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.

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.

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.

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.

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.

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 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.

Intraspecific variation of organisms is of great importance to correctly carry out taxonomic work, which is a prerequisite for key disciplines in paleontology such as community paleoecology, biostratigraphy, and biogeography. However, intraspecific variation is rarely studied in ectocochleate cephalopods (ammonoids and nautiloids), for which an excessive number of taxa was established during the past centuries. Because intraspecific variation of fossilized organisms suffers from various biases (time averaging and taphonomy), an extant example is needed for actualistic comparison. We applied 3D morphometry to 93 specimens of Nautilus pompilius from three different geographic populations. This data set was used to examine the intraspecific variation throughout ontogeny in detail. Although there are slight differences between the populations as well as some measurement biases, a common pattern of intraspecific variation appears to be present. High variation in morphometric variables appears early in ontogeny and then decreases gradually in the following ontogenetic stages. Subsequently, the variation shows an increase again before maturity until a sharp increase or decrease occurs toward the end of ontogeny. Comparison with intraspecific variation of ammonoids and belemnites illustrated that some groups have ontogenetic patterns of intraspecific variation that are similar to that of N. pompilius. This implies that the abovementioned ontogenetic pattern of intraspecific variation might be common in some major cephalopod clades.

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.

The per-stage extinction rate is the product of the per-taxon extinction rate and stage length, and the per-stage origination rate is defined similarly. These rates decline from ancient to recent times because of the pull of the Recent, because there is more young than old fossiliferous rock, and because average stage length increases from the recent to the past. More specifically, the present model assumes that the graphs of ln(per-stage extinction rate) and ln(per-stage origination rate) versus geologic time have slope zero in the absence of sampling biases, and shows how sampling biases cause both these graphs to appear to have slope min(h,q) + s in the distant past, where h and q are the fossil loss and actual per-taxon extinction rates, and the stratigraphic constant, s, quantifies how stage length changes through time.

Although the per-stage rates of bivalve families and marine invertebrate genera decline toward the recent, the magnitudes of these declines are entirely consistent with what the present model predicts sampling biases will produce. Hence there is no need to postulate a biological explanation for these patterns.

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.

Many apparent homeomorphs have been recognized among genera assigned to the Paleozoic stenolaemate bryozoan orders Trepostomata and Cryptostomata. Morphologies are evaluated to determine whether such homeomorphy should be expected, or is likely to have resulted from incomplete taxonomic analysis. Historical and constructional constraints prevalent in the phylum appear to provide ample opportunity for adaptive convergence, a conclusion supported by the occurrence of similar morphologies in distantly related post-Paleozoic bryozoans.

Cryptostomes are distinguished in part by the presence of restricted budding loci. Loci pattern is hypothesized to be the key innovation in the establishment of the clade and the pattern also is considered critical to the evolution of the relatively slender branches and short zooecia typical of cryptostomes.

Loci development does not provide a taxonomic panacea. This is because the hypothesis does not preclude convergent evolution of broadly similar restricted loci in Paleozoic non-cryptostome groups, although presumably the cryptostomes in general would have been best equipped to succeed under conditions favoring restricted loci.

Environmental conditions for the cryptostomes in general and changing life history strategies for rhabdomesoids in particular provide possible controlling factors for the evolution of these bryozoans.

The stratophenetic approach to phylogeny reconstruction, developed in numerous recent papers by Gingerich, has its strongest data base in comprehensive collections from early Eocene rocks in the Big Horn Basin of northwestern Wyoming. Other examples have been criticised for lack of well-documented collection data, making suitable testing of stratophenetic interpretations of evolutionary modes virtually impossible.

Study of Hyopsodus from the middle Eocene Bridger Formation of southwestern Wyoming provides new collection data. Adequate stratigraphic documentation is available, so Gingerich's graphical presentation can be essentially duplicated. In contrast to the complex branching pattern Gingerich interpreted from his data, Bridger Formation Hyopsodus data seems to show little size change through approximately one million years. This stasis or equilibrium condition, which is considered rare by Bookstein et al. (1978), is the only well developed pattern in Bridger Hyopsodus.

Fusion occurred between pairs of conspecific colonies of Permian fenestrate bryozoans that were of approximately equal radius at time of contact. In contrast, no fusion occurred in pairs of conspecific colonies that were of unequal radius at time of contact. It is suggested that histologically compatible colonies developed from larvae that settled essentially simultaneously and that the larvae were siblings, lecithotrophic with low mobility, and of the same genotype (i.e., polyembryonic). Thus polyembryony appears to have existed as a reproductive “strategy” for at least 275 Myr, and its scarcity in modern taxa cannot be due to recentness of evolution.

As the climate changes and ecosystems shift toward novel combinations of species, the methods and metrics of conservation science are becoming less species-centric. To meet this growing need, marine conservation paleobiologists stand to benefit from the addition of new, taxon-free benthic indices to the live–dead analysis tool kit. These indices, which were developed to provide actionable, policy-specific data, can be applied to the readily preservable component of benthic communities (e.g., mollusks) to assess the ecological quality status of the entire community. Because these indices are taxon-free, they remain applicable even as the climate changes and novel communities develop—making them a potentially valuable complement to traditionally applied approaches for live–dead analysis, which tend to focus on maintaining specific combinations of species under relatively stable environmental conditions. Integrating geohistorical data with these established indices has potential to increase the salience of the live–dead approach in the eyes of resource managers and other stakeholders.

The end-Permian mass extinction occurred alongside a large swath of environmental changes that are often invoked as extinction mechanisms, even when a direct link is lacking. One way to elucidate the cause(s) of a mass extinction is to investigate extinction selectivity, as it can reveal critical information on organismic traits as key determinants of extinction and survival. Here we show that machine learning algorithms, specifically gradient boosted decision trees, can be used to identify determinants of extinction as well as to predict extinction risk. To understand which factors led to the end-Permian mass extinction during an extreme global warming event, we quantified the ecological selectivity of marine extinctions in the well-studied South China region. We find that extinction selectivity varies between different groups of organisms and that a synergy of multiple environmental stressors best explains the overall end-Permian extinction selectivity pattern. Extinction risk was greater for genera that had a low species richness, narrow bathymetric ranges limited to deep-water habitats, a stationary mode of life, a siliceous skeleton, or, less critically, calcitic skeletons. These selective losses directly link the extinctions to the environmental effects of rapid injections of carbon dioxide into the ocean–atmosphere system, specifically the combined effects of expanded oxygen minimum zones, rapid warming, and potentially ocean acidification.

Multivariate methods such as cluster analysis and ordination are basic to paleoecology, but the messy nature of fossil occurrence data often makes it difficult to recover clear patterns. A recently described faunal similarity index based on the Forbes coefficient improves results when its complement is employed as a distance metric. This index involves adding terms to the Forbes equation and ignoring one of the counts it employs (that of species found in neither of the samples under consideration). Analyses of simulated data matrices demonstrate its advantages. These matrices include large and small samples from two partially overlapping species pools. In a cluster analysis, the widely used Dice coefficient and the Euclidean distance metric both create groupings that reflect sample size, the Simpson index suggests large differences that do not exist, and the corrected Forbes index creates groupings based strictly on true faunal overlap. In a principal coordinates analysis (PCoA) the Forbes index almost removes the sample-size signal but other approaches create a second axis strongly dominated by sample size. Meanwhile, species lists of late Pleistocene mammals from the United States capture biogeographic signals that standard ordination methods do recover, but the adjusted Forbes coefficient spaces the points out more sensibly. Finally, when biome-scale lists for living mammals are added to the data set and extinct species are removed, correspondence analysis misleadingly separates out the biome lists, and PCoA based on the Dice coefficient places them to the edge of the cloud of fossil assemblage data points. PCoA based on the Forbes index places them in more reasonable positions. Thus, only the adjusted Forbes index is able to recover true biological patterns. These results suggest that the index may be useful in analyzing not only paleontological data sets but any data set that includes species lists having highly variable lengths.

The tailbend, a downward flexure of the vertebral column, is a prominent feature of post-Triassic ichthyosaurs. However, due to the vagaries of preservation and of preparation, its presence cannot be verified in all skeletons. Computed tomography offers a solution to the problem by identifying the wedge-shaped centra that contribute to the tailbend. Leptopterygius tenuirostris appears to have a tailbend, albeit slightly downturned. There is also evidence that its close relative Eurhinosaurus longirostris had a tailbend, too.