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.

For mammals today, mountains are diverse ecosystems globally, yet the strong relationship between species richness and topographic complexity is not a persistent feature of the fossil record. Based on fossil-occurrence data, diversity and diversification rates in the intermontane western North America varied through time, increasing significantly during an interval of global warming and regional intensification of tectonic activity from 18 to 14 Ma. However, our ability to infer origination and extinction rates reliably from the fossil record is affected by variation in preservation history. To investigate the influence of preservation on estimates of diversification rates, I simulated fossil records under four alternative diversification hypotheses and six preservation scenarios. Diversification hypotheses included tectonically controlled speciation pulses, while preservation scenarios were based on common trends (e.g., increasing rock record toward the present) or derived from fossil occurrences and the continental rock record. For each scenario, I estimated origination, extinction, and diversification rates using three standard methods—per capita, three-timer, and capture–mark–recapture (CMR) metrics—and evaluated the ability of the simulated fossil records to accurately recover the underlying diversification dynamics. Despite variable and low preservation probabilities, simulated fossil records retained the signal of true rates in several of the scenarios. The three metrics did not exhibit similar behavior under each preservation scenario: while three-timer and CMR metrics produced more accurate rate estimates, per capita rates tended to better reproduce true shifts in origination rates. All metrics suffered from spurious peaks in origination and extinction rates when highly volatile preservation impacted the simulated record. Results from these simulations indicate that elevated diversification rates in relation to tectonic activity during the middle Miocene are likely to be evident in the fossil record, even if preservation in the North American fossil record was variable. Input from the past is necessary to evaluate the ultimate mechanisms underlying speciation and extinction dynamics.

We know that the fossil record is incomplete. But how incomplete? Here we very coarsely estimate the completeness of the mammalian record in the Miocene, assuming that the duration of a mammalian species is about 1 Myr and the species diversity has stayed constant and is structurally comparable to the taxonomic diversity today. The overall completeness under these assumptions appears to be around 4%, but there are large differences across taxonomic groups. We find that the fossil record of proboscideans and perissodactyls as we know it for the Miocene must be close to complete, while we might know less than 15% of the species of artiodactyl or carnivore fossil species and only about 1% of primate species of the Miocene. The record of small mammals appears much less complete than that of large mammals.

The Neogene species Petaloconchus sculpturatus presents a contradiction in terms, for it grows whorl “packages” of nearly perfect regularity, but ranks within the most geometrically irregular family of uncoiled gastropods, the Vermetidae. We perform a first biometric study of vermetids (only possible because sufficient regularity of growth permits us to number and identify whorls) to specify and characterize the factors on both sides of this “exquisite tension” between promotion and prevention of recoiling. Promoting factors include the older phyletic heritage of preserved dextral coiling, and the more immediate vermetid (or specifically petaloconchid) features of growth toward open spaces (where regular coiling might proceed in an unimpeded fashion); radular excision of discordant feeding tubes with shaping of the resulting scar so that growth may proceed in conformity with previous whorls; and locking of subsequent whorls upon a keel formed by longitudinal bead-rows of the previous whorl. Preventing factors include prominent phyletic heritage of all vermetids—maximal early irregularity enjoined by discordance between larval and subsequent growth (with teleoconch wrapping itself around the protoconch), thus precluding an ordered substrate to act as a foundation for regular whorl “packages” of intermediary growth—and a set of features specific to this lineage and acting as geometric constraints. In this category, we particularly document the exceedingly low rate of whorl expansion and the consequently wide umbilical space that produces a shell akin to winding a cylindrical coil of narrow-diameter rope around the periphery of a wide circular platform. This complex combination of promoting and preventing factors produces a shell that is tantalizingly close to fully regular, but cannot truly reattain this previous phyletic state—thus providing a fine example of Dollo's Law at the centenary of his formation of irreversibility.

Identifying biological traits that promote evolutionary success is fundamental for understanding biodiversity dynamics and for assessing the evolutionary response of organisms to global change. We tested the hypothesis that image-forming eyes have contributed to the diversification of taxa in the geological past. Using fossil occurrences in the Paleobiology Database, we analyzed the diversity and evolutionary rates of more than 17,000 Phanerozoic genera of marine invertebrates living on or above the shallow-water seafloor according to their visual capabilities. Analysis of the complete data set shows a peak in the proportional diversity of sighted genera early in the Phanerozoic, and their continuance at a relatively low and stable level after the Ordovician. As an explanation of this pattern we suggest that selection pressure to develop eyes rose in the Cambrian, and that behavioral constraints had a balancing effect thereafter. In contrast to the pooled data, a clade-level study of those subgroups that contain both sighted and blind genera revealed that—in trilobites, all epifaunal bivalves, pectinoid bivalves, gastropods, and echinoderms—sighted genera diversified more strongly than blind genera. This difference is controlled by significantly raised extinction rates of blind genera. These more finely resolved patterns support the hypothesis that good vision is a key trait that promoted preferential diversification.

George Gaylord Simpson was one of the first paleontologists to apply survivorship analysis to the study of fossil taxa. His finding that the survivorship curve for extant bivalve genera plotted above that for extinct genera led him to conclude that bivalve genera are drawn from at least two distinct distributions of longevities, and formed the fundamental basis for his influential concepts of horotelic and bradytelic evolutionary rates. Survivorship curves presented in this paper show the same pattern of disjunct survivorship in genera from the Treatise on Invertebrate Paleontology and in families from Sepkoski's compendium.

Some of the observed differences between survivorship curves are artificial, occurring because long-lived genera and families are more likely to survive to the Recent than short-lived genera and families. The living fauna thus contains a disproportionate number of long-lived genera and families, and the survivorship curve for the living fauna is expected to lie above that for the extinct fauna for this reason alone—even if all longevities are drawn from the same distribution. Recognition of this bias led Raup (1975) to question the significance of the survivorship patterns presented by Van Valen (1973), and Stanley's (1984) acceptance of Raup's argument led him to dismiss the survivorship pattern discovered by Simpson. But statistical analysis using bootstrapping shows that this bias accounts for only a small proportion of the difference between survivorship curves. Other biases considered, such as “pull of the Recent,” “asymmetrical range truncation,” and erroneous concatenation of stratigraphic ranges, do not account for the pattern either. Although still other biases, as yet unknown, cannot definitively be ruled out, it appears that the longevities of extinct and living bivalve taxa are meaningfully different, and that the fundamental causes are biological.

Polycystine radiolarians axe the most widely distributed (geographically and geologically) of the well-preserved microzooplankton. To correctly interpret the tempo and mode of radiolarian microevolution, speciation and macroevolution, the zoogeography and ecological niches of extant, and paleozoogeography and paleoecological niches of extinct subspecies, species and higher taxa of the studied lineages should be carefully considered. Such studies of the Stichocorys and Lamprocyrtis lineages suggest that allopatric speciation as peripheral isolates is important. Sympatric speciation is also a possible mode of evolution in these lineages. Hybridization may play a role in the evolution of one subspecies and one species. Allopatrically evolved subspecies and species require some time to inhabit their maximum geographical range after evolving in an isolated and peripheral part of that “environment,” whereas the supposedly sympatrically evolved forms do not. Cooling trends and water mass reorganization may be related to the speciation events. Similar, but much less controlled, studies on a macroevolutionary scale (evolution above the species level, essentially the “family” level) suggest that there have been about half a dozen periods of major adaptive breakthroughs resulting in quantum, or macro, evolution. Global coolings and the initiations of “new” cold-water spheres and related water masses appear to have allowed these macroevolutionary steps during the Ordovician, Devonian-Carboniferous, Permian, and early Neogene. Ecological pressure from diatoms and planktonic foraminiferans appears to have been related to macroevolutionary events bounding the Cretaceous-Tertiary transition.

Eurypterids are generally considered to comprise a mixture of active nektonic to nektobenthic predators and benthic scavenger-predators exhibiting a mode of life similar to modern horseshoe crabs. However, two groups of benthic stylonurine eurypterids, the Stylonuroidea and Mycteropoidea, independently evolved modifications to the armature of their anterior appendages that have been considered adaptations toward a sweep-feeding life habit, and it has been suggested the evolution toward sweep-feeding may have permitted stylonurines to capture smaller prey species and may have been critical for the survival of mycteropoids during the Late Devonian mass extinction. There is a linear correlation between the average spacing of feeding structures and prey sizes among extant suspension feeders. Here, we extrapolate this relationship to sweep-feeding eurypterids in order to estimate the range of prey sizes that they could capture and examine prey size in a phylogenetic context to determine what role prey size played in determining survivorship during the Late Devonian. The mycteropoid Cyrtoctenus was the most specialized sweep-feeder, with comblike appendage armature capable of capturing mesoplankton out of suspension, while the majority of stylonurines possess armature corresponding to a prey size range of 1.6–52 mm, suggesting they were suited for capturing small benthic macroinvertebrates such as crustaceans, mollusks, and wormlike organisms. There is no clear phylogenetic signal to prey size distribution and no evolutionary trend toward decreasing prey sizes among Stylonurina. Rather than prey size, species survivorship during the Late Devonian was likely mediated by geographic distribution and ability to capitalize on the expanding freshwater benthos.

We describe statistical methods to formulate and validate statements about survival rates given a small number of individuals. These methods allow one to estimate the age-specific survival rate and assess its uncertainty, to assess whether the survival rates during some age range differ from the survival rates during another age range, and to assess whether the survivorship curve has a particular shape. We illustrate these methods by applying them to a sample of 22 Albertosaurus sarcophagus individuals. We show that this sample is too small to provide any confidence in the claim that this species had a “convex” survivorship curve arising from age-specific survival rates that decreased monotonically with age. However, we show that a sample of 50 to 100 individuals has reasonable statistical power to support such a claim. There is evidence for the much weaker claim that average survival rates for ages 2 to 15 were higher than survival rates for later ages. Finally, we describe one way to account for size-dependent fossilization rates and show that a plausible positively-size-dependent fossilization rate results in a substantially non-convex survivorship curve for A. sarcophagus.

Posterior eccentricity has evolved independently in three lineages of northern Pacific sand dollars; it is best known in the genus Dendraster. In these forms, the anterior areas of the aboral surface are much more highly developed than the posterior areas; consequently, the apical system is located posteriorly, rather than centrally. This morphology is linked to an unusual and highly successful mode of suspension-feeding. The evolution of eccentricity appears to be related to regulatory mechanisms found in many non-eccentric sand dollars, such as Echinarachnius parma. During the ontogeny of this form, the growth rates of the ambulacra and interambulacra are correlated with their position along the longitudinal axis. Early in ontogeny, the anterior areas develop at a faster rate than the posterior areas; later in ontogeny, this relationship is completely reversed. Normally, these two phases of unequal growth counterbalance each other, and the mature test appears symmetrical. However, if the balance between the two phases were upset, eccentricity would naturally ensue. In fact, aberrant Recent and fossil Echinarachnius with the predicted anteriorly-and posteriorly-eccentric morphologies actually do exist. Posterior eccentricity is apparently produced by retention of the earlier unequal growth pattern, which favors anterior development. This represents trait neoteny; however, since the retained trait is a regulatory mechanism that controls growth rates over the entire aboral surface, the morphological effects are particularly profound. Thus, the seemingly bizarre morphology of Dendraster can be derived by a change in the timing of an existing regulatory mechanism. This may help to explain the sudden appearance of Dendraster in the fossil record and the absence of transitional forms. The unusual suspension-feeding behavior of Dendraster may have been derived from a righting response that is common among other sand dollars.

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.

As a label for a distinct category of life, “living fossil” is controversial. The term has multiple definitions, and it is unclear whether the label can be genuinely used to delimit biodiversity. Even taking a purely phylogenetic perspective in which a proxy for the living fossil is evolutionary distinctness (ED), an inconsistency arises: Does it refer to “dead-end” lineages doomed to extinction or “panchronic” lineages that survive through multiple epochs? Recent tree-growth model studies indicate that speciation rates must have been unequally distributed among species in the past to produce the shape of the tree of life. Although an uneven distribution of speciation rates may create the possibility for a distinct group of living fossil lineages, such a grouping could only be considered genuine if extinction rates also show a consistent pattern, be it indicative of dead-end or panchronic lineages. To determine whether extinction rates also show an unequal distribution, we developed a tree-growth model in which the probability of speciation and extinction is a function of a tip’s ED. We simulated thousands of trees in which the ED function for a tip is randomly and independently determined for speciation and extinction rates. We find that simulations in which the most evolutionarily distinct tips have lower rates of speciation and extinction produce phylogenetic trees closest in shape to empirical trees. This implies that a distinct set of lineages with reduced rates of diversification, indicative of a panchronic definition, is required to create the shape of the tree of life.

Occupancy statistics in ecology and paleontology are biased upward by the fact that we generally do not have solid data on species that exist but are not found. The magnitude of this bias increases as the average occupancy probability decreases and as the number of sites sampled decreases. A maximum-likelihood method is developed to estimate the underlying distribution of occupancy probabilities of all species based only on the sample of observed species with nonzero occupancy. The method is based on determining the probability that the number of occupied sites will take on any specific value for a given occupancy probability, integrated over the entire distribution of occupancy probabilities. If the shape of the underlying distribution is well modeled, the resulting occupancy estimates circumvent the bias inherent in failing to observe some species and the fact that this bias depends on the number of sites. For occupancy data on marine animal genera drawn from the Paleobiology Database, the underlying distribution is reasonably approximated as a right-truncated log-normal, but the methods developed can be extended to any distribution. Examples are presented to illustrate some observations that are robust and others that need to be revised in light of this bias correction. The method is compared to a recently developed, distribution-free approach to the same problem.

Echinoderms make up a substantial component of Ordovician marine invertebrates, yet their speciation and dispersal history as inferred within a rigorous phylogenetic and statistical framework is lacking. We use biogeographic stochastic mapping (BSM; implemented in the R package BioGeoBEARS) to infer ancestral area relationships and the number and type of dispersal events through the Ordovician for diploporan blastozoans and related species. The BSM analysis was divided into three time slices to analyze how dispersal paths changed before and during the great Ordovician biodiversification event (GOBE) and within the Late Ordovician mass extinction intervals. The best-fit biogeographic model incorporated jump dispersal, indicating this was an important speciation strategy. Reconstructed areas within the phylogeny indicate the first diploporan blastozoans likely originated within Baltica or Gondwana. Dispersal, jump dispersal, and sympatry dominated the BSM inference through the Ordovician, while dispersal paths varied in time. Long-distance dispersal events in the Early Ordovician indicate distance was not a significant predictor of dispersal, whereas increased dispersal events between Baltica and Laurentia are apparent during the GOBE, indicating these areas were important to blastozoan speciation. During the Late Ordovician, there is an increase in dispersal events among all paleocontinents. The drivers of dispersal are attributed to oceanic and epicontinental currents. Speciation events plotted against geochemical data indicate that blastozoans may not have responded to climate cooling events and other geochemical perturbations, but additional data will continue to shed light on the drivers of early Paleozoic blastozoan speciation and dispersal patterns.

The origin of endothermic homeothermy and of high metabolic rate in mammals is currently believed to be the result of early (Mesozoic) selection in advanced cynodont therapsids and/or early mammals for either (1) enhanced thermoregulatory capacity or (2) increased powers of endurance and stamina. Selective factors underlying the origin of specialized respiration/ventilation-support systems in mammals are possible indices of the validity of these two hypotheses. One such support structure is the diaphragm, a specialized muscle that facilitates lung ventilation. We tested capacity for maintenance of resting metabolic rate, thermoregulation, and for extended, intense exercise in laboratory rats (Rattus rattus) in which diaphragm function had been completely ablated. The results were virtual elimination of aeroboic scope (active metabolic rate — resting metabolic rate) but resting metabolic rate was unaffected. Thermoregulatory capacity was unimpaired to at least 8° below lower critical temperature. These and other data suggest that the origin of the mammalian diaphragm, as well as mammalian metabolic rates, may have been related to selection for greater levels of sustainable activity rather than for functions associated with thermoregulation.

Comparisons between death assemblages and their source living communities are among the most common actualistic methods of evaluating the preservation of compositional and environmental information in fossil assemblages. Although live-dead studies have commonly focused on marine mollusks, the potential of diatoms to preserve ecological information in continental settings has been overlooked. Thus, little is known about the nature and magnitude of the taphonomic biases affecting live-dead agreement of diatom assemblages, despite their extensive application as modern and fossil bioindicators in paleoecological and paleoenvironmental reconstructions. In this study, I analyzed three live-dead data sets in order to evaluate the compositional and environmental fidelity exhibited by diatom death assemblages in shallow lakes. I find that diatom death assemblages (DAs) do differ significantly in their taxonomic composition from living assemblages (LAs), mainly as a consequence of (1) differences in the temporal resolution between time-averaged DAs and non-averaged LAs, and (2) differential preservation of diatom taxa related to the intrinsic properties of their valves. Despite compositional dissimilarities, DAs were able to capture the same environmental gradients as LAs, with high significance. This decoupling between live-dead agreement in community composition and community response to gradients can be related to the existence of at least two mutually exclusive subsets of species that significantly captured compositional dissimilarities based on the full set of the species in the three lakes. This functional redundancy implies that the between-sample relationships of living assemblages can be significantly preserved by DAs even if some taxa are removed by taphonomic processes. The preservation of environmental gradients thus does not require good preservation of all living taxa. Structural redundancy compensates for the loss of compositional fidelity caused by postmortem processes in the diatom data set.

Ontogenetic sequence reconstruction is challenging particularly for extinct taxa because of when, where, and how fossils preserve. Different methods of reconstruction exist, but the effects of preservational bias, the applicability of size-independent methods, and the prevalence of sequence polymorphism (intraspecific variation) remain unexplored for paleontological data. Here I compare five different methods of ontogenetic sequence reconstruction and their effects on the detection of sequence polymorphism, using a large collection of the extinct vertebrates Microbrachis pelikani and Hyloplesion longicostatum. The postcranial ossification sequences presented here for those taxa are the first examples known for extinct lepospondyls. Sequences were reconstructed according to skull length, trunk length, increasing number of ontogenetic events, majority-rule consensus, and Ontogenetic Sequence Analysis (OSA). Results generally were in agreement, demonstrating that paleontological data may be used to robustly reconstruct developmental patterns. When reconstructing sequences based on fossils, size-based methods and OSA are more objective and less dependent on preservational bias than other techniques. Apart from the other methods, OSA also allows for statistical analysis of observed and predicted polymorphism. However, OSA requires a large sample size to yield meaningful results, and size-based methods are justified in paleontological studies when sample size is limited by poor preservation. Different methods of reconstruction detected different patterns of sequence polymorphism, although across all methods the magnitude of sequence variation for M. pelikani and H. longicostatum (1.3−3.4%) was within the lower range of values reported for extant vertebrates. Compared with other extinct and extant tetrapods, all sequence reconstruction methods consistently showed that M. pelikani and H. longicostatum exhibit advanced ossification of the pubis and delayed ossification of the scapula. However, the postcranial ossification sequences of these two taxa largely are congruent with those of other tetrapods, suggesting an underlying conservative ancestral pattern that evolved early in tetrapod history.

The typical pelecypod form, long thought to be primitively adaptive to burrowing, is likely to have been originally adaptive to a suspension feeding, epifaunal, possibly crawling mode of life. At small body size (< 1 cm), pelecypods possessing typical burrowing features can function as epifaunal crawlers. Pelecypods arose at small body sizes and are part of a molluscan evolutionary sequence in which relative size of the mantle cavity increased to accommodate a few large gills specialized for suspension feeding.

Acquisition of a bivalved shell by ancestral epifaunal suspension feeders may have offered protection from sediment clogging on soft bottoms, additional control over the direction, volume, and rate of water flow through the mantle cavity, more effective protection from predators, and better short-term control of the internal environment. Consideration of invertebrate groups analogous to the pelecypods (Branchiopoda, Cladocera, Ostracoda, Phyllocarida) support the view that the bivalve condition is primarily an adaptation for suspension feeding and predator avoidance in benthic environments.

The earliest known pelecypod, Fordilla troyensis Barrande, was not necessarily infaunal just because it had features similar to much larger, Recent burrowers. The size, shell morphology and environment of preservation of F. troyensis all suggest that it is reasonable to envision Cambrian pelecypods as epifaunal suspension feeders, possibly crawling on sedimentary bottoms. Moreover, the sudden Ordovician expansion of pelecypods and increase in individual size may be explained as a result of invasion of the infaunal adaptive zone.

The hypothesis that there is a characteristic rate of exponential radiation for the Insecta is tested for forty-nine of the most diverse family-level taxa in the Coleoptera, Diptera, and Hymenoptera. Data used are estimates of Recent species diversity and age of first appearance in the fossil record, as in the original statement of the hypothesis by Stanley (1979). There is no evidence of a characteristic radiation rate for the insects. A more exact method is proposed for identifying clades that are radiating exponentially. When applied to Stanley's data for the mammalian family Bovidae, it indicates that the Bovidae are not radiating exponentially at a characteristic rate. Future research might emphasize the reliable identification of clades that are radiating exponentially, prior to drawing conclusions about rates that might characterize higher taxa.