Spectroscopy on the wing: Investigating possible differences in protein secondary structures in feather shafts of birds using Raman spectroscopy.

The central shaft of a bird's flight feather bears most of the aerodynamic load during flight and exhibits some remarkable mechanical properties. The shaft comprises two parts, the calamus and the rachis. The calamus is at the base of the shaft, while the rachis is the longer upper part which supports the vanes. The shaft is composed of a fibrous outer cortex, and an inner foam-like core. Recent nanoindentation experiments have indicated that reduced modulus values, Er, for the inner and outer regions of the cortex can vary, with the Er values of the inner region slightly greater than those of the outer region. In this work, Raman spectroscopy is used to investigate the protein secondary structures in the inner and outer regions of the feather cortex. Analysis of the Amide I region of Raman spectra taken from four birds (Swan, Gull, Mallard and Kestrel) shows that the ß-sheet structural component decreases between the inner and outer region, relative to the protein side-chain components. This finding is consistent with the proposal that Er values are greater in the inner region than the outer region. This work has shown that Raman spectroscopy can be used effectively to study the change in protein secondary structure between the inner and outer regions of a feather shaft.

Imaging techniques for observing laminar geometry in the feather shaft cortex.

Bird feather shafts are light, stiff and strong, but the fine details of how their structure, mechanics and function relate to one another remains poorly understood. The missing piece in our understanding may be the various fibrous layers that make up the shaft's cortex. Detailed imaging techniques are needed to enable us to capture, analyse and quantify these layers before we can begin to unravel the relationship between their structure, mechanics and function. We show that Serial-Block-Face scanning electron microscopy, scanning confocal polarised microscopy and synchrotron-based computed tomography are three suitable techniques to investigate layer thickness and fibre orientation in the feather cortex. These techniques and other are discussed in terms of their ability to resolve the fibrous laminar structure of the feather cortex, on sample preparation, and on throughput. Annotated images are presented for each and less suitable techniques are presented in the Supplementary Material. LAY DESCRIPTION: Bird feathers have a light, stiff and strong central shaft. However, the fine details of how their structure, mechanics and function relate to one another remains poorly understood. The missing piece in our understanding may have to do with how fibrous layers within the shaft vary in thickness and alignment. Detailed imaging techniques are needed so that we can quantify some of this variation before we can revisit some long-unanswered questions about the feather shaft's structure, mechanics and function. We investigate a number of microscopy techniques and show that three techniques are suitable for the sort of investigation that is required. These techniques and others are discussed in terms of their ability to resolve the layers' thickness and alignment, on sample preparation, and on the sample sizes they are able to process. Annotated images are presented and discussed for each of the three techniques and unsuitable techniques receive the same examination in the Supplementary Material.

An abelisaurid (Dinosauria: Theropoda) ilium from the Upper Cretaceous (Cenomanian) of the Kem Kem beds, Morocco.

Abelisaurid theropods first appear in the fossil record in the early Jurassic and survived at least until the end of the Mesozoic. They were known to have dominated South America, India and Madagascar but were not so abundant in North America or Asia. Much less is known about their presence in Africa, although there has been several recent discoveries of abelisaurid material in Morocco. Here we add a partially preserved ilium to a growing body of evidence that suggests abelisaurs might also have dominated Africa.

Ultraviolet light illuminates the avian nature of the Berlin Archaeopteryx skeleton.

The question of whether the iconic avialan Archaeopteryx was capable of active flapping flight or only passive gliding is still unresolved. This study contributes to this debate by reporting on two key aspects of this fossil that are visible under ultraviolet (UV) light. In contrast to previous studies, we show that most of the vertebral column of the Berlin Archaeopteryx possesses intraosseous pneumaticity, and that pneumatic structures also extend beyond the anterior thoracic vertebrae in other specimens of Archaeopteryx. With a minimum Pneumaticity Index (PI) of 0.39, Archaeopteryx had a much more lightweight skeleton than has been previously reported, comprising an air sac-driven respiratory system with the potential for a bird-like, high-performance metabolism. The neural spines of the 16th to 22nd presacral vertebrae in the Berlin Archaeopteryx are bridged by interspinal ossifications, and form a rigid notarium-like structure similar to the condition seen in modern birds. This reinforced vertebral column, combined with the extensive development of air sacs, suggests that Archaeopteryx was capable of flapping its wings for cursorial and/or aerial locomotion.

A mixed vertebrate eggshell assemblage from the Transylvanian Late Cretaceous.

A Late Cretaceous-aged multi-taxon nesting site from Romania preserved in three dimensions reveals the earliest example of nest site sharing yet known from the vertebrate fossil record. Eggshell and osteological evidence combined in this single accumulation demonstrate that at least four vertebrate taxa including enantiornithine birds and another avian of indeterminate affinities as well as crocodylomorphs and gekkotan squamates nested together in the same place. Colonial nesting in enantiornithines was previously described from this site; here, we present the first fossil evidence that other vertebrates also nested in the same place, perhaps exploiting the presence of the large bird colony. We describe four distinct eggshell morphotypes that have been collected from this site and draw palaeoecological inferences based on this unique multi-taxon nesting association.

Older birds have better feathers: A longitudinal study on the long-distance migratory Sand Martin, Riparia riparia.

Feather quality is of critical importance to long-distance migratory birds. Here, we report a series of analyses of a unique data set encompassing known-age individuals of the long-distance migratory Sand Martin (Riparia riparia). Sampling over 17 years along the Tisza River, eastern Hungary, has resulted in the recapture of numerous individuals enabling longitudinal and cross-sectional investigation of the role of adaptation to variable environmental conditions on feather morphology. We show that older individuals tend to possess better quality feathers, measured using bending stiffness, feather length and thickness as proxies. Bending stiffness and feather thickness do not change with individual age, in contrast with increases in feather length and declines in daily feather growth versus age of individual alongside moult duration. Individuals who live to older ages tend to have similar, or higher, feather growth rates and better feather quality than individuals captured at younger ages. Thus, on the basis of strong selection against individuals with slow feather growth, as seen in other species of swallows and martins, which causes a delay in moult completion, the results of this analysis highlight the potential cost of producing better quality feathers when this depends on moult duration. Feather length also does change during the lifetime of the individual and thus enabled us to further investigate influence of individual and environmental conditions during the moult. The results of this analysis provide important insights on the adaptive significance of these traits, and the potential use of physical characteristics in unravelling the reasons why long distance migratory bird populations are in global decline.

The four-flipper swimming method of plesiosaurs enabled efficient and effective locomotion.

The extinct ocean-going plesiosaurs were unique within vertebrates because they used two flipper pairs identical in morphology for propulsion. Although fossils of these Mesozoic marine reptiles have been known for more than two centuries, the function and dynamics of their tandem-flipper propulsion system has always been unclear and controversial. We address this question quantitatively for the first time in this study, reporting a series of precisely controlled water tank experiments that use reconstructed plesiosaur flippers scaled from well-preserved fossils. Our aim was to determine which limb movements would have resulted in the most efficient and effective propulsion. We show that plesiosaur hind flippers generated up to 60% more thrust and 40% higher efficiency when operating in harmony with their forward counterparts, when compared with operating alone, and the spacing and relative motion between the flippers was critical in governing these increases. The results of our analyses show that this phenomenon was probably present across the whole range of plesiosaur flipper motion and resolves the centuries-old debate about the propulsion style of these marine reptiles, as well as indicating why they retained two pairs of flippers for more than 100 million years.

Complex neuroanatomy in the rostrum of the Isle of Wight theropod Neovenator salerii.

The discovery of large, complex, internal canals within the rostra of fossil reptiles has been linked with an enhanced tactile function utilised in an aquatic context, so far in pliosaurids, the Cretaceous theropod Spinosaurus, and the related spinosaurid Baryonyx. Here, we report the presence of a complex network of large, laterally situated, anastomosing channels, discovered via micro-focus computed tomography (µCT), in the premaxilla and maxilla of Neovenator, a mid-sized allosauroid theropod from the Early Cretaceous of the UK. We identify these channels as neurovascular canals, that include parts of the trigeminal nerve; many branches of this complex terminate on the external surfaces of the premaxilla and maxilla where they are associated with foramina. Neovenator is universally regarded as a 'typical' terrestrial, predatory theropod, and there are no indications that it was aquatic, amphibious, or unusual with respect to the ecology or behaviour predicted for allosauroids. Accordingly, we propose that enlarged neurovascular facial canals shouldn't be used to exclusively support a model of aquatic foraging in theropods and argue instead that an enhanced degree of facial sensitivity may have been linked with any number of alternative behavioural adaptations, among them defleshing behaviour, nest selection/maintenance or social interaction.

Exploring the Relationship between Skeletal Mass and Total Body Mass in Birds.

Total body mass (TBM) is known to be related to a number of different osteological features in vertebrates, including limb element measurements and total skeletal mass. The relationship between skeletal mass and TBM in birds has been suggested as a way of estimating the latter in cases where only the skeleton is known (e.g., fossils). This relationship has thus also been applied to other extinct vertebrates, including the non-avian pterosaurs, while other studies have used additional skeletal correlates found in modern birds to estimate TBM. However, most previous studies have used TBM compiled from the literature rather than from direct measurements, producing values from population averages rather than from individuals. Here, we report a new dataset of 487 extant birds encompassing 79 species that have skeletal mass and TBM recorded at the time of collection or preparation. We combine both historical and new data for analyses with phylogenetic control and find a similar and well-correlated relationship between skeletal mass and TBM. Thus, we confirm that TBM and skeletal mass are accurate proxies for estimating one another. We also look at other factors that may have an effect on avian body mass, including sex, ontogenetic stage, and flight mode. While data are well-correlated in all cases, phylogeny is a major control on TBM in birds strongly suggesting that this relationship is not appropriate for estimating the total mass of taxa outside of crown birds, Neornithes (e.g., non-avian dinosaurs, pterosaurs). Data also reveal large variability in both bird skeletal and TBM within single species; caution should thus be applied when using published mass to test direct correlations with skeletal mass and bone lengths.

The paleoenvironments of azhdarchid pterosaurs localities in the Late Cretaceous of Kazakhstan.

Five pterosaur localities are currently known from the Late Cretaceous in the northeastern Aral Sea region of Kazakhstan. Of these, one is Turonian-Coniacian in age, the Zhirkindek Formation (Tyulkili), and four are Santonian in age, all from the early Campanian Bostobe Formation (Baibishe, Akkurgan, Buroinak, and Shakh Shakh). All so far collected and identifiable Late Cretaceous pterosaur bones from Kazakhstan likely belong to Azhdarchidae: Azhdarcho sp. (Tyulkili); Aralazhdarchobostobensis (Shakh Shakh); and Samrukianessovi (Akkurgan). These latter two taxa, both from the Bostobe Formation might be synonyms. Azhdarcho sp. from the Zhirkindek Formation lived in a tropical-to-subtropical relatively humid climate on the shore of an estuarine basin connected to the Turgai Sea. Known fossils were collected in association with brackish-water bivalves and so the overall paleoenvironment of this pterosaur was likely an estuarine marsh as indicated by the dominance of conifers and low relative counts of ferns and angiosperms. Aralazhdarchobostobensis, from the Bostobe Formation, lived on a coastal fluvial plain along the Turgai Sea. This paleoenvironment was either floodplain (Akkurgan, Buroinak, and Shakh Shakh) or estuarine (Baibishe). In the Santonian - early Campanian, shallow waters near this coastal plain were sites for the intensive accumulation of phosphates under upwelling conditions caused by strong winds from the ancient Asian landmass. These winds also caused significant aridization of the climate during this time. We speculate that pterosaurs may have been attracted to this area by the abundant resources in the bio-productive estuaries and nearshore upwelling waters.

Nanomechanical properties of bird feather rachises: exploring naturally occurring fibre reinforced laminar composites.

Flight feathers have evolved under selective pressures to be sufficiently light and strong enough to cope with the stresses of flight. The feather shaft (rachis) must resist these stresses and is fundamental to this mode of locomotion. Relatively little work has been done on rachis morphology, especially from a mechanical perspective and never at the nanoscale. Nano-indentation is a cornerstone technique in materials testing. Here we use this technique to make use of differentially oriented fibres and their resulting mechanical anisotropy. The rachis is established as a multi-layered fibrous composite material with varying laminar properties in three feathers of birds with markedly different flight styles; the Mute Swan (Cygnus olor), the Bald Eagle (Haliaeetus leucocephalus) and the partridge (Perdix perdix). These birds were chosen not just because they are from different clades and have different flight styles, but because they have feathers large enough to gain meaningful results from nano-indentation. Results from our initial datasets indicate that the proportions and orientation of the laminae are not fixed and may vary either in order to cope with the stresses of flight particular to the bird or with phylogenetic lineage.

Dinosaur evolution. Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds.

Recent discoveries have highlighted the dramatic evolutionary transformation of massive, ground-dwelling theropod dinosaurs into light, volant birds. Here, we apply Bayesian approaches (originally developed for inferring geographic spread and rates of molecular evolution in viruses) in a different context: to infer size changes and rates of anatomical innovation (across up to 1549 skeletal characters) in fossils. These approaches identify two drivers underlying the dinosaur-bird transition. The theropod lineage directly ancestral to birds undergoes sustained miniaturization across 50 million years and at least 12 consecutive branches (internodes) and evolves skeletal adaptations four times faster than other dinosaurs. The distinct, prolonged phase of miniaturization along the bird stem would have facilitated the evolution of many novelties associated with small body size, such as reorientation of body mass, increased aerial ability, and paedomorphic skulls with reduced snouts but enlarged eyes and brains.

A reversal of fortunes: climate change 'winners' and 'losers' in Antarctic Peninsula penguins.

Climate change is a major threat to global biodiversity. Antarctic ecosystems are no exception. Investigating past species responses to climatic events can distinguish natural from anthropogenic impacts. Climate change produces 'winners', species that benefit from these events and 'losers', species that decline or become extinct. Using molecular techniques, we assess the demographic history and population structure of Pygoscelis penguins in the Scotia Arc related to climate warming after the Last Glacial Maximum (LGM). All three pygoscelid penguins responded positively to post-LGM warming by expanding from glacial refugia, with those breeding at higher latitudes expanding most. Northern (Pygoscelis papua papua) and Southern (Pygoscelis papua ellsworthii) gentoo sub-species likely diverged during the LGM. Comparing historical responses with the literature on current trends, we see Southern gentoo penguins are responding to current warming as they did during post-LGM warming, expanding their range southwards. Conversely, Adélie and chinstrap penguins are experiencing a 'reversal of fortunes' as they are now declining in the Antarctic Peninsula, the opposite of their response to post-LGM warming. This suggests current climate warming has decoupled historic population responses in the Antarctic Peninsula, favoring generalist gentoo penguins as climate change 'winners', while Adélie and chinstrap penguins have become climate change 'losers'.

Pectoral fin morphology of batoid fishes (Chondrichthyes: Batoidea): explaining phylogenetic variation with geometric morphometrics.

The diverse cartilaginous fish lineage, Batoidea (rays, skates, and allies), sister taxon to sharks, comprises a huge range of morphological diversity which to date remains unquantified and unexplained in terms of evolution or locomotor style. A recent molecular phylogeny has enabled us to confidently assess broadscale aspects of morphology across Batoidea. Geometric morphometrics quantifies the major aspects of shape variation, focusing on the enlarged pectoral fins which characterize batoids, to explore relationships between ancestry, locomotion and habitat. A database of 253 specimens, encompassing 60 of the 72 batoid genera, reveals that the majority of morphological variation across Batoidea is attributable to fin aspect-ratio and the chordwise location of fin apexes. Both aspect-ratio and apex location exhibit significant phylogenetic signal. Standardized independent linear contrast analysis reveals that fin aspect-ratio can predict locomotor style. This study provides the first evidence that low aspect-ratio fins are correlated with undulatory-style locomotion in batoids, whereas high aspect-ratio fins are correlated with oscillatory locomotion. We also show that it is phylogeny that determines locomotor style. In addition, body- and caudal fin-locomotors are shown to exhibit low aspect-ratio fins, whereas a pelagic lifestyle correlates with high aspect-ratio fins. These results emphasize the importance of phylogeny in determining batoid pectoral fin shape, however, interactions with other constraints, most notably locomotor style, are also highlighted as significant.

Skin pigmentation provides evidence of convergent melanism in extinct marine reptiles.

Throughout the animal kingdom, adaptive colouration serves critical functions ranging from inconspicuous camouflage to ostentatious sexual display, and can provide important information about the environment and biology of a particular organism. The most ubiquitous and abundant pigment, melanin, also has a diverse range of non-visual roles, including thermoregulation in ectotherms. However, little is known about the functional evolution of this important biochrome through deep time, owing to our limited ability to unambiguously identify traces of it in the fossil record. Here we present direct chemical evidence of pigmentation in fossilized skin, from three distantly related marine reptiles: a leatherback turtle, a mosasaur and an ichthyosaur. We demonstrate that dark traces of soft tissue in these fossils are dominated by molecularly preserved eumelanin, in intimate association with fossilized melanosomes. In addition, we suggest that contrary to the countershading of many pelagic animals, at least some ichthyosaurs were uniformly dark-coloured in life. Our analyses expand current knowledge of pigmentation in fossil integument beyond that of feathers, allowing for the reconstruction of colour over much greater ranges of extinct taxa and anatomy. In turn, our results provide evidence of convergent melanism in three disparate lineages of secondarily aquatic tetrapods. Based on extant marine analogues, we propose that the benefits of thermoregulation and/or crypsis are likely to have contributed to this melanisation, with the former having implications for the ability of each group to exploit cold environments.

Aerodynamic performance of the feathered dinosaur Microraptor and the evolution of feathered flight.

Understanding the aerodynamic performance of feathered, non-avialan dinosaurs is critical to reconstructing the evolution of bird flight. Here we show that the Early Cretaceous five-winged paravian Microraptor is most stable when gliding at high-lift coefficients (low lift/drag ratios). Wind tunnel experiments and flight simulations show that sustaining a high-lift coefficient at the expense of high drag would have been the most efficient strategy for Microraptor when gliding from, and between, low elevations. Analyses also demonstrate that anatomically plausible changes in wing configuration and leg position would have made little difference to aerodynamic performance. Significant to the evolution of flight, we show that Microraptor did not require a sophisticated, 'modern' wing morphology to undertake effective glides. This is congruent with the fossil record and also with the hypothesis that symmetric 'flight' feathers first evolved in dinosaurs for non-aerodynamic functions, later being adapted to form lifting surfaces.

A Jurassic avialan dinosaur from China resolves the early phylogenetic history of birds.

The recent discovery of small paravian theropod dinosaurs with well-preserved feathers in the Middle-Late Jurassic Tiaojishan Formation of Liaoning Province (northeastern China) has challenged the pivotal position of Archaeopteryx, regarded from its discovery to be the most basal bird. Removing Archaeopteryx from the base of Avialae to nest within Deinonychosauria implies that typical bird flight, powered by the forelimbs only, either evolved at least twice, or was subsequently lost or modified in some deinonychosaurians. Here we describe the complete skeleton of a new paravian from the Tiaojishan Formation of Liaoning Province, China. Including this new taxon in a comprehensive phylogenetic analysis for basal Paraves does the following: (1) it recovers it as the basal-most avialan; (2) it confirms the avialan status of Archaeopteryx; (3) it places Troodontidae as the sister-group to Avialae; (4) it supports a single origin of powered flight within Paraves; and (5) it implies that the early diversification of Paraves and Avialae took place in the Middle-Late Jurassic period.