When transitional fossils blur previously clear boundaries between major groups, drawing that line can be problematic. While the need to rigorously define formal taxon names is widely acknowledged (e.g., de Queiroz and Gauthier 1992; Cantino et al. 1997), the need for similar precision in the scientific use of vernacular terms is not widely appreciated. The lack of accepted usages for common names has engendered endless arguments about when a fish becomes (also?) a tetrapod (e.g., Clack 1997), when a dinosaur becomes (also?) a bird (e.g., Padian and Chiappe 1998), and when a mammal-like reptile becomes (also?) a mammal (e.g., Rowe and Gauthier 1992). Recent descriptions of fossil snakes with well-developed hindlimbs have raised similar questions about where to draw the line between lizards and snakes and initiated a lively debate over the origin of snakes. However, lack of a precise definition of the vernacular term “snake,” as well as lack of a consensus on what constitutes a higher taxon's “origins,” has seriously hindered discussion of “snake origins.” Here, precise definitions of both terms are proposed and justified and their paleobiological implications discussed. The origin of higher taxa remains one of the most intriguing macroevolutionary problems, but scientists risk arguing at cross-purposes unless they agree on the exact boundaries of vernacular groups, and the exact meaning of the term “origin.”

Sideritic “coprolites” from the late Miocene of southwest Washington, the Upper Cretaceous of Saskatchewan and Madagascar, and the Permian of China have often been claimed to be pseudofossils. They are here interpreted as intestinal casts (cololites) prefossilized by bacterial activity and later transformed into siderite with no traces of original food particles left. All occurrences are found within fluvial overbank deposits that carry no other vertebrate remains. Their absence could be due to aquifer roll-fronts that destroyed phosphatic bones and teeth but favored siderite precipitation.

Analyses of limb joint morphology in nonmammalian therapsid “mammal-like reptiles” have suggested that among many lineages, individual animals were capable of shifting between sprawling and upright hindlimb postures, much like modern crocodilians. The ability to use multiple limb postures thus might have been ancestral to the generally more upright posture that evolved during the transition from “mammal-like reptiles” to mammals. Here I derive a biomechanical model to test this hypothesis through calculations of expected posture-related changes in femoral stress for therapsid taxa using different limb postures. The model incorporates morphological data from fossil specimens and experimental data from force platform experiments on iguanas and alligators.

Experimental data suggest that the evolutionary transition from sprawling to nonsprawling posture was accompanied by a change in the predominant loading regime of the limb bones, from torsion to bending. Changes in the cross-sectional morphology of the hindlimb bones between sphenacodontid “pelycosaurs” and gorgonopsid therapsids are consistent with the hypothesis that bending loads increased in importance early in therapsid evolution; thus, bending stresses are an appropriate model for the maximal loads experienced by the limb bones of theriodont therapsids. Results from the model used to estimate stresses in these taxa do not refute the use of both sprawling and more upright stance among basal theriodont therapsids. Thus, the hypothesis that the use of multiple postures was ancestral to the more upright posture typical of most mammals is biomechanically plausible. Model calculations also indicate that the axial rotation of the femur typical in sprawling locomotion can reduce peak bending stresses. Therefore, as experimental data from alligators and iguanas suggest, the evolution of nonsprawling limb posture and kinematics in therapsids might have been accompanied by increased limb bone bending stress.

Histologic studies of embryonic and perinatal longbones of living birds, non-avian dinosaurs, and other reptiles show a strong phylogenetic signal in the distribution of tissues and patterns of vascularization in both the shafts and the bone ends. The embryonic bones of basal archosaurs and other reptiles have thin-walled cortices and large marrow cavities that are sometimes subdivided by erosion rooms in early stages of growth. The cortices of basal reptiles are poorly vascularized, and osteocyte lacunae are common but randomly organized. Additionally, there is no evidence of fibrolamellar tissue organization around the vascular spaces. Compared with turtles, basal archosaurs show an increase in vascularization, better organized osteocytes, and some fibrolamellar tissue organization. In dinosaurs, including birds, vascularization is greater than in basal archosaurs, as is cortical thickness, and the osteocyte lacunae are more abundant and less randomly organized. Fibrolamellar tissues are evident around vascular canals and form organized primary osteons in older perinates and juveniles.

Metaphyseal (“epiphyseal”) morphology varies with the acquisition of new features in derived groups. The cartilage cone, persistent through the Reptilia (crown-group reptiles, including birds), is completely calcified in ornithischian dinosaurs before it is eroded by marrow processes; cartilage canals, absent in basal archosaurs, are present in Dinosauria; a thickened calcified hypertrophy zone in Dinosauria indicates an acceleration of longitudinal bone growth.

Variations in this set of histological synapomorphies overlap between birds and non-avian dinosaurs. In birds, these variations are strongly correlated with life-history strategies. This overlap, plus independent evidence from nesting sites, reinforces the hypothesis that variations in bone growth strategies in Mesozoic dinosaurs reflect different life-history strategies, including nesting behavior of neonates and parental care.

Theoretical models of skeletal structures provide suitable frameworks to assess macroevolutionary patterns of form change. We discuss three theoretical approaches to account for morphological patterns of the pelvic girdle in archosaurs. Every approach targets a different level of organization within the concept of morphospace. First, we build a morphocline by applying a mathematical transformation to the outline of the hip of the theropod dinosaur Deinonychus antirrhopus, in order to look at theoretical paths of evolutionary change based on changes of proportion. Second, we analyze the variability of a sample of 86 hips within a theoretical construction that incorporates information about the spatial orientation of the three paired bones that build this skeletal compound. Finally, we look at boundary patterns within these hips as a basis for generating a formalism based on graph theory. Insights about the evolution and development of the archosaur triradiate pelvis and its morphological trends are suggested in the light of each theoretical approach, with a special focus on the convergent evolution of a retroverted pubis in ornithischians and birds.

We infer the absolute completeness of the mammalian fossil record of the Iberian Neogene, from a compiled database of preserved stratigraphic ranges for both species and genera and by means of the analytical tools developed by Foote and Raup (1996). We conclude that the mammalian fossil record from the Neogene of the Iberian Peninsula is very complete (more than 75% at the specific level, and more than 90% at the generic one), being a good indicator of how complete the record of terrestrial organisms can be at least under certain favorable conditions. Comparison with previously published results for well-known marine invertebrates indicates that the continental Iberian Neogene record is not significantly less complete, thus raising doubts about the importance of more episodic deposition in continental environments. It remains to be seen if continental faunas in general are as complete as the marine invertebrate record.

Many Tertiary species of Crassostrea appear to have inhabited shallow-marine environments where they produced extremely large and thick shells. In contrast, living Crassostrea species are restricted primarily by marine predation to brackish, hypersaline, and intertidal environments where they produce comparatively smaller and thinner shells. If Crassostrea populations have used estuarine environments as a refuge from predation since the Cretaceous, then their presence in fully marine environments after the Cretaceous is puzzling. In order to interpret differences in environment and shell size, I examined the paleoecology and sclerochronology of two marine and two estuarine populations. Results are consistent with the hypothesis that thicker shells in Tertiary Crassostrea titan deterred increased exposure to fully marine predation. Life spans and growth rates estimated from annually formed growth increments show that C. titan grew significantly faster in shell thickness, as well as lived two to three times longer, than Quaternary Crassostrea virginica. Similar or lower valve-height growth rates in C. titan, as well as thinner shell walls in the attachment area, are consistent with exposure to marine predation, but not with alternative factors, such as higher salinity or alkalinity. Thicker valves in C. titan resulted from the successive addition of chalky deposit layers, in contrast to C. virginica valves, which contain significantly less of this unusual shell structure. A high incidence of incomplete drill holes in juvenile C. titan shells demonstrates that their thick valves were successful in deterring muricid predation. The association of C. titan with other large suspension feeders (barnacles and pectenids), as well as with phosphatic-pellet sediments, suggests that elevated planktic productivity may have supported this reefal community and enabled C. titan to grow thicker shells. The occurrence of both shallow-marine and estuarine Crassostrea since the Cretaceous raises the possibility that estuaries have served as refugia from which populations have dispersed into fully marine environments multiple times through the Cenozoic.

Globorotalia truncatulinoides is an extant species of planktic foraminiferans commonly used for stratigraphic and paleoenvironmental analyses. It originated ∼2.8 m.y. ago in subtropical areas of the South Pacific, spread to all subtropical and temperate regions of the world ocean, and expanded its range to southern subantarctic waters between 500 and 200 Ka. The wide geographic distribution of G. truncatulinoides is associated with a latitudinal morphological variability considered as an ecophenotypic variation within a single species. Here, we present the first molecular, morphological, and ecological evidence that G. truncatulinoides corresponds to a complex of four genetic species adapted to particular hydrographic conditions. The different species are separated by significant genetic distances in several ribosomal genes (SSU, ITS-1, 5.8S, ITS-2). Species 1 and species 2 characterize subtropical waters, species 3 is abundant exclusively in the Subantarctic Convergence, while species 4 inhabits subantarctic waters. By using an absolute molecular clock, we deduce the time of divergence between the subtropical and frontal/subantarctic species at ∼300 Ka, which is in agreement with stratigraphic data and suggests an adaptive radiation of the species allowing it to colonize the nutrient-rich and cold subantarctic waters. This genetic dichotomy is associated with a morphological differentiation identified using outline analysis. Species of the same regions are more similar in test shape but can be distinguished by coiling direction. The evolutionary patterns recognized here by combining DNA and morphological analyses from plankton-tow specimens mirror and allow a new interpretation of the data available from Recent sediments. They highlight the importance of adaptation and heterochronic processes, leading to cryptic speciation, in planktic foraminifera.

Recent works have suggested that the fossil record exhibits a fractal structure; i.e., that processes, such as extinction, follow a power-law size distribution and their time series show a 1/f power spectrum. This structure has been used as evidence that evolutionary dynamics are an example of a self-organized critical (SOC) process. We have reexamined this claim by analyzing a detailed record of marine genus-level extinctions and originations. Our results indicate that neither extinctions nor origination metrics show the power-law size distribution or a 1/f power spectrum characteristic of SOC and related models. We also believe that the underlying assumptions of SOC are incompatible with our understanding of the processes controlling macroevolutionary patterns.

Statistical analyses of the data sets are compatible, however, with the presence of multifractal self-similarity in both records, consistent with a hierarchical and multiplicative generating process. This model assumes that multiple causal mechanisms, acting over many spatial and temporal scales, interact to promote or inhibit originations and extinctions. In this view, the same event can have quite different impacts depending on the state of the biotic or physical system at the time that it occurs. This may at least partially explain such phenomena as the imperfect correlation between eustatic sea-level changes and macroevolutionary processes and the apparent nonlinear response of biotic systems to bolide impacts.

Previous estimates of the global generic diversity loss for echinoids at the Cretaceous/Tertiary boundary have been as high as 65%. However, these estimates are based on compilations of occurrence data from the existing literature and are plagued by problems of inconsistent taxonomic usage. Analysis of a taxonomically standardized, phylogenetically framed data set demonstrates that the generic extinction rate for heart urchins was 33%, and that the two constituent orders suffered markedly different fates. Whereas holasteroids lost 56% of their generic diversity at the end of the Cretaceous, only 17% of spatangoid genera became extinct. Correlation of extinction with a range of geographical, environmental, and biological factors has been explored. Survivorship is significantly correlated only with feeding strategy, implying that the extinctions of atelostomate echinoids at the Cretaceous/Tertiary boundary were nutrient driven. In addition, feeding strategy is correlated with atelostomate clade affinity, explaining the differential fates of holasteroids and spatangoids at the end of the Cretaceous.

A method is presented for the digital reconstruction of weakly calcified fossils within the Nama Group, Namibia. These recently described fossils (Grotzinger et al. 2000) are preserved as calcitic void-fill in a calcite matrix, and individual specimens cannot be freed by conventional techniques. The technique presented here has several integrated steps: (1) the analysis of cross-sections of fossil specimens, (2) the construction of a three-dimensional “tomographic” model that is assembled from the cross-sections, (3) the development of an idealized mathematical model based upon geometric parameters measured from the tomographic model, and (4) the visualization of randomly oriented cross-sections through the mathematical model, which can be compared with fossil cross-sections in outcrop.

In this procedure, rocks containing the fossils are ground and digitally photographed at thickness intervals of 25 μm. A battery of image-processing techniques is used to obtain the contour outlines of the fossils in serial cross-sections. A Delaunay triangulation method is then used to reconstruct the morphology from tetrahedrons which connect the contours in adjacent layers. We found that most of the fossils represent a single morphology with some well-defined characters that vary slightly among individual specimens. This fossil morphology was described by Grotzinger et al. (2000) as Namacalathus hermanastes. A mathematical description of the morphology is used to obtain a database of randomly oriented synthetic cross-sections. This database reproduces the vast majority of cross-sections observed in outcrop.

In a recent Matters of the Record, Vermeij (1999) identifies what he regards as a fundamental problem with cladistic analysis. “The phylogenetic method,” he states (p. 431), “derives phylogeny in one part of the tree by relying on character-taxon relationships in another part of the tree, in direct violation of the principle that clades, once they have diverged from each other, are independent of one another.” Vermeij fails to appreciate the distinction between pattern-based cladograms, which are hierarchies founded on homology hypotheses, and logically contingent, process-based trees, which are depictions of temporal evolution. As a result, he treats cladograms as literal and direct estimates of evolution and thus confuses the treatment of characters and taxa in parsimony analyses with biological processes and interactions.

The use of geologic age or range data in phylogenetic reconstruction is strongly debated (Cracraft and Eldredge 1979; Smith 1994; Fox et al. 1999; Heyning and Thacker 1999). Vermeij (1999) voiced concern regarding ‘rectangular data matrices’ and concluded that stratigraphic data are particularly suitable for improving phylogenetic inference. We find two major problems with his conclusion and question the validity of stratocladistics or any other phylogenetic method incorporating temporal data (e.g., Wagner 1998).

Phylogenetic methodology has always attracted more than its share of controversy, so I expected critical responses to my 1999 piece on the evolutionary implications of character-taxon matrices. In that piece, I argued that the topology of a clade, as inferred from cladistic parsimony analysis of a rectangular matrix of characters and taxa, is influenced by all the taxa considered, including those that fall outside the clade in question. The inferred pattern of branching in the clade is therefore statistically influenced by and dependent on the inferred evolutionary pattern among the other taxa. This dependence is at odds with the principle that, once sister-groups of eukaryotes have diverged, their subsequent pathways of evolution are independent of each other. I also suggested that, along with evidence from ontogeny, times of appearance of taxa as inferred from stratigraphic data be allowed to influence interpretations of which characters are primitive and which are derived.