Estimates of taxonomic richness and abundance are complicated by sampling biases. The failure to sample rare taxa is most often attributed to inadequate sampling and to removal during the process of sample-size standardization. Here I present two methods for unveiling rare diversity by integrating species presence/absence data from museum collections and the literature with quantitative estimates of species richness and abundance gathered from field-based bulk samples. Combining museum, literature, and field data can provide a more comprehensive estimate of taxonomic richness and abundance without substantial increase in current sampling effort. First, in a given bulk sample, the lowest proportional abundance value observed can be used to estimate the maximum abundance of rare species known to have occurred at the locality at least once but not recorded in the current sample. Second, a model-selection approach can be used, in which a set of relative abundance distribution models are fit to the bulk-sample abundance data and the parameter estimates for the best model used to calculate the abundance distribution for all species known from the locality. The Paleogene marine fossil record of the U.S. Gulf Coastal Plain is suitable for applying these methods, because (1) the molluscan fauna is well represented in museum collections and the literature, (2) the molluscan fauna has been taxonomically standardized, and (3) many classic localities remain accessible for standardized bulk sampling. I introduce these methods by applying them to a single locality and then, using the faunas of the Gosport, Moodys Branch, and Red Bluff Formations, I demonstrate how the model-fitting approach can be used to compare taxonomic richness among multiple localities. A substantial fraction of the molluscan richness known from each locality is not captured in bulk samples and much of this unobserved richness may be attributed to the rarity of species. The multiple-locality comparison suggests that the greatest Paleogene decline in standing richness occurred in the middle Eocene and that the recovery of richness following the Eocene-Oligocene extinction was quite rapid despite substantial loss of taxa. These analyses underscore the magnitude of veiled diversity in marine fossil assemblages and the potential of existing sources of data to unveil rare taxa, allowing them to be incorporated into quantitative diversity studies.

The silicoflagellates are a class of enigmatic chrysophytes characterized by netlike skeletons composed of opaline silica. Other major groups of siliceous plankton—the diatoms and radiolarians—exhibit evidence of decreasing size or silicification over the Cenozoic. We investigated trends in the silicoflagellate fossil record by constructing a species-level database of diversity and morphological metrics. This new database reveals a proliferation of silicoflagellate species with spined skeletons along with an increase in the mean number of spines per species over the Cenozoic. Although there is little change in skeleton size or silicification among species with spines, those without spines are larger than species with spines and exhibit a decrease in size toward the present. Increased grazing pressure combined with declining surface silicate availability may have shifted the costs and benefits of silicification, causing divergent responses in skeletal morphology between these different morphological lineages of silicoflagellates over time. We postulate that diminishing Cenozoic surface silicic acid availability may have predisposed large spineless silicoflagellate species to extinction, whereas increased grazing pressure may have contributed to the extinction of all remaining spineless species within the edible size range of grazers.

Periodicity has recently been reported in the extinction rates of fossil marine families since the Permian. The analysis used appears particularly sensitive to parameter estimation techniques, particularly in the definition of mass extinctions. It also fails to incorporate autocorrelation in the fossil record into its null hypothesis and rests on an inappropriate a posteriori comparison to the null hypothesis. An alternative analysis, examining the time-lags between periods of high extinction rates, produces no evidence of a cycle.

We have devised a simple model for assessing the role of development in shaping the evolution of morphological disparity. Disparity of a clade at any given time is expressed in terms of the developmental dynamics that lead to the variety of adult morphotypes observed. We use assumed phenotypic manifestations of developmental processes, as they could be detected from allometric characterizations, to distinguish a few, nonexclusive types of evolutionary changes in ontogeny. On the basis of this formalization, we describe the diversification of hypothetical clades, using the standard curve of adult morphological disparity, the curve of juvenile disparity, and the curve of allometric disparity, the latter quantifying the diversification of clades in allometric space. Contrasts of these curves reflect the underlying developmental scheme that drives temporal changes in disparity. We then vary the parameters of the model to assess the expected signature of each metric under specific conditions: changes in the relative frequencies of the types of evolutionary developmental changes, changes in the transition magnitude attached to each of them, and effects of temporal variation in average adult size on disparity curves and patterns of morphospace occupation. Results emphasize the potential contribution of these proxies for developmental dynamics—juvenile morphological disparity, allometric disparity, and average adult size—in enriching the interpretation of standard disparity curves and the description of clade histories, with possible process-oriented inferences.

A neurological method for assessment of nasal cavity homologies in extant archosaurs is extended to lambeosaurine hadrosaurids (Dinosauria: Ornithischia) to test functional hypotheses associated with their hypertrophied nasal passages and highly derived cranial crests. The olfactory system and associated cranial nerve pathways that have consistent relationships to soft tissue divisions of the nasal cavity are reconstructed in lambeosaurines on the basis of new paleoneurological data and a comparative phylogenetic approach. The new model of the lambeosaurine olfactory system and nasal cavity shows that a significant portion of nasal cavity proper was located outside the crest cavities and that the primary olfactory region was located rostromedial to the orbits.

All available data indicate that the evolutionary hypertrophy of the nasal cavity occurred predominantly within the non-olfactory nasal vestibule, and that crest development was not causally associated with olfaction. The high level of interspecific and ontogenetic variation in crest shape and nasal vestibule development in lambeosaurine dinosaurs is most consistent with proposed behavioral functions, notably acoustic resonance for intraspecific communication. Despite significant modification to the nasal cavity within Archosauria and its extreme hypertrophy and supraorbital development in Lambeosaurinae, the neural olfactory system and the olfactory region of the nasal cavity proper retain their plesiomorphic positions and associations, suggesting that this system is highly conserved in vertebrate evolution.

The purpose of this paper is to explore the possibility and utility of estimating multivariate selection in fossil assemblages, using naticid gastropods as a case study. We used the presence or the absence of a naticid borehole as an index of survival with respect to drilling attacks, enabling us to estimate the multivariate selection gradient exerted by this predator on the shell length and shell thickness of two bivalve genera, Astarte and Spisula. We hypothesized that naticid selection pressure would favor the survival of large, thick-shelled bivalve prey throughout the Cenozoic.

Differential survival of prey was recorded over geologic time using processed bulk assemblages from the Miocene, Pliocene, and Pleistocene Epochs. Multivariate logistic regressions were performed by time period to determine if length and thickness were important factors affecting survival. The direction and magnitude of selection on length and thickness for the two genera ranged from zero (no selection) to large positive or negative values. Only two selection coefficients were significant after sequential Bonferroni corrections: thin-shelled Astarte survived substantially better than thick-shelled Astarte during the Pleistocene (βavggrad = −1.23) and large Spisula survived slightly better than small Spisula during the Miocene Epoch (βavggrad = 0.05).

This is the first study using fossils to calculate multivariate selection gradients. It suggests that naticids were not necessarily strong agents of selection on two traits previously thought to be important to survival of drilling attacks for two of their common prey species. We also show that multivariate selection gradient estimates differ from traditional predation intensity estimates but are superior for estimating the magnitude and direction of natural selection because they use differential mortality of different prey phenotypes rather than just absolute mortality from predation. This work is especially significant for research that involves estimating the relative importance of predation (naticid or otherwise) as an evolutionary force and will be useful for fossil studies where differential survival can be recorded.

To assess evolutionary processes in deep time, it is essential to understand the roles of development and environment, both recorded through the morphological variability of fossil assemblages. Thanks to their great abundance and the high temporal resolution of their fossil record, conodont elements are ideal to address this issue. In this paper, we present the first quantitative study of a Carnian–Norian (Late Triassic) assemblage of closely related P1 conodont elements. Using geometric morphometrics (landmarks, sliding landmarks, and elliptic Fourier analysis), we explore the main axes of phenotypic variation and relate them to classically used taxonomic characters. We show that some important taxonomic features follow laws of covariation, hence highlighting developmental constraints. Furthermore, the intraspecific variation within all considered species, either Carnian or Norian forms, is similarly restricted, emphasizing, for the first time in conodont P1 elements, a common line of least resistance to evolution, which means that similar intrinsic (developmental) factors were acting on these taxa and likely biased the evolutionary trajectories of all these taxa in a similar way. Because the evolution between Carnian and Norian forms is known to have followed a trajectory that is significantly different from the line of least resistance, strong extrinsic pressures, such as environmental disturbances, were probably at play around the Carnian/Norian boundary to counteract the effects of these intrinsic, developmental constraints.

Analyses of ancient food webs reveal important paleoecological processes and responses to a range of perturbations throughout Earth's history, such as climate change. These responses can inform our forecasts of future biotic responses to similar perturbations. However, previous analyses of ancient food webs rarely accounted for key differences between modern and ancient community data, particularly selective loss of soft-bodied taxa during fossilization. To consider how fossilization impacts inferences of ancient community structure, we (1) analyzed node-level attributes to identify correlations between ecological roles and fossilization potential and (2) applied selective information loss procedures to food web data for extant systems. We found that selective loss of soft-bodied organisms has predictable effects on the trophic structure of “artificially fossilized” food webs because these organisms occupy unique, consistent food web positions. Fossilized food webs misleadingly appear less stable (i.e., more prone to trophic cascades), with less predation and an overrepresentation of generalist consumers. We also found that ecological differences between soft- and hard-bodied taxa—indicated by distinct positions in modern food webs—are recorded in an early Eocene web, but not in Cambrian webs. This suggests that ecological differences between the groups have existed for ≥48 Myr. Our results indicate that accounting for soft-bodied taxa is vital for accurate depictions of ancient food webs. However, the consistency of information loss trends across the analyzed food webs means it is possible to predict how the selective loss of soft-bodied taxa affects food web metrics, which can permit better modeling of ancient communities.

The study of tracks is often regarded as a fringe subdiscipline outside the scientific mainstream. Papers dealing with footprints traditionally appear either in popular magazines like Natural History (Bird 1939, 1944; Brown 1938), or in very obscure publications (Sarjeant 1974). Usually it is only the spectacular discoveries, which are directly applicable to topical debates, that rouse much scientific interest. For example, the discovery of Pliocene hominid tracks (Leakey and Hay 1979) provided unequivocal evidence for the antiquity of bipedalism (cf., Napier 1967). Similarly the tracks of a running theropod allowed for direct estimates of the speed attained by dinosaurs (Farlow 1981), and the tracks of a herd of running theropods fueled debate about gregariousness and stampede behavior (Thulborn and Wade 1984).

Evolutionary inferences from fossil data often require accurately reconstructing differences in richness and morphological disparity between fossil sites across space and time. Biases such as sampling and rock availability are commonly accounted for in large-scale studies; however, preservation bias is usually dealt with only in smaller, more focused studies. Birds represent a diverse, but taphonomically fragile, group commonly used to infer environmental conditions in recent (Pleistocene and later) fossil assemblages, and their relative scarcity in the fossil record has led to controversy over the timing of their radiation. Here, I use simulations to show how even weak taphonomic biases can distort estimates of richness, and render variance sensitive to sample size. I then apply an ecology-based filtering model to recent bird assemblages to quantify the distortion induced by taphonomy. Certain deposit types, such as caves, show less evidence of taphonomic distortion than others, such as fluvial and lacustrine deposits. Archaeological middens unsurprisingly show some of the strongest evidence for taphonomic bias, and they should be avoided when reconstructing Pleistocene and early Holocene environments. Further, these results support previously suggested methods for detecting fossil assemblages that are relatively faithfully preserved (e.g., presence of difficult-to-preserve taxa), and I use these results to recommend that future large-scale studies include facies diversity along with metrics such as rock volume, or compare only sites with similar taphonomic histories.

Fish scales accumulating in marine laminated sediments can provide a record of population variability of small pelagic fishes. Although some studies have noted signs of scale degradation that could affect estimates of population variability, there are presently no well-developed means to evaluate degradation. We developed several indices as indicators of fish scale preservation in two box-cores that we collected off Pisco (14°S), one at 301 m near the center of the oxygen minimum zone (OMZ), and the other at 201 m near the upper limit of the OMZ. These indices include (1) an index of fish scale integrity (estimate of scale wholeness relative to fragmentation), (2) the fungi-free area of fish scales and vertebrae, (3) the ratio of fish scales to vertebrae (as well as fish scales to vertebrae and bones), and (4) the ratio of whole scales to fragments. We address whether lower numbers of anchovy scales occurring in association with reduced total organic carbon fluxes and higher bottom-water oxygen concentrations are due entirely to lower abundances of anchovy or whether differential preservation of the fish scales in the sediments plays an important role in reduced scale abundances. Comparison of temporal sequences between the two cores provides the means to assess whether there are differences in the preservation of fish scales. The combined indices indicate that the lower numbers of fish scales in the earliest period have been affected by degradation, and to a greater degree in the box-core from 201 meters, which can be subject to higher oxygen concentrations. On the other hand, decadal-scale variations in fish scale abundance within the period of better preservation are unlikely to be caused by degradation. We discuss the utility and drawbacks of different indices of preservation for reconstructing past changes in fish population sizes with fluxes of fish debris and also briefly discuss the utility of these indices to other paleobiological systems.

Amecystis Ulrich and Kirk is a rhombless rhombiferan cystoid exhibiting adaptation to an active mode of life in the bilaterally symmetrical, dorso-ventrally compressed theca and to an active mode of respiration suggested by the lack of pore rhombs and greatly enlarged periproct. Like other members of the Pleurocystitidae, Amecystis probably wriggled along the bottom, but may have adopted a temporarily sessile habit by pushing the distal stele into the substrate or by grasping. Evolution of the genus began in the Middle Ordovician, probably as a development from Pleurocystites. General trends in the stratigraphic succession of recognized morphospecies: A. raymondi Parsley, A. woodi n.sp., and A. laevis (Raymond) show a reduction in angularity of thecal outline and obsolescence of surface features on the thecal plates. The use of the periproct as a pumping organ in respiration is regarded as an advanced trend that was probably utilized by many rhomb-bearing cystoids as an accessory respiratory mode; alone, it proved to be an unsuccessful adaptation in Amecystis.

Improvements in the perceived completeness of the fossil record may be driven both by new discoveries and by reinterpretation of known fossils, but disentangling the relative effects of these processes can be difficult. Here, we propose a new methodology for evaluating historical trends in the perceived completeness of the fossil record, demonstrate its implementation using the freely available software ASCC (version 4.0.0), and present an example using crown-group birds (Aves). Dates of discovery and recognition for the oldest fossil representatives of 75 major lineages of birds were collected for the historical period ranging from 1910 to 2010. Using a comprehensive phylogeny, we calculated minimum implied stratigraphic gaps (MIG range) across these 75 lineages. Our results show that a reduction in global MIG values of 1.35 Ga (billion years) occurred over the past century in avian paleontology. A pronounced increase in the average rate of global MIG reduction is noted in the post-1970s interval (290.5 Myr per decade) compared to the pre-1970s interval (31.9 Myr per decade). Although the majority of the improvement in the fossil record of birds has come from new discoveries, substantial improvement (∼22.5%) has resulted from restudy and phylogenetic revision of previously described fossils over the last 40 years. With a minimum estimate indicating that at least 1.34 Gyr of gaps remain to be filled between the predicted and observed first appearances of major lineages of crown Aves, there is much progress to be made. However, a notable tapering off in the rate of global MIG reduction occurs between 1990 and 2010, suggesting we may be approaching an asymptote of oldest record discoveries for birds. Only future observations can determine whether this is a real pattern or a historical anomaly. Either way, barring the discovery of fossils that substantially push back the minimum age for the origin of crown-clade Aves, new discoveries cannot continue to reduce global MIG values at the average post-1970s rate over the long term.

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.

The emergence of shell forms in the growth of foraminifera is an essential problem in the morphogenesis of these microorganisms. We present a model of foraminiferal shells that applies a moving-reference system. Previous models have referred to fixed-reference axes and have neglected apertures. Our model focuses on real morphologic characteristics and follows stepwise natural biological processes. It introduces apertures based on minimization of the local communication path and applies three parameters, which are either predetermined or selected at random from given ranges. Expression of stochastic parameters mimics phenotypic variability of a shell. We also present a detailed description of the method with examples of simulated shells and the first step toward analyses of the theoretical morphospace. The morphospace is divided into certain regions (phases) separated by transitional planes (phase transitions). Further prospects for foraminiferal modeling, which should focus on more in-depth models based on realistic intracellular dynamics, are also presented.

Over the last 50 years, access to new data and analytical tools has expanded the study of analytical paleobiology, contributing to innovative analyses of biodiversity dynamics over Earth's history. Despite—or even spurred by—this growing availability of resources, analytical paleobiology faces deep-rooted obstacles that stem from the need for more equitable access to data and best practices to guide analyses of the fossil record. Recent progress has been accelerated by a collective push toward more collaborative, interdisciplinary, and open science, especially by early-career researchers. Here, we survey four challenges facing analytical paleobiology from an early-career perspective: (1) accounting for biases when interpreting the fossil record; (2) integrating fossil and modern biodiversity data; (3) building data science skills; and (4) increasing data accessibility and equity. We discuss recent efforts to address each challenge, highlight persisting barriers, and identify tools that have advanced analytical work. Given the inherent linkages between these challenges, we encourage discourse across disciplines to find common solutions. We also affirm the need for systemic changes that reevaluate how we conduct and share paleobiological research.

Most geometric morphometric studies are underpinned by sets of photographs of specimens. The camera lens distorts the images it takes, and the extent of the distortion will depend on factors such as the make and model of the lens and camera and user-controlled variation such as the zoom of the lens. Any study that uses populations of geometric data digitized from photographs will have shape variation introduced into the data set simply by the photographic process. We illustrate the nature and magnitude of this error using a 30-specimen data set of Recent New Zealand Mactridae (Mollusca: Bivalvia), using only a single camera and camera lens with four different photographic setups. We then illustrate the use of retrodeformation in Adobe Photoshop and test the magnitude of the variation in the data set using multivariate Procrustes analysis of variance. The effect of photographic method on the variance in the data set is significant, systematic, and predictable and, if not accounted for, could lead to misleading results, suggest clustering of specimens in ordinations that has no biological basis, or induce artificial oversplitting of taxa. Recommendations to minimize and quantify distortion include: (1) that studies avoid mixing data sets from different cameras, lenses, or photographic setups; (2) that studies avoid placing specimens or scale bars near the edges of the photographs; (3) that the same camera settings are maintained (as much as practical) for every image in a data set; (4) that care is taken when using full-frame cameras; and (5) that a reference grid is used to correct for or quantify distortion.

The morphological and ecological diversity of lemurs and lorisiformes once rivaled that of the rest of the primate order. Here, we assemble a dataset of 3D models representing the second mandibular molars of a wide range of extant and fossil strepsirrhines encompassing this diversity. We use these models to distill quantitative descriptors of tooth form and then analyze these data using new analytical methods. We employ a recently developed dental topography metric (ariaDNE), which is less sensitive to details of random error in 3D model quality than previously used metrics (e.g., DNE); Bayesian multinomial modeling with metrics designed to measure overfitting risk; and a tooth segmentation algorithm that allows the shapes of disaggregated tooth surface features to be quantified using dental topography metrics. This approach is successful at reclassifying extant strepsirrhine primates to known dietary ecology and indicates that the averaging of morphological information across the tooth surface does not interfere with the ability of dental topography metrics to predict dietary adaptation. When the most informative combination of dental topography metrics is applied to extinct species, many subfossil lemurs and the most basal fossil strepsirrhines are predicted to have been primarily frugivorous or gummivorous. This supports an ecological contraction among the extant lemurs and the importance of frugivory in the origins of crown Strepsirrhini, potentially to avoid competition with more insectivorous and folivorous members of Paleogene Afro-Arabian primate faunas.

Simulations are playing an increasingly important role in paleobiology. When designing a simulation study, many decisions have to be made and common challenges will be encountered along the way. Here, we outline seven rules for executing a good simulation study. We cover topics including the choice of study question, the empirical data used as a basis for the study, statistical and methodological concerns, how to validate the study, and how to ensure it can be reproduced and extended by others. We hope that these rules and the accompanying examples will guide paleobiologists when using simulation tools to address fundamental questions about the evolution of life.