Vertebrate tracks are a unique, abundant source of fossil data that supplements the skeletal record in many ways. However, the utility of ichnofossil data depends on how specifically the authors of tracks can be identified. Despite this fact, there is little consensus about how to identify potential trackmakers, and existing methods differ in their bases, assumptions, and corresponding implications.

In this paper we support the proposal that trackmakers should be identified primarily by skeletal structures that are both preserved in the ichnofossils and synapomorphies of some body-fossil clade. This synapomorphy-based technique enables certain taxa to be positively identified as candidate trackmakers and others to be excluded from consideration. In addition, the diagnostic level of the synapomorphy (i.e., to a higher or lower level) corresponds to that of the trackmaker. Additional features, such as body size and provenance, can be used in association with synapomorphies as additional differentiae of trackmaker identity.

Trackway analyses are dependent on the level of trackmaker diagnosis, but not all analyses require the same diagnostic specificity. Palichnostratigraphic correlations to the stage level are shown to require at least a genus-level identification of a trackmaker, whereas studies of vertebrate distributions (i.e., origins, extinctions, ranges) accommodate much coarser designations. Anachronistic occurrences of trace and body fossils result in range extensions for either the skeletal taxon or the feature in question. For example, the temporal distribution of theropods can be extended on the basis of the footprint record, resulting in an earlier estimated divergence time for Dinosauria.

Populations of planktic foraminifera display “proportionate” coiling (approximately 50% sinistral and dextral individuals given the data at hand) or may have “biased“ coiling, in which populations are dominated by either sinistral or dextral individuals. The major radiations of planktic foraminifera in the Late Cretaceous, the Paleocene to early Eocene, the middle Eocene, and the Neogene were each initiated by clades with proportionate coiling but subsequently accumulated sinistral and dextral species over time. Upper Maastrichtian foraminifera were predominantly dextral, but only the small number of species with proportionate coiling actually survived the Cretaceous/Paleogene mass extinction. The first Paleocene species with biased coiling appeared about four million years after the extinction and gradually came to represent as much as 50–60% of the tropical species diversity by the latest Paleocene. Tropical taxa with biased coiling suffered a second extinction in the late early Eocene and renewed a trend toward an increased abundance of species with biased coiling in the middle Eocene.

Our results for the Paleogene reflect a recurring theme in foraminifer evolution. In each radiation, once the founding species of a clade developed a biased-coiling mode, the descendants tended to maintain biased coiling until the extinction of the clade. The iterative evolution of biased coiling appears to represent an example in which a fundamental feature of development becomes fixed in a clade and inhibits reversion to an ancestral state. Apparently, coiling patterns are heritable in contrast with previous interpretations that coiling is environmentally controlled. On evolutionary timescales, species with proportionate coiling are less susceptible to extinction than species dominated by sinistral or dextral forms. Differential survivorship ensures that each radiation is initiated from founders with proportionate coiling following mass extinction. Hence, coiling preferences represent a case where the establishment of an evolutionary trend is caused by drift away from a “limiting boundary,” much like the evolution of large body size from ubiquitous small ancestors.

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.

The Ordovician Radiation exhibited a global transition in dominance from the Cambrian evolutionary fauna (e.g., trilobites), to the Paleozoic and Modern faunas (e.g., articulate brachiopods and bivalve molluscs). Although its causes have yet to be determined definitively, the transition coincided with increased global tectonism. Erosion of source areas uplifted during orogenic activity increased the siliciclastic richness of marine substrates in many venues, and it has been hypothesized previously that higher taxa with affinities for siliciclastics diversified in association with these environmental changes, whereas higher taxa not exhibiting such affinities either failed to radiate or declined in diversity. Here, we provide an initial test of this substrate affinity hypothesis by evaluating the Ordovician affinities of trilobites and articulate brachiopods.

Our analyses—at the class level for both trilobites and articulate brachiopods, and at the order level for orthid and strophomenid brachiopods—were based on the affinities of constituent genera for siliciclastic, carbonate, and mixed siliciclastic/carbonate settings. Individual genus affinities are calculated with a database of genus occurrences encompassing nine Ordovician paleocontinents. Using these values, we developed a standardized relative affinity (SRA) metric to compare the propensities of higher taxa, and to assess changes in relative affinities of individual higher taxa from series to series.

A simple comparison of trilobites and articulate brachiopods for the Ordovician in aggregate does not appear to support the substrate affinity hypothesis: articulate brachiopods, which contributed increasingly to overall diversity through the period, exhibit an overall affinity for carbonates and an aversion to siliciclastics. However, a rather different view emerges when we consider the affinity trajectories of higher taxa through the period: articulate brachiopods exhibit a growing affinity for siliciclastics and a declining affinity for carbonates, whereas the opposite is the case among trilobites. Among constituent articulate brachiopod orders, the affinity trajectories of orthids and strophomenids mirror that of the class. Thus, the increasing dominance of articulate brachiopods in the Middle and Late Ordovician may have been linked to the affinity for siliciclastics of a diversifying subset of the group, but further investigation will be required to verify this claim.

A spatial approach was employed to test whether the conchological differentiation of the Recent land snail Albinaria terebra from southern central Crete (Greece) is decreased in areas that have been more recently colonized by the species. The eastern Mediterranean genus Albinaria has produced more than 120 species, probably in pre-Tortonian events of radiation. A. terebra occupies a compact range of 550 km2 consisting partly of late Cenozoic deposits of different ages, partly of pre-Cenozoic formations. The morphological study was based on 300 samples distributed over the entire range of the species. Shell size, shape, whorls, and teleoconch rib densities exhibited no evident correlation with environment but were subjected to considerable spatial variations. The differentiation, determined as the difference of the mentioned shell parameters between one population and another population 2–4 km distant, was found to increase continuously with the time (1–12 Myr) the land has been exposed to air. The populations with the highest degrees of spatial variation came from two areas that have never been submerged in the late Cenozoic, possibly the oldest populations of the species. It is plausible that the other areas were colonized by range expansion after late Neogene periods of tectonic uplift. The results are consistent with previous conclusions derived from molecular studies setting the radiation of Albinaria prior to the Tortonian and imply that we might be in possession of a new tool to detect information on the phylogeographic history of land snail species.

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.

Teleost otoliths are located in the membranous labyrinth and are mainly composed of aragonite and a small amount of organic matrix. Their rhythmic growth may provide important data about age, growth, maturity, and life-history events.

This article presents insights into paleoecological and evolutionary details from a study of the otolith microstructure of Trisopterus kasselensis, Trisopterus sculptus, and Pterothrissus umbonatus (Oligo-Miocene, North Sea Basin). Otoliths of Recent Trisopterus minutus were analyzed using the same methods (light and electron microscopy, thin slides) as a basis for comparison with the fossil sample.

Growth structures similar in size and aspect to the seasonal and daily growth increments in living fish indicate both individual age and early life transitions in habitat and life strategy suggesting planktonic larvae and benthic juveniles. The aspect of rhythmic growth patterns is due to lunar periodicity, a common feature in fish otoliths. Moreover, fossil Trisopterus show an phylogenetic increase in otolith—and consequently—somatic growth, indicating a change of life strategy during evolution (Oligocene to Recent).

Thus the internal structure of fossil otoliths allows the determination of growth, age composition, and early life history of fossil fish, as well as their direct comparison with living relatives.

During the Ordovician Radiation, domination of benthic marine communities shifted away from trilobites, toward articulate brachiopods, and, to a lesser degree, toward bivalves and gastropods. In this paper, we identify the patterns in origination and extinction probabilities that gave rise to these transitions. Using methods adapted from capture-mark-recapture (CMR) population studies, we estimate origination, extinction, and sampling probabilities jointly to avoid confounding patterns in turnover rates with temporal variation in the quality of the fossil record. Not surprisingly, higher extinction probabilities in trilobites relative to articulate brachiopods, bivalves, and gastropods were partly responsible for relative decreases in trilobite diversity. However, articulate brachiopods also had higher origination probabilities than trilobites, indicating that relative increases in articulate brachiopod diversity would have occurred even in the absence of between-class differences in extinction probabilities. This contrasts with inferences based on earlier Phanerozoic-scale, long-term averages of turnover probabilities, and it indicates that a major cause of this faunal transition has been overlooked.

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).

The Neogene paleoisland from the area of Gargano, Italy, has yielded numerous fossil vertebrates, some of them showing extraordinary morphological peculiarities due to island evolution. Among them, Microtia (Freudenthal 1976) is the dominant rodent genus in the Gargano palaeofauna and is represented by at least three evolutionary lineages. The incisors are used to describe the size evolution in these lineages, and we come to the conclusion that these lineages did not follow the same evolutionary trend: two of them evolve toward larger size, while the third one shows a slight decrease in size. In addition, we describe the evolution of the curvature of the lower incisor, compared with that of body-size. The evolution of Microtia is characterized by a specialization for burrowing, which may be accompanied by either an increase or a decrease in size. Finally, we propose that the evolutionary change among these three sympatric lineages allowed Microtia to minimize competition between species, by avoiding size overlaps.

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.

Clypeasteroid echinoids are a familiar and easily defined clade with a cryptic origin. They first appear in the late Paleocene and are believed to have arisen from cassiduloid ancestry, but identifying sister-group relationships more precisely has proved difficult. Two factors are responsible for this problem, the extreme morphological conservatism of cassiduloids, which has given rise to high levels of character exhaustion, and the origin of crown-group clypeasteroids through paedomorphosis. Previous analyses, based on extant representatives alone or including all Mesozoic to Recent genera, have proved unsatisfactory.

Here a parsimony analysis is undertaken using a restricted set of all stem-group clypeasteroids and cassiduloid taxa that existed immediately prior to the appearance of crown-group clypeasteroids. Inclusion of Togocyamus, the fossil taxon lying closest to the origin of crown-group clypeasteroids, is phylogenetically uninformative because that taxon is highly paedomorphic and has only generalized juvenile characteristics. However, earlier stem-group plesions provide critical data that identify Apatopygidae as extant sister group to the Clypeasteroida. Stratigraphically restricted analyses cannot eradicate the problems that arise from character exhaustion, but can minimize these with respect to specific phylogenetic questions.

The degree of hierarchical structure of organisms—the number of levels of nesting of lower-level entities within higher-level individuals—has apparently increased a number of times in the history of life, notably in the origin of the eukaryotic cell from an association of prokaryotic cells, of multicellular organisms from clones of eukaryotic cells, and of integrated colonies from aggregates of multicellular individuals. Arranged in order of first occurrence, these three transitions suggest a trend, in particular a trend in the maximum, or an increase in the degree of hierarchical structure present in the hierarchically deepest organism on Earth. However, no rigorous documentation of such a trend—based on operational and consistent criteria for hierarchical levels—has been attempted. Also, the trajectory of increase has not been examined in any detail. One limitation is that no hierarchy scale has been developed with sufficient resolution to document more than these three major increases. Here, a higher-resolution scale is proposed in which hierarchical structure is decomposed into levels and sublevels, with levels reflecting number of layers of nestedness, and sublevels reflecting degree of individuation at the highest level. The scale is then used, together with the body-fossil record, to plot the trajectory of the maximum. Two alternative interpretations of the record are considered, and both reveal a long-term trend extending from the Archean through the early Phanerozoic. In one, the pattern of increase was incremental, with almost all sublevels arising precisely in order. The data also raise the possibility that waiting times for transitions between sublevels may have decreased with increasing hierarchical level (and with time). These last two findings—incremental increase in level and decreasing waiting times—are tentative, pending a study of possible biases in the fossil record.