Approaches to patterns of diversification based on counting taxa at a given rank can be misleading, even when all taxa are monophyletic. Such “rank-based” approaches are unable to reflect a hierarchy of evolutionary events because taxa of the same rank cannot be nested within one another. Phylogenetic trees specify an order of origination of characters and clades and can therefore be used in some cases to test hypotheses on causal relationships between characters and changes in diversity. “Tree-thinking” also clarifies discussions of the age of groups, by distinguishing between splitting of the stem-lineage from its sister group and splitting of the crown-group into extant clades.

Cladistic evidence that Pentoxylon, Bennettitales, and Gnetales are the sister group of angiosperms implies that the angiosperm line (angiophytes) existed by the Late Triassic. The presence of primitive members of five basic angiosperm clades indicates that the crown-group (angiosperms) had begun to diversify by the mid-Early Cretaceous (Barremian-Aptian), but not necessarily much earlier. The greatest unresolved issue raised by cladistic analyses concerns the fact that the angiosperm tree can be rooted in two almost equally parsimonious positions. Trees rooted near Magnoliales (among “woody magnoliids”) suggest that the angiosperm radiation may have been triggered by the origin of intrinsic traits, e.g., a fast-growing, rhizomatous habit in the paleoherb and eudicot subgroup. However, trees rooted among paleoherbs, which are favored by rRNA data, imply that these traits are basic for angiosperms as a whole. This could mean that the crown-group originated not long before its radiation, or, if it did originate earlier, that its radiation was delayed due to extrinsic factors. Such factors could be a trend from environmental homogeneity and stability in the Jurassic to renewed tectonic activity and disturbance in the Early Cretaceous. Potentially relevant pre-Cretaceous fossils cannot be placed with confidence, but may be located along the stem-lineage (stem angiophytes); their generally paleoherb-like features favor the paleoherb rooting. The history of angiophytes may parallel that of Gnetales: some diversification of the stem-lineage in the Late Triassic, near disappearance in the Jurassic, and vigorous radiation of the crown-group in the Early Cretaceous.

The problem of how accurately paraphyletic taxa versus monophyletic (i.e., holophyletic) groups (clades) capture underlying species patterns of diversity and extinction is explored with Monte Carlo simulations. Phylogenies are modeled as stochastic trees. Paraphyletic taxa are defined in an arbitrary manner by randomly choosing progenitors and clustering all descendants not belonging to other taxa. These taxa are then examined to determine which are clades, and the remaining paraphyletic groups are dissected to discover monophyletic subgroups. Comparisons of diversity patterns and extinction rates between modeled taxa and lineages indicate that paraphyletic groups can adequately capture lineage information under a variety of conditions of diversification and mass extinction. This suggests that these groups constitute more than mere “taxonomic noise” in this context. But, strictly monophyletic groups perform somewhat better, especially with regard to mass extinctions. However, when low levels of paleontologic sampling are simulated, the veracity of clades deteriorates, especially with respect to diversity, and modeled paraphyletic taxa often capture more information about underlying lineages. Thus, for studies of diversity and taxic evolution in the fossil record, traditional paleontologic genera and families need not be rejected in favor of cladistically-defined taxa.

Morphological and taxonomic diversity each provide insight into the expansion and contraction of major biological groups, while the nature of the relationship between these two aspects of diversity also has important implications for evolutionary mechanisms. In this paper, I compare morphological and taxonomic diversity within the classes Blastoidea and Trilobita, and within the trilobite clades Libristoma, Asaphina, Proetida, Phacopida, and Scutelluina. Blastoid morphology is quantified with homologous landmarks on the theca, and trilobite form is measured with a Fourier description of the cranidium. Morphological diversity is measured as the total variance among forms in morphological space (proportional to the mean squared distance among forms). Blastoid taxonomic diversity is based on published compilation of stratigraphic ranges of genera. The Zoological Record was used to determine the number of new species of trilobites described since the publication of the Treatise; temporal patterns in species richness are similar to those for generic richness based on the Treatise, suggesting a common underlying signal.

Morphological variety and taxonomic richness often increase together during the initial diversification of a clade. This pattern is consistent with diffusion through morphospace, although some form of adaptive radiation cannot be ruled out. Morphological diversity varies little throughout much of the history of Proetida, a pattern that may suggest major constraints on the magnitude and direction of evolution, and that agrees with the perception of Proetida as a morphologically conservative group. Two major patterns are seen during the decline of clades. In Blastoidea, Trilobita, Libristoma, and Asaphina, morphological diversity is maintained at substantial levels, and in fact continues to increase, even in the face of striking reductions in taxonomic richness. This pattern suggests continued diffusion through morphospace and taxonomic attrition that is effectively non-selective with respect to morphology. In Phacopida, Scutelluina, and to some extent in Proetida, morphological diversity decreases along with taxonomic diversity. This pattern suggests heterogeneities such as elevated extinction and/or reduced origination in certain regions of morphospace. As found previously for the echinoderm subphylum Blastozoa, all studied clades of trilobites except Proetida show maximal morphological diversity in the Mid–Late Ordovician and maximal taxonomic diversity sometime during the Ordovician, suggesting some degree of common control on diversification patterns in these groups.

This analysis examines the evolution of the greater diversity of species with non-planktonic larval types relative to species with planktonic larval types in the turritellid gastropods. This sort of trend has been documented in both the fossil and recent biota of several gastropod families. Two mechanisms for generating diversity gradients in larval types have been proposed in the literature. The first, species selection, focuses on the population biology of larval types. The second proposes that factors in development that are mediated by organismal adaptation are responsible. Turritellids have been cited as a classic example of species selection. In order to examine the relevance of these two proposed mechanisms, a phylogenetic analysis of the turritellids using molecular sequence data was performed to determine the evolution of larval types in this clade. The resultant phylogeny suggests that species selection is not the only process driving the trend toward increasing numbers of non-planktonic species through time. Developmental processes, apart from those involving organismal adaptation (except in the trivial sense), are implicated as playing a role in this trend. In particular, these processes may involve changes in the timing of germ-line sequestration in organisms. Germ-line sequestration governs how accessible organisms are to heritable variation during ontogeny. Embryological evidence from gastropods suggests that non-planktonic species have early germ-line sequestration relative to planktonic species, making them more resistant to developmental change. Thus, non-planktonic lineages will only rarely revert to a planktonic larval mode.

The 18 m.y. history of the subfamily Equinae (exclusive of Archaeohippus and “Parahippus”) in North America consisted of a 3-m.y. radiation phase, a 9-m.y. steady-state diversity phase, and a 6-m.y. reduction phase. During the steady-state phase, species richness varied between 14 and 20, with two maxima at about 13.5 and 6.5 Ma. Species richness of the tribes Hipparionini and Equini was about equal through the middle Miocene, but hipparionines consistently had more species in the late Miocene and early Pliocene. Overall mean species duration was 3.2 m.y. (n = 50), or an average extinction rate of 0.31 m.y.-1 During the radiation phase, speciation rates were very high (0.5 to 1.4 m.y.-1), while extinction rates were low (<0.10 m.y.-1). Speciation and extinction rates both averaged about 0.15 m.y.-1 during the steady-state phase, with extinction rates having more variation. Extinction rates increased fourfold during the reduction phase, while speciation rates declined slightly. Late Hemphillian extinctions affected both tribes severely, not just the three-toed hipparionines, and were correlated with global climatic change.

After having been very abundant in the Early Maastrichtian Globotruncana gansseri zone, Inoceramus remains disappear from five stratigraphic sections in the Basque region of France and Spain in the lower Abathomphalus mayaroensis zone, ~2.5 m.y. before the Cretaceous–Tertiary boundary. Several lines of evidence demonstrate that these shell fragments are preserved in place and accurately record the pattern of the decline and disappearance of the group. The dominant taphonomic process seems to have been passive disaggregation of the shell as shell proteins decayed. The resulting shell fragments were dispersed only locally by burrowing organisms. Shell fragments decline in abundance over tens of meters of section and there are subtle differences between sections which suggests Inoceramus was eliminated by gradual changes in ecological conditions that affected the basin roughly simultaneously but with some geographic variability.

Analysis of molluscan collections from a 3+ m.y. interval around the Cretaceous–Tertiary (K–T) interval in east Texas suggests that molluscs suffered an extinction at or near the K–T boundary, followed by a prolonged period of stress which lasted through the P0 and P1a planktic foraminiferal zones. The stressed period was characterized by low species richness, low abundances of individuals, high species turnover and a dominance of deposit feeders. Species richness and the relative abundance of deposit feeders generally track the 13C depletion curve suggesting that the stress was caused by a lack of primary production. A stable, relatively diverse, suspension feeding molluscan community was reestablished less than two million years after the K–T boundary. The total number of species within the habitat did not recover to Cretaceous levels within the study interval.

We examined the radiocarbon age, taphonomic condition and stratigraphic position of shells of the venerid bivalve Chione spp. from the tidal flats of Bahia la Choya, Sonora, Mexico. Shells in Bahia la Choya are time-averaged. Thirty shells yielded radiocarbon dates from modern (A.D. 1950 or younger) to 3569 years before present. The median calendar age of inner flat shells is 483 years; the median age of tidal channel shells is 427 years. We interpret such long shell survival to be the result of frequent shallow burial. Such burial retards bioerosion of shells.

The taphonomic condition of shells varied with environment. Shells from the surface of the inner flats were better preserved than shells from the tidal channel. Shells are more likely to be physically worn and biologically degraded in the waters of the channel than on the quieter and more frequently exposed inner tidal flat. Taphonomic condition is an unreliable indicator of a shell's time-since-death. Poorly-preserved shells on the inner flats tended to be old, but in general shell condition was much more variable than shell age. A shell's condition is more likely the result of its total residence time on the surface than its time-since-death (surface time plus burial time).

Two composite short (44 cm and 50 cm) cores revealed varying degrees of stratigraphic disorder (the departure from perfect correlation between relative stratigraphic position and relative age). One of eight shells in the inner flats core was disordered; four of nine shells in the tidal channel were disordered. The actual age range of surface shells approximates the age range of shells in cores. Stratigraphic disorder is a consequence of both time-averaging and physical and biogenic mixing.

Time-averaging controls the degree of precision possible in paleoecological studies. Environmental changes and ecological phenomena occurring within a span of 3500 years would not be recognized in deposits like those of Bahia la Choya. Time-averaging and stratigraphic disorder also constrain the temporal resolution possible in microstratigraphic studies of evolution. The extent of time-averaging and stratigraphic disorder will dictate an appropriate sample interval. In order to prevent temporal overlap between successive samples in deposits like Bahia la Choya, sample spacing should not be less than approximately 0.5 m.