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 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.

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 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.

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.

All else being equal, species with short life spans are expected to be overrepresented in time-averaged death assemblages relative to their standing abundance in the living community, but the magnitude of the distortion of proportional abundance and assemblage evenness has received little attention. Here, information from 30 data sets on the living and dead abundances of marine bivalves in local habitats is combined with a global compilation of bivalve life spans to determine whether bias from mortality rate can explain observed differences in species proportional abundances. Although bivalve maximum life spans range from one to 75 years in these data sets, indicating annual mortality rates of 0.97 to 0.09, the “life span bias” (LB) of a species–the difference between its proportional abundance expected dead and that observed alive–is consistently small in magnitude (average change <2%, maximum about 20%) and random in sign relative to observed discordance (OD = difference between that species' proportional abundance observed dead and that observed alive). The aggregate result for 413 living species occurrences is a significantly positive but weak correlation of OD to LB, with only 10% of variation in OD explained. The model performs better among longer-lived species than among shorter-lived species, probably because longer-lived species conform better to the model assumption that species maintain a constant proportional abundance in the living assemblage over time. Among individual data sets, only seven exhibit significant positive correlations between OD and LB. The model also under-predicts the cases where a death assemblage is dominated by a species that is shorter lived than the dominant species in the living assemblage, indicating that some factor(s) other than or in addition to mortality rate is responsible for OD. We can find no evidence of preservational bias linked to life span, for example through body size. This negative outcome reflects a weak biological relationship between life span and living abundance among bivalves in local habitats, contrary to the terrestrial paradigm, and points toward a simpler model of time-averaged death assemblage formation where higher abundances reflect (under-sampled) past populations. Contrary to long-held expectations, variation in population turnover among species is not a major source of taphonomic bias in time-averaged death assemblages among bivalves and perhaps among other marine groups: bias must arise largely from other factors.

Bone-collecting behavior in the harvester ant, Messor barbarus, has been observed for the first time. Excavation to the depth of the packed substrate of a single ant hill yielded 1167 modern bones derived from nine or more species of small vertebrates. Since harvester ants of various species are well-known from the Americas, Africa, and Eurasia, ants may have served as important agents of concentration for micromammal assemblages in the fossil record. Analysis of the faunal and skeletal representation of the ant hill assemblages reveals characteristic patterns that might be used to distinguish such assemblages from those collected by avian or mammalian predators.

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.

—Stable isotope ratios of carbon and nitrogen in archaeological and modern bone samples have been used to reconstruct the dietary changes of the South American sea lion Otaria flavescens from the late Holocene to the present in the southwestern Atlantic. We sampled bones from archaeological sites in northern-central and southern Patagonia, Argentina, and bones housed in modern scientific collections. Additionally, we analyzed the stable isotope ratios in ancient and modern shells of intertidal molluscs to explore changes in the isotope baseline and allow comparison between bone samples from different periods after correction for baseline shifts. Results confirmed the trophic plasticity of the South American sea lion, demonstrated the much larger impact of modern exploitation of marine resources as compared with that of hunter-gatherers, and underscored the dissimilarity between the past and modern niches of exploited species. These conclusions are supported by the rather stable diet of South American sea lions during several millennia of aboriginal exploitation, in both northern-central and southern Patagonia, and the dramatic increase in trophic level observed during the twentieth century. The recent increase in trophic level might be related to the smaller population size resulting from modern sealing and the resulting reduced intraspecific competition. These results demonstrate how much can be learned about the ecology of modern species thanks to retrospective studies beyond the current, anthropogenically modified setting where ecosystem structure is totally different from that in the pristine environments where current species evolved.

The evolution of powered flight has traditionally been associated with the origin of birds, the most successful clade of modern tetrapods, as exemplified by the nearly 10,000 species alive today. Flight requires a suite of morphological changes to skeletal anatomy to create a light yet resistant framework for an airfoil and advanced nervous motor control. Given the level of morphological integration necessary to create a suitable aerofoil, the origin of flight may be intuitively assumed to be coupled with high evolutionary rates of wing-related morphologies. Here we show that the origin of birds is associated with little or no evolutionary change to the skeletal anatomy of the forelimb, and thus Archaeopteryx is unlikely to be the “Rosetta Stone” for the origin of flight it was once believed to be. Using comparative statistics and time-series analyses on a data set constructed from all known forelimb skeletal anatomy of non-avian theropod dinosaurs and a diverse assemblage of early birds, we demonstrate three focused peaks of rapid forelimb evolution at Tetanurae, Eumaniraptora, and Ornithothoraces. The peaks are not associated with missing data and remain stable under multiple perturbations to the phylogenetic arrangements. Different regions of the forelimbs are demonstrated to have undergone asynchronous periods of evolutionary peaks and stasis. Our results evince a more complicated stepwise mode of forelimb evolution before and after the origin of Aves than previously supposed.

Laboratory and field collected sediments were x-rayed to document the array of biogenic sedimentary structures produced by the burrowing and feeding behavior of six species of marine intertidal annelid (Glycera robusta, Nephtys caecoides, Pectinaria californiensis, Notomastus magnus, Eupolymnia crescentis, and Cirriformia spirabrancha). Polychaete burrows were found to vary greatly in structural complexity with both errant (N. magnus) and relatively sessile forms (C. spirabrancha) producing a variety of biogenic structures. Sediment mixing by the tentacle-feeding polychaete C. spirabrancha was observed by sequentially x-raying an experimental field enclosure stratified with an opaque substance. The experiment demonstrates that tentacle-feeding polychaetes can influence the topography of the sediment-water interface and transport substantial amounts of near surface material downward.

Criteria by which fossil biogenic sedimentary structures, presumably produced by soft-bodied organisms, can be assigned a feeding function have been advanced by Walker (1972). Some of the assumptions inherent in feeding function analysis were applied, with varying degrees of success, to the biogenic structures of modern soft-sediment polychaetes.

Previous attempts to quantify the test-flattening trend in Heterostegina depressa with water depth have been rather unsuccessful. Due to its broad depth distribution, H. depressa is a perfect model species to calibrate test flattening as a bathymetric signal for fossil assemblages. This might enable us to better reconstruct paleoenvironments of fossil communities of larger foraminifera or even provide clues to the degree of transport in allochthonous deposits. In this study, we used growth-independent functions to describe the change of test thickness throughout ontogeny. Four growth-invariant characters, deriving from these functions, clearly quantify a transition of individuals with thicker to thinner central parts along the water-depth gradient. This transition is probably controlled by light intensity, because the photosymbionts of H. depressa (diatoms) are most effective at low irradiation levels. Thus, specimens at shallower depths grow thicker to reduce light penetration, whereas specimens living deeper than the light optimum increase their surface by flattening to obtain better exposure to light.

Changes in shape and in the pattern of the reticulate carapace ornament of 63 representative female ostracode specimens of the deep-sea genus Poseidonamicus from 28 Deep Sea Drilling Project Sites, extending over a geographic distance of 40,000 miles and a geologic age of 40 × 106 yr, have been analyzed by Resistant Fit Theta-Rho Analysis, conventional least-squares Theta-Rho Analysis, and by inspection of homologies in the fossae of the reticulum. Through comparison of the relative rates of morphological change on at least three levels of integrated complexity, it is possible to demonstrate that a sudden evolutionary change in the architectural framework of the carapace can be the product of mechanical accommodation under stress to more gradual and general changes in carapace shape. Certain geometric imperatives related to these mechanical needs determine morphologic stability and consequently rates of evolutionary change. In the western deep South Atlantic (near the Vema Channel on the Rio Grande Rise), an important evolutionary “punctuational event” seems to have taken place at about 14 Myr, whereas its concomitant, more gradual transformation is traceable in the shallower eastern South Atlantic (Walvis Ridge). This evolutionary event in Poseidonamicus probably reflects the relatively sudden invasion of deep Antarctic Bottom Water through the Vema Channel resulting from the formation of the East Antarctic Ice Cap, while the more gradual transition in shallower depths of Walvis Ridge represents a temporary transitory refuge. The problems of recognizing allopatric origins of species in the deep sea compared to in situ sudden transitions caused by biomechanical instability are considered.

It has generally been argued that the majority of fossil benthic foraminifera, the most common proxy for paleo bottom oceanic conditions, could not tolerate anoxia. Here we present evidence that fossil foraminifera were able to successfully colonize anoxic–dysoxic bottom waters, by using adaptations similar to those found in living species. Our study is based on a multi proxy micropaleontological and geochemical investigation of the Upper Cretaceous sediments from the Levant upwelling regime. A shift from buliminid to diverse trochospiral dominated assemblages was recorded in an interval with a distinct anoxic geochemical signature coinciding with a regional change in lithology. This change was triggered by an alteration in the type of primary producers from diatoms to calcareous nannoplankton, possibly causing modifications in benthic foraminiferal morphological and physiological adaptations to life in the absence of oxygen.

Our data show that massive blooms of triserial (buliminid) benthic foraminifera with distinct apertural and test morphologies during the Campanian were enabled by their ability to sequester diatom chloroplasts and associate with bacteria, in a similar manner as their modern analogs. Diverse trochospiral forms existed during the Maastrichtian by using nitrate instead of oxygen for their respiratory pathways in a denitrifying environment. Species belonging to the Stilostomellidae and Nodosariidae families might have been affected by the change in food type arriving to the seafloor after the phytoplankton turnover at the Campanian/Maastrichtian boundary, in a similar manner as their mid Pleistocene descendants prior to their extinction. This study promotes the need for a re-evaluation of the current models used for interpreting paleoceanographic data and demonstrates that the identification of adaptations and mechanisms involved in promoting sustained life under anoxic to dysoxic conditions should become a standard in faunal paleoceanographic studies.

The late Albian (Early Cretaceous) lineage of Actinoceramus sulcatus (Parkinson 1819) is a remarkable example of macro- and microevolution within the Bivalvia. Immediately following cladogenesis from ancestral A. concentricus, the lineage displays a conspicuous, short-term excursion through morphospace followed by a return to the ancestral form. This excursion is marked by the acquisition, and subsequent loss, of large radial folds affecting some part or all of the shell. The pattern is noteworthy because of the gross scale and rate of morphological evolution, the relatively short life span of an “extreme” morphology, an apparent evolutionary reversal, the presence of phenotypic clines through time, the extent of phenotypic variation within populations and abundance of morphological intermediates between disparate end-member types, the wide geographic distributions of phenotypic clines and variants, and the subtle asymmetry of morphological transitions bounding the evolutionary excursion.

From census and biometric analyses of stratigraphically constrained samples, we conclude that morphological change was not focused at speciation and the pattern of evolution does not conform to the classical paradigm of punctuated equilibrium. Instead, we infer that observed patterns are best explained by phyletic evolution, at widely varying rates, combined with ecophenotypic plasticity. Evolution targeted the potential to form radial folds; the expression of those in any individual was determined, in part at least, by environmental cues. Ecophenotypic plasticity in A. sulcatus was itself probably an evolutionary response favored by the presence of long-lived planktotrophic larvae and wide dispersal of the species. In A. sulcatus, there is a continuum of pattern between intrapopulational, ecophenotypic variation that can be observed on bedding planes, interregional variation, and phyletic change through time. We argue that this continuity of pattern is most easily explained by continuity of process: in the case of the visually striking radial folds in A. sulcatus, there is no reason to invoke distinct hierarchies of macro- and microevolution; instead, these seem to be parts of a continuum.

Paleobiologists must propose a priori hypotheses of homology when conducting a phylogenetic analysis of extinct taxa. The distributions of such “primary” homologies among species are fundamental to phylogeny reconstruction because they reflect a prior belief in what constitutes comparable organismal elements and are the principal determinants of the outcome of phylogenetic analysis. Problems arise when fossil morphology presents seemingly equivocal hypotheses of homology, herein referred to as antinomies. In groups where homology recognition has been elusive, such as echinoderms, these problems are commonly accompanied by the presence (and persistence) of poor descriptive terminology in taxonomic literature that confounds an understanding of characters and stymy phylogenetic research. This paper combines fossil morphology, phylogenetic systematics, and insights from evolutionary developmental biology to outline a research program in Phylogenetic Paleo-ontogeny. A “paleo” ontogenetic approach to character analysis provides a logical basis for homology recognition and discerning patterns of character evolution in a phylogenetic context. To illustrate the utility of the paleo-ontogenetic approach, I present a reassessment of historically contentious plate homologies for “pan-cladid” crinoids (Cladida, Flexibilia, Articulata). Developmental patterns in living crinoids were combined with the fossil record of pan-cladid morphologies to investigate primary posterior plate homologies. Results suggest the sequence of morphologic transitions unfolding during the ontogeny of extant crinoids are developmental relics of their Paleozoic precursors. Developmental genetic modules controlling posterior plate development in pan-cladid crinoids have likely experienced considerable constraint for over 250 million years and limited morphologic diversity in the complexity of calyx characters. Future phylogenetic analyses of pan-cladids are recommended to consider the presence of a single plate in the posterior region homologous with the radianal, rather than the anal X, as is commonly assumed.