Extant‐only comparative methods fail to recover the disparity preserved in the bird fossil record

Most extant species are in clades with poor fossil records, and recent studies of comparative methods show they have low power to infer even highly simplified models of trait evolution without fossil data. Birds are a well‐studied radiation, yet their early evolutionary patterns are still contentious. The fossil record suggests that birds underwent a rapid ecological radiation after the end‐Cretaceous mass extinction, and several smaller, subsequent radiations. This hypothesized series of repeated radiations from fossil data is difficult to test using extant data alone. By uniting morphological and phylogenetic data on 604 extant genera of birds with morphological data on 58 species of extinct birds from 50 million years ago, the “halfway point” of avian evolution, I have been able to test how well extant‐only methods predict the diversity of fossil forms. All extant‐only methods underestimate the disparity, although the ratio of within‐ to between‐clade disparity does suggest high early rates. The failure of standard models to predict high early disparity suggests that recent radiations are obscuring deep time patterns in the evolution of birds. Metrics from different models can be used in conjunction to provide more valuable insights than simply finding the model with the highest relative fit.     

More than one way to spin a crystallite: multiple trajectories through liquid crystallinity to solid silk

Arthropods face several key challenges in processing concentrated feedstocks of proteins (silk dope) into solid, semi-crystalline silk fibres. Strikingly, independently evolved lineages of silk-producing organisms have converged on the use of liquid crystal intermediates (mesophases) to reduce the viscosity of silk dope and assist the formation of supramolecular structure. However, the exact nature of the liquid-crystal-forming-units (mesogens) in silk dope, and the relationship between liquid crystallinity, protein structure and silk processing is yet to be fully elucidated. In this review, we focus on emerging differences in this area between the canonical silks containing extended-β-sheets made by silkworms and spiders, and ‘non-canonical’ silks made by other insect taxa in which the final crystallites are coiled-coils, collagen helices or cross-β-sheets. We compared the amino acid sequences and processing of natural, regenerated and recombinant silk proteins, finding that canonical and non-canonical silk proteins show marked differences in length, architecture, amino acid content and protein folding. Canonical silk proteins are long, flexible in solution and amphipathic; these features allow them both to form large, micelle-like mesogens in solution, and to transition to a crystallite-containing form due to mechanical deformation near the liquid–solid transition. By contrast, non-canonical silk proteins are short and have rod or lath-like structures that are well suited to act both as mesogens and as crystallites without a major intervening phase transition. Given many non-canonical silk proteins can be produced at high yield in E. coli, and that mesophase formation is a versatile way to direct numerous kinds of supramolecular structure, further elucidation of the natural processing of non-canonical silk proteins may to lead to new developments in the production of advanced protein materials.     

Allometric space and allometric disparity: a developmental perspective in the macroevolutionary analysis of morphological disparity

Here, we advance novel uses of allometric spaces--multidimensional spaces specifically defined by allometric coefficients--with the goal of investigating the focal role of development in shaping the evolution of morphological disparity. From their examination, operational measures of allometric disparity can be derived, complementing standard signals of morphological disparity through an intuitive and process-oriented refinement of established analytical protocols used in disparity studies. Allometric spaces thereby become a promising context to reveal different patterns of evolutionary developmental changes and to assess their relative prevalence and importance. Such spaces offer a novel domain of investigation of phenotypic variation and should help in detecting large-scale trends, thus placing various macroevolutionary phenomena in an explicitly developmental context. Ammonoidea (Cephalopoda) at the Lower-Middle Jurassic transition were chosen as a case study to illustrate this methodological approach. We constructed two phenotypic spaces: a static, adult one (adult morphospace) and a dynamic, developmental one (allometric space). Comparative disparity analyses show a strikingly stable occupation in both spaces, despite extensive change in taxonomic composition. In contrast, disparity analyses of subclades reveal clearly distinct morphological and allometric disparity dynamics. Allometric approaches allow developmental insights into morphological diversification otherwise intractable from the analysis of adult morphospace alone.     

More than one way to be an herbivore: convergent evolution of herbivory using different digestive strategies in prickleback fishes (Stichaeidae)

In fishes, the evolution of herbivory has occured within a spectrum of digestive strategies, with two extremes on opposite ends: (i) a rate-maximization strategy characterized by high intake, rapid throughput of food through the gut, and little reliance on microbial digestion or (ii) a yield-maximization strategy characterized by measured intake, slower transit of food through the gut, and more of a reliance on microbial digestion in the hindgut. One of these strategies tends to be favored within a given clade of fishes. Here, we tested the hypothesis that rate or yield digestive strategies can arise in convergently evolved herbivores within a given lineage. In the family Stichaeidae, convergent evolution of herbivory occured in Cebidichthys violaceus and Xiphister mucosus, and despite nearly identical diets, these two species have different digestive physiologies. We found that C. violaceus has more digesta in its distal intestine than other gut regions, has comparatively high concentrations (>11 mM) of short-chain fatty acids (SCFA, the endpoints of microbial fermentation) in its distal intestine, and a spike in β-glucosidase activity in this gut region, findings that, when coupled to long retention times (>20 h) of food in the guts of C. violaceus, suggest a yield-maximizing strategy in this species. X. mucosus showed none of these features and was more similar to its sister taxon, the omnivorous Xiphister atropurpureus, in terms of digestive enzyme activities, gut content partitioning, and concentrations of SCFA in their distal intestines. We also contrasted these herbivores and omnivores with other sympatric stichaeid fishes, Phytichthys chirus (omnivore) and Anoplarchus purpurescens (carnivore), each of which had digestive physiologies consistent with the consumption of animal material. This study shows that rate- and yield-maximizing strategies can evolve in closely related fishes and suggests that resource partitioning can play out on the level of digestive physiology in sympatric, closely related herbivores.     

More than one way to evolve a weed: parallel evolution of US weedy rice through independent genetic mechanisms

Many different crop species were selected for a common suite of ‘domestication traits’, which facilitates their use for studies of parallel evolution. Within domesticated rice (Oryza sativa), there has also been independent evolution of weedy strains from different cultivated varieties. This makes it possible to examine the genetic basis of parallel weed evolution and the extent to which this process occurs through shared genetic mechanisms. We performed comparative QTL mapping of weediness traits using two recombinant inbred line populations derived from crosses between an indica crop variety and representatives of each of the two independently evolved weed strains found in US rice fields, strawhull (S) and blackhull awned (B). Genotyping‐by‐sequencing provided dense marker coverage for linkage map construction (average marker interval <0.25 cM), with 6016 and 13 730 SNPs mapped in F₅ lines of the S and B populations, respectively. For some weediness traits (awn length, hull pigmentation and pericarp pigmentation), QTL mapping and sequencing of underlying candidate genes confirmed that trait variation was largely attributable to individual loci. However, for more complex quantitative traits (including heading date, panicle length and seed shattering), we found multiple QTL, with little evidence of shared genetic bases between the S and B populations or across previous studies of weedy rice. Candidate gene sequencing revealed causal genetic bases for 8 of 27 total mapped QTL. Together these findings suggest that despite the genetic bottleneck that occurred during rice domestication, there is ample genetic variation in this crop to allow agricultural weed evolution through multiple genetic mechanisms.     

More than one way to splice an RNA: branching without a bulge and splicing without branching in group II introns.

Domain 6 (D6) of group II introns contains a bulged adenosine that serves as the branch-site during self-splicing. In addition to this adenosine, other structural features in D6 are likely to contribute to the efficiency of branching. To understand their role in promoting self-splicing, the branch-site and surrounding nucleotides were mutagenized. Detailed kinetic analysis on the self-splicing efficiency of the mutants revealed several interesting features. First, elimination of the branch-site does not preclude efficient splicing, which takes place instead through a hydrolytic first step. Second, pairing of the branch-site does not eliminate branching, particularly if the adenosine is involved in a mispair. Third, the G-U pairs that often surround group II intron branch-points contribute to the efficiency of branching. These results suggest that there is a strong driving force for promoting self-splicing by group II introns, which employ a versatile set of different mechanisms for ensuring that splicing is successful. In addition, the behavior of these mutants indicates that a bulged adenosine per se is not the important determinant for branch-site recognition in group II introns. Rather, the data suggest that the branch-site adenosine is recognized as a flipped base, a conformation that can be promoted by a variety of different substructures in RNA and DNA.     

Cytokinesis in flowering plants: more than one way to divide a cell

Several different cytokinetic mechanisms operate in flowering plants. During 'conventional' somatic cytokinesis, the mitotic spindle remnants give rise to a phragmoplast that serves as a framework for the assembly of the cell plate. Cell plates fuse with the parental plasma membrane at specific cortical sites previously defined by the preprophase band of microtubules. In nuclear endosperms, meiocytes, and gametophytic cells, cytokinesis occurs without preprophase bands. The position of the new cell walls is determined instead by interacting arrays of microtubules that radiate from the nuclear envelope surfaces. The nuclear cytoplasmic domains defined by these microtubule arrays demarcate the boundaries of the future cells. Recent studies have provided new insights into the ultrastructural similarities and dissimilarities between conventional and non-conventional cytokinesis. Numerous proteins have also been localized to cytokinesis-related cytoskeletal arrays and cell plates but the functions of most of them have yet to be elucidated.     

Shaking a leg and hot to trot: the effects of body size and temperature on running speed in ants

Abstract.  1. Data were compiled from the literature and our own studies on 24 ant species to characterise the effects of body size and temperature on forager running speed.
2. Running speed increases with temperature in a manner consistent with the effects of temperature on metabolic rate and the kinetic properties of muscles.
3. The exponent of the body mass-running speed allometry ranged from 0.14 to 0.34 with a central tendency of approximately 0.25. This body mass scaling is consistent with both the model of elastic similarity, and a model combining dynamic similarity with available metabolic power.
4. Even after controlling for body size or temperature, a substantial amount of inter-specific variation in running speed remains. Species with certain lifestyles [e.g. nomadic group predators, species which forage at extreme (>60 °C) temperatures] may have been selected for faster running speeds.
5. Although ants have a similar scaling exponent to mammals for the running speed allometry, they run slower than predicted compared with a hypothetical mammal of similar size. This may in part reflect physiological differences between invertebrates and vertebrates.     

No gastric mill in sauropod dinosaurs: new evidence from analysis of gastrolith mass and function in ostriches

Polished pebbles occasionally found within skeletons of giant herbivorous sauropod dinosaurs are very likely to be gastroliths (stomach stones). Here, we show that based on feeding experiments with ostriches and comparative data for relative gastrolith mass in birds, sauropod gastroliths do not represent the remains of an avian-style gastric mill. Feeding experiments with farm ostriches showed that bird gastroliths experience fast abrasion in the gizzard and do not develop a polish. Relative gastrolith mass in sauropods (gastrolith mass much less than 0.1% of body mass) is at least an order of magnitude less than that in ostriches and other herbivorous birds (gastrolith mass approximates 1% of body mass), also arguing against the presence of a gastric mill in sauropods. Sauropod dinosaurs possibly compensated for their limited oral processing and gastric trituration capabilities by greatly increasing food retention time in the digestive system. Gastrolith clusters of some derived theropod dinosaurs (oviraptorosaurs and ornithomimosaurs) compare well with those of birds, suggesting that the gastric mill evolved in the avian stem lineage.     

More than one way to control hair growth: regulatory mechanisms in enterobacteria that affect fimbriae assembled by the chaperone/usher pathway

Many gram-negative enterobacteria produce surface-associated fimbriae that facilitate attachment and adherence to eucaryotic cells and tissues. These organelles are believed to play an important role during infection by enabling bacteria to colonize specific niches within their hosts. One class of these fimbriae is assembled using a periplasmic chaperone and membrane-associated scaffolding protein that has been referred to as an usher because of its function in fimbrial biogenesis. The presence of multiple types of fimbriae assembled by the chaperone/usher pathway can be found both within a single bacterial species and also among different genera. One way of controlling fimbrial assembly in these bacteria is at the genetic level by positively or negatively regulating fimbrial gene expression. This minireview considers the mechanisms that have been described to control fimbrial gene expression and uses specific examples to demonstrate both unique and shared properties of such regulatory mechanisms.     

Testing the effect of the rock record on diversity: a multidisciplinary approach to elucidating the generic richness of sauropodomorph dinosaurs through time

The accurate reconstruction of palaeobiodiversity patterns is central to a detailed understanding of the macroevolutionary history of a group of organisms. However, there is increasing evidence that diversity patterns observed directly from the fossil record are strongly influenced by fluctuations in the quality of our sampling of the rock record; thus, any patterns we see may reflect sampling biases, rather than genuine biological signals. Previous dinosaur diversity studies have suggested that fluctuations in sauropodomorph palaeobiodiversity reflect genuine biological signals, in comparison to theropods and ornithischians whose diversity seems to be largely controlled by the rock record. Most previous diversity analyses that have attempted to take into account the effects of sampling biases have used only a single method or proxy: here we use a number of techniques in order to elucidate diversity. A global database of all known sauropodomorph body fossil occurrences (2024) was constructed. A taxic diversity curve for all valid sauropodomorph genera was extracted from this database and compared statistically with several sampling proxies (rock outcrop area and dinosaur‐bearing formations and collections), each of which captures a different aspect of fossil record sampling. Phylogenetic diversity estimates, residuals and sample‐based rarefaction (including the first attempt to capture ‘cryptic’ diversity in dinosaurs) were implemented to investigate further the effects of sampling. After ‘removal’ of biases, sauropodomorph diversity appears to be genuinely high in the Norian, Pliensbachian–Toarcian, Bathonian–Callovian and Kimmeridgian–Tithonian (with a small peak in the Aptian), whereas low diversity levels are recorded for the Oxfordian and Berriasian–Barremian, with the Jurassic/Cretaceous boundary seemingly representing a real diversity trough. Observed diversity in the remaining Triassic–Jurassic stages appears to be largely driven by sampling effort. Late Cretaceous diversity is difficult to elucidate and it is possible that this interval remains relatively under‐sampled. Despite its distortion by sampling biases, much of sauropodomorph palaeobiodiversity can be interpreted as a reflection of genuine biological signals, and fluctuations in sea level may account for some of these diversity patterns.     

More than energy cost: multiple benefits of the long Achilles tendon in human walking and running

Elastic strain energy that is stored and released from long, distal tendons such as the Achilles during locomotion allows for muscle power amplification as well as for reduction of the locomotor energy cost: as distal tendons perform mechanical work during recoil, plantar flexor muscle fibres can work over smaller length ranges, at slower shortening speeds, and at lower activation levels. Scant evidence exists that long distal tendons evolved in humans (or were retained from our more distant Hominoidea ancestors) primarily to allow high muscle–tendon power outputs, and indeed we remain relatively powerless compared to many other species. Instead, the majority of evidence suggests that such tendons evolved to reduce total locomotor energy cost. However, numerous additional, often unrecognised, advantages of long tendons may speculatively be of greater evolutionary advantage, including the reduced limb inertia afforded by shorter and lighter muscles (reducing proximal muscle force requirement), reduced energy dissipation during the foot–ground collisions, capacity to store and reuse the muscle work done to dampen the vibrations triggered by foot–ground collisions, reduced muscle heat production (and thus core temperature), and attenuation of work-induced muscle damage. Cumulatively, these effects should reduce both neuromotor fatigue and sense of locomotor effort, allowing humans to choose to move at faster speeds for longer. As these benefits are greater at faster locomotor speeds, they are consistent with the hypothesis that running gaits used by our ancestors may have exerted substantial evolutionary pressure on Achilles tendon length. The long Achilles tendon may therefore be a singular adaptation that provided numerous physiological, biomechanical, and psychological benefits and thus influenced behaviour across multiple tasks, both including and additional to locomotion. While energy cost may be a variable of interest in locomotor studies, future research should consider the broader range of factors influencing our movement capacity, including our decision to move over given distances at specific speeds, in order to understand more fully the effects of Achilles tendon function as well as changes in this function in response to physical activity, inactivity, disuse and disease, on movement performance.     

At the feet of the dinosaurs: the early history and radiation of lizards

Lizards, snakes and amphisbaenians together constitute the Squamata, the largest and most diverse group of living reptiles. Despite their current success, the early squamate fossil record is extremely patchy. The last major survey of squamate palaeontology and evolution was published 20 years ago. Since then, there have been major changes in systematic theory and methodology, as well as a steady trickle of new fossil finds. This review examines our current understanding of the first 150 million years of squamate evolution in the light of the new data and changing ideas. Contrary to previous reports, no squamate fossils are currently documented before the Jurassic. Nonetheless, indirect evidence predicts that squamates had evolved by at least the middle Triassic, and had diversified into existing major lineages before the end of this period. There is thus a major gap in the squamate record at a time when key morphological features were evolving. With the exception of fragmentary remains from Africa and India, Jurassic squamates are known only from localities in northern continents (Laurasia). The situation improves in the Early Cretaceous, but the southern (Gondwanan) record remains extremely poor. This constrains palaeobiogeographic discussion and makes it difficult to predict centres of origin for major squamate clades on the basis of fossil evidence alone. Preliminary mapping of morphological characters onto a consensus tree demonstrates stages in the sequence of acquisition for some characters of the skull and postcranial skeleton, but many crucial stages--most notably those relating to the acquisition of squamate skull kinesis--remain unclear.     

More than one ring to bind them all: Recent insights into the structure of the axon

This brief review outlines recent developments in the understanding of the ultrastructural organization of the axonal and growth cone actin filament cytoskeleton. A novel form of structural organization has arisen as a regulator of the actin cytoskeleton: ring‐like structures. Rings may represent a conserved functional theme exhibited by diverse molecular systems and have implications for the understanding of the axon in development, maturity, and disease. © 2013 Wiley Periodicals, Inc. Develop Neurobiol 73:799–805, 2013     

Diversity patterns amongst herbivorous dinosaurs and plants during the Cretaceous: implications for hypotheses of dinosaur/angiosperm co‐evolution

Abstract Palaeobiologists frequently attempt to identify examples of co‐evolutionary interactions over extended geological timescales. These hypotheses are often intuitively appealing, as co‐evolution is so prevalent in extant ecosystems, and are easy to formulate; however, they are much more difficult to test than their modern analogues. Among the more intriguing deep time co‐evolutionary scenarios are those that relate changes in Cretaceous dinosaur faunas to the primary radiation of flowering plants. Demonstration of temporal congruence between the diversifications of co‐evolving groups is necessary to establish whether co‐evolution could have occurred in such cases, but is insufficient to prove whether it actually did take place. Diversity patterns do, however, provide a means for falsifying such hypotheses. We have compiled a new database of Cretaceous dinosaur and plant distributions from information in the primary literature. This is used as the basis for plotting taxonomic diversity and occurrence curves for herbivorous dinosaurs (Sauropodomorpha, Stegosauria, Ankylosauria, Ornithopoda, Ceratopsia, Pachycephalosauria and herbivorous theropods) and major groups of plants (angiosperms, Bennettitales, cycads, cycadophytes, conifers, Filicales and Ginkgoales) that co‐occur in dinosaur‐bearing formations. Pairwise statistical comparisons were made between various floral and faunal groups to test for any significant similarities in the shapes of their diversity curves through time. We show that, with one possible exception, diversity patterns for major groups of herbivorous dinosaurs are not positively correlated with angiosperm diversity. In other words, at the level of major clades, there is no support for any diffuse co‐evolutionary relationship between herbivorous dinosaurs and flowering plants. The diversification of Late Cretaceous pachycephalosaurs (excluding the problematic taxon Stenopelix) shows a positive correlation, but this might be spuriously related to poor sampling in the Turonian–Santonian interval. Stegosauria shows a significant negative correlation with flowering plants and a significant positive correlation with the nonflowering cycadophytes (cycads, Bennettitales). This interesting pattern is worthy of further investigation, and it reflects the decline of both stegosaurs and cycadophytes during the Early Cretaceous.