogene Caribbean benthic communities.

This paper takes an alternative approach to the problem of inferring patterns of phenotypic evolution in the fossil record. Reconstructing temporal biological signal from noisy stratophenetic data is an inverse problem analogous to subsurface reconstructions in geophysics, and similar methods apply. To increase the information content of stratophenetic series, available geological data on sample ages and environments are included as prior knowledge, and all inferences are conditioned on the uncertainty in these geological variables. This uncertainty, as well as data error and the stochasticity of fossil preservation and evolution, prevents any unique solution to the stratophenetic inverse problem. Instead, the solution is defined as a distribution of model parameter values that explain the data to varying degrees. This distribution is obtained by direct Monte Carlo sampling of the parameter space, and evaluated with Bayesian integrals. The Bayesian inversion is illustrated with Miocene stratigraphic data from the ODP Leg 174AX Bethany Beach borehole. A sample of the benthic foraminifer Pseudononion pizarrensis is used to obtain a phenotypic covariance matrix for outline shape, which constrains a model of multivariate shape evolution. The forward model combines this evolutionary model and stochastic models of fossil occurrence with the empirical sedimentary record to generate predicted stratophenetic series. A synthetic data set is inverted, using the Neighbourhood Algorithm to sample the parameter space and characterize the posterior probability distribution. Despite small sample sizes and noisy shape data, most of the generating parameter values are well resolved, and the underlying pattern of phenotypic evolution can be reconstructed, with quantitative measures of uncertainty. Inversion of a stratigraphic series into a time series can significantly improve our perception and interpretation of an evolutionary pattern.

We studied the morphological diversity of gastropod shell forms from the viewpoint of theoretical morphology, emphasizing the relationships of shell form to postural stability and the available space for soft body, which we assessed in terms of the moment of force and soft-tissue ratio calculations, respectively. The results of computer simulations suggest a functional trade-off between postural stability and available space for soft body: a compact shell possessing a low spire and small umbilicus exhibits high postural stability, whereas a less overlapped shell form with a high spire and large umbilicus makes available space for soft body. A functional morphospace analysis using theoretical models reveals that outward and downward inclination of the aperture moderates the functional trade-off between these parameter values and permits compatibility between stable posture and efficient shell construction. The hypothetical optimum that realizes this compatibility is consistent with the observed range of forms estimated from 359 extant gastropod species. The biometric results also suggest that land snails are more highly constrained than marine species in achieving a balance between postural stability and available space for soft body.

Phenotypic variation within species provides the raw material acted upon by natural selection and other evolutionary mechanisms. As such, the range and variation of morphology within a species can play an important role in determining the tempo of evolution. The range and variance of aspects of cranidial morphology for nine lower Paleozoic trilobites were measured to identify microevolutionary correlates of macroevolutionary patterns. Comparisons were made among sets of homologous landmarks or upon partial warp vector matrices containing similar proportions of variance. Rarefaction and bootstrap analyses helped estimate the effects of sampling. Levels of variance and range of morphology differed considerably within and among time periods. There is no significant temporal decline in the variance or range of morphology, suggesting that developmental or genomic constraints may not have been the primary factors controlling the tempo of trilobite macroevolution. The spatial distribution of cranidial variance differed considerably among taxa, suggesting that a complex set of developmental processes governed the morphogenesis of cranidia within trilobites.

The middle Carboniferous was an interval of global change when the climate was transitioning from greenhouse to icehouse conditions. Field collections of paleotropical brachiopod assemblages across the Mississippian/Pennsylvanian boundary reveal a taxonomic turnover event in which the overall diversity structure is conserved, despite an apparent regional extinction of 63% of latest Mississippian genera and an apparent regional origination of 50% of earliest Pennsylvanian. An analysis of the global ranges of the brachiopods encountered in the field reveals that turnover was driven primarily by extirpation and immigration rather than true extinctions and originations. Taxonomic richness and evenness are indistinguishable between the latest Mississippian and earliest Pennsylvanian stages. Additive diversity partitioning shows that the within-collection, between-collections (i.e., within-bed), and between-bed diversity components do not change across the Mississippian/Pennsylvanian boundary for richness or evenness. Rank-abundance plots of genera show the same distribution for both stages, but with no correlation between the Mississippian abundances of range-through genera and their abundance in the Pennsylvanian. Detrended correspondence analysis shows a major change in taxonomic composition across that Mississippian/Pennsylvanian boundary and consistency in the general gradient along which genera were distributed. An estimation of spatio-temporal heterogeneity of taxonomic composition within each stage reveals that the earliest Pennsylvanian was significantly more homogeneous. These results suggest that middle Carboniferous brachiopod assemblages from tropical shallow-water carbonate platform settings were organized by some factor that was independent of the specific taxa present. Furthermore, the increased homogeneity in taxonomic composition in the Morrowan did not affect the overall diversity structure. Strong competitive interactions among taxa do not appear to be important in determining the taxonomic compositions and abundances of brachiopod stage-level assemblages.

Problems of taphonomy and sampling adequacy hinder direct evolutionary interpretations of pattern in the Precambrian paleontological record; however, molecular studies of microbial phylogeny and comparative physiological and ecological investigations of living microorganisms can be combined with geological research to establish patterns of early evolution. The Late Proterozoic record of planktonic algae resembles those of Phanerozoic plants, animals, and microplankton in its patterns of diversification and turnover, as well as in the importance of major extinction events in shaping the course of evolution. Late Proterozoic eukaryotes thus appear to be discussable in terms of the macroevolutionary issues that have become central to Phanerozoic paleobiology. In contrast, evolutionary patterns in Precambrian prokaryotes appear to be different from those of plants and animals, a possible consequence of their differing systems of genetic organization and recombination.

The “niche-variation” model predicts that increase in environmental stability should be accompanied by increase in homozygosity and reduction in morphological variability. All Late Cambrian trilobite biomeres show an increase in regional species diversity from low in the biomere toward the top. This change in diversity is believed to reflect increasing environmental stability and consequently affords the opportunity to indirectly test the “niche-variation” hypothesis in a paleontological context. Measurements were made of eight cranidial features of samples of 17 species populations from the Pterocephaliid Biomere of the Great Basin. Coefficients of variation and a multivariate analog of them failed to reveal a relationship between morphological variability and species diversity. Consideration of these data together with contradictory, but limited, informaton for other organisms suggests that the predicted decrease in genetic variability may either be absent or be readily masked in naturally occurring populations, which typically retain a high degree of genetic polymorphism. If heterozygosity is common, it would appear that accidents of geography, rather than the genetic consequences of stable or unstable environments, are among the primary factors controlling the probability of speciation.

Numerous methods exist for estimating the true stratigraphic range of a fossil taxon based on the stratigraphic positions of its fossil occurrences. Many of these methods require the assumption of uniform fossil recovery potential—that fossils are equally likely to be found at any point within the taxon's true range. This assumption is unrealistic, because factors such as stratigraphic architecture, sampling effort, and the taxon's abundance and geographic range affect recovery potential. Other methods do not make this assumption, but they instead require a priori quantitative knowledge of recovery potential that may be difficult to obtain. We present a new Bayesian method, the Adaptive Beta method, for estimating the true stratigraphic range of a taxon that works for both uniform and non-uniform recovery potential. In contrast to existing methods, we explicitly estimate recovery potential from the positions of the occurrences themselves, so that a priori knowledge of recovery potential is not required. Using simulated datasets, we compare the performance of our method with existing methods. We show that the Adaptive Beta method performs well in that it achieves or nearly achieves nominal coverage probabilities and provides reasonable point estimates of the true extinction in a variety of situations. We demonstrate the method using a dataset of the Cambrian mollusc Anabarella.

The relative numbers of sexually and asexually recruited colonies and the proportion of brooding zooids were determined in 26 species of cheilostome bryozoans of Late Cretaceous and Early Tertiary ages. Asexual reproduction seems to be much more widespread than previously realized, although its relative importance is related to growth habit. Arborescent species of these fossil assemblages reproduce mainly asexually via fragmentation; encrusting species reproduce sexually via motile larvae. Free-living species use both methods; some reproduce sexually, whereas other species have enhanced the ability to break and reproduce predominantly asexually. Mode of reproduction was stable over a period of 3 m.y. in all species except the vinelike Columnotheca cribrosa. In this species both the proportion of asexual recruits and brooding zooids varied in accord with environmental parameters. In all cases populations dominated by asexual propagation had a significantly lower proportion of brooding zooids than populations dominated by sexual propagation.

The reconstruction of the Tree of Life has been a primary goal in biology since Darwin coined the expression, the “great Tree of Life” in On the Origin of Species: “The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species…. As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications” (Darwin 1859: pp. 129–130). Ernst Haeckel was the first biologist who attempted to reconstruct the Darwinian Tree of Life. However, he could not reach his goal because his method of tree reconstruction was deeply anchored in the pre-Darwinian scala naturae (Dayrat 2003). A segment of the Darwinian Tree of Life is illustrated in the unique figure published in On the Origin of Species. This figure, which Darwin referred to as a “branching diagram,” represents ancestor-descendant relationships (ADR).

The Early Jurassic Toarcian Oceanic Anoxic Event is considered one of the most dramatic environmental perturbations of the Mesozoic. An elevated extinction rate among marine invertebrates accompanied rapid environmental changes, but effects on large vertebrates are less understood. We examined changes in ichthyosaur body size in the Posidonia Shale of the Southwest German Basin spanning the extinction interval to assess how environmental changes and biotic crisis among prey species affected large reptiles. We report no species-level extinction among the ichthyosaurs coinciding with peak invertebrate extinction. Large ichthyosaurs were absent from the fauna during the extinction interval, but became more abundant in the immediate aftermath. Stenopterygius quadriscissus, the most abundant species during the extinction interval, increased in body size after the biotic event. Rapid invasion by large taxa occurred immediately following the extinction event at the end of the first ammonite zone of the early Toarcian. Greater mobility permitting exploitation of ephemeral resources and opportunistic feeding behavior may minimize the impacts of environmental change on large vertebrates.

The evolutionary bootstrap is a new approach to the analysis of patterns of taxonomic diversity. In general, the evolutionary bootstrap works by surveying the diversity history of a taxon, learning its dynamic properties, and then generating randomly large numbers of artificial diversity histories based upon what was learned. The distribution of artificial—or bootstrapped—diversity histories approximates the distribution of diversity histories that were possible for taxa with the dynamic properties of the real taxon, and serves as a paleontological null hypothesis for studying statistically the diversity history of the real taxon.

Two null hypotheses were established, the additive and the multiplicative. The additive null hypothesis assumes that the amount of diversity change that occurs in a higher taxon during an interval of time is independent of the number of member subtaxa present at the beginning of the interval. The multiplicative null hypothesis, in contrast, assumes that the amount of diversity change that occurs is dependent upon the number of member subtaxa present at the start. Thus the two null hypotheses represent end members of a diversity-independent/diversity-dependent continuum of possibilities.

Detailed analyses using the evolutionary bootstrap, in conjunction with the clade statistics of Gould et al. (1977), show that several of the 17 higher taxa studied have diversity histories that are statistically significantly different from the random expectation under one or both null hypotheses. Analyses of multiple taxa in aggregate also reveal several properties of diversity histories that are statistically significantly different from random. Real taxa tend to have higher uniformities and lower maximum diversities than expected under the multiplicative null hypothesis. They have lower uniformities, higher maximum diversities, and longer durations than expected under the additive null hypothesis. And, they have lower centers of gravity than expected under either null hypothesis. Overall, the results provide a possible statistical verification of the process of taxonomic (traditionally, adaptive) radiation and suggest the need to consider deterministic explanations for observed diversity patterns.

Evolution of photosymbiotic ecology is an important adaptation for planktic foraminifers that enhances the ecological advantage of living in oligotrophic oceans. Therefore, detecting photosymbiotic ecology in fossil species is one of the keys to understanding the paleobiodiversity dynamics of planktic foraminifers. Because foraminiferal tests record the ontogenetic history of ecological information in geochemical signatures, analyzing individual geochemical profiles with growth can reveal a species’ ecology. This study examined chamber-by-chamber stable isotopes (δ13C and δ18O) of foraminiferal individuals to identify photosymbiotic signals. We observed an ontogenetic δ13C increase of up to 2.4‰, accompanied by relatively stable, negative δ18O, in the symbiotic species Globigerinoides conglobatus and Globigerinoides sacculifer. In contrast, δ13C and δ18O showed significant positive correlation during ontogeny in the asymbiotic species Globorotalia truncatulinoides. These two ecological groups produce contrasting isotopic profiles, thereby allowing us to use our ontogenetic isotopic analyses of individual specimens to identify algal photosymbiosis in fossil foraminifers. The chamber-by-chamber isotope analyses with individual ontogeny have great advantages in analyzing rare species because only one individual is required to describe ontogenetic isotopic history. In addition to photosymbiotic identification, our methods hold great potential to provide new insight into species paleoecological studies such as the ontogenetic history of calcification depth.

The logistic model provides a useful geometric description of coiling for larger Foraminifera. This model represents a spiral in polar coordinates by means of a logistic equation. The model describes the spires of the genera Alveolina, Nummulites, and Assilina very well. The logistic model is a consequence of allometric growth in these genera. The spires of Nummulites do not fit the logarithmic spiral model well, because the model does not accommodate ontogenetic change of form. Computer simulations using the logistic model also show the very different morphologies of the genus Alveolina. The model allows study of geometrical constraints on test form and of pathways followed by the evolution of the genus (or genera). The logistic model describes ontogenetic change in the organism's functional requirements. The main physiological requirements are nourishment, general exchanges of matter and energy with the environment, and light for the photosynthetic symbionts that live in the cytoplasm of these larger Foraminifera. All these functions require suitable area/volume ratios, that mandate changes of form during growth. The possible biological meaning of the parameters of the model is explored. The use of the more meaningful parameters is proposed in statistical multivariate studies.