Landmark-based geometric morphometrics is a powerful approach to quantifying biological shape, shape variation, and covariation of shape with other biotic or abiotic variables or factors. The resulting graphical representations of shape differences are visually appealing and intuitive. This paper serves as an introduction to common exploratory and confirmatory techniques in landmark-based geometric morphometrics. The issues most frequently faced by (paleo)biologists conducting studies of comparative morphology are covered. Acquisition of landmark and semilandmark data is discussed. There are several methods for superimposing landmark configurations, differing in how and in the degree to which among-configuration differences in location, scale, and size are removed. Partial Procrustes superimposition is the most widely used superimposition method and forms the basis for many subsequent operations in geometric morphometrics. Shape variation among superimposed configurations can be visualized as a scatter plot of landmark coordinates, as vectors of landmark displacement, as a thin-plate spline deformation grid, or through a principal components analysis of landmark coordinates or warp scores. The amount of difference in shape between two configurations can be quantified as the partial Procrustes distance; and shape variation within a sample can be quantified as the average partial Procrustes distance from the sample mean. Statistical testing of difference in mean shape between samples using warp scores as variables can be achieved through a standard Hotelling's T2 test, MANOVA, or canonical variates analysis (CVA). A nonparametric equivalent to MANOVA or Goodall's F-test can be used in analysis of Procrustes coordinates or Procrustes distance, respectively. CVA can also be used to determine the confidence with which a priori specimen classification is supported by shape data, and to assign unclassified specimens to pre-defined groups (assuming that the specimen actually belongs in one of the pre-defined groups).

Examples involving Cambrian olenelloid trilobites are used to illustrate how the various techniques work and their practical application to data. Mathematical details of the techniques are provided as supplemental online material. A guide to conducting the analyses in the free Integrated Morphometrics Package software is provided in the appendix.

Detrital zircon geochronology is rapidly evolving into a very powerful tool for determining the provenance and maximum depositional age of clastic strata. This rapid evolution is being driven by the increased availability of ion probes and laser ablation ICP mass spectrometers, which are able to generate age determinations rapidly, at moderate to low cost, and of sufficient accuracy for most applications. Improvements in current methods will probably come from enhanced precision/accuracy of age determinations, better tools for extracting critical information from age spectra, abilities to determine other types of information (e.g., REE patterns, O and Hf isotope signatures, and/or cooling ages) from the dated grains, and construction of a database that provides access to detrital zircon age determinations from around the world.

Over recent decades ostracods have become established indicators of ecosystem health, biodiversity and environmental change. With applications ranging across the earth sciences (from modern pollution studies to sea-level change, basin evolution, plate tectonics, palaeoceanography) and related disciplines such as archaeology, ecology and genetics, their utility extends to almost every aquatic and semi-aquatic habitat, from the deep ocean to high mountain springs. Their temporal range is now known to cover the last 500 million years of earth history.

The study of fossil ostracod assemblages follows traditional palaeontological lines of investigation, including taphonomy, morphometries and diversity, but there are a number of methodological approaches, specific to the ostracods, that render them potentially one of the most versatile organisms in the fossil record. Ostracods have been employed on a range oftemporal and spatial scales to reconstruct past environments, from world-wide, geological-scale global events in the deep-sea through to smaller-scale studies of lakes and their archives of local environmental change over recent centuries.

Much information can be obtained from ostracod assemblages but it is particularly through recent advances in the chemical and physical study of single shells or carapaces that the utility of these organisms has been brought to the fore. In this paper the potential palaeoenvironmental information derived from an ostracod assemblage, a single species, or an individual shell is reviewed. The main applications for ostracods are outlined for marine and non-marine ecosystems. Finally, the role of the ostracods in detailing the recent history of the Aral Sea is outlined.

Paleontological research on predation has been expanding rapidly in scope, methods, and goals. The growing assortment of research strategies and goals has led to increasing differences in sampling strategies, types of data collected, definition of variables, and even reporting style. This methodological overview serves as a starting point for erecting some general methodological guidelines for studying the fossil record of predation. I focus here on trace fossils left by predators in the skeleton of their prey, arguably one of the most powerful sources of direct data on predator-prey interactions available in the fossil record. A critical survey of sampling protocols (data collecting strategy, sieve size, and sample size) and analytical approaches (predation intensity metrics, strategies for evaluating behavioral selectivity of predators, and taphonomic tests) reveals that various approaches can be fruitful depending on logistic circumstances and scientific goals of paleoecological projects. Despite numerous caveats and uncertainties, trace fossils left by predators on skeletons of their prey remain one of the most promising directions of research in paleoecology and evolutionary paleobiology.

Advancement of understanding in paleontology and biology has always been hindered by difficulty in accessing comparative data. With current and burgeoning technology, the severity of this hindrance can be substantially reduced. Researchers and museum personnel generating three-dimensional (3-D) digital models of museum specimens can archive them using internet repositories that can then be explored and utilized by other researchers and private individuals without a museum trip. We focus on MorphoSource, the largest web archive for 3-D museum data at present. We describe the site, how to use it most effectively in its current form, and best practices for file formats and metadata inclusion to aid the growing community wishing to utilize it for distributing 3-D digital data. The potential rewards of successfully crowd sourcing the digitization of museum collections from the research community are great, as it should ensure rapid availability of the most important datasets. Challenges include long-term governance (i.e., maintaining site functionality, supporting large amounts of digital storage, and monitoring/updating file to prevent bit rot, which is the slow and random corruption of electronic data over time, and data format obsolescence, which is the problem of data becoming unreadable or ineffective because of the loss of functional software necessary for access), and utilization by the community (i.e., detecting and minimizing user error in creating data records, incentivizing data sharing by researchers and institutions alike, and protecting stakeholder rights to data, while maximizing accessibility and discoverability).

MorphoSource serves as a proof-of-concept of how these kinds of challenges can be met. Accordingly, it is generally recognized as the most appropriate repository for large, raw datasets of fossil organisms and/or comparative samples. Its existence has begun to transform data transparency standards because journal reviewers, editors, and grant officers now often suggest or require that 3-D data be made available through this site.

Paleobiologists are reaching a consensus that biases in diversity curves, origination rates, and extinction rates need to be removed using statistical estimation methods. Diversity estimates are biased both by methods of counting and by variation in the amount of fossil data. Traditional counts are essentially tallies of age ranges. Because these counts are distorted by interrelated factors such as the Pull of the Recent and the Signor-Lipps effect, counts of taxa actually sampled within intervals should be used instead. Sampling intensity biases can be addressed with randomized subsampling of data records such as individual taxonomic occurrences or entire fossil collections. Fair subsampling would yield taxon counts that track changes in the species pool size, i.e., the diversity of all taxa that could ever be sampled. Most of the literature has overlooked this point, having instead focused on making sample sizes uniform through methods such as rarefaction. These methods flatten the data, undersampling when true diversity is high. A good solution to this problem involves the concept of frequency distribution coverage: a taxon's underlying frequency is said to be “covered” when it is represented by at least one fossil in a data set. A fair subsample, but not a uniform one, can be created by drawing collections until estimated coverage reaches a fixed target (i.e., until a “shareholder quorum” is attained). Origination and extinction rates present other challenges. For many years they were thought of in terms of simple counts or ratios, but they are now treated as exponential decay coefficients of the kind featuring in simple birth-death models. Unfortunately, these instantaneous rates also suffer from counting method biases (e.g., the Pull of the Recent). Such biases can be removed by only examining taxa sampled twice consecutively, three times consecutively, or in the first and third of three intervals but not the second (i.e., two timers, three timers, and part timers). Two similar equations involving these counts can be used. Alternative methods of estimating diversity and turnover through extrapolation share some of the advantages of quorum subsampling and two-timer family equations, but it remains to be shown whether they produce precise and accurate estimates when applied to fossil data.

Predation, in the broad sense of an organism killing another organism for nutritional purposes, is probably as old as life itself and has originated many times during the history of life. Although little of the beginnings is caught in the fossil record, observations in the rock record and theoretical considerations suggest that predation played a crucial role in some of the major transitions in evolution. The origin of eukaryotic cells, poorly constrained to about 2.7 Ga by geochemical evidence, was most likely the ultimate result of predation among prokaryotes. Multicellularity (or syncytiality), as a means of acquiring larger size, is visible in the fossil record soon after 2 Ga and is likely to have been mainly a response to selective pressure from predation among protists. The appearance of mobile predators on bacteria and protists may date back as far as 2 Ga or it may be not much older than the Cambrian explosion, or about 600 Ma. The combined indications from the decline of stromatolites and the diversification of acritarchs, however, suggest that such predation may have begun around 1 Ga. The Cambrian explosion, culminating around 550 Ma, represents the transition from simple, mostly microbial, ecosystems to ones with complex food webs and second- and higher-order consumers. Macrophagous predators were involved from the beginning, but it is not clear whether they originated in the plankton or in the benthos. Although predation was a decisive selective force in the Cambrian explosion, it was a shaper rather than a trigger of this evolutionary event.

Foraminiferal tests are a common component of many marine sediments. The oxygen isotope ratio (δ18O) of test calcite is frequently used to reconstruct aspects of their life environment. The δ18O depends mainly on the isotope ratio of the water it is precipitated from, the temperature of calcification, and, to a lesser extent, the carbonate ion concentration. Foraminifera and other organisms can potentially preserve their original isotope ratio for many millions of years, although diagenetic processes can alter the ratios. Work on oxygen isotope ratios of foraminifera was instrumental in the discovery of the orbital theory of the ice ages and continues to be widely used in the study of rapid climate change. Compilations of deep sea benthic foraminifer oxygen isotopes have revealed the long history of global climate change over the past 100 million years. Planktonic foraminifer oxygen isotopes are used to investigate the history of past sea surface temperatures, revealing the extent of past ‘greenhouse’ warming and global sea surface temperatures.

Burgess Shale-type fossil assemblages provide a unique record of animal life in the immediate aftermath of the so-called “Cambrian explosion.” While most soft-bodied faunas in the rock record were conserved by mineral replication of soft tissues, Burgess Shale-type preservation involved the conservation of whole assemblages of soft-bodied animals as primary carbonaceous remains, often preserved in extraordinary anatomical detail. Burgess Shale-type preservation resulted from a combination of influences operating at both local and global scales that acted to drastically slow microbial degradation in the early burial environment, resulting in incomplete decomposition and the conservation of soft-bodied animals, many of which are otherwise unknown from the fossil record. While Burgess Shale-type fossil assemblages are primarily restricted to early and middle Cambrian strata (Series 2–3), their anomalous preservation is a pervasive phenomenon that occurs widely in mudstone successions deposited on multiple paleocontinents. Herein, circumstances that led to the preservation of Burgess Shale-type fossils in Cambrian strata worldwide are reviewed. A three-tiered rank classification of the more than 50 Burgess Shale-type deposits now known is proposed and is used to consider the hierarchy of controls that regulated the operation of Burgess Shale-type preservation in space and time, ultimately determining the total number of preserved taxa and the fidelity of preservation in each deposit. While Burgess Shale-type preservation is a unique taphonomic mode that ultimately was regulated by the influence of global seawater chemistry upon the early diagenetic environment, physical depositional (biostratinomic) controls are shown to have been critical in determining the total number of taxa preserved in fossil assemblages, and hence, in regulating many of the important differences among Burgess Shale-type deposits.

The Paleozoic body fossil record of potential benthic predators includes nautiloid and ammonoid cephalopods, phyllocarids, decapods, and several lineages of gnathostomes. The latter group, in particular, radiated rapidly during the Devonian. In the pelagic realm, predator-prey interactions involving cephalopods and some nektonic arthropods probably appeared in the Ordovician. Again, evidence indicates intensification of pelagic predation, much of it by arthrodires and sharks on other fishes, during the Devonian radiation of gnathostomes.

Trace fossils provide direct evidence of predatory attack from the Ediacarian and Early Cambrian onward, but with a substantial increase in the Siluro-Devonian. Brachiopod and molluscan shells and trilobite exoskeletons show evidence of healed bite marks and peeling from the Cambrian onward, but with an increased frequency in the Devonian. Predatory drill holes with stereotypical position and prey-species preference are found in brachiopods (Cambrian onward) and mollusks (Ordovician onward); boreholes also show increased frequency in the middle Paleozoic. Certain of these boreholes are tentatively attributable to platyceratid gastropods.

Hard-shelled benthic organisms with thicker, more spinose skeletons may have had a selective advantage as durophagous predators increased. Brachiopods, gastropods, trilobites, and crinoids show an abrupt increase in spinosity beginning in the Siluro-Devonian. But spinosity decreases after the early Carboniferous. Late Paleozoic benthos may have taken refuge in smaller size and resistant, thick-walled skeletons, as well as endobenthic and cementing modes of life. Conversely, in the pelagic realm, external armor was reduced, while more efficient, fast-swimming modes of life (e.g., in sharks) increased in the post-Devonian.

Taphonomic study of echinoderms provides useful information on sedimentary conditions before, during, and after burial. Taphonomic studies of Recent echinoderms indicate that much skeletal disarticulation occurs within a few days after death. However, experiments also indicate that within a short period after death echinoderm carcasses remain rather resistant to disarticulation, and thus may be transported a considerable distance by currents; following periods of a few hours of decay, more delicate portions of echinoderm skeletons are readily disarticulated. Some skeletal modules (e.g., crinoid pluricolumnals) may resist disarticulation for periods of months in quiet- and or cool-water environments. Anoxia promotes intact preservation by excluding scavenging metazoans. Echinoderm ossicles may undergo minor abrasion and/or corrosion if left exposed, and less dense stereom corrodes much more rapidly than dense plates, such as echinoid spines. However, heavily abraded ossicles may indicate prefossilization and reworking.

Various groups of echinoderms (e.g., pelmatozoans, asterozoans, echinoids) have differing propensities for degradation and, therefore, produce different arrays of preserved fossil material primarily depending upon the relative rates of burial, bottom-water oxygenation, and turbulence. Echinoderms may be divided into three groups based upon the relative ease of skeletal disarticulation. Type 1 echinoderms include weakly articulated forms (e.g., asteroids and ophiuroids) that rapidly disintegrate into individual ossicles. Type 2 includes those echinoderms whose bodies contain portions in which are more tightly sutured, as well as portions in which the ossicles are somewhat more delicately bound (e.g., crinoids, regular echinoids). Such echinoderms display more varied taphonomic grades from fully intact to mixtures of isolated ossicles and articulated modules. Type 3 comprises those echinoderms (e.g., irregular echinoids) in which major portions of the skeleton are so resistant to disarticulation that they may be broken across sutures rather than coming apart at plate boundaries.

Comparative taphonomy of particular types of echinoderm skeletal remains leads to recognition of distinctive taphofacies that characterize particular depositional environments. Taphofacies include two types of characteristic modes of fossil preservation: event taphonomic signatures and background taphonomic signatures. Depending upon normal conditions of environmental energy and rates of sedimentation, the background condition of various types of echinoderms for a given facies may range from articulated, unabraded skeletal modules (in Types 2 and 3) to highly corroded and/or abraded ossicles. Conversely, the occurrence of fully intact fossil echinoderms provides unambiguous evidence of rapid and deep burial of benthic communities. Such well-preserved fossil assemblages can provide a wealth of information regarding the paleobiology of echinoderms, as well as the nature of the depositional events and burial histories.

This paper presents a preliminary classification and characterization of background and event aspects of echinoderm taphofacies for carbonate- (9 taphofacies, including reefs and hardgrounds) and siliciclastic-dominated (5 taphofacies) environments. In each case, we recognize a spectrum of echinoderm taphofacies that coincides with a gradient of environments, ranging from nearshore, high energy shoreface through proximal and distal storm-influenced shelf, to deeper ramp and dysoxic basinal settings. Most taphofacies also feature particular styles of obrution (smothered bottom) Lagerstätten. These range from scattered lenses of articulated fossils in some high energy sandstone and grainstone facies to bedding planes of articulated, pyrite coated specimens in dark shales. We classify and discuss the genesis of these types of Lagerstätten and list typical examples. Finally, we present a simple model that integrates the occurrence of various echinoderm taphofacies with concepts of cyclic and sequence stratigraphy.

Morphological integration and modularity are closely related concepts about how different traits of an organism are correlated. Integration is the overall pattern of intercorrelation; modularity is the partitioning of integration into evolutionarily or developmentally independent blocks of traits. Modularity and integration are usually studied using quantitative phenotypic data, which can be obtained either from extant or fossil organisms. Many methods are now available to study integration and modularity, all of which involve the analysis of patterns found in trait correlation or covariance matrices. We review matrix correlation, random skewers, fluctuating asymmetry, cluster analysis, Euclidean distance matrix analysis (EDMA), graphical modelling, two-block partial least squares, RV coefficients, and theoretical matrix modelling and discuss their similarities and differences. We also review different coefficients that are used to measure correlations. We apply all the methods to cranial landmark data from and ontogenetic series of Japanese macaques, Macaca fuscata to illustrate the methods and their individual strengths and weaknesses. We conclude that the exploratory approaches (cluster analyses of various sorts) were less informative and less consistent with one another than were the results of model testing or comparative approaches. Nevertheless, we found that competing models of modularity and integration are often similar enough that they are not statistically distinguishable; we expect, therefore, that several models will often be significantly correlated with observed data.

Mesozoic and Cenozoic evolution of predators involved a series of episodes. Predators rebounded rather rapidly after the Permo-Triassic extinction and by the Middle Triassic a variety of new predator guilds had appeared, including decapod crustaceans with crushing claws, shell-crushing sharks and bony fish, as well as marine reptiles adapted for crushing, smashing, and piercing shells. While several groups (e.g., placodonts, nothosaurs) became extinct in the Late Triassic crises, others (e.g., ichthyosaurs) survived; and the Jurassic to Early Cretaceous saw the rise of malacostracan crustaceans with crushing chelae and predatory vertebrates—in particular, the marine crocodilians, ichthyosaurs, and plesiosaurs. The late Cretaceous saw unprecedented levels of diversity of marine predaceous vertebrates including pliosaurids, plesiosaurs, and mosasaurs. The great Cretaceous-Tertiary extinction decimated marine reptiles. However, most invertebrate and fish predatory groups survived; and during the Paleogene, predatory benthic invertebrates showed a spurt of evolution with neogastropods and new groups of decapods, while the teleosts and neoselachian sharks both underwent parallel rapid evolutionary radiations; these were joined by new predatory guilds of sea birds and marine mammals. Thus, although escalation is sometimes cast as an ongoing “arms race,” in actuality the predatory record shows long interludes of relative stability puncturated by episodes of abrupt biotic reorganization during and after mass extinctions. This pattern suggests episodic, but generally increasing, predation pressure on marine organisms through the Mesozoic-Cenozoic interval. However, review of the Cenozoic record of predation suggests that there are not unambiguous escalatory trends in regard to antipredatory shell architecture, such as conchiolin and spines; nor do shell drilling and shell repair data show a major increase from the Late Mesozoic through the Cenozoic. Most durophagous groups are generalists, and thus it may be that they had a diffuse effect on their invertebrate prey.

The Cambrian explosion can be thought of as the culmination of a diversification of eukaryotes that had begun several hundred million years before. Eukaryotes - one of the three domains of life — originated by late Archean time, and probably underwent a long period of stem group evolution during the Paleoproterozoic Era. A suite of taxonomically resolved body fossils and biomarkers, together with estimates of acritarch and compression fossil diversity, suggest that while divergences among major eukaryotic clades or 'super-groups' may have occurred as early as latest Paleoproterozoic through Mesoproterozoic time, the main phase of eukaryotic diversification took place several hundred million years later, during the middle Neoproterozoic Era. Hypotheses for Neoproterozoic diversification must therefore explain why eukaryotic diversification is delayed several hundred million years after the origin of the eukaryotic crown group, and why diversification appears to have occurred independently within several eukaryotic super-groups at the same time. Evolutionary explanations for eukaryotic diversification (the evolution of sex; the acquisition of plastids) fail to account for these patterns, but ecological explanations (the advent of microbial predators) and environmental explanations (changes in ocean chemistry) are both consistent with them. Both ecology and environment may have played a role in triggering or at least fueling Neoproterozoic eukaryotic diversification.

The fossil record contains far more coprolites produced by carnivorous animals than by herbivores. This inequity reflects the fact that feces generated by diets of flesh and bone (and other skeletal materials) contain chemical constituents that may precipitate out under certain conditions as permineralizing phosphates. Thus, although coprolites are usually less common than fossil bones, they provide a significant source of information about ancient patterns of predation. The identity of a coprolite producer often remains unresolved, but fossil feces can provide new perspectives on prey selection patterns, digestive efficiency, and the occurrence of previously unknown taxa in a paleoecosystem. Dietary residues are often embedded in the interior of coprolites, but much can be learned from analyses of intact specimens. When ample material is available, however, destructive analyses such as petrography or coprolite dissolution may be used to extract additional paleobiological information.

The impressive array of disparity within the Echinodermata can be explained by the interplay of components (particularly skeletal elements) making up two major body wall regions: axial and extraxial. Axial skeleton comprises paired plate columns of the ambulacra, formed according to the Ocular Plate Rule (OPR) and in association with the water vascular system. Extraxial skeleton (subdivided into two subtypes: perforate and imperforate) is not formed according to the OPR, and new elements can be added anywhere and at any time within extraxial body wall. Recent work on early development of echinoderms reveals that axial skeleton is formed as an integral part of the rudiment, but that extraxial skeleton is derived from the non-rudiment part of the larval body. In addition to displaying such fundamental embryological and ontogenetic differences, the body wall regions have distinctive distributions and topologies that can be used to formulate criteria for their identification in any echinoderm regardless of how esoteric their morphology might be. Like the system of homologies that has long been established for vertebrates, the model of axial and extraxial skeletal types can be used to explore relationships among Recent and fossil taxa alike. Application of the model also leads to reassessment of previously published morphological characters and phylogenies.

Morphological data can be used effectively in phylogenetic analyses to determine relationships among echinoderm clades. These data in the form of characters are simply hypotheses that any observed morphological state among taxa results from a single character state transformation and is therefore, homologous. All such character states must be scored as potentially homologous unless the hypothesis of homology can be rejected by the tests of similarity, conjunction (a priori), or character congruence (a posteriori). Fossils are not always more incomplete than extant forms and incompleteness originates from non-preservation and long phylogenetic branches. The greatest strength of fossil data lies in its ability to effectively shorten long phylogenetic branches by occurring on the tree nearer to the nodes than extant terminal taxa and thus circumventing positively misleading results encountered in parsimony analysis under long branch conditions.

The paleontological literature on marine invertebrates is rich in supposed examples of parasitism and our tabulation shows a nearly even distribution of reported cases through the post-Cambrian Phanerozoic. Slightly lower frequencies characterize the Triassic and Jurassic and higher frequencies the Cretaceous and Tertiary, and the pattern roughly mirrors Sepkoski's (1984) marine diversity curve. The total number of parasitic associations for any geologic period rarely exceeds a dozen, yet few of the reported examples provide explicit criteria distinguishing parasitism from predation, commensalism, or mutualism. We evaluated the published examples using the following criteria: (1) evidence of a long-term relationship between two organisms, (2) benefit of interaction to supposed parasite, and (3) detriment of interaction to the host We found that only in exceptional cases were these criteria fulfilled. One example that provides much information on parasitic interactions involves platyceratids and crinoids and we summarize the evidence for the parasitic interaction between these two groups of organisms.

Trace fossils, as everyone knows by now, provide us with direct information about fossil behavior, and they offer us a wide variety of mysteries to solve in the area of paleoethology (literally, “the study of ancient behavior”). Chief among these mysteries are “what?”, “who?”, “why?” and “where?”. What we especially want to know is what a given trace fossil looks like in three dimensions, what type of organism(s) created it, for what reason(s) they made it, and under what type of environmental conditions the trace was made.

Since their first appearance in the Middle-Late Silurian, land plants have played an increasingly important role in shaping terrestrial ecosystems and landscapes. It is difficult to overestimate their role because they form the framework for terrestrial ecosystems, provide habitats for terrestrial animals, form an important part of the food chain, affect weathering processes and have a direct impact on soil formation, and, last but not least, play a primary role in the oxygen/carbon cycles.