Despite a global fossil record, Metatheria are now largely restricted to Australasia and South America. Most metatherian paleodiversity studies to date are limited to particular subclades, time intervals, and/or regions, and few consider uneven sampling. Here, we present a comprehensive new data set on metatherian fossil occurrences (Barremian to end Pliocene). These data are analyzed using standard rarefaction and shareholder quorum subsampling (including a new protocol for handling Lagerstätte-like localities).

Global metatherian diversity was lowest during the Cretaceous, and increased sharply in the Paleocene, when the South American record begins. Global and South American diversity rose in the early Eocene then fell in the late Eocene, in contrast to the North American pattern. In the Oligocene, diversity declined in the Americas, but this was more than offset by Oligocene radiations in Australia. Diversity continued to decrease in Laurasia, with final representatives in North America (excluding the later entry of Didelphis virginiana) and Europe in the early Miocene, and Asia in the middle Miocene. Global metatherian diversity appears to have peaked in the early Miocene, especially in Australia. Following a trough in the late Miocene, the Pliocene saw another increase in global diversity. By this time, metatherian biogeographic distribution had essentially contracted to that of today.

Comparison of the raw and sampling-corrected diversity estimates, coupled with evaluation of “coverage” and number of prolific sites, demonstrates that the metatherian fossil record is spatially and temporally extremely patchy. Therefore, assessments of macroevolutionary patterns based on the raw fossil record (as in most previous studies) are inadvisable.

The Signor-Lipps effect states that even a sudden mass extinction will invariably appear gradual in the fossil record, due to incomplete fossil preservation. Most previous work on the Signor-Lipps effect has focused on testing whether taxa in a mass extinction went extinct simultaneously or gradually. However, many authors have proposed scenarios in which taxa went extinct in distinct pulses. Little methodology has been developed for quantifying characteristics of such pulsed extinction events. Here we introduce a method for estimating the number of pulses in amass extinction, based on the positions of fossil occurrences in a stratigraphic section. Rather than using a hypothesis test and assuming simultaneous extinction as the default, we reframe the question by asking what number of pulses best explains the observed fossil record.

Using a two-step algorithm, we are able to estimate not just the number of extinction pulses but also a confidence level or posterior probability for each possible number of pulses. In the first step, we find the maximum likelihood estimate for each possible number of pulses. In the second step, we calculate the Akaike information criterion and Bayesian information criterion weights for each possible number of pulses, and then apply a k-nearest neighbor classifier to these weights. This method gives us a vector of confidence levels for the number of extinction pulses—for instance, we might be 80% confident that there was a single extinction pulse, 15% confident that there were two pulses, and 5% confident that there were three pulses. Equivalently, we can state that we are 95% confident that the number of extinction pulses is one or two. Using simulation studies, we show that the method performs well in a variety of situations, although it has difficulty in the case of decreasing fossil recovery potential, and it is most effective for small numbers of pulses unless the sample size is large. We demonstrate the method using a data set of Late Cretaceous ammonites.

Numerical simulations of neutral metacommunities are used here to predict the effects of growth and shrinkage of metacommunities, as well as their separation and merging caused by continental collision and rifting and their secondary eustatic effects. Although growth and shrinkage of metacommunities predictably change diversity, separating and merging metacommunities have counterintuitive effects. Separating and merging metacommunities change diversity within the individual areas, especially so for smaller areas, but they cause no change in total diversity of the system, contrary to previous predictions. The response times of metacommunities are likely to be geologically undetectable except for enormously large systems. These models can be used to predict the plate-tectonic effects on the diversity of terrestrial, coastal-marine, deep-marine, and oceanic-island systems. Of these, global and regional coastal-marine systems are the most acutely sensitive to the changes in area and fragmentation caused by plate tectonics. Oceanic-island systems also experience global and regional changes in diversity during supercontinent breakup and assembly, with the global effects driven by the changing length of volcanic arcs, and the regional effects also driven by secondary eustatic changes in shallow-marine area. Although individual terrestrial provinces or continents may experience substantial changes in diversity from rifting and collision, global terrestrial diversity should be unchanged except for the relatively modest contributions caused by the secondary eustatic effects on land area. These changes in diversity may be reinforced or counteracted by the changing latitudinal position of metacommunities.

Vertebrates with terrestrial or freshwater ancestors colonized the sea from the Early Triassic onward and became competitively dominant members of many marine ecosystems throughout the Mesozoic and Cenozoic eras. The circumstances that led to initial marine colonization have, however, received little attention. One hypothesis is that mass extinction associated with ecosystem collapse provided opportunities for clades of amphibians, reptiles, birds, and mammals to enter marine environments. Another is that competitive pressures in donor ecosystems on land and in freshwater, coupled with abundant food in nearshore marine habitats, favored marine colonization. Here we test these hypotheses by compiling all known secondarily marine amniote clades and their times of colonization. Marine amniotes are defined as animals whose diet consists primarily of marine organisms and whose locomotion includes swimming, diving, or wading in salt water. We compared the number of clades entering during recovery phases from mass extinctions with the rate of entry of clades during nonrecovery intervals of the Mesozoic and Cenozoic. We conservatively identify 69 marine colonizations by amniotes. The only recovery interval for which prior mass extinction could have been a trigger for marine entry is the Early Triassic, when four clades colonized the sea over 7 Myr, significantly above the rates at which clades entered during other intervals. High nearshore productivity was a greater enticement to colonization than was a low diversity of potential marine competitors or predators in nearshore environments of a highly competitive terrestrial or freshwater donor biota. Rates of marine entry increased during the Cenozoic, in part because of rising productivity and in part thanks to the participation of warm-blooded birds and mammals, which broadened the range of thermal environments in which initial colonization of the sea became possible.

The environmental transformations that occurred during the Neogene had profound effects on spatiotemporal biodiversity patterns, yet the modulating role of traits (i.e., physiological, ecological, and life-history traits) remains little understood. We tested this idea using the Neogene fossil record of chondrichthyans along the temperate Pacific coast of South America (TPSA). Information for georeferenced occurrences and ecological and life-history information of 38 chondrichthyan fossil genera in 42 Neogene sites was collected. Global georeferenced records were used to estimate present-day biogeographic distributions of the genera and to characterize the range of oceanographic conditions in which each genus lives as a proxy of their realized niche. Biogeographic range shifts (Neogene-present) were evaluated at regional and local scales. The role of traits as drivers of different range dynamics was evaluated using random forest models. The magnitude and direction of biogeographic range shifts were different at both spatial scales. At a regional scale, 34% of genera contracted their ranges, disappearing from the TPSA. At a local scale, a similar proportion of genera expanded and contracted their southern endpoints of distribution. The models showed a high precision at both spatial scales of analyses, but the relative importance of predictor variables differed. At a regional scale, disappearing genera tended to have a higher tolerance to salinity, lower sea surface temperature (SST) range, and smaller body sizes. At a local scale, genera contracting their ranges tended to live at greater depths, tolerate lower levels of primary productivity, and show a reduced tolerance to higher and lower SST ranges. The magnitude and direction of the changes in the range distribution were scale dependent and variable across the genera. Hence, multiple environmental exogenous factors interacted with taxon traits during the Neogene, creating a mosaic of biogeographic dynamics.

Recent studies have shown that modes of evolution, namely directional trend, random walk, and stasis, vary across morphologic traits and over the geographic range of a taxon. If so, is it possible that our interpretation of evolutionary modes is actually driven by our selection of traits in a study? In an attempt to answer this question, we have restudied the middle Miocene planktonic foraminifera Fohsella lineage, an iconic example of gradual morphologic evolution. In contrast to previous studies that have focused on the gross morphology as embodied by the edge view of tests, we analyze here multiple phenotypic traits chosen because their biologic and ecologic significance is well understood in living populations. We find that traits in the lineage did not evolve in concert. The timing and geographic pattern of changes in shape, coiling direction, size, and ecology were different. The evolution of this lineage is a mosaic combination of different evolutionary modes for different traits. We suggest that overemphasis on the evolution of some single trait, such as the edge-view outline, from narrow geographic ranges has significantly underestimated the dynamic evolutionary history of this group.

The fossil conchs of ammonoids provide valuable information about the life habits of this extinct group. A new conch measurement, the apertural surface area (ASarea), is introduced here along with modeled sizes of the buccal mass and the hyponome, based on ratios of these organs in comparison with the aperture height from the Recent Nautilus pompilius. A principal components analysis was performed using the three main characters: (1) apertural surface area index (i.e., the ratio of the apertural surface and the conch diameter), (2) buccal mass area index (i.e., the ratio between the buccal mass area and the ASarea), and (3) coiling rate of the conch. It revealed an ecomorphospace where life history traits can be tentatively assigned to species of the Ammonoidea. In this morphospace, Recent Nautilus has a marginal position, being one of the ectocochleate cephalopods with best properties for active life (capacity for handling large food items, rather good mobility). In contrast, most ammonoids possessed, at comparable conch sizes, much smaller buccal apparatuses and hyponomes, suggesting a more passive life history with reduced mobility potential and reduced capacities for larger prey items.

Evolving interactions between predators and prey constitute one of the major adaptive influences on marine animals during the Paleozoic. Crinoids and fish constitute a predator—prey system that may date back to at least the Silurian, as suggested by patterns of crinoid regeneration and spinosity in concert with changes in the predatory fauna. Here we present data on the frequency of breakage and regeneration in the spines of the Middle Devonian camerate Gennaeocrinus and late Paleozoic cladids, as well as an expanded survey of the prevalence of spinosity and infestation by platyceratid gastropods on crinoid genera during the Paleozoic. Spine regeneration frequency in the measured populations is comparable to arm regeneration frequencies from Mississippian Rhodocrinites and from modern deepwater crinoid populations. The prevalence of spinosity varies by taxon, time, and anatomy among Paleozoic crinoids; notably, spinosity in camerates increased from the Silurian through the Mississippian and decreased sharply during the Pennsylvanian, whereas spines were uncommon in cladids until their Late Mississippian diversification. Among camerates, tegmen spinosity is positively correlated with the presence of infesting platyceratid gastropods. These results allow us to evaluate several hypotheses for the effects of predation on morphological differences between early, middle, and late Paleozoic crinoid faunas. Our data corroborate the hypothesis that predators targeted epibionts on camerate crinoids and anal sacs on advanced cladids and suggest that the replacement of shearing predators by crushing predators after the Hangenberg extinction affected the locations of spines in Mississippian camerates.

Graphoglyptids are biogenic structures commonly found in deep-sea flysch deposits and occasionally detected on the modern deep-sea floor. They extend principally horizontally and take a variety of geometric patterns, whose functional morphology remains an enigma in ichnology and paleoceanography. Based on published materials from 1850 to 2017 (79 ichnotaxa from 28 ichnogenera of graphoglyptids) and systematic observations of one of the largest deep-sea trace fossil collections in the world, this paper proposes that topological analysis is an important ingredient in the taxonomy and functional interpretation of graphoglyptids. Accordingly, graphoglyptids are classified into line, tree, and net forms by their key topological architecture, and are further attributed to 19 topological prototypes by detailed secondary topological features. Line graphoglyptids are single-connected structures with uniform tunnel width, representing primarily the feeding patterns of solitary animals. Tree graphoglyptids, the most diverse architectural group of graphoglyptids, are ascribed to 11 topological prototypes according to the connectivity features of burrow segments and the number and distributional pattern of the branching points. Net graphoglyptids are subdivided into three topological prototypes on the basis of the connectivity features and/or the regularity of the meshes. Multiconnected net forms are considered as a continuous morphological spectrum with different levels of complexity in the net formation. The various connected components in multiconnected tree and net graphoglyptids generally exhibit small and uniform tunnel diameter in a given structure (suggesting a tiny trace maker[s]). The whole structure shows relatively extensive linear or surface coverage and overall good preservation, indicating sustained processes of burrow construction. It is highly probable that certain multiconnected tree and net graphoglyptids represent some emergent patterns from self-organized collective behaviors of conspecific animals. Graphoglyptids thus provide us with a new perspective on the study of solitary and collective behaviors of macrobenthos in the deep-sea environment.

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).