In their “alternative interpretation” Marshall and Hecht raise two interesting questions:

1. I) Is “Taxocene Analysis” a permissible approach to community evolution, and if so under what conditions?

2. II) What really happened to the ten South American ungulate genera that vanished during the Early Pleistocene?

As these are fundamentally different questions, I shall consider each separately.

The multibrachiate grade of organization in camerate crinoids was principally attained through pinnule differentiation: the accelerated development of a proximal pinnule that ultimately became a pinnule-bearing arm. Although pinnule differentiation is not the only means of achieving a multibrachiate organization in modern crinoids, it was the primary mode in producing both dichotomous and exotomous branching patterns in multibrachiate camerates. Whereas most of the proximal branchings, commonly fixed in the cup of camerates, were due to pinnule differentiaton, the first dichotomy and distal dichotomies above the cup apparently developed from direct modification of a brachial plate at the growing tip of the immature crinoid arm.

Inferences on the development and morphology of extinct brachiopods must be informed by the ontogeny and shell ornamentation of extant brachiopods. Although the adult shells of extant brachiopods are well studied, detailed descriptions of the embryonic and juvenile shells of extant lingulides are lacking. Here, we describe in detail the shells of juveniles of Lingula anatina Lamarck, 1801 from Vietnam and the Republic of the Philippines. The following previously unknown properties of the lingulide shell are described: (1) a distinct border between the protegulum and the brephic shell; (2) drapes that develop on both the protegulum and brephic shell; and (3) the notched anterior margin of the brephic shell. The drapes and cogs on the brephic shell may be caused by the formation of setal follicles during the planktonic stage. Specimens of L. anatina from the Philippines have larger brephic shells than those from Vietnam, probably because the former have a longer planktonic stage. Based on comparisons of the first-formed shells of extant brachiopods with published data on fossil brachiopods, we suggest that the life cycle of extant lingulides, in which planktotrophic juveniles with a shell hatch from the egg envelope, is the most evolutionarily advanced brachiopod life cycle and appeared in the early Silurian. We suggest criteria for determining the type of life cycle based on the structure of the first-formed shell of brachiopods. Finally, we consider hypothetical scenarios of life cycles of fossil brachiopods, including true planktotrophic larvae in the Cambrian linguliforms.

Vertebrate microfossil assemblages in a stratigraphic sequence often yield similar assortments of taxa but at different relative abundances, potentially indicative of marginal paleocommunity changes driven by paleoenvironmental change over time. For example, stratigraphically younger assemblages in the Dinosaur Park Formation (DPF) yield proportionally more aquatic taxa, consistent with marine transgression. However, individual deposits may have received specimens from multiple source paleocommunities over time, limiting our ability to confidently identify ecologically significant, paleocommunity differences through direct assemblage comparisons. We adapted a three-source, two-tracer Bayesian mixing model to quantify proportional contributions from different source habitats to DPF microfossil assemblages. Prior information about the compositions of separate, relatively unmixed terrestrial, freshwater, and marine assemblages from the Belly River Group allowed us to define expected taxon percent abundances for the end-member habitats likely contributing specimens to the mixed deposits. We compared the mixed assemblage and end-member distributions using 21 different combinations of vertebrate taxa. Chondrichthyan, dinosaur, and amphibian occurrence patterns ultimately allowed us to parse the contributions from the potential sources to 14 of the 15 mixed assemblages. The results confirmed a significant decline in terrestrial contributions at younger DPF sites, driven primarily by increased freshwater specimen inputs—not incursions from the adjacent marine paleocommunity. A rising base level likely increased lateral channel migration and the prevalence of freshwater habitats on the landscape, factors that contributed to increased paleocommunity mixing at younger channel deposit sites. Bayesian methods can account for source-mixing bias, which may be common in assemblages associated with major paleoenvironmental changes.

According to when they attained high diversity, major taxa of marine animals have been clustered into three groups, the Cambrian, Paleozoic, and Modern Faunas. Because the Cambrian Fauna was a relatively minor component of the total fauna after mid-Ordovician time, the Phanerozoic history of marine animal diversity is largely a matter of the fates of the Paleozoic and Modern Faunas. The fact that most late Cenozoic genera belong to taxa that have been radiating for tens of millions of years indicates that the post-Paleozoic increase in diversity indicated by fossil data is real, rather than an artifact of improvement of the fossil record toward the present.

Assuming that ecological crowding produced the so-called Paleozoic plateau for family diversity, various workers have used the logistic equation of ecology to model marine animal diversification as damped exponential increase. Several lines of evidence indicate that this procedure is inappropriate. A plot of the diversity of marine animal genera through time provides better resolution than the plot for families and has a more jagged appearance. Generic diversity generally increased rapidly during the Paleozoic, except when set back by pulses of mass extinction. In fact, an analysis of the history of the Paleozoic Fauna during the Paleozoic Era reveals no general correlation between rate of increase for this fauna and total marine animal diversity. Furthermore, realistically scaled logistic simulations do not mimic the empirical pattern. In addition, it is difficult to imagine how some fixed limit for diversity could have persisted throughout the Paleozoic Era, when the ecological structure of the marine ecosystem was constantly changing. More fundamentally, the basic idea that competition can set a limit for marine animal diversity is incompatible with basic tenets of marine ecology: predation, disturbance, and vagaries of recruitment determine local population sizes for most marine species. Sparseness of predators probably played a larger role than weak competition in elevating rates of diversification during the initial (Ordovician) radiation of marine animals and during recoveries from mass extinctions. A plot of diversification against total diversity for these intervals yields a band of points above the one representing background intervals, and yet this band also displays no significant trend (if the two earliest intervals of the initial Ordovician are excluded as times of exceptional evolutionary innovation). Thus, a distinctive structure characterized the marine ecosystem during intervals of evolutionary radiation—one in which rates of diversification were exceptionally high and yet increases in diversity did not depress rates of diversification.

Particular marine taxa exhibit background rates of origination and extinction that rank similarly when compared with those of other taxa. Rates are correlated in this way because certain heritable traits influence probability of speciation and probability of extinction in similar ways. Background rates of origination and extinction were depressed during the late Paleozoic ice age for all major marine invertebrate taxa, but remained correlated. Also, taxa with relatively high background rates of extinction experienced exceptionally heavy losses during biotic crises because background rates of extinction were intensified in a multiplicative manner; decimation of a large group of taxa of this kind in the two Permian mass extinctions established their collective identity as the Paleozoic Fauna.

Characteristic rates of origination and extinction for major taxa persisted from Paleozoic into post-Paleozoic time. Because of the causal linkage between rates of origination and extinction, pulses of extinction tended to drag down overall rates of origination as well as overall rates of extinction by preferentially eliminating higher taxa having relatively high background rates of extinction. This extinction/origination ratchet depressed turnover rates for the residual Paleozoic Fauna during the Mesozoic Era. A decline of this fauna's extinction rate to approximately that of the Modern Fauna accounts for the nearly equal fractional losses experienced by the two faunas in the terminal Cretaceous mass extinction.

Viewed arithmetically, the fossil record indicates slow diversification for the Modern Fauna during Paleozoic time, followed by much more rapid expansion during Mesozoic and Cenozoic time. When viewed more appropriately as depicting geometric—or exponential—increase, however, the empirical pattern exhibits no fundamental secular change: the background rate of increase for the Modern Fauna—the fauna that dominated post-Paleozoic marine diversity—simply persisted, reflecting the intrinsic origination and extinction rates of constituent taxa. Persistence of this overall background rate supports other evidence that the empirical record of diversification for marine animal life since Paleozoic time represents actual exponential increase. This enduring rate makes it unnecessary to invoke environmental change to explain the post-Paleozoic increase of marine diversity.

Because of the resilience of intrinsic rates, an empirically based simulation that entails intervals of exponential increase for the Paleozoic and Modern Faunas, punctuated by mass extinctions, yields a pattern that is remarkably similar to the empirical pattern. It follows that marine animal genera and species will continue to diversify exponentially long into the future, barring disruption of the marine ecosystem by human-induced or natural environmental changes.

Understanding the mechanisms that prevent or promote the coexistence of taxa at local scales is critical to understanding how biodiversity is maintained. Competitive exclusion and environmental filtering are two processes thought to limit which taxa become established in a community. However, determining the relative importance of the two processes is a complex task, especially when the critical initial stages of colonization cannot be directly observed. Here, we explore the use of phylogenetic community structure for identifying filtering mechanisms in a fossil community. We integrated a time-calibrated molecular phylogeny of bivalve genera with a spatial dataset of late Cenozoic bivalves from the Pacific coast of North America to characterize how the community that was present in the semirestricted San Joaquin Basin (SJB) embayment of present-day California was phylogenetically structured. We employed phylogenetic distance-based metrics across six time bins spanning 27–2.5 Ma and found no evidence of significant clustering or evenness in the SJB community when compared with communities randomly assembled from the regional source pool. Additionally, we found that new colonizers into the SJB were not significantly more or less closely related to native taxa than expected by chance. These findings suggest that neither competitive exclusion nor environmental filtering were overwhelmingly influential factors shaping the composition of the SJB community over time. We further discuss interpretations of these patterns in light of current understandings in community phylogenetics and reiterate the critical role historical perspectives play in how community assembly rules are assessed.

The Cenozoic genus Terebratula seems to be an exception to the post-Permian trend in brachiopod retreat to offshore habitats, because it was species rich and numerically abundant in warm-temperate shallow-water environments in the Mediterranean and the Paratethys realms. This was so despite the general dominance of bivalves and the pervasive bioturbation and predation pressure during the Neogene. Terebratula, however, went extinct in the Calabrian (Pleistocene). The optimal environmental conditions for Terebratula during its prime are poorly known. The Águilas Basin (SE Spain) is an ideal study area to investigate the habitat of Terebratula, because shell beds of this brachiopod occur there cyclically in early Pliocene deposits. We evaluate the paleoecological boundary conditions controlling the distribution of Terebratula by estimating its environmental tolerances using benthic and planktic foraminiferal and nannoplanktic assemblages and oxygen isotopes of the secondary layer brachiopod calcite. Our results suggest that Terebratula in the Águilas Basin favored oligotrophic to mesotrophic, well-oxygenated environments at water depths of 60–90 m. Planktic foraminiferal assemblages and oxygen isotopes point to sea-surface temperatures between ~16°C and 22°C, and bottom-water temperatures between 17°C and 24°C. The analyzed proxies indicate that Terebratula tolerated local variations in water depth, bottom temperature, oxygenation, productivity, and organic enrichment. Terebratula was probably excluded by grazing pressure from well-lit environments and preferentially occupied sediment-starved, current-swept upper offshore habitats where coralline red algae were absent. Narrow temperature ranges of Terebratula species might have been a disadvantage during the high-amplitude seawater temperature fluctuations that started about 1 Ma, when the genus went extinct.

The Burgess Shale-type Lagerstätten of the Early Cambrian Maotianshan Shale record an apparently sudden conquest of pelagic niches by ten phyla of metazoans. One of these phyla is Chaetognatha, a group of predatory marine worms. Given their role as major predators in modern planktonic ecosystems, the chaetognaths discovered in the Maotianshan Shale (Yunnan Province, South China) suggest that the pelagos at the time was already quite complex. Modern chaetognaths, however, can be divided into benthic and pelagic forms; the pelagic nature of Eognathacantha ercainella should therefore be validated by strong morphological evidence.

Knowing that planktonic animals present morphological adaptations that increase their buoyancy, we studied the drag produced during the active phase of chaetognath locomotion for the modern forms Paraspadella gotoi (benthic) and Sagitta elegans (pelagic). By using a motion model developed by Jordan in 1992, we could calculate the resistive force produced by the undulatory movement of chaetognaths' bodies.

This mechanistic approach evaluates the effect of three motion parameters (relative speed, total length, and tail ratio) on the drag force produced during locomotion. Our results show that the increase of size contributes to higher drag while the shorter tail of the pelagic form balances this effect by reducing the wetted surface subject to friction. For chaetognaths, therefore, a bigger body (both in length and width) and a shorter tail indicate a pelagic lifestyle, a finding that can be applied to the study of the fossil Eognathacantha ercainella. A discriminant analysis can confirm that the Early Cambrian chaetognath presents a pelagic morphology with similarities to modern bathypelagic and mesopelagic species.

The unique body plan of frogs (Lissamphibia: Anura) has been largely conserved from at least 200 Myr, and its evolution from a more generalized tetrapod condition is still poorly understood, in part due to the scarce early fossil record of Salientia, the anuran total-group. The origin of the anuran Bauplan has been classically explained as an adaptation to jumping, but recent studies incorporating new data in a phylogenetic context have challenged the popular jumping hypothesis. Here we revisit and test this hypothesis from a paleobiological perspective by integrating limb data from a wide range of extant and fossil frogs. We first explored the evolution of limb proportions from the Jurassic to the Paleogene to understand when the present limb diversity originated and whether, and to what extent, limb proportions have been conserved over the last 200 Myr. We then inferred the locomotor capabilities of extinct species by phylogenetic flexible discriminant analysis, and from these inferences, we studied the locomotor diversity of frogs over geological time and reconstructed the ancestral state for frog-like salientians. The evolution of limb proportions is characterized by an early diversification that was underway in the Jurassic, followed by a repeated convergence over a limited area of the morphospace that was already explored by the Early Cretaceous. In agreement with this early limb diversity, the Jurassic stem species were also locomotory diverse, and their inferred locomotor modes do not support the jumping hypothesis. We propose that the patterns found herein of repeated convergent evolution of both limb proportions and locomotor capabilities over geological time hamper any attempt to confidently infer the ancestral locomotion mode and, it therefore might be time to start focusing on other hypotheses on the origin of the anuran Bauplan that are not related to locomotion.

Biodiversity patterns in the fossil record are often interpreted as functions of only origination and extinction whereas the migration of taxa among regions or paleocontinents is rarely considered. A null biogeographic model is presented that evaluates the role of migration in shaping global biodiversity patterns across evolutionary time scales. As taxa are allowed to originate, go extinct, and migrate among continents, the model keeps track of global richness and differentiation diversity (the diversity gained by pooling continents). The model's results highlight the difference between global-scale and continental-scale origination and extinction rates. Intuitively, origination and extinction have opposite effects on global richness at the global scale, but they interact with migration at the continental scale to influence differentiation diversity and global richness in surprising ways. The model shows that the migration of taxa among paleocontinents can facilitate an increase in global richness, even when continental extinction is greater than continental origination. Additionally, the model shows that differentiation diversity reaches a dynamic equilibrium that is dictated by the combination of migration, origination, and extinction rates. A test of the model with Ordovician macroinvertebrate data indicates that migration rates were low during the Ordovician and that differentiation diversity was high and varied little. Overall, the Ordovician was an interval of high provinciality. It also shown that widespread genera were less prone to global extinction, even though extinction of genera on individual paleocontinents was common.

The geographic distribution of 293 Modern bivalve genera has been analyzed and found to be statistically correlated with distance. In particular, a least-squares regression analysis of the data indicates that the distance between faunal realms (D) in kilometers can be estimated using the equation D = (ln(d) + 0.4233)/−0.00013, where d is the Dice coefficient of faunal similarity. Analysis of 59 genera of Late Ordovician bivalves indicates that the above equation also describes their biogeographic distribution.

Using this formula, the distance between Laurentia and Scotland/Northwest Ireland was estimated to be 5500 kilometers. This is consistent with the reconstruction of a connection among these areas during the Late Ordovician based on brachiopod and graptolite biogeographic data.

Paleomagnetic and paleoclimatic data also suggest that Avalonia, Baltica, and Laurentia were at tropical latitudes. Distances between these paleocontinents can therefore be used to estimate paleolongitudes. If the location of England on the eastern side of Avalonia is used as zero degrees paleolongitude for the Late Ordovician as it is today, the paleolongitude for South America, Laurentia, Scotland and northwest Ireland, and Baltica would be 125°W, 45°W, 10°W, and 15°E, respectively. Because of drifting of the Avalonia plate, these paleolongitudes probably do not coincide with the longitudinal grid used today. The paleolongitudes indicate only the relative spacing between continents in the past. The methodology in this study should be useful for improving the accuracy of paleogeographic reconstructions for the Late Ordovician throughout the Cenozoic, and especially the Paleozoic periods for which magnetic seafloor anomaly data are not available.

A fundamental question in paleobiology is whether ecology is correlated with evolutionary history. By combining time-calibrated phylogenetic trees with genus occurrence data through time, we can understand how environmental preferences are distributed on a tree and evaluate support for models of ecological similarity. Exploring parameters that lend support to each evolutionary model will help address questions that lie at the nexus of the evolutionary and ecological sciences. We calculated ecological difference and phylogenetic distance between species pairs for 83 taxa used in recent phylogenetic revisions of the brachiopod order Strophomenida. Ecological difference was calculated as the pairwise distance along gradients of water depth, carbonate, and latitudinal affinity. Phylogenetic distance was calculated as the pairwise branch length between tips of the tree. Our results show no relationship between ecological affinity and phylogeny. Instead results suggest an ecological burst during the initial radiation of the clade. This pattern likely reflects scaling at the largest macroevolutionary and macroecological scales preserved in the fossil record. Hierarchical scaling of ecological and evolutionary processes is complex, but phylogenetic paleoecology is an avenue for better evaluating these questions.

Understanding the life orientation of fossil organisms, such as brachiopods, is not only important for understanding the biology of the organism in question, but it also can be used to interpret paleoecological information about the assemblages from which the specimens were derived. The dorsibiconvex brachiopod morphology is particularly common, especially among the Order Atrypida, yet there have been few independent, biomechanical studies to assess the life orientation of these brachiopods. In this study, we assess potential orientations of two end-member morphologies of a dorsibiconvex brachiopod, Pseudoatrypa lineata, from the Mid–Late Devonian of North America by placing realistic models in a flume.

Using materials with the specific gravity of calcium carbonate, we modeled two well-preserved Pseudoatrypa lineata from the Waterways Formation (Givetian–Frasnian, Alberta, Canada) to represent the original shell. The hydrodynamic stability of the models was assessed by placing the models in a recirculating flume in one of three initial orientations: (1) anterior commissure upstream, (2) umbo upstream, and (3) lateral (specimen perpendicular to flow), each with the dorsal and ventral valve topmost. The entire process was conducted both on a Plexiglas substrate and on well-sorted, mediumgrained sand. All scenarios were repeated five times for a total of sixty trials per specimen (120 total).

Flume trials indicate that neither brachiopod had a true hydrodynamically stable orientation.

Reorientations occurred at low velocities (~0.2 m/s), with transport occurring soon after (~0.3 m/s).

Assuming that a juvenile, pedunculate, dorsibiconvex brachiopod would initially have been oriented with its ventral valve topmost, our results suggest two outcomes: the brachiopods either (1) were attached via pedicles throughout their lives or (2) lived in quiet, undisturbed waters. Given the abundance of dorsibiconvex brachiopods in observed high-energy environments, our results indicate it is more conservative to assume dorsibiconvex brachiopods retained pedicles throughout their lives.

Lithification, the transition of unconsolidated sediments to fully indurated rocks, can potentially bias estimates of species richness, evenness, and body size distribution derived from fossil assemblages. Fossil collections made from well-indurated rocks consistently exhibit lower species richness, lower evenness, and larger average specimen size relative to collections made from unconsolidated sediments, even when collections are drawn from the same assemblage. This phenomenon is known as “lithification bias.” While the bias itself has been demonstrated empirically, much less attention has been paid to its causes. Proposed causes include taphonomic processes (e.g., destruction of small specimens during early diagenesis) and methodological differences (e.g., sieving vs. counting specimens on outcrops, bedding surfaces, or mechanically split surfaces). Here we investigate the potential effects of preferential intersection that could also result in a methodologically related bias: the preferential sampling of larger specimens relative to smaller ones when fossils are counted on rock surfaces. We used an analogue model to simulate preferential intersection (fossil collection via splitting fossiliferous rocks) and compare the results with a random-draw model that approximates the effects of sieving. The model was parameterized using nine different combinations of species abundance and species size distributions. The results show that, with rare exceptions, species richness is 5–23% lower, evenness 5–25% lower, and average specimen size 24–150% larger in preferential-intersection than in random-draw simulations. We conclude that preferential intersection can impose a significant bias independent of other mechanisms (e.g., preferential destruction of smaller specimens during diagenetic or sampling processes), that the magnitude of this bias is partially dependent on the species abundance and size distributions, and that this bias alone does not fully account for empirically observed lithification bias on species richness (i.e., other sources of bias are also at work).

Ricklefs (1980) suggested the use of neontological data to distinguish between puncuated equilibrium and gradualism as modes of evolution. This paper investigates his model and finds it contains oversimplifications that make any test difficult. We modify his model slightly and use it as a limited test of punctuated equilibrium by large morphological shifts at speciation. This test is applied to a data set of 110 species from two families of bats, the Emballonuridae and the Molossidae. We find no evidence of consistently large morphological shifts at the formation of subspecies, species or genera.

The Cambrian saw a dramatic increase in metazoan diversity and abundance. Between-assemblage diversity (beta diversity) soared in the first three Cambrian stages, suggesting a rapid increase in the geodisparity of marine animals during the Cambrian radiation. However, it remains unclear how these changes scale up to first-order biogeographic patterns. Here we outline time-traceable provinces for marine invertebrates across the Cambrian period using a compositional network based on species-level fossil occurrence data. Results confirm an increase in regional differences of faunal composition and a decrease in by-species geographic distribution during the first three stages. We also show that general biogeography tends to be reshaped after global extinction pulses. We suggest that the abrupt biogeographic differentiation during the Cambrian radiation was controlled by a combination of tectonics, paleoclimate, and dispersal capacity changes.