Gill function in an early arthropod and the widespread adoption of the countercurrent exchange mechanism.

Rising but fluctuating oxygen levels in the Early Palaeozoic provide an environmental context for the radiation of early metazoans, but little is known about how mechanistically early animals satisfied their oxygen requirements. Here we propose that the countercurrent gaseous exchange, a highly efficient respiratory mechanism, was effective in the gills of the Late Ordovician trilobite Triarthrus eatoni. In order to test this, we use computational fluid dynamics to simulate water flow around its gills and show that water velocity decreased distinctly in front of and between the swollen ends, which first encountered the oxygen-charged water, and slowed continuously at the mid-central region, forming a buffer zone with a slight increase of the water volume. In T. eatoni respiratory surface area was maximized by extending filament height and gill shaft length. In comparison with the oxygen capacity of modern fish and crustaceans, a relatively low weight specific area in T. eatoni may indicate its low oxygen uptake, possibly related to a less active life mode. Exceptionally preserved respiratory structures in the Cambrian deuterostome Haikouella are also consistent with a model of countercurrent gaseous exchange, exemplifying the wide adoption of this strategy among early animals.

Shared patterns of segment size development in trilobites and vertebrates.

The relative sizes of body segments are a major determinant of the shape and functionality of an animal. Developmental biases affecting this trait can therefore have major evolutionary implications. In vertebrates, a molecular activator/inhibitor mechanism, known as the inhibitory cascade (IC), produces a simple and predictable pattern of linear relative size along successive segments. The IC model is considered the default mode of vertebrate segment development and has produced long-term biases in the evolution of serially homologous structures such as teeth, vertebrae, limbs, and digits. Here we investigate whether the IC model or an IC-like model also has controls on segment size development in an ancient and hyperdiverse group of extinct arthropods, the trilobites. We examined segment size patterning in 128 trilobite species, and during ontogenetic growth in three trilobite species. Linear relative segment size patterning is prominent throughout the trunk of trilobites in the adult form, and there is strict regulation of this patterning in newly developing segments in the pygidium. Extending the analysis to select stem and modern arthropods suggests that the IC is a common default mode of segment development capable of producing long-term biases in morphological evolution across arthropods as it does in vertebrates.

Long-term clade-wide shifts in trilobite segment number and allocation during the Palaeozoic.

Arthropods are characterized by having an exoskeleton, paired jointed appendages and segmented body. The number and shape of those segments vary dramatically and unravelling the evolution of segmentation is fundamental to our understanding of arthropod diversification. Because trilobites added segments to the body post-hatching which were expressed and preserved in biomineralized exoskeletal sclerites, their fossil record provides an excellent system for understanding the early evolution of segmentation in arthropods. Over the last 200 years, palaeontologists have hypothesized trends in segment number and allocation in the trilobite body, but they have never been rigorously tested. We tabulated the number of segments in the post-cephalic body for over 1500 species, selected to maximize taxonomic, geographical and temporal representation. Analysis reveals long-term shifts in segment number and allocation over the 250-million-year evolutionary history of the clade. For most of the Palaeozoic, the median number of segments in the body did not change. Instead, the total range decreased over time and there was long-term increase in the proportion of segments allocated to the fused terminal sclerite relative to the articulated thoracic region. There was also increased conservation of thoracic segment number within families. Neither taxonomic turnover nor trends in functionally relevant defensive behaviour sufficiently explain these patterns.

Modularity in the trilobite head consistent with the hypothesized segmental origin of the eyes.

The trilobite head served multiple functions and was composed of several fused segments. Yet, the underlying organization of the trilobite head, and whether patterns are conserved across trilobites, remains unclear. Modeling the head as being composed of modules, or subunits that vary and thus have the potential to evolve semi-independently can reveal underlying patterns of organization. Hypotheses of modular organization based on the comparative developmental biology of arthropods were evaluated using geometric morphometrics. Two-dimensional (semi)landmark datasets collected from the cranidia of two Ordovician trilobite species, Calyptaulax annulata (Phacopida) and Cloacaspis senilis (Olenida sensu Adrain, 2011) were analyzed. The degree and pattern of modularity were assessed using the covariance ratio (CR), which compares the covariation within putative modules to the covariation between them, and the fit of different models was compared using an effect size measure derived from the CR. When treating the eyes as a distinct module, the best modular hypothesis identified for C. annulata shows the eyes and anteriormost region of the head integrated as a single module. The best modular hypotheses for C. senilis are more complex but the eyes still covary mostly strongly with the anterior part of the head. The latter is also the case for all other well-supported models for both species. These results can be interpreted as a developmental signal corresponding to the anteriormost ocular segment of early arthropods that is retained throughout development, despite any likely selective pressures related to functional needs.

Selectivity and the effect of mass extinctions on disparity and functional ecology.

Selectivity of mass extinctions is thought to play a major role in coupling or decoupling of taxonomic, morphological, and ecological diversity, yet these measures have never been jointly evaluated within a single clade over multiple mass extinctions. We investigate extinction selectivity and changes in taxonomic diversity, morphological disparity, and functional ecology over the ~160-million-year evolutionary history of diplobathrid crinoids (Echinodermata), which spans two mass extinctions. Whereas previous studies documented extinction selectivity for crinoids during background extinction, we find no evidence for selectivity during mass extinctions. Despite no evidence for extinction selectivity, disparity remains strongly correlated with richness over extinction events, contradicting expected patterns of disparity given nonselective extinction. Results indicate that (i) disparity and richness can remain coupled across extinctions even when selective extinction does not occur, (ii) simultaneous decreases in taxonomic diversity and disparity are insufficient evidence for extinction selectivity, and (iii) selectivity differs between background and mass extinction regimes.

The trilobite upper limb branch is a well-developed gill.

Whether the upper limb branch of Paleozoic "biramous" arthropods, including trilobites, served a respiratory function has been much debated. Here, new imaging of the trilobite Triarthrus eatoni shows that dumbbell-shaped filaments in the upper limb branch are morphologically comparable with gill structures in crustaceans that aerate the hemolymph. In Olenoides serratus, the upper limb's partial articulation to the body via an extended arthrodial membrane is morphologically comparable to the junction of the respiratory book gill of Limulus and differentiates it from the typically robust exopod junction in Chelicerata or Crustacea. Apparently limited mechanical rotation of the upper branch may have protected the respiratory structures. Partial attachment of the upper branch to the body wall may represent an intermediate state in the evolution of limb branch fusion between dorsal attachment to the body wall, as in Radiodonta, and ventral fusion to the limb base, as in extant Euarthropoda.

Incorporating Hierarchical Characters into Phylogenetic Analysis.

Popular optimality criteria for phylogenetic trees focus on sequences of characters that are applicable to all the taxa. As studies grow in breadth, it can be the case that some characters are applicable for a portion of the taxa and inapplicable for others. Past work has explored the limitations of treating inapplicable characters as missing data, noting that this strategy may favor trees where internal nodes are assigned impossible states, where the arrangement of taxa within subclades is unduly influenced by variation in distant parts of the tree, and/or where taxa that otherwise share most primary characters are grouped distantly. Approaches that avoid the first two problems have recently been proposed. Here, we propose an alternative approach which avoids all three problems. We focus on data matrices that use reductive coding of traits, that is, explicitly incorporate the innate hierarchy induced by inapplicability, and as such our approach extend to hierarchical characters, in general. In the spirit of maximum parsimony, the proposed criterion seeks the phylogenetic tree with the minimal changes across any tree branch, but where changes are defined in terms of dissimilarity metrics that weigh the effects of inapplicable characters. The approach can accommodate binary, multistate, ordered, unordered, and polymorphic characters. We give a polynomial-time algorithm, inspired by Fitch's algorithm, to score trees under a family of dissimilarity metrics, and prove its correctness. We show that the resulting optimality criteria is computationally hard, by reduction to the NP-hardness of the maximum parsimony optimality criteria. We demonstrate our approach using synthetic and empirical data sets and compare the results with other recently proposed methods for choosing optimal phylogenetic trees when the data includes hierarchical characters. [Character optimization, dissimilarity metrics, hierarchical characters, inapplicable data, phylogenetic tree search.].

Air Breathing in an Exceptionally Preserved 340-Million-Year-Old Sea Scorpion.

Arachnids are the second most successful terrestrial animal group after insects [1] and were one of the first arthropod clades to successfully invade land [2]. Fossil evidence for this transition is limited, with the majority of arachnid clades first appearing in the terrestrial fossil record. Furthermore, molecular clock dating has suggested a Cambrian-Ordovician terrestrialization event for arachnids [3], some 60 Ma before their first fossils in the Silurian, although these estimates assume that arachnids evolved from a fully aquatic ancestor. Eurypterids, the sister clade to terrestrial arachnids [4-6], are known to have undergone major macroecological shifts in transitioning from marine to freshwater environments during the Devonian [7, 8]. Discoveries of apparently subaerial eurypterid trackways [9, 10] have led to the suggestion that eurypterids were even able to venture on land and possibly breathe air [11]. However, modern horseshoe crabs undertake amphibious excursions onto land to reproduce [12], rendering trace fossil evidence alone inconclusive. Here, we present details of the respiratory organs of Adelophthalmus pyrrhae sp. nov. from the Carboniferous of Montagne Noire, France [13], revealed through micro computed tomography (µ-CT) imaging. Pillar-like trabeculae on the dorsal surface of each gill lamella indicate eurypterids were capable of subaerial breathing, suggesting that book gills are the direct precursors to book lungs while vascular ancillary respiratory structures known as Kiemenplatten represent novel air-breathing structures. The discovery of air-breathing structures in eurypterids indicates that characters permitting terrestrialization accrued in the arachnid stem lineage and suggests the Cambrian-Ordovician ancestor of arachnids would also have been semi-terrestrial.

Disparities in the analysis of morphological disparity.

Analyses of morphological disparity have been used to characterize and investigate the evolution of variation in the anatomy, function and ecology of organisms since the 1980s. While a diversity of methods have been employed, it is unclear whether they provide equivalent insights. Here, we review the most commonly used approaches for characterizing and analysing morphological disparity, all of which have associated limitations that, if ignored, can lead to misinterpretation. We propose best practice guidelines for disparity analyses, while noting that there can be no 'one-size-fits-all' approach. The available tools should always be used in the context of a specific biological question that will determine data and method selection at every stage of the analysis.

Ignoring stratigraphic age uncertainty leads to erroneous estimates of species divergence times under the fossilized birth-death process.

Fossil information is essential for estimating species divergence times, and can be integrated into Bayesian phylogenetic inference using the fossilized birth-death (FBD) process. An important aspect of palaeontological data is the uncertainty surrounding specimen ages, which can be handled in different ways during inference. The most common approach is to fix fossil ages to a point estimate within the known age interval. Alternatively, age uncertainty can be incorporated by using priors, and fossil ages are then directly sampled as part of the inference. This study presents a comparison of alternative approaches for handling fossil age uncertainty in analysis using the FBD process. Based on simulations, we find that fixing fossil ages to the midpoint or a random point drawn from within the stratigraphic age range leads to biases in divergence time estimates, while sampling fossil ages leads to estimates that are similar to inferences that employ the correct ages of fossils. Second, we show a comparison using an empirical dataset of extant and fossil cetaceans, which confirms that different methods of handling fossil age uncertainty lead to large differences in estimated node ages. Stratigraphic age uncertainty should thus not be ignored in divergence time estimation and instead should be incorporated explicitly.

A new family of dissimilarity metrics for discrete character matrices that include inapplicable characters and its importance for disparity studies.

The use of discrete character data for disparity analyses has become more popular, partially due to the recognition that character data describe variation at large taxonomic scales, as well as the increasing availability of both character matrices co-opted from phylogenetic analysis and software tools. As taxonomic scope increases, the need to describe variation leads to some characters that may describe traits not found across all the taxa. In such situations, it is common practice to treat inapplicable characters as missing data when calculating dissimilarity matrices for disparity studies. For commonly used dissimilarity metrics like Wills's GED and Gower's coefficient, this can lead to the reranking of pairwise dissimilarities, resulting in taxa that share more primary character states being assigned larger dissimilarity values than taxa that share fewer. We introduce a family of metrics that proportionally weight primary characters according to the secondary characters that describe them, effectively eliminating this problem, and compare their performance to common dissimilarity metrics and previously proposed weighting schemes. When applied to empirical datasets, we confirm that choice of dissimilarity metric frequently affects the rank order of pairwise distances, differentially influencing downstream macroevolutionary inferences.

The oldest known digestive system consisting of both paired digestive glands and a crop from exceptionally preserved trilobites of the Guanshan Biota (Early Cambrian, China).

The early Cambrian Guanshan biota of eastern Yunnan, China, contains exceptionally preserved animals and algae. Most diverse and abundant are the arthropods, of which there are at least 11 species of trilobites represented by numerous specimens. Many trilobite specimens show soft-body preservation via iron oxide pseudomorphs of pyrite replacement. Here we describe digestive structures from two species of trilobite, Palaeolenus lantenoisi and Redlichia mansuyi. Multiple specimens of both species contain the preserved remains of an expanded stomach region (a "crop") under the glabella, a structure which has not been observed in trilobites this old, despite numerous examples of trilobite gut traces from other Cambrian Lagerstätten. In addition, at least one specimen of Palaeolenus lantenoisi shows the preservation of an unusual combination of digestive structures: a crop and paired digestive glands along the alimentary tract. This combination of digestive structures has also never been observed in trilobites this old, and is rare in general, with prior evidence of it from one juvenile trilobite specimen from the late Cambrian Orsten fauna of Sweden and possibly one adult trilobite specimen from the Early Ordovician Fezouata Lagerstätte. The variation in the fidelity of preservation of digestive structures within and across different Lagerstätten may be due to variation in the type, quality, and point of digestion of food among specimens in addition to differences in mode of preservation. The presence and combination of these digestive features in the Guanshan trilobites contradicts current models of how the trilobite digestive system was structured and evolved over time. Most notably, the crop is not a derived structure as previously proposed, although it is possible that the relative size of the crop increased over the evolutionary history of the clade.

Development, Trait Evolution, and the Evolution of Development in Trilobites.

Trilobites offer one of the best fossil records of any arthropod group. This is due to a number of factors, most notably the combination of (1) having inhabited areas where organisms are more likely to be buried and ultimately fossilized; and (2) having had a highly biomineralized exoskeleton more likely to survive the stresses of fossilization. This biomineralized exoskeleton was also morphologically complex, bearing traits that had ecological significance, and was present throughout postembryonic development, from larval to adult stages. Because the morphology of the exoskeleton changed gradually across molts during development, it is possible to reconstruct ontogenetic series for many species. Over the last decade, studies have documented both variation in modularity among closely related species and conserved developmental patterns among modules. In the latter case, trait evolution could still occur through modification of rates of morphological change along otherwise conserved ontogenetic trajectories. At the clade level, the pattern of expression and release of new exoskeletal segments during post-embryonic development was generally conserved across most species, but the relative timing of different segmentation events could vary, and developmental traits appear to have been relatively labile across the clade's evolutionary history. Most recently, comparative analyses indicate that the association between segmentation events and the timing of shifts in the rate of ontogenetic shape change varies across species. Despite these advances, we still know relatively little about how development constrained or contributed to trait evolution in trilobites, and almost nothing about the origin of novel traits in trilobites. A major (but removable) obstacle is the current lack of well-supported trilobite phylogenies that span higher taxonomic levels.

Phylogenetic Paleoecology: Tree-Thinking and Ecology in Deep Time.

The new and emerging field of phylogenetic paleoecology leverages the evolutionary relationships among species to explain temporal and spatial changes in species diversity, abundance, and distribution in deep time. This field is poised for rapid progress as knowledge of the evolutionary relationships among fossil species continues to expand. In particular, this approach will lend new insights to many of the longstanding questions in evolutionary biology, such as: the relationships among character change, ecology, and evolutionary rates; the processes that determine the evolutionary relationships among species within communities and along environmental gradients; and the phylogenetic signal underlying ecological selectivity in background and mass extinctions and in major evolutionary radiations.

Simple versus complex models of trait evolution and stasis as a response to environmental change.

Previous analyses of evolutionary patterns, or modes, in fossil lineages have focused overwhelmingly on three simple models: stasis, random walks, and directional evolution. Here we use likelihood methods to fit an expanded set of evolutionary models to a large compilation of ancestor-descendant series of populations from the fossil record. In addition to the standard three models, we assess more complex models with punctuations and shifts from one evolutionary mode to another. As in previous studies, we find that stasis is common in the fossil record, as is a strict version of stasis that entails no real evolutionary changes. Incidence of directional evolution is relatively low (13%), but higher than in previous studies because our analytical approach can more sensitively detect noisy trends. Complex evolutionary models are often favored, overwhelmingly so for sequences comprising many samples. This finding is consistent with evolutionary dynamics that are, in reality, more complex than any of the models we consider. Furthermore, the timing of shifts in evolutionary dynamics varies among traits measured from the same series. Finally, we use our empirical collection of evolutionary sequences and a long and highly resolved proxy for global climate to inform simulations in which traits adaptively track temperature changes over time. When realistically calibrated, we find that this simple model can reproduce important aspects of our paleontological results. We conclude that observed paleontological patterns, including the prevalence of stasis, need not be inconsistent with adaptive evolution, even in the face of unstable physical environments.

Dynamic evolutionary change in post-Paleozoic echinoids and the importance of scale when interpreting changes in rates of evolution.

How ecological and morphological diversity accrues over geological time has been much debated by paleobiologists. Evidence from the fossil record suggests that many clades reach maximal diversity early in their evolutionary history, followed by a decline in evolutionary rates as ecological space fills or due to internal constraints. Here, we apply recently developed methods for estimating rates of morphological evolution during the post-Paleozoic history of a major invertebrate clade, the Echinoidea. Contrary to expectation, rates of evolution were lowest during the initial phase of diversification following the Permo-Triassic mass extinction and increased over time. Furthermore, although several subclades show high initial rates and net decreases in rates of evolution, consistent with "early bursts" of morphological diversification, at more inclusive taxonomic levels, these bursts appear as episodic peaks. Peak rates coincided with major shifts in ecological morphology, primarily associated with innovations in feeding strategies. Despite having similar numbers of species in today's oceans, regular echinoids have accrued far less morphological diversity than irregular echinoids due to lower intrinsic rates of morphological evolution and less morphological innovation, the latter indicative of constrained or bounded evolution. These results indicate that rates of evolution are extremely heterogenous through time and their interpretation depends on the temporal and taxonomic scale of analysis.

Differential niche dynamics among major marine invertebrate clades.

The degree to which organisms retain their environmental preferences is of utmost importance in predicting their fate in a world of rapid climate change. Notably, marine invertebrates frequently show strong affinities for either carbonate or terrigenous clastic environments. This affinity is due to characteristics of the sediments as well as correlated environmental factors. We assessed the conservatism of substrate affinities of marine invertebrates over geological timescales, and found that niche conservatism is prevalent in the oceans, and largely determined by the strength of initial habitat preference. There is substantial variation in niche conservatism among major clades with corals and sponges being among the most conservative. Time-series analysis suggests that niche conservatism is enhanced during times of elevated nutrient flux, whereas niche evolution tends to occur after mass extinctions. Niche evolution is not necessarily elevated in genera exhibiting higher turnover in species composition.

Extinction space--a method for the quantification and classification of changes in morphospace across extinction boundaries.

Three main modes of extinction are responsible for reductions in morphological disparity: (1) random (caused by a nonselective extinction event); (2) marginal (a symmetric, selective extinction event trimming the margin of morphospace); and (3) lateral (an asymmetric, selective extinction event eliminating one side of the morphospace). These three types of extinction event can be distinguished from one another by comparing changes in three measures of morphospace occupation: (1) the sum of range along the main axes; (2) the sum of variance; and (3) the position of the centroid. Computer simulations of various extinction events demonstrate that the pre-extinction distribution of taxa (random or normal) in the morphospace has little influence on the quantification of disparity changes, whereas the modes of the extinction events play the major role. Together, the three disparity metrics define an "extinction-space" in which different extinction events can be directly compared with one another. Application of this method to selected extinction events (Frasnian-Famennian, Devonian-Carboniferous, and Permian-Triassic) of the Ammonoidea demonstrate the similarity of the Devonian events (selective extinctions) but the striking difference from the end-Permian event (nonselective extinction). These events differ in their mode of extinction despite decreases in taxonomic diversity of similar magnitude.

Evolutionary mode routinely varies among morphological traits within fossil species lineages.

Recent studies have revitalized interest in methods for detecting evolutionary modes in both fossil sequences and phylogenies. Most of these studies examine single size or shape traits, often implicitly assuming that single phenotypic traits are adequate representations of species-level change. We test the validity of this assumption by tallying the frequency with which traits vary in evolutionary mode within fossil species lineages. After fitting models of directional change, unbiased random walk, and stasis to a dataset of 635 traits across 153 species lineages, we find that within the majority of lineages, evolutionary mode varies across traits and the likelihood of conflicting within-lineage patterns increases with the number of traits analyzed. In addition, single traits may show variation in evolutionary mode even in situations where the overall morphological evolution of the lineage is dominated by one type of mode. These quantified, stratigraphically based findings validate the idea that morphological patterns of mosaic evolution are pervasive across groups of organisms throughout Earth's history.

Mosaic heterochrony and evolutionary modularity: the trilobite genus Zacanthopsis as a case study.

Logical connections exist between evolutionary modularity and heterochrony, two unifying and structuring themes in the expanding field of evolutionary developmental biology. The former sees complex phenotypes as being made up of semi-independent units of evolutionary transformation; the latter requires such a modular organization of phenotypes to occur in a localized or mosaic fashion. This conceptual relationship is illustrated here by analyzing the evolutionary changes in the cranidial ontogeny of two related species of Cambrian trilobites. With arguments from comparative developmental genetics and functional morphology, we delineate putative evolutionary modules within the cranidium and examine patterns of evolutionary changes in ontogeny at both global and local scales. Results support a case of mosaic heterochrony, that is, a combination of local heterochronies affecting the different parts individuated in the cranidium, leading to the complex pattern of allometric repatterning observed at the global scale. Through this example, we show that recasting morphological analyses of complex phenotypes with a priori knowledge or hypotheses about their organizational and variational properties can significantly improve our interpretation and understanding of evolutionary changes among related taxa, fossil and extant. Such considerations open avenues to investigate the large-scale dynamics of modularity and its role in phenotypic evolution.