The nature of phenotypic evolution within lineages is central to many unresolved questions in paleontology and evolutionary biology. Analyses of evolutionary time series of ancestor–descendant populations in the fossil record are likely to make important contributions to many of these debates. However, the limited number of models that have been applied to these types of data may restrict our ability to interpret phenotypic evolution in the fossil record. Using uni- and multivariate models of trait evolution that make different assumptions regarding the dynamics of the adaptive landscape, I evaluate contrasting hypotheses to explain evolution of size in the radiolarian Eucyrtidium calvertense and armor in the stickleback Gasterosteus doryssus. Body-size evolution in E. calvertense is best explained by a model in which the lineage evolves as a consequence of a shift in the adaptive landscape that coincides with the initiation of neosympatry with its sister lineage. Multivariate evolution of armor traits in a stickleback lineage (G. doryssus) shows evidence of adaptation toward independent optima on the adaptive landscape at the same time as traits change in a correlated fashion. The fitted models are available in the R package evoTS, which builds on the paleoTS framework.

Extant species of the genus Equus (e.g., horses, asses, and zebras) have a widespread distribution today on all continents except Antarctica. Extinct species of Equus represented by fossils were likewise widely distributed in the Pliocene and even more so during the Pleistocene. In order to understand the efficacy of “big data” for (paleo)biogeographic analyses, location records (latitude, longitude) and fossil occurrences for the genus Equus were mined and further explored from six databases, including iDigBio, Paleobiology Database, VertNet, BISON, Neotoma, and GBIF. These were chosen from a priori knowledge of where relevant data might be aggregated. We also realized that these databases have different objectives and data sources and therefore would provide a useful comparative study of the widespread taxon Equus in space and time.

The mining of Equus data from these six sources yielded a combined total of 123.8 K location records, including 116.2K fossil specimens. These include individual points that are unique, that is, only occurring in one of these databases, and those that are duplicated in multiple databases. Of the six databases, three (iDigBio, Paleobiology Database, and GBIF) were judged to be the most useful in the Equus use case. Most of the databases are biased toward North American records, thus limiting the reconstruction of the actual distribution of the genus Equus in space and time outside of this continent. Although Equus has a large number of digitally accessible records, fundamentally interesting questions pertaining to evolutionary dynamics and extinction geography are still a challenge for these kinds of biodiversity databases due primarily to the lack of sufficiently dense and precise temporal data.

Interpreting the impact of climate change on vertebrates in the fossil record can be complicated by the effects of potential biotic drivers on morphological patterns observed in taxa. One promising area where this impact can be assessed is a high-resolution terrestrial record from the Bighorn Basin, Wyoming, that corresponds to the Paleocene–Eocene thermal maximum (PETM), a geologically rapid (~170 kyr) interval of sustained temperature and aridity shifts about 56 Ma. The PETM has been extensively studied, but different lines of research have not yet been brought together to compare the timing of shifts in abiotic drivers that include temperature and aridity proxies and those of biotic drivers, measured through changes in floral and faunal assemblages, to the timing of morphological change within mammalian species lineages. We used a suite of morphometric tools to document morphological changes in molar crown morphology of three lineages of stem erinaceid eulipotyphlans. We then compared the timing of morphological change to that of both abiotic and other biotic records through the PETM. In all three species lineages, we failed to recover any significant changes in tooth crown shape or size within the PETM. These results contrast with those documented previously for lineages of medium-sized mammals, which show significant dwarfing within the PETM. Our results suggest that biotic drivers such as shifts in community composition may have also played an important role in shaping species-level patterns during this dynamic interval in Earth history.

Previous descriptions and interpretations of the Cycadeoidea pollen organ are followed by a new interpretation based upon its presumed neotenous condition. The sexually mature pollen organ represents a juvenile morphological condition that persisted into the adult stage of the organism and was inherited ultimately from a seed fern ancestor. The neotenous organ is considered to have come into existence abruptly and the altered morphology to have been achieved without an intervening series of intermediates. Abrupt establishment of higher taxa by heterochrony constitutes a mechanism capable of decoupling microevolutionary processes from macrevolutionary differences and poses a distinct challenge to current evolutionary theory.

The record of the taxonomic evolution of North American ungulates is critical to our understanding of mammalian evolution and environmental change throughout the Cenozoic. The distribution of sampling in the ungulate fossil record over time and geographic space and the degree to which this biases the observed patterns of taxonomic evolution is poorly understood. To address these issues, I placed fossil collections and occurrences drawn from the Paleobiology Database into 2-Myr time intervals between 55 and 1 Ma. I determined the variation in numbers of fossil collections and occurrences, using three metrics to measure geographic variation: first, the area of the convex hull containing all collections in an interval, to determine the areal coverage of sampling; second, the mean pairwise geographic distance among collections as a measurement of the dispersion of collections within that area; and third, the interval-to-interval migration of the geographic centroid of all collections, to calculate changes in the geographic location of sampling. Each of these showed considerable variation over the Cenozoic, and both the area of the convex hull (ACH) encompassing all collections in an interval, and mean pairwise distance (MPWD) among them showed increasing trends over time.

To minimize the effect of variation in numbers of fossil samples over time, I used standard sample-standardization procedures. To minimize the effect of geographic variation in sampling over time, I standardized the area of sampling among intervals. I also employed both standardizations sequentially. Each standardization procedure had surprisingly little effect on observed patterns of taxonomic richness and rates. This indicates that, for North American ungulates, neither variation in number nor geographic distribution of fossil samples exerts an overwhelming influence on perceived macroevolutionary patterns. These results confirm the ungulate fossil record as a critical and faithful record for our understanding of Cenozoic environmental change and the mammalian evolutionary response.

For centuries, paleontologists have sought functional explanations for the uniquely complex internal walls (septa) of ammonoids, extinct shelled cephalopods. Ammonoid septa developed increasingly complex fractal margins, unlike any modern shell morphologies, throughout more than 300 million years of evolution. Some have suggested these morphologies provided increased resistance to shell-crushing predators. We perform the first physical compression experiments on model ammonoid septa using controlled, theoretical morphologies generated by computer-aided design and 3D printing. These biomechanical experiments reveal that increasing complexity of septal margins does not increase compression resistance. Our results raise the question of whether the evolution of septal shape may be tied closely to the placement of the siphuncle foramen (anatomic septal hole). Our tests demonstrate weakness in the centers of uniformly thick septa, supporting work suggesting reinforcement by shell thickening at the center of septa. These experiments highlight the importance of 3D reconstruction using idealized theoretical morphologies that permit the testing of long-held hypotheses of functional evolutionary drivers by recreating extinct morphologies once rendered physically untestable by the fossil record.

Troodon formosus, a theropod from the Late Cretaceous, is one of the few species of dinosaurs with multiple nest sites uncovered. It has been consistently demonstrated that eggs within these nests would have been partially buried in life—an exceedingly rare state in modern vertebrates. There has been debate over Troodon's capacity to engage in thermoregulatory contact incubation, especially regarding an adult's ability to efficiently supply partially buried eggs with energy. An actualistic investigation was undertaken to determine the thermodynamic efficiency of contact incubating partially buried eggs. An efficient system would keep eggs at temperatures closer to the surrogate parent than the ambient, without prohibitively high energy input. For the experiment, a surrogate dinosaur was created and used in both indoor controlled ambient temperature trials and in an outdoor variant. Even with ambient temperatures that were likely cooler than Cretaceous averages, the results showed that contact incubating partially buried eggs did seem to confer an energetic advantage; egg temperatures remained closer to the surrogate than ambient in both indoor and outdoor tests. Still, critics of contact incubating partially buried eggs are correct in that there is a depth at which adult energy would fail to make much of an impact—perhaps more relevant to buried eggs, as partially buried eggs would be in contact with an adult and likely above the thermal input threshold. Additionally, results from this experiment provide evidence for a possible evolutionary path from guarding behavior to thermoregulatory contact incubation.

The use of sclerobiosis as a tool for paleoenvironmental and paleoecological research is undermined by a lack of comparable methods for sclerobiont data collection and analysis. We present a new method for mapping sclerobiont distributions across any host, and offer an example of how the method may be used to interpret sclerobiont data in relation to host orientation. This approach can also be used to assess the suitability of beds and fossil material for paleoenvironmental reconstruction.

A sample of 150 encrusted dorsibiconvex atrypide brachiopods were selected from six beds in the Waterways Formation (latest Givetian – Early Frasnian; Alberta, Canada). The dorsal and ventral valves of each brachiopod were photographed. Sclerobiont taxa were mapped onto the photographs, and the maps were used to create stacked images with each of the 25 brachiopod specimens from each bed. Based on the life orientation of dorsibiconvex atrypides, three zones were designated on the host: the post mortem zone, (only available to sclerobionts after death and reorientation of the host); the shaded zone (brachial valve, excluding the post mortem zone); and the exposed zone (ventral valve).

Randomization simulation results indicate that all beds likely exhibit non random encrustation patterns, and corroborate the hypotheses that: (1) much of the encrustation occurred while the hosts were alive, and (2) these beds and fossils have experienced little physical reworking or transport and would be suitable for paleoenvironmental analysis. Mapping sclerobionts across hosts can serve as a unifying method to increase the recognition and use of sclerobiosis in paleontological studies.

The paleoecologist has been hampered in his studies of ancient communities by an inability to obtain reasonable estimates of standing crops and diversities. Finding the diversity of an ancient community is no simple matter, because a fossil assemblage is a mixture of living and recently dead individuals from that community. Considerable numbers of each group may be missing. The relationship of the elements in a fossil population for an individual species can be expressed as follows: F = Fl + Fd, where F is the average number of fossil individuals collected per unit area, Fl is the part of the sample produced by the burial of live individuals, and Fd is the part produced by the individuals already dead at the time of burial. Fl is a product of the standing crop S (number of individuals per unit area), multiplied by the probability of failure P (proportion of the standing crop which can be expected to fail to escape anastrophic burial), or Fl = (S) (P). Fd is the product of the death rate D (number of individuals which die per age-class time unit) multiplied by the residence time R (average length of time expressed in age-class time units that the remains of an individual will persist after death), or Fd = (D) (R). The probability of failure, residence time, and death rate can all be estimated from modern communities; the death rate can also be estimated from the fossils. Thus, the standing crop of an individual species can be expressed as follows:

This equation can be modified to eliminate the need to estimate D, as follows where i is the subscript indicating the number of the specific age class where the youngest is 1 and oldest is n. Once the standing crop for each species in the community has been estimated, a meaningful diversity can be calculated. Study of the model reveals that in populations where high-early mortality is the rule the likelihood of error in estimating population parameters is lower than for constant and low-early mortality populations.

Species diversity is a product of both biological interactions and physical-geographic factors. A model which eliminates biological interactions as a determinant of diversity can be used to assess the potential impact of physical and geographic factors operating alone on temporal trends in diversity (succession) and on spatial differences along latitudinal or environmental gradients. If a biologically neutral model can generate diversity patterns similar to those we observe, it can be argued that traditional hypotheses which depend on biological interactions are not the most parsimonious explanations for diversity patterns. If the neutral model approach supports a spectrum of possible hypotheses, perhaps the entire concept of species diversity can be discarded as a useful measure of community structure.

An earlier analysis of this type supported the notion that diversity patterns can be adequately explained by physical disturbance, global geography gradients, and stochastic immigration and extinction events. Our neutral model analysis does not affirm this view. We argue that the coarse level at which simple colonization models operate does not permit strong conclusions regarding the underlying mechanisms. Detailed community analyses may provide the best evidence for the nature of structuring processes. Based on the evidence available in the literature, species diversity is likely to be generated by a small number of biological processes interacting with physical-geographic gradients.

Lunules have evolved independently in several groups of clypeasteroids, including the Rotulidae, Astriclypeidae, Mellitidae and Scutasteridae. In this paper, only the monophyletic assemblage Monophorasteridae plus Mellitidae is considered. Lunules result from modifications of the growth patterns of test plates which bring about changes in relative growth in specific directions. It is unnecessary to postulate resorption of the test. Ambulacral lunules, which are known to have hydrodynamic functions, originated as part of a series of changes: 1) bifurcation of food grooves, 2) formation of pressure drainage channels, 3) lobulation of the ambitus (as in Monophoraster), 4) complete lunule formation. The anal lunule shares the hydrodynamic function but arose separately, as a developmental aberration. The position of the periproct is highly variable but it is most commonly located at the junction of suture lines, at plate corners. In Scutella it is located between the first and second post-basicoronal plates. In Monophoraster the periproct is located further forward, between the first post-basicoronal plates, and the small anal lunule occupies the junction point between first and second post-basicoronals. It is hypothesized that the anal lunule originated as an all-or-nothing event following the forward migration of the periproct and failure to resume normal plate growth at the sutural junction point between first and second post-basicoronal plates. Its walls were derived from paired interambulacral supports. The hypothesis is discussed in connection with the ontogenetic formation of the anal lunule in living mellitid sand dollars.

A basic hypothesis in extinction theory predicts that more abundant taxa have an evolutionary advantage over less abundant taxa, which should manifest as increased survivorship during major extinction events and longer fossil-record durations. Despite this, various paleontologic studies have found conflicting patterns, indicating a more complex relationship between abundance and extinction in the geologic past. This study tests the relationship between abundance and extinction among brachiopod genera within seven third-order depositional sequences spanning the Late Ordovician to Early Silurian (Katian–Aeronian) of the Cincinnati Arch.

Contrary to predictions, abundance is not positively correlated with duration in this study. Abundance and duration range from strongly negatively correlated to uncorrelated depending on the spatial scale of analysis and the geologic intervals included, but correlations never indicate that abundance is an evolutionary advantage. In contrast, abundance was an advantageous trait prior to the Ordovician/Silurian extinction, and brachiopods with higher abundances were more likely to survive the event than less abundant brachiopods. While this result is in keeping with common models of extinction, it has not been observed previously at a mass extinction boundary. This may be further evidence that the Ordovician/Silurian extinction was not accompanied by a shift in the macroevolutionary selectivity regime.

Conodont fossils are highly valuable for Paleozoic biostratigraphy and for interpreting evolutionary change, but identifying and describing conodont morphologies, and characterizing gradual shape variation remain challenging. We used geometric morphometric (GM) analysis to conduct the first landmark-based morphometric analysis of the biostratigraphically useful conodont genus Neognathodus. Our objective is to assess whether previously defined morphotype groups are reliably distinct from one another. As such, we reevaluate patterns of morphologic change in Neognathodus P1elements, perform maximum-likelihood tests of evolutionary modes, and construct novel, GM-based biozonations through a Desmoinesian (Middle Pennsylvanian) section in the Illinois Basin. Our GM results record the entire spectrum of shape variability among Neognathodus morphotypes, thus alleviating the problem of documenting and classifying gradual morphologic transitions between morphotypes. Statistically distinct GM groups support previously established classifications of N. bassleri, N. bothrops, and N. roundyi. Statistically indistinct pairs of GM groups do not support literature designations of N. medadultimus and N. medexultimus, and N. dilatus and N. metanodosus, and we synonymize each pair. Maximum-likelihood tests of evolutionary modes provide the first statistical assessment of Neognathodus evolutionary models in the Desmoinesian. The most likely evolutionary models are an unbiased random walk or a general random walk. We name four distinct biozones through the Desmoinesian using GM results, and these align with previous biozonation structure based on the Neognathodus Index (NI), illustrating that Neognathodus-based biostratigraphic correlations would not change between GM or NI methods. The structural similarity between both biozonations showcases that determining GM-based biozones is not redundant, as this comparison validates using landmark-based GM work to construct viable biozonations for subsequent stratigraphic correlations. Although this study is limited to the Illinois Basin, our quantitative methodology can be applied broadly to test taxonomic designations of additional genera, interpret statistically robust evolutionary patterns, and construct valid biozones for this significant chordate 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.

Living crinoids are exclusively passive suspension feeders and benthic as adults. However, in the past they adapted to a broad range of ecological niches. For instance, the stratigraphically important middle Paleozoic scyphocrinoids are hypothesized to have been planktonic, employing their inferred gas-filled globular, chambered structure at the distal end of the stem, the so-called lobolith, as a buoyancy device with the crinoid calyx suspended below it. Here, we evaluate this hypothesis using evidence from skeletal micromorphology and theoretical biomechanical modeling. Lobolith walls are typically composed of ossicles, which are exclusively composed of constructional labyrinthic stereom. In plates from the distal side of the lobolith, this stereom extends into microperforate stereom layer, forming wavy ridges and spines. No microscale adaptations for preventing gas leaks and/or ingress of water (such as internal and external imperforate stereom layers) are known. Furthermore, theoretical calculations suggest that the scyphocrinoid tow-net mode of feeding would have resulted in small relative velocities between the towed filter and the ambient water, thus making it an ineffective passive filter feeder. We suggest that the lobolith of these crinoids acted as a modified holdfast rather than as a floating buoy. Its globular shape and distally positioned microspines served as adaptations for living in unconsolidated sediments, analogous to iceberg- and snowshoe-like strategies used by some mollusks and brachiopods. Like modern isocrinids, scyphocrinoids could have maintained an upright feeding posture by extending the distal portion of the stalk along the bottom. In this recumbent posture, the distal part of the stalk with the lobolith might have functioned as a drag anchor. As a consequence of the ~3-m-long stem, even with this posture, the benthic scyphocrinoids could have risen to the highest epifaunal tier in the Paleozoic.

It has been shown in laboratory experiments that viruses can transfer DNA from the host cell to other cells and even to those of another species. In nature such transfers could facilitate convergent evolution. Studied cases of convergent evolution indicate that a gene might be successfully transferred to another species to produce a similar phenotypic effect as frequently as once per 1–10 ma and the effects of gene transfer on evolution in general are likely to be considerable. There are many constraints on the cases of convergent evolution that might be considered as possible examples of gene transfer. First, both co-occurrence in space and time of the taxa in question and presence of complete reproductive isolation must be assessed. Further, both the limited space available in a virus particle and the necessity that the transferred DNA functions well in both mitosis and meiosis in heterozygotic individuals indicate that only rather short pieces of DNA would be expected to be transferred. This limits the possible effects of any gene transfer. Examples of convergent evolution in five Siluro-Devonian conodont lineages are briefly presented and assessed in terms of possible mechanisms of convergence.

The coastal environment of the Changjiang delta has been influenced by recent anthropogenic activities such as dam construction and increased sewage and fertilizer inputs. Previous work examined the compositional shift of marine plankton to assess ecological impacts of these activities on marine ecosystems in the Changjiang discharge area. Here we used benthic marine ostracodes collected in the Changjiang estuary and the adjacent East China Sea in the 1980s and the 2010s, respectively, to investigate temporal changes of the benthic community and controlling factors for the benthic fauna. Our results revealed more shoreward distribution of some well-known offshore ostracode species in the 2010s compared with the 1980s and a relatively more important role for environmental processes (e.g., bottom-water temperature, bottom-water salinity, and eutrophic conditions of surface water) than spatial processes (e.g., the flow of ocean currents) in structuring ostracode compositions. The temporal changes in the ostracode community are likely attributable to the combined effects of reduced fresh water and sediment discharge and eutrophic conditions of the Changjiang due to the many dams constructed along the Changjiang and population expansion in the Changjiang Basin. Results of redundancy analysis and variation partitioning suggest that ocean currents facilitated environmental filtering of ostracode species such that they could disperse to preferred environmental conditions. These findings highlight the potential uses of marine microfossils to better understand ecological impacts on benthic ecosystems in vulnerable Asian mega-deltas and provide insights into the integration of metacommunity concepts in disentangling dynamics of marine benthic communities.

The inner ear of the two higher clades of modern cetaceans (Neoceti) is highly adapted for hearing infrasonic (mysticetes) or ultrasonic (odontocetes) frequencies. Within odontocetes, Platanistoidea comprises a single extant riverine representative, Platanista gangetica, and a diversity of mainly extinct marine species from the late Oligocene onward. Recent studies drawing on features including the disparate tympanoperiotic have not yet provided a consensus phylogenetic hypothesis for platanistoids. Further, cochlear morphology and evolutionary patterns have never been reported. Here, we describe for the first time the inner ear morphology of late Oligocene–early Miocene extinct marine platanistoids and their evolutionary patterns. We initially hypothesized that extinct marine platanistoids lacked a specialized inner ear like P. gangetica and thus, their morphology and inferred hearing abilities were more similar to those of pelagic odontocetes. Our results reveal there is no “typical” platanistoid cochlear type, as the group displays a disparate range of cochlear anatomies, but all are consistent with high-frequency hearing. Stem odontocete Prosqualodon australis and platanistoid Otekaikea huata present a tympanal recess in their cochlea, of yet uncertain function in the hearing mechanism in cetaceans. The more basal morphology of Aondelphis talen indicates it had lower high-frequency hearing than other platanistoids. Finally, Platanista has the most derived cochlear morphology, adding to evidence that it is an outlier within the group and consistent with a >9-Myr-long separation from its sister genus Zarhachis. The evolution of a singular sound production morphology within Platanistidae may have facilitated the survival of Platanista to the present day.

It was once thought that the endemic carnivorous mammals of South America, the metatherian sparassodonts, were driven extinct by North American carnivorans through competitive exclusion. However, sparassodonts went extinct before most groups of carnivorans entered South America; only the endemic Cyonasua-group procyonids (Cyonasua and Chapalmalania), which immigrated to South America nearly 4 million years earlier than other carnivorans, significantly overlapped with sparassodonts in time. In this study, we examine the functional morphology of the dentition of Cyonasua and Chapalmalania through quantitative analysis to determine the dietary habits of these taxa and the degree to which they may have ecologically overlapped sparassodonts and large predatory Neogene didelphimorphians. We find Cyonasua and Chapalmalania to be more carnivorous than extant procyonids, other than Bassariscus, in agreement with previous studies, but more omnivorous than most other carnivorans and all meat-eating South American metatherians, including sparassodonts. The extreme ecological dissimilarity between Cyonasua-group procyonids and members of the endemic South American predator guild may explain why procyonids were able to successfully establish themselves in South America several million years earlier than most other northern mammals (including all other carnivorans): they moved into a previously unoccupied ecological niche (large omnivore) and avoided direct competition with incumbent native species, a situation similar to that documented in historical cases of biological invasion. The omnivorous diets and climbing/swimming abilities of procyonids may have increased their chances for a successful over-water dispersal relative to other carnivorans, further favoring their successful establishment in South America.