In recent years several authors have questioned the reality of a widely accepted and apparently large increase in marine biodiversity through the Cenozoic. Here we use collection-level occurrence data from the rich and uniquely well documented New Zealand (NZ) shelfal marine mollusc fauna to test this question at a regional scale. Because the NZ data were generated by a small number of workers and have been databased over many decades, we have been able to either avoid or quantify many of the biases inherent in analyses of past biodiversity. In particular, our major conclusions are robust to several potential taphonomic and systematic biases and methodological uncertainties, namely non-uniform loss of aragonitic faunas, biostratigraphic range errors, taxonomic errors, choice of time bins, choice of analytical protocols, and taxonomic rank of analysis.

The number of taxa sampled increases through the Cenozoic. Once diversity estimates are standardized for sampling biases, however, we see no evidence for an increase in marine mollusc diversity in the NZ region through the middle and late Cenozoic. Instead, diversity has been approximately constant for much of the past 40 Myr and, at the species and genus levels, has declined over the past ~5 Myr. Assuming that the result for NZ shelfal molluscs is representative of other taxonomic groups and other temperate faunal provinces, then this suggests that the postulated global increase in diversity is either an artifact of sampling bias or analytical methods, resulted from increasing provinciality, or was driven by large increases in diversity in tropical regions. We see no evidence for a species-area effect on diversity. Likewise, we are unable to demonstrate a relationship between marine temperature and diversity, although this question should be re-examined once refined shallow marine temperature estimates become available.

Biological veracity of the sharp diversity increase observed in many analyses of the post-Paleozoic marine fossil record has been debated vigorously in recent years. To assess this question for sample-level (“alpha”) diversity, we used bulk samples of shelly invertebrates, representing three major fossil groups (brachiopods, bivalves, and gastropods), to compare the Jurassic and late Cenozoic sample-level diversity of marine benthos. After restricting the data set to single-bed, whole-fauna, bulk samples (n ≥ 30 specimens) from comparable open marine siliciclastic facies, we were able to retain 427 samples (255 Jurassic and 172 late Cenozoic), with most of those samples originating from our own empirical work.

Regardless of the diversity metric applied, the initial results suggest that standardized sample-level species (or genus) diversity, driven by evenness and/or richness of the most common taxa, increased between the Jurassic and late Cenozoic by at least a factor of 1.6. When the data are partitioned into the three dominant higher taxa, it becomes clear that (1) the bivalves, which dominated the samples for both time intervals, increased in sample-level diversity between the Jurassic and the late Cenozoic by a much smaller factor than the total fauna; (2) the removal of brachiopods, which were a noticeable component of the Jurassic samples, did not significantly affect standardized sample-level diversity estimates; and (3) the gastropods, which were rare in the Jurassic but common in many late Cenozoic samples, contributed notably to the increase in sample-level diversity observed between the two time intervals. Parallel to these changes, the samples revealed secular trends in ecological structure, including Jurassic to late Cenozoic increases in proportion of (1) infauna, (2) mobile forms, and (3) non-suspension-feeding organisms. These trends mostly persist when data are restricted to bivalves.

Supplementary analyses indicate that these patterns cannot be attributed to sampling heterogeneities in paleolatitudinal range, lithology, or paleoenvironment of deposition. Likewise, when data are restricted to samples dominated by species with originally aragonitic shells, the observed temporal changes persist at a comparable magnitude, suggesting that the pervasive loss of aragonite in the older fossil record is unlikely to have been the primary cause of the observed patterns. The comparable ratio of identified to unidentified species and genera, observed when comparing the Jurassic and late Cenozoic samples, indicates that the relatively poorer (mold/cast) preservation of Jurassic aragonite species also is unlikely to have been responsible for the observed patterns. However, the diagenesis-related taphonomic and methodological artifacts cannot be ruled out as an at least partial contributor to the observed post-Paleozoic changes in diversity, taxonomic composition, and ecology (the outcomes of the three tests of the diagenetic bias available to us are incongruent).

The study demonstrates that the post-Paleozoic trends in the sample-level diversity, ecology, and taxonomic structure of common taxa can be replicated across multiple studies. However, the diversity increase estimated here is much less prominent than suggested by many previous analyses. The results also narrow the list of causative explanations down to two testable hypotheses. The first is diagenetic bias—a spurious trend driven by either (a) increasing taphonomic loss of small specimens in the older fossil record or (b) a shift in sampling procedures between predominantly lithified rocks of the Mesozoic and predominately unlithified, and therefore sievable, sediments of the late Cenozoic. The second hypothesis is genuine biological changes—macroevolutionary trends in the structure of marine benthic associations through time, consistent with predictions of several related models such as evolutionary escalation, increased ecospace utilization, and the Mesozoic marine revolution. Future studies should focus on testing these two rival models, a key remaining challenge for identifying the primary causative mechanism for the long-term changes in sample-level diversity, ecology, and taxonomic structure observed in the Phanerozoic marine fossil record.

Inferring the causes for change in the fossil record has been a persistent problem in evolutionary biology. Three independent lines of evidence indicate that a lineage of the fossil stickleback fish Gasterosteus doryssus experienced directional natural selection for reduction of armor. Nonetheless, application to this lineage of three methods to infer natural selection in the fossil record could not exclude random process as the cause for armor change. Excluding stabilizing selection and genetic drift as the mechanisms for biostratigraphic patterns in the fossil record when directional natural selection was the actual cause is very difficult. Biostratigraphic sequences with extremely fine temporal resolution among samples and other favorable properties must be used to infer directional selection in the fossil record.

For almost 30 years, paleontologists have analyzed evolutionary sequences in terms of simple null models, most commonly random walks. Despite this long history, there has been little discussion of how model parameters may be estimated from real paleontological data. In this paper, I outline a likelihood-based framework for fitting and comparing models of phyletic evolution. Because of its usefulness and historical importance, I focus on a general form of the random walk model. The long-term dynamics of this model depend on just two parameters: the mean (μstep) and variance (σ2step) of the distribution of evolutionary transitions (or “steps”). The value of μstep determines the directionality of a sequence, and σ2step governs its volatility. Simulations show that these two parameters can be inferred reliably from paleontological data regardless of how completely the evolving lineage is sampled.

In addition to random walk models, suitable modification of the likelihood function permits consideration of a wide range of alternative evolutionary models. Candidate evolutionary models may be compared on equal footing using information statistics such as the Akaike Information Criterion (AIC). Two extensions to this method are developed: modeling stasis as an evolutionary mode, and assessing the homogeneity of dynamics across multiple evolutionary sequences. Within this framework, I reanalyze two well-known published data sets: tooth measurements from the Eocene mammal Cantius, and shell shape in the planktonic foraminifera Contusotruncana. These analyses support previous interpretations about evolutionary mode in size and shape variables in Cantius, and confirm the significantly directional nature of shell shape evolution in Contusotruncana. In addition, this model-fitting approach leads to a further insight about the geographic structure of evolutionary change in this foraminiferan lineage.

Ontogenetic stages of trilobites have traditionally been recognized on the basis of the development of exoskeletal segmentation. The established protaspid, meraspid, and holaspid phases relate specifically to the development of articulated joints between exoskeletal elements. Transitions between these phases were marked by the first and last appearances of new trunk segment articulations. Here we propose an additional and complementary ontogenetic scheme based on the generation of new trunk segments. It includes an anamorphic phase during which new trunk segments appeared, and an epimorphic phase during which the number of segments in the trunk remained constant. In some trilobites an ontogenetic boundary can also be recognized at the first appearance of morphologically distinct posterior trunk segments. Comparison of the phase boundaries of these different aspects of segment ontogeny highlights rich variation in the segmentation process among Trilobita. Cases in which the onset of the holaspid phase preceded onset of the epimorphic phase are here termed protarthrous, synchronous onset of both phases is termed synarthromeric, and onset of the epimorphic phase before onset of the holaspid phase is termed protomeric. Although these conditions varied among close relatives and perhaps even intraspecifically in some cases, particular conditions may have been prevalent within some clades.

Trilobites displayed hemianamorphic development that was accomplished over an extended series of juvenile and mature free-living instars. Although developmental schedules varied markedly among species, morphological transitions during trilobite development were generally regular, limited in scope, and extended over a large number of instars when compared with those of many living arthropods. Hemianamorphic, direct development with modest change between instars is also seen among basal members of the Crustacea, basal myriapods, pycnogonids, and in some fossil chelicerates. This mode may represent the ancestral condition of euarthropod development.

The discrete cosine transform (DCT) is a Fourier-related transform widely used in signal processing and well suited to analyzing open outlines such as ammonite ribs. The method is applied here to depict and decipher the ribbing morphospace of a large group of Lower Jurassic ammonites composed of the Oxynoticeratidae and their close ancestors. Because they are clearly associated with buoyancy and/or swimming ability, the usually clearly involute, comparatively smooth and compressed shells of these ammonites may well be misleading taxonomic markers. In this context, quantitative analysis of the ribbing pattern using the DCT may significantly improve our perception of the ornamental patterns expressed within the group. A set of 251 specimens illustrating the worldwide fauna and selected from more than 80 publications is analyzed. Big differences are found in the evolutionary patterns of the two main lineages of Oxynoticeratidae currently accepted in the literature. A previously unsuspected Mediterranean group comprising principally the genus Parasteroceras is identified from its distinctive ornamentation. The northwest European and Mediterranean genera Eparietites, Oxynoticeras, and Parasteroceras do not feature among the American (East Pacific) faunas. This finding calls into question some generally accepted correlations between European and American stratigraphic frameworks. The study shows that the DCT is a valuable tool for discriminating between species within the huge and often puzzling range of ornamental variation of the main genera (e.g., Gleviceras and Radstockiceras).

Spinal ossified tendons are a defining character for Ornithischia, one of the two major clades of dinosaurs. The function of these bony rods has remained a mystery since their first detailed description in 1886. Qualitative approaches to understand ossified tendon function have resulted in different ecological and behavioral interpretations for ornithopod dinosaurs. To evaluate ossified tendon function, this study constructed finite element models of the vertebral column for two ornithopod taxa: Tenontosaurus, which shows the plesiomorphic condition of longitudinally arrayed tendons along the spinous processes, and Brachylophosaurus, which exhibits a lattice of tendons along the spinous processes. Both models predict that ossified tendons stiffened the vertebral column, especially the tail, but the derived lattice of ossified tendons in iguanodontoidean dinosaurs, like Brachylophosaurus, increased spinal stiffness more than the plesiomorphic condition. Caudofemoral muscles that retracted the hindlimb during locomotion attached the femur to the tail in ornithopods. Increased tail stiffness caused by intratendinous ossification may have influenced locomotion by rigidly anchoring M. caudofemoralis longus to the tail, thereby allowing a more forceful retraction of the hindlimb by reducing ventral flexion of the tail during muscle contraction. Ossified tendons may also have been important for storing elastic energy throughout the gait cycle. Moreover, the lattice of ossified tendons stiffened the trunk and tail nearly equally in Brachylophosaurus, indicating the evolution of a postural function by passively supporting the epaxial musculature in maintaining a horizontal vertebral column.

We describe three giant palaeobatrachid fossil tadpoles of the genus Palaeobatrachus (Nieuwkoop-Faber [NF] stages 60–64) from the Miocene of Randecker Maar, Germany. The largest was 150 mm at the beginning of metamorphosis (stage 60), whereas the smallest was 100 mm and approaching the end of metamorphosis (stage 64). In contrast, normal palaeobatrachid tadpoles and their pipid relatives, both extinct and extant, rarely exceed 60 mm in length. We review here both ecological and pathological conditions that are conducive to the development of gigantism in tadpoles. Tadpoles that lack a thyroid gland become exceptionally large and arrest development at early hindlimb stages (NF stages 53–56). However, the advanced metamorphic stages of the giant Palaeobatrachus tadpoles indicate that they were able to metamorphose, and thus were not athyroid. Environmental factors—pond size and permanence, predators, duration of the growing season—may all contribute to tadpole gigantism in certain extant anuran species. We identify suites of ecological features that distinguish extant anurans with large tadpoles from high-latitude and high-altitude permanent lakes in temperate regions (e.g., certain Rana and Telmatobius) from tropical species, such as Pseudis paradoxa, whose tadpoles normally achieve large size in temporary seasonal ponds. The paleoecology of Randecker Maar suggests that Palaeobatrachus tadpoles lived in a permanent semitropical lake, but one with few predators.