The origin and diversification of terrestrial communities has long been associated with the Devonian. The earliest known substantial assemblage of land plants and animals preserved in or close to their original habitats is still that of the Rhynie Chert peat bog, from Scotland, which is of Siegenian age.

Paleontologists have long stressed the need to know how sampling the fossil record might influence our knowledge of the evolution of life. Here, we combine fossil occurrences of North American marine invertebrates from the Paleobiology Database with lithologic data from Macrostrat to identify sampling patterns in carbonate and siliciclastic rocks. We aim to quantify temporal trends in sampling effort within and between lithologies, focusing on the proportion of total available volume that has been sampled (sampled fossiliferous proportion, here called κ). Results indicate that the sampled fossiliferous proportion was stable during the Paleozoic, and variable during the post-Paleozoic, but showed no systematic increase through time. Fossiliferous carbonate rocks are proportionally more sampled than siliciclastic rocks, with intervals where the carbonate κ is double the siliciclastic κ. Among possible explanations for the apparent oversampling of fossiliferous carbonate rocks, analyses suggest that barren units, taphonomic dissolution, or data entry errors cannot completely explain sampling patterns. Our results suggest that one of the important drivers might be that paleontologists publish taxonomic descriptions from carbonate rocks more frequently. The higher diversity in carbonate rocks might account for an ease in the description of unknown species and therefore a higher rate of published fossils. Finally, a strong effect in favor of carbonate rocks might distort our perception of diversity through time, even under commonly used standardization methods. Our results also confirm that previous descriptions of an increase in the proportion of sampled fossiliferous rocks over time were driven by the sampling of the nonmarine fossil record.

Principal coordinates analysis (PCoA) is a statistical ordination technique commonly applied to morphology-based cladistic matrices to study macroevolutionary patterns, morphospace occupation, and disparity. However, PCoA-based morphospaces are dissociated from the original data; therefore, whether such morphospaces accurately reflect body-plan disparity or extrinsic factors, such as body size, remains uncertain. We collated nine character–taxon matrices of dinosaurs together with body-mass estimates for all taxa and tested for relationships between body size and both the principal axis of variation (i.e., PCo1) and the entire set of PCo scores. The possible effects of body size on macroevolutionary hypotheses derived from ordinated matrices were tested by reevaluating evidence for the accelerated accumulation of avian-type traits indicated by a strong directional shift in PCo1 scores in hypothetical ancestors of modern birds. Body mass significantly accounted for, on average, approximately 50% and 16% of the phylogenetically corrected variance in PCo1 and all PCo scores, respectively. Along the avian stem lineage, approximately 30% of the morphological variation is attributed to the reconstructed body masses of each ancestor. When the effects of body size are adjusted, the period of accelerated trait accumulation is replaced by a more gradual, additive process. Our results indicate that even at low proportions of variance, body size can noticeably affect macroevolutionary hypotheses generated from ordinated morphospaces. Future studies should thoroughly explore the nature of their character data in association with PCoA-based morphospaces and use a residual/covariate approach to account for potential correlations with body size.

For the past twenty years, Ralph Gordon Johnson contributed significantly in three areas of paleobiology: understanding the dynamics of benthic marine communities, exploring the mode of formation of fossil assemblages, and describing the remarkably preserved Mazon Creek fauna.

Late Eocene foraminiferal extinction shows diverse patterns of selective morphologic and latitudinal extinction. Taxa with discoidal shape, calcareous tests, and narrow and low-latitudinal ranges are at significantly greater risk of extinction. Elevated extinction intensities in calcareous tests are mainly due to the presence of larger benthic foraminifera that evolved in late Paleocene and diversified through the lower to middle Eocene. Selectivity of late Eocene foraminiferal extinction indicates that this extinction event was not a globally uniform event. Although this result does not verify an extraterrestrial impact or any other proposed cause of extinction, it does constrain the causes of late Eocene extinction. Furthermore, the geography of late Eocene foraminiferal extinction, and previously studied Cenomanian/Turonian extinction, demonstrates that mass extinctions exhibit different patterns of selectivity.

Mark and Flessa (1977) have argued that the evolutionary equilibrium hypothesis requires that there should be significant correlation between generic origins and extinctions, and they presented data on Phanerozoic brachiopods and Cenozoic mammals. Their data are re-examined and the correlations are found not to support their version of the evolutionary equilibrium hypothesis. We argue that the equilibrium hypothesis may not be falsifiable using paleontological data.

Levinton notes that the number of individuals available to my study of patterns in the evolution of Homo erectus is low, especially when cranial base breadth is considered. If measurements of biauricular breadth are related to stratigraphic age of the fossils using linear regression, the slope obtained is small (−1.52). The confidence interval includes zero, and there is no evidence that a real trend is present. At the same time, the .95 interval is large (±26.81), so slopes differing by even a substantial margin cannot be distinguished. Levinton suggests that this negates a claim for stasis, and I agree that there are grounds for doubt. But by his reasoning, a case for stasis can never be established. While it is true that the occurrence of (very small) trends can never be denied, even if an analysis of many fossils shows a zero slope bracketed by narrow confidence limits, surely these “trends” must be dismissed as insignificant. Given such an outcome, a conclusion of no (directional) change would be quite justified.

Evolutionary rates and selection intensities in eight cladistically defined species-level evolutionary sequences of the Middle and Upper Ordovician bryozoan genus Peronopora were calculated for comparison with values published for fossil and living taxa. Calculations were restricted to statistically significant unidirectional segments of anagenetic series to minimize the mixing of different modes, directions, and rates of evolutionary change.

Rates and selection intensities ranged from 10−7 to 10−6 darwins and from 10−6 to 10−5 haldanes. Across characters, the weighted mean evolutionary rate equaled 5.86 × 10−7 darwins and the mean selection intensity was 6.44 × 10−7. Mean rates of 2.15 × 10−6, 4.31 × 10−6, and 8.61 × 10−6 haldanes, and corresponding mean selection intensities equaling 2.39 × 10−6, 4.78 × 10−6, and 9.56 × 10−6, were calculated for generation lengths of 0.5, 1, and 2 years, respectively.

The magnitudes of positive and negative evolutionary rates and selection intensities do not differ statistically, individual characters display no consistent pattern of positive or negative values, and no character complexes were detectable. A mosaic pattern of change occurs across characters in evolutionary sequences.

Eighty percent of analyzed evolutionary series were multispecies lineages. Both individual and mean values provide direct estimates of the rates of evolution within those lineages at the moment of speciation.

Rates of anagenetic evolution in Peronopora were low and similar to published rates for a variety of fossil protists, invertebrates, and vertebrates. However, earlier rate calculations did not isolate the effect of unidirectional anagenesis from that of stasis, random walks, trend reversals, or rate variations. Eight percent of characters in Peronopora produced anagenetic series that were statistically significant, a percentage similar to the 5% calculated in a study of 251 sequences of evolving traits in 53 fossil lineages (Hunt 2007). Stasis and mutation-drift are the most common patterns detectable in the fossil record, although anagenesis remains a potentially important force in shaping the course of both micro- and macroevolution.

Antarctic Hoploparia exhibit morphologic changes upsection in a stratigraphic record considered to be long (approximately 15 m.y.) and free of major hiatuses. Five characters exhibit change upsection, and the overall morphologies of the geologically oldest and youngest lobsters are different. The observed patterns could be the result of either phyletic evolution or gradual invasion of one or more species into the range of the original species. The most parsimonious interpretation of the data argues against the invasion hypothesis but supports the phyletic evolution hypothesis.

Calcareous nannoplankton have been one of the dominant primary producers in the surface oceans since the late Triassic. The bolide impact at the Cretaceous/Paleogene (K/Pg) boundary ~66.0 Ma, led to the elimination of >90% of nannoplankton species: the largest extinction event in their evolutionary history. One of the few nannoplankton genera to survive the K/Pg mass extinction and even thrive in its aftermath was Braarudosphaera, which precipitates pentagonal calcite plates (pentaliths). The only Braarudosphaera species to span the K/Pg boundary (B. bigelowii) is extant and has formed geographically and temporally restricted “blooms” throughout geologic time. Four morphologically and genetically distinct cryptic species of B. bigelowii have been identified in the modern ocean. However, it is uncertain whether these cryptic species have disparate ecophysiological tolerances that have allowed them to adapt to varying environmental conditions. For the first time, we assess changes in the size and shape of Braarudosphaera pentaliths following the K/Pg mass extinction at three geographically and environmentally disparate sites that have early Paleocene Braarudosphaera blooms. Our results show that different Braarudosphaera morphotypes were dominant in the Gulf of Mexico compared with the Tethys Ocean, likely due to regional environmental differences. In addition, we provide evidence that the dominant Braarudosphaera morphotypes shifted in response to changes in upper water column stratification. This ability to rapidly adapt to unstable environments likely helped Braarudosphaera thrive in the aftermath of the K/Pg extinction and explains why this lineage has enjoyed such a long evolutionary history.

Despite the paleontological relevance and paleobiological interest of trigoniid bivalves, our knowledge of their ontogeny—an aspect of crucial evolutionary importance—remains limited. Here, we assess the intra- and interspecific ontogenetic variations exhibited by the genus Steinmanella Crickmay (Myophorellidae: Steinmanellinae) during the early Valanginian–late Hauterivian of Argentina and explore some of their implications. The (ontogenetic) allometric trajectories of seven species recognized for this interval were estimated from longitudinal data using 3D geometric morphometrics, segmented regressions, and model selection tools, and then compared using trajectory analysis and allometric spaces. Our results show that within-species shell shape variation describes biphasic ontogenetic trajectories, decoupled from ontogenetic changes shown by sculpture, with a gradual decay in magnitude as ontogeny progresses. The modes of change characterizing each phase (crescentic growth and anteroposterior elongation, respectively) are conserved across species, thus representing a feature of Steinmanella ontogeny; its evolutionary origin is inferred to be a consequence of the rate modification and allometric repatterning of the ancestral ontogeny. Among species, trajectories are more variable during early ontogenetic stages, becoming increasingly conservative at later stages. Trajectories’ general orientation allows recognition of two stratigraphically consecutive groups of species, hinting at a potentially higher genus-level diversity in the studied interval. In terms of functional morphology, juveniles had a morphology more suited for active burrowing than adults, whose features are associated with a sedentary lifestyle. The characteristic disparity of trigoniids could be related to the existence of an ontogenetic period of greater shell malleability betrayed by the presence of crescentic shape change.

Understanding the drivers of macroevolutionary trends through the Phanerozoic has been a central question in paleobiology. Increasingly important is understanding the regional and environmental variation of macroevolutionary patterns and how they are reflected at the global scale. Here we test the role of biotic interactions on regional ecological patterns during the Mesozoic marine revolution. We test for escalatory trends in Jurassic marine benthic macroinvertebrate ecosystems using occurrence data from the Paleobiology Database parsed by region and environment. The escalation hypothesis posits that taxonomic groups that could adapt to intense predation and bioturbation proliferated, whereas groups unable to adapt were reduced in diversity and abundance or driven to extinction. We tested this hypothesis in five regions during Jurassic stages and among four depositional environments in Europe. Few escalatory trends were detected, although at least one escalatory trend was observed in every region, with the greatest number and strongest trends observed in Europe. These trends include increases in shallow infauna and cementing epifauna and occurrences of facultatively mobile invertebrates and decreases in pedunculate, free-lying, and sessile epifauna. Within Europe, escalatory trends occur in shallow-water environments but also in deeper-water environments, where they are predicted not to occur. When regional trends are aggregated, trends in Europe drive the global signal. The results of this study suggest that while evidence of escalation is rare globally, it is plausible that escalation drove macroevolutionary patterns in Europe. Furthermore, these results underline the need to dissect global fossil data at the regional scale to understand global macroevolutionary dynamics.

Tree-based paleobiological studies use inferred phylogenies as models to test hypotheses about macroevolution and the quality of the fossil record. Such studies raise two concerns. The first is how model trees might bias results. The second is testing hypotheses about parameters that affect tree inference.

Bias introduced by model trees is explored for tree-based assessments of the quality of the fossil record. Several nuisance parameters affect tree-based metrics, including consistency of sampling probability, rates of speciation / extinction, patterns of speciation, applied taxonomic philosophy, and assumed taxonomy. The first two factors affect probabilistic assessments of sampling, but also can be tested and accommodated in sophisticated probability tests. However, the final three parameters (and the assumption of a correct phylogeny) do not affect probabilistic assessments.

Often paleobiologists wish to test hypotheses such as rates of character change or rates of preservation. Assumptions about such parameters are necessary in simple phylogenetic methods, even if the assumptions are that rates are homogeneous or that sampling is irrelevant. Likelihood tests that evaluate phylogenies in light of stratigraphic data and / or alternative hypotheses of character evolution can reduce assumptions about unknowns by testing numerous unknowns simultaneously. Such tests have received numerous criticisms, largely based in philosophy. However, such criticisms are based on incorrect depictions of the logical structures of parsimony and likelihood, misunderstandings about when arguments are probabilistic (as opposed to Boolean), overly restrictive concepts of when data can test a hypothesis, and simply incorrect definitions of some terms.

Likelihood methods can test multiparameter hypotheses about phylogeny and character evolution (i.e., rates, independence, etc.). The best hypothesis positing a single rate of independent character change (with no variation among character states) is determined for each topology. Hypotheses about rate variation among characters or across phylogeny, character independence, and different patterns of state evolution then are examined until one finds the simplest (i.e., fewest varying parameters) hypothesis that cannot be rejected given knowledge of a more complicated hypothesis. This is repeated for alternative topologies. An example is presented using hyaenids. Two trees are contrasted, one of which requires the minimum necessary steps and the other of which requires at least seven additional steps. Given either tree, likelihood rejects fewer than three general rates of character change and also rejects the hypothesis of independence among the characters. However, hypotheses of changes in rates across the tree do not add substantially to the tree likelihood. The likelihoods of the trees given stratigraphic data also are determined. Both morphologic and stratigraphic data suggest that the multiparameter hypothesis including the parsimony tree is significantly less likely than the multiparameter hypothesis including a different tree.