News Article | April 20, 2017
Famed British naturalist David Attenborough is going to become a virtual reality hologram with the help of UK broadcaster Sky and Londons Natural History Museum. Attenborough will appear in a VR experience titled Hold the World, which will let viewers navigate the museums collection, picking up and examining rare items. When they do, Attenborough will appear to offer insights about different objects, explaining their significance to the viewer. These artifacts will include fossils, bones, and skulls. I have enjoyed helping people to discover more about the natural world, and Hold The World offers people a unique opportunity: to examine rare objects, some millions of years old, up close, said Attenborough in a press statement. It... Continue reading… You can wake up Microsoft's Surface Studio by talking to it Waking up your PC from sleep is as easy as tapping the touchscreen, moving the mouse or pressing a button on the keyboard -- but if you have a Microsoft Surface Studio, it just got ... Sir David Attenborough will be turned into a HOLOGRAM The broadcasting legend will talk about his favourite fossils from the Natural History Museum in London during a new immersive experience developed by London-based Sky VR. David Attenborough wants to show you some fossils (in VR) - CNET A virtual reality experience takes you inside the Natural History Museum's collection with a little help from Sky and everyone's favourite naturalist. You can now shout hey Cortana to wake up the Surface Studio Microsoft is making its first big update to the Surface Studio this week. A new audio driver, available on Windows Update, will now let Surface Studio owners wake their machines simply ... David Attenborough's hologram will help you study fossils in VR Sir David Attenborough is no stranger to VR. The beloved naturalist and TV presenter has worked on immersive, look-where-you-like films for the Natural History Museum (NHM) in London, ... Sky will be adding 4K test cricket to its slate of sports offerings, and working alongside HBO on world class drama
News Article | February 15, 2017
No statistical methods were used to predetermine sample size. The experiments were not randomized and the investigators were not blinded to allocation during experiments and outcome assessment. We measured 2,028 species, representing 2,028 of 2,091 genera across 194 families. Specimens were obtained primarily from the avian skin collection at the Natural History Museum, Tring, and also from the Manchester Museum. Study skins, rather than skeletal material, were used because they are generally better represented in museum collections with more species and specimens available than in skeletons, and secondly because the rhamphotheca (the keratinous sheath surrounding the fused premaxilla, maxilla and nasal bones) is often absent from skeletonized specimens. This is the portion of the bill that interacts directly with the environment and is thus the subject of selection. Where available, one mature male per species was selected for scanning. This was necessary to achieve the taxonomic sampling required within a reasonable time frame and because males are generally better represented in the collections than females. Care was taken to select specimens that were undamaged, with all the landmarks visible and unobstructed (see below). When undamaged males were unavailable, females were preferentially chosen over unsexed specimens. Some species (for example, Strigiformes, Podargidae, and others) have bills that are obscured by protruding feathers or rictal bristles that ‘shade’ the bill from the scanner. For specimens where this was an issue, or for specimens that were not represented in the skins collections, specimens were chosen from the skeletons collection at Tring. 3D scans of the bills were taken using white or blue structured light scanning (FlexScan3D, LMI Technologies, Vancouver, Canada). The use of 3D scans provides a more complete and nuanced estimate of bill diversity than standard linear measures (length, width, depth) that reflect only the relative proportions of the bill and effectively assume that bills are no more than proportional variations on a cone shape. For bills of lengths >5 cm, an R3X white-light scanner (LMI Technologies; calibration boards 10–25 mm, resolution 0.075 mm) was used, and for bills of lengths <3 cm a MechScan white-light macro scanner (MechInnovation Limited; calibration boards 1.3–4 mm, resolution 0.010 mm) was used. For bills intermediate between these lengths, a pre-calibrated HDI 109 blue-light scanner (LMI Technologies; resolution 0.080 mm) was used. In some cases, larger bills (for example, those with a high aspect ratio, such as hummingbirds) were scanned on the higher resolution scanner. To fully capture 3D geometry, approximately 5–25 scans per bill were obtained, and aligned and combined in the FlexScan software before being exported as ‘.ply’ files. Scans were imported into Geomagic Studio (3D Systems), automatically decimated to approximately 500,000 faces, and cleaned to remove mesh errors (holes, reversed normals, high aspect ratio spikes). In some specimens, it was necessary to remove feathers or scanning artefacts that had obstructed portions of the geometry by manual cleaning of the mesh. Following cleaning, meshes were exported as ‘.obj’ files. Landmark-based geometric morphometric analysis is a method for analysing variation in geometric shape on the basis of the positions of equivalent homologous points (landmarks) placed on every specimen in the study31, 32. Although ‘homologous’ in this context is usually taken to mean developmentally homologous, in practice the key to landmark selection is that the points chosen must be easily identifiable, such that they can be accurately placed and repeatable within and between specimens32. This is difficult to do on the rhamphotheca because, other than the tip of the bill, it lacks any obvious landmarks, especially as the nostrils are not exposed in many bird species. We therefore opted to identify four true landmarks: (1) the tip of the beak and the posterior margin of the keratinous rhamphotheca, along the (2) midline dorsal profile, (3) left and (4) right tomial edges. Three semi-landmark curves joined point 1 to points 2, 3 and 4 to represent the dorsal profile, and the left and right tomial edges, respectively (Extended Data Fig. 1). In order to facilitate landmarking of such a high number of species, a crowdsourcing website http://www.markmybird.org was developed to allow members of the public to participate in the research by placing landmarks on to the bill scans. After registration, volunteers were required to landmark two training bills with easily identifiable (shoebill, Balaeniceps rex) and more challenging (brown-chested alethe, Alethe poliocephala) landmarks. Instructions were shown to all users for every landmark, with links to more detailed instructions provided. Bills were assigned to users by randomly selecting a bill from the 100 scans most recently uploaded. To account for the fact that different users tend to place homologous landmarks in slightly different places33, each bill was marked by three to four different users. Custom R scripts were used to check for common mistakes that may not have been caught by real-time error checks (confusing left and right, large asymmetries in landmark position, incorrect order of semi-landmarks, and semi-landmarks that deviated from the correct curve owing to user failure to rotate the bill and assess their landmark placement in three dimensions). If any landmark configuration failed these tests, the data was manually checked and if necessary removed with the bill made re-available for landmarking. Finally, the three/four repetitions for each bill were averaged to find the mean shape between users, and tested to ensure that all users had placed the landmarks within an acceptable range (Procrustes distance < 0.2) of each another. The average bill shapes were then used for geometric morphometric analysis. Using ANOVA approaches for assessing measurement error in geometric morphometrics33, we found that repeatability was consistently high among users when comparing among PC axes (see below; Extended Data Table 2). All geometric morphometric analysis was performed in the R package Geomorph34. First, landmark configurations were subjected to a generalized Procrustes analysis to remove the effects of size and translational and rotational position on the landmark configurations. This is a common first step in geometric morphometric analyses as it removes all the geometric information from the landmark coordinates that is not related to shape31. During alignment, symmetry was enforced so that slight user-introduced differences in the left or right positions of landmarks were removed. Semi-landmarks were slid to minimize bending energy35. The Procrustes aligned coordinates were then assessed using PCA to identify the major axes of shape variation within bird bills, which were plotted as morphospaces. PC scores for the first eight axes are available in the Supplementary Information. As morphospaces are projections of multidimensional Kendall’s shape space into two-dimensional tangent space, they may be prone to distortions the further one moves from the central coordinates of the morphospace. In other words, extreme bill morphologies plotted at the edges of morphospace have the potential to distort the projection such that Procrustes distances at the edges of a morphospace are not equivalent to those at the centre of a morphospace. To assess the extent to which projected tangent space differed from the underlying Kendall’s shape space, the Procrustes aligned coordinates were analysed using tpsSmall 1.30 (ref. 36). We found no evidence of distortion: distance in tangent was very tightly correlated with Procrustes distance (uncentred correlation, 0.999; regression through the origin slope, 0.985; root mean squared error, <0.001). Similarly, Procrustes distances (D) were consistently close to tangent distances (d; minimum Procustes D: 0.024, minimum tangent d: 0.024; mean Procustes D: 0.194, mean tangent d: 0.192; maximum Procustes D: 0.525, maximum tangent d: 0.501). Warps of the associated shape changes with each PC were generated by transforming the landmarks of the bill closest to the average shape (rusty-fronted barwing, Actinodura egertoni) to landmarks representing the extremes of a given PC when all other PCs = 0, and interpolating the surface in between. To assess any possible distortion of PCA by the underlying phylogenetic non-independence among species, we also ran a phylogenetic PCA (pPCA)37, 38. As with the standard PCA, the first eight PCs accounted for >99% of total shape variance. We found that the first two pPCs did not correlate with the first two original PCs—pPC1 was more closely correlated with PC2 and pPC2 was more closely correlated with PC1. The remaining PCs and pPCs were closely correlated and retained the same order in terms of the proportion of variance explained. We also re-ran rate variable models on the first eight pPCs (see below). For this analysis we allowed the pPCs to be correlated because a property of pPCA is that the axes are not expected to be orthogonal. The multivariate results are similar regardless of the choice of PCA or pPCA (Extended Data Fig. 3). Recently identified problems inherent with using PCA (or pPCA) that can lead to misidentifying macroevolutionary models are expected to arise when individual PCs are analysed, particularly when the variance explained is distributed fairly evenly across multiple PCs39. Because we use a multivariate approach these problems are minimized. We based our analyses on the phylogenetic tree distributions from http://www.birdtree.org11. For both ‘Hackett’40 and ‘Ericson’41 backbones, we sampled 10,000 ‘stage 2’ trees (that is, those containing all 9,993 species) from http://www.birdtree.org, which were pruned to generate tree distributions for the 2,028 species in our dataset. We also generated similar tree distributions using ‘stage 1’ trees from the same source, which contain only the subset of species placed using genetic data. Of the 2,028 species in the full dataset, 1,627 (80%) were represented in stage 1 trees. On the basis of these distributions, we used TreeAnnotator42 to generate maximum clade credibility (MCC) trees, setting branch lengths equal to ‘Common Ancestor’ node heights. In addition, we constructed a composite of the trees from ref. 11 and the genomic backbone tree from ref. 43 (Extended Data Fig. 4) by grafting sub-clades of the stage 2 Hackett MCC tree onto nodes in the phylogeny from ref. 41 at positions where the two trees could be sensibly combined (see Supplementary Material for node-matching data and R code to combine the trees). This process resulted in a composite tree combining the genus level resolution afforded by the ref. 11 tree with the branching topology and age estimates of the ref. 43 backbone, which are notably younger than those in the trees in ref. 11. We calculated the phylogenetic signal of bill shape by estimating Pagel’s λ using the R package MOTMOT44. λ can vary between 0 and 1, with a value of 0 indicating no phylogenetic signal and a value of 1 indicating similar levels of phylogenetic covariance as expected under a Brownian motion model. Univariate variable rates models were estimated using the software BayesTraits (available from http://www.evolution.rdg.ac.uk/) using default priors and a single-chain Markov chain Monte Carlo (MCMC) run for at least 1 billion (1,000,000,000) iterations. From each chain, we sampled parameters every 100,000 iterations and final parameter estimates for each model were based on 5,000 post-burn in samples. Uncorrelated multivariate models were estimated using the same approach. At each iteration in the MCMC chain, the multivariate models fit a single-branch length transformation to the tree across all trait (that is, PC) axes. An uncorrelated multivariate model is justified because PC axes are inherently orthogonal; however, this may limit inference of some forms of rate change. Specifically, the uncorrelated multivariate model is informative with respect to changes in the variances among clades and shifts in the morphospace centroids of clades (that is, single-branch shifts) but cannot detect cases where variances and centroids are similar but covariances among clades differ. We summarized the results of each run by calculating (1) the mean rate and (2) the probability of a rate shift (branch or clade) over all posterior samples for each node in the tree. It is often challenging to pinpoint the precise location of rate shifts in the tree, particularly when such shifts involve clades of species with short internode intervals at their base. In such cases it becomes difficult to assign the location of a shift to a single node and the inference of a rate shift is then often distributed across two or more nested nodes in the phylogeny. To account for this, we also summarized our results using a second approach in which the posterior probability for a particular rate shift was calculated as the sum of the probability of a shift having occurred on a focal node or on either of the nodes immediately descending from it. We focus on the multivariate analyses because bill shape is a high-dimensional trait. In the main text (Figs 2, 3) we report results from the stage 2 Hackett tree but found comparable results regardless of tree choice (Extended Data Figs 3, 4). We checked for biases in rate estimates across the phylogeny by comparing our observed multivariate rate estimates of bill-shape evolution to results generated using simulated data. Using the stage 2 Hackett MCC tree, we generated 10 null multivariate datasets (simulated under Brownian motion) and estimated rates using runs of 200 million iterations and 1,000 post-burn samples. We found that, on average, branch-specific rates derived from simulated datasets were uncorrelated with observed rates of bill-shape evolution (Spearman’s rho = 0.03; P = 0.34), indicating that our results are unlikely to be affected by underlying biases in rate estimation. In addition to BayesTraits we compared the fit of three single-process models (Brownian motion (BM), early burst and Ornstein–Uhlenbeck), fit using the ‘fitContinuous’ function and default settings in the R package Geiger v2.0 (ref. 45), as well as alternative formulations of the BAMM model46 that differed in their handling of temporal rate variation (time constant (t constant), time variable (t var.) and time flip (t flip)). The BayesTraits, BAMM and single-process models are not fitted in a common framework with consistent likelihood calculations. We therefore compared the fit of the alternative models within each shape axis by calculating the likelihood of a BM model fit to the mean rate-transformed trees (from ref. 11) derived from each model. In the absence of support for alternative models (Extended Data Table 3), and because BAMM does not currently allow analyses of multivariate data, we focus our interpretation on analyses using BayesTraits. We estimated ancestral values for each component axis of bill-shape variation using a maximum likelihood approach implemented in the R package phytools38. We estimated ancestral states using the mean rate-transformed trees for each component axis to account for unequal rates of evolution across the tree and among shape axes. To generate estimates of ancestral disparity through time, we took time slices at 1-million-year intervals starting at the root of the tree. For each time slice, we extracted ancestral state estimates for each component axis for the lineages in the phylogeny existing at that particular time point. We then quantified multivariate disparity in trait values by calculating the sum of the variances across all eight trait axes21. Unlike other disparity metrics, the sum of the variances is expected to be independent of richness and sensitive to changes in both expansion and packing of trait space, thus providing an indication of the relative strength of these two patterns19. We generated two alternative null models of morphospace filling based on BM models of trait evolution to assess whether the observed patterns of bill-shape disparity through time were distinct from unbiased patterns of disparity accumulation. In the first, we assumed that trait variation accumulates at a constant rate (CR) that is homogeneous with respect to time and also to the position of a lineage in the phylogeny. In the second we relaxed these assumptions of rate constancy and instead simulated traits using the mean rate-transformed trees for each axis, thereby providing a null model of disparity accumulation incorporating variable rates (VR) of trait evolution. For each model, we simulated 500 replicate datasets and used these to calculate two sets of null disparity through time curves using identical approaches to those described above. Irrespective of whether evolutionary rates are fixed to be constant or allowed to vary, an important feature of both null models is that the underlying balance between morphospace expansion and packing is expected to be effectively equal and constant over time. This is due to the inherently non-directional nature of trait change simulated using the BM model. Consequently, any deviation in the observed rate of disparity accumulation compared to the null rates suggests that one process (either expansion or packing) has dominated over the other. For each 1-million-year time slice, we calculated the mean rate of evolution across all branches present at that time point. We repeated this procedure for each tree in the posterior distribution to generate a distribution of average rate estimates in 1 million year intervals. We examined the consistency of bill-shape evolution within and among avian clades using Bayesian estimates of phenotypic variance–covariance matrices (P matrices) of bill-shape within higher taxa (families, superfamilies and orders)26, 27. First, we estimated the number of independent axes (that is, eigenvectors of P) that are required to adequately explain the total trait variance in P in each higher taxon. We then tested whether the dominant eigenvector of bill-shape variation (P ) is consistent among clades. P is the first principal component of P and an estimate of the major axis of phenotypic variation. We estimated phenotypic variance–covariance matrices for higher taxa containing ≥ 20 sampled species. Posterior distributions of variance–covariance matrices were generated using Bayesian MCMC MANOVA models implemented in the R package MCMCglmm27. We used weak uniform priors and ran each model for 80,000 iterations with a burn-in of 40,000 and sampling that produced 1,000 estimates of the posterior distribution. On the basis of these distributions, we used a set of Bayesian matrix quantification approaches26 to extract information on (1) centroid position, (2) subspace orientation, (3) individual trait loadings onto and variance explained by P , and (4) number of significant eigenvectors associated with each P. Scan and landmark data that support the findings of this study have been deposited in the NHM Data Portal with the identifier http://dx.doi.org/10.5519/0005413. All other data analysed during this study are included as Source Data and Supplementary Information files.
News Article | December 21, 2015
Using X-ray scattering at the ESRF facility in France to examine the blue and white feathers of the Jay, researchers from the University of Sheffield found that birds demonstrate a surprising level of control and sophistication in producing colours. Instead of simply using dyes and pigments that would fade over time, the birds use well-controlled changes to the nanostructure to create their vividly coloured feathers - which are possibly used for Jays to recognise one another. The Jay is able to pattern these different colours along an individual feather barb - the equivalent of having many different colours along a single human hair. The Jay's feather, which goes from ultra violet in colour through to blue and into white, is made of a nanostructured spongy keratin material, exactly the same kind of material human hair and fingernails are made from. The researchers found that the Jay is able to demonstrate amazing control over the size of the holes in this sponge-like structure and fix them at very particular sizes, determining the colour that we see reflected from the feather. This is because when light hits the feather the size of these holes determines how the light is scattered and therefore the colour that is reflected. As a result, larger holes mean a broader wavelength reflectance of light, which creates the colour white. Conversely, a smaller, more compact structure, results in the colour blue. If the colours were formed using pigments created from the bird's diet, the feather colour would fade over time. However, since nature has developed a way to create the colours through structural changes, any nanostructure will remain intact, explaining why birds never go grey as they age. In contrast, humans rely on pigments to colour hair. As these are not produced to the same extent as we age, we consequently go grey. The research findings are being published today in Nature Scientific Reports today (21 December 2015). Dr Andrew Parnell, from the University of Sheffield's Department of Physics and Astronomy said: "Conventional thought was that to control light using materials in this way we would need ultra precise and controlled structures with many different processing stages, but if nature can assemble this material 'on the wing', then we should be able to do it synthetically too." Dr Parnell added: "This discovery means that in the future, we could create long-lasting coloured coatings and materials synthetically. We have discovered it is the way in which it is formed and the control of this evolving nanostructure - by adjusting the size and density of the holes in the spongy like structure - that determines what colour is reflected. "Current technology cannot make colour with this level of control and precision - we still use dyes and pigments. Now we've learnt how nature accomplishes it, we can start to develop new materials such as clothes or paints using these nanostructuring approaches. It would potentially mean that if we created a red jumper using this method, it would retain its colour and never fade in the wash." Researcher Dr Daragh McLoughlin of AkzoNobel Decorative Paints Material Science Research Team added: "At AkzoNobel, the makers of Dulux paint, we aim to encourage and stimulate the innovation of more sustainable products that have eco-premium benefits. This exciting new insight may help us to find new ways of making paints that stay brighter and fresher-looking for longer, while also having a lower carbon footprint." The work used feathers selected from the extensive collection at the Natural History Museum (NHM) in London. Dr Adam Washington from the University of Sheffield added: "The research also answers the longstanding conundrum of why non-iridescent structural greens are rare in nature. This is because to create the colour green, a very complex and narrow wavelength is needed, something that is hard to produce by manipulating this tuneable spongy structures. As a result, nature's way to get round this and create the colour green - an obvious camouflage colour - is to mix the structural blue like that of the Jay with a yellow pigment that absorbs some of the blue colour." Explore further: Rainbows without pigments offer new defense against fraud
News Article | November 28, 2016
London’s Natural History Museum (the NHM) is one of the world’s greatest and most famous of natural history museums, and one thing the museum is synonymous with is dinosaurs. Even without its soon-to-be-touring Diplodocus replica, the museum is still home to both a dinosaur display gallery that brings in millions of visitors each year, and to one of the world’s most important scientific collections of dinosaur fossils. So it stands to reason that the museum has long been associated with books that seek to educate and entertain the public as goes the world of dinosaurs and their ilk. For years, William Swinton’s Fossil Amphibians and Reptiles was the museum’s main offering. It was reprinted on numerous occasions following its publication in 1954. Then there was Alan Charig’s A New Look at the Dinosaurs, first published in 1979 and also reprinted as numerous later editions. By the 1990s, Charig’s rather technical tome was looking dated (see Moody & Naish 2010) and the time was right for a more popular, prettier volume. And thus Tim Gardom and Angela Milner’s 1993 The Natural History Museum Book of Dinosaurs came to pass. Gardom & Milner (1993) is not bad at all as a popular-level volume and ran for three editions, the newest appearing in 2007. But the time came when it, too, began to look dated (check out all those scaly-skinned maniraptorans). A new book was needed, and the task of writing it fell to current NHM dinosaur expert Paul Barrett... who, so kindly, approached the present author with an offer of collaboration. And thus it was that we teamed up and wrote what might just be the best popular-level dinosaur book written so far*. * As usual: a nod to worthy predecessors. Check out Thomas Holtz’s Dinosaurs: The Most Complete, Up-to-Date Encyclopedia for Dinosaur Lovers of All Ages and Farlow et al.’s The Complete Dinosaur (2nd edition) if you can. Our new book – Dinosaurs: How They Lived and Evolved (Naish & Barrett 2016) – is a sturdy hardback of some 224 pages. It’s extensively illustrated in colour throughout and features scores of photos, diagrams and life reconstructions. There’s a lot of text, the style of which is mostly pitched at older teenagers and adults but which could easily be followed by a smart person of 11 or 12. Having said this, an interested kid of 10 could follow it too. I cannot yet confirm plans for a softback, nor do I know anything about a digital version (follow me on twitter for news: @TetZoo). The contents. The six chapters variously cover (1) History, Origins and their World, (2) The Dinosaur Family Tree, (3) Anatomy, (4) Biology, Ecology and Behaviour, (5) The Origin of Birds, and (6) The Great Extinction and Beyond. Let’s talk about the contents of those chapters a little. Chapter 1 features the preamble you expect for a dinosaur book: there’s a little bit about taxonomy and geological time, the popularity of dinosaurs, and a brief look at the science of dinosaur research and at what sort of things experts aim to find out. We also get one thing out of the way right up-front – on the third page of text in fact. This is the fact that birds are dinosaurs, and thus that dinosaurs are not extinct and that constant reference has to be made to ‘non-bird dinosaurs’ where appropriate. It is, in my view (and Paul’s), misleading and downright wrong to ignore birds when discussing the group termed Dinosauria. The rest of that first chapter reviews the history of dinosaur research. We are in a post-Bakkerian world where, again, it is wrong to pretend that the writings of Ostrom and Bakker – whatever you make of them – did not inspire that which followed, and so it is that we have a section on the impact of their work during the late 20th century. As we note, however, things might actually have been more complex and more study is needed. Anyway, cue the graph showing how more than 85% of recognised non-bird dinosaurs have been named since 1990. Also from the intro chapter: we briefly discuss Mesozoic climate, weather and palaeobiogeography. Things have turned out to be less simple than people used to think. Cool temperatures during part of the Mesozoic? Dinosaurs specialised for life on island continents? Dinosaurs in polar regions during prolonged periods of seasonal darkness? Our anatomy chapter aims to bring many of the idea familiar to specialist dinosaur researchers to a broader audience: think of all that work on neck flexibility, tail musculature and tail flexibility, on the saurischian pneumatic system and so on that’s there in the technical literature but little known to lay-readers. We make use of those sexy diagrams by Mike Taylor and Heinrich Mallison that depict sauropod neck and stegosaur tail flexibility, respectively. Biology, ecology, behaviour. I suspect that a favourite chapter for many will be the one on biology, ecology and behaviour. If you’re familiar with Paul’s research, and my own interests and research interests, you might guess what the contents include. We cover the increasingly complex world of ornithischian feeding biology and jaw function, the debate on diplodocid feeding behaviour (spoiler: maybe anything goes), maniraptoran predation and use of those sickle-claws, finite element analysis and its application, locomotion and running speed, sexual selection, parental care, ontogeny, the composition of dinosaur communities… and more. Many of the things that will be new to a generalist readership will be familiar to readers of this blog: the ‘ontogenetic morphology hypothesis’ as it pertains to pachycephalosaurs (yes) and chasmosaurines (well, ok… except for that Torosaurus idea), Just Say No To Nanotyrannus, kids, the race-to-death in Tyrannosaurus (longevity of less than 30 years), and the idea of aquatic or amphibious life in Spinosaurus… we’re sceptical of the Ibrahim et al. idea, and we wrote what we did before Evers et al. (2015) appeared. We’re a bit open-ended on the issue of dinosaur physiology. I think that the evidence indicating full-blown physiological endothermy (and not just inertial endothermy) in at least some non-bird dinosaurs is good (Pontzer et al. 2009) but I’m also not offended by the idea that a more intermediate ‘mesothermy’ (Grady et al. 2014) might have applied to some lineages. The Cenozoic has dinosaurs too. People who read my stuff (here at Tet Zoo or in various books: see Naish 2012) will know that I consider it important that the Cenozoic history of birds should be included in any review of dinosaur diversity that allows it. All too often authors stop with Cretaceous lineages, meaning that interested parties have no option but to turn to Feduccia’s books when it comes to post-Cretaceous birds, and those works are as misleading on Cenozoic birds as they are on bird origins and the Mesozoic history of birds. Anyway, our last chapter includes a brief review of post-Mesozoic bird history and diversity that I think does a pretty good job. It ends with chickens. Always with the chickens. There are over 20 billion of them in the world right now, you know. As for the extinction event, Paul and I endorse the ‘integrated scenario’: the idea that it was the giant rock from outer space that mostly killed all those animals, but that other issues of the time had already put them in a very vulnerable place. How awesome is this book exactly? Reviewers respond. What have people said about the text so far? People seem to like the way it’s pitched and the stuff it covers. I have to say that I roll my eyes when I see reviewers making (as one has) some snide aside to our apparent use of the “passive voice”. I know what ‘passive voice’ means and I avoid it where I can, but it gets so frequently called out as a criticism of scientific writing (my own included) that it no longer means anything to me and I’m not sure that it can be avoided when writing about science. I saw one review which claimed that the “least successful” chapter is the one on the dinosaur family tree (Chapter 2). I find that description amusing: reviewers (who typically review books because they review books, not because they’re especially interested in the book or its subject) tend not to get that the let’s-walk-through-the-family-tree section of a book is often one of the highlights for dinosaur fans, and I can’t see that this subject (nor our review specifically) is dry or monotonous. What, you think that disagreements over the evolutionary position of heterodontosaurids are boring? Huh, I do not envy your view of reality, my friend. And, checking that chapter again in an effort to quell my paranoia, I find it pretty satisfying: when discussing a relevant group, we talk about its anatomy, palaeobiology and inferred lifestyle, it’s not just a “group x gave rise to give y which gave rise to group z” tirade of tree structure and nothing else. Let’s talk about the pictures. OK, the Giganotosaurus in the room is the cover. I will say that I don’t like it, but I don’t want to say much more than that, other than that I bowed to pressure and recognised that – aesthetics aside – the image was chosen for reasons of impact. I will remind those who dislike the image not to judge a book by its cover. And indeed… the artwork elsewhere in the book includes some of the best, most cutting-edge content produced by anyone. Excellent pieces by Bob Nicholls (some of them brand new), Emily Willoughby, John Conway, Julius Csotonyi, Mark Witton, Andrey Atuchin, Davide Bonadonna, John Sibbick and Berislav Krzic appear. My cladograms feature throughout. Even if you don’t want to read the text you might buy the book for its pictures alone, I feel. This book is also packed with excellent colour photos and features a great many of the NHM’s prize dinosaur specimens (many of which are not on display but in the collections). Among my favourites are the Stegoceras skull (one of the most complete pachycephalosaur skulls in the world), the Proceratosaurus and Baryonyx holotypes, Cutler’s amazing Scolosaurus specimen (an image I was sadly unable to procure for the relevant section of my 2012 The Great Dinosaur Discoveries) and the many images of Sophie the famous Stegosaurus. Non-NHM specimens put to good use include the Erlikosaurus skull, Scipionyx (thanks to Cristiano Dal Sasso and Simone Maganuco for those pictures), the bristle-tailed Psittacosaurus you all know and love, the quill knobs of Velociraptor and the gracile hand of Berlin’s Giraffatitan. Sometimes, tracking down the images took quite some effort. The NHM might be home to many of the world’s most awesome dinosaur fossils but that doesn’t mean that good photos of the specimens (which are often on display behind glass, or in deep storage and awkward to pull out) are readily available. A tip-off from Dean Lomax (author of the recent Dinosaurs of the British Isles) led to the discovery of the excellent colour, whole-specimen shot of the Scelidosaurus I wanted. And I think that will do. I hope people like the book; initial indications from reviews online and word of mouth is that they do. For a particularly nice review I will point you to Marc Vincent’s at Love in the Time of Chasmosaurs. Finally, there are a few minor typos that I wish we’d caught (“titonosaurs” in one figure caption… d’oh!), but it’s hard to be perfect. So – what’s next? Ah yes, that… Darren Naish & Paul Barrett. 2016. Dinosaurs: How They Lived and Evolved. The Natural History Museum/Smithsonian Book. £18.00/$29.95. Hardback, index, glossary, pp. 224. ISBN 978-0-56509311-2. Here from the Natural History Museum. Here on amazon. Here on amazon.co.uk (I have no idea why amazon.co.uk are selling it at £24, retail price is £18.00). For previous articles relevant to things mentioned here, see... Dal Sasso, C. & Signore, M. 1998. Exceptional soft-tissue preservation in a theropod dinosaur from Italy. Nature 392, 383-387. Evers, S. W., Rauhut, O. W. M., Milner, A. C., McFeeters, B. & Allain, R. 2015. A reappraisal of the morphology and systematic position of the theropod dinosaur Sigilmassasaurus from the “middle” Cretaceous of Morocco. PeerJ 3:e1323 https://doi.org/10.7717/peerj.1323 Mallison, H. 2010. CAD assessment of the posture and range of motion of Kentrosaurus aethiopicus Henning 1915. Swiss Journal of Geosciences 103, 211-233. Moody, R. T. J. & Naish, D. 2010. Alan Jack Charig (1927-1997): an overview of his academic accomplishments and role in the world of fossil reptile research. In Moody, R. T. J., Buffetaut, E., Naish, D. & Martill, D. M. (eds) Dinosaurs and Other Extinct Saurians: A Historical Perspective. Geological Society, London, Special Publications 343, pp. 89-109. Naish, D. 2012. Birds. In Brett-Surman, M. K., Holtz, T. R. & Farlow, J. O. (eds) The Complete Dinosaur (Second Edition). Indiana University Press (Bloomington & Indianapolis), pp. 379-423. Naish, D. & Barrett, P. M. 2016. Dinosaurs: How They Lived and Evolved. The Natural History Museum, London. Pontzer, H., Allen, V. & Hutchinson. J. R. 2009. Biomechanics of running indicates endothermy in bipedal dinosaurs. PLoS ONE 4 (11): e7783. doi:10.1371/journal.pone.0007783
News Article | January 8, 2016
Sherborn's Index Animalium is available online through the Smithsonian Libraries. Credit: Smithsonian Libraries From the outside, it can seem that taxonomy has a commitment issue with scientific names. They shift for reasons that seem obscure and unnecessarily wonkish to people who simply want to use names to refer to a consistent, knowable taxon such as species, genus or family. However, the relationship between nomenclature and taxonomy, as two quite separate but mutually dependent systems, is a sophisticated way of balancing what we know and what is open to further interpretation. Nomenclature is a bureaucracy that follows rules and is tied to published records and type specimens. It provides a rigid framework or skeleton for knowledge. Taxonomy, on the other hand, is a data-driven science, influenced by interpretation and resulting in concepts that are open to further test and change. To actually get the answers right, taxonomy needs to be responsive and fluid as a system of knowledge. The link between nomenclature and the published record is also the junction with the data that fuels taxonomic interpretation. Biodiversity informatics aims to solve this issue, and its founding father is Charles Davies Sherborn. His magnum opus, Index Animalium, provided the bibliographic foundation for current zoological nomenclature. In the 43 years he spent working on this extraordinary resource, he anchored our understanding of animal diversity through the published scientific record. No work has equaled it, and it is still in current and critical use. This special volume of the open-access journal ZooKeys celebrates Sherborn, his contributions, context and the future for the discipline of biodiversity informatics. The papers in this volume fall into three general areas of history, current practice and frontiers. The first section presents facets of Sherborn as a man, scientist and bibliographer, and describes the historical context for taxonomic indexing from the 19th century to today. The second section discusses existing tools and innovations for bringing legacy biodiversity information into the modern age. The final section tackles the future of biological nomenclature, including digital access, innovative publishing models and the changing tools and sociology needed for communicating taxonomy. In the late 1880s Charles Davies Sherborn recognised the need for a full index of names to the original sources that gave them legitimacy, their first publications. He set about making a complete index for names of animals, which are the largest group of described organisms (1.4 million of the current 1.8 million described species are animals). Because this work began while the very basics of nomenclatural rules were being thrashed out, the work itself affected how those rules were codified. Sherborn's monumental work, Index Animalium, comprises more than 9,000 pages in 11 volumes and about 440,000 names. This was on the scale of other hugely ambitious tasks at the time that changed the course of communication such as the Oxford English Dictionary. The error rates are astonishingly low, and it became, and it remains to date the most complete reference source for animal nomenclature. Taxonomic studies rely on Sherborn's work today. While the future for information access is one of the most exciting frontiers for our increasingly interconnected, accelerated society, biodiversity information will continue to be grounded in this seminal work. The future for biodiversity informatics is built on Sherborn's work, and is expanding to be digital, diversified and accessible. The publisher of this volume, the journal ZooKeys, is itself a pioneer in developing a more stable and accessible scientific nomenclature. Together with PhytoKeys, ZooKeys is piloting an innovative workflow with a pre-publication automated pipeline for registration of nomenclatural acts. This initiative comes from the EU FP7 project pro-iBiosphere, and in close collaboration with ZooBank (the official online registry for scientific names of animals), Zoological Record, IPNI, MycoBank and Index Fungorum, and the Global Names project. The volume was inspired by a symposium held in Sherborn's honour at the Natural History Museum (NHM), London, on the 150th year of his birth in 2011, organised by the International Commission on Zoological Nomenclature (ICZN), in collaboration with the Society for the History of Natural History (SHNH). Sherborn was a man with a vision for the future and respect for the accomplishments of the past. He would have celebrated the new tools for the ambitious goal of linking all biological information through names that are readable for both machines and humans. He would have understood the tremendous power of interconnected names for biodiversity science overall. And he would have knuckled down and got to work to make it happen. Explore further: Zoologists are no longer restricted to publish new species on paper More information: Ellinor Michel. Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond, ZooKeys (2016). DOI: 10.3897/zookeys.550.7460
News Article | November 15, 2016
The UK's most famous dinosaur is going to start its national tour on southern England's Jurassic Coast. Dorset County Museum will be the first place to host Dippy the Diplodocus when it temporarily moves out of its London home. The capital's Natural History Museum is having a big front-of-house makeover. A blue whale skeleton is being put in the dinosaur's prominent position by the main entrance - and so Dippy is going on the road. The plaster-of-Paris model - so loved by generations of visitors - will be on show in London for the last time on 4 January. Conservators will then spend the next 12 months getting it ready for its trip around the UK. This will involve re-making some parts and giving it a new, modular support structure, or armature, to facilitate frequent packing and unpacking. After Dorset, 21m-long Dippy will visit Birmingham Museum; Ulster Museum; Kelvingrove Art Gallery and Museum, Glasgow; Great North Museum, Newcastle; the National Assembly for Wales; Number One Riverside, Rochdale; and Norwich Cathedral. At each location, the dinosaur will be used as the centrepiece of a display that will highlight local natural history and nature collections. The tour will end in late 2020. Director of the Dorset County Museum, Dr Jon Murden, said: "We are so excited to be welcoming Dippy on Tour here in 2018 at the heart of the Jurassic Coast World Heritage Site. As the birthplace of palaeontology, there is nowhere in the UK more appropriate for Dippy to start the tour than Dorset." Specialists are already deep into the task of preparing the blue whale ready for its new role. It is due to be suspended in a dramatic diving pose from the ceiling of the NHM's Hintze Hall. The grand opening will be next summer. The bones were recently removed from their old display position in the mammals gallery and taken into a laboratory. "There was an amazing carpet of dust on the whale's bones," said Lorraine Cornish, the head of conservation at the NHM. "In many ways it was very beautiful - like a Mars or a Moon surface. And so the first thing we had to do was clean all that away using vacuum cleaners, to see the surface more clearly, to check if there were cracks or issues we hadn't spotted before," she told BBC News. The near-4.5-tonne whale specimen is more than 100 years old, and - unlike Dippy - is the real deal; it is not a cast. It was acquired for the NHM shortly after the institution opened in 1881. The animal had beached at Wexford on the southeast coast of Ireland, and London's curators paid £250 for the carcass. Nearly every bone is present, and they still leach oil. The workmen who first put the whale on public display in 1935 probably thought it would never be taken out of its gallery. This might explain why it was shot through with long iron rods and cables. Some of the alterations made to accommodate this scaffolding are really quite brutal. "They just drilled very big holes and put very large bolts in the bones, and very large pieces of wire cabling. As conservators, we'd not now drill a hole in a specimen," said Lorraine Cornish. "It's scientific data for us; it's one of our collection items. Wherever possible we'll re-use some of those holes but we'll add additional armature to the outside to make sure the whale is protected when it suspends above the public." The museum team made a quick lidar scan of the bones before moving them to the lab, to help understand how they fit together and to begin designing the new display pose. A more comprehensive, 3D mapping exercise will be conducted in the next few weeks, however. This is key to the NHM's big digitisation strategy, which seeks to make virtual copies of 20 million of its more than 80 million specimens over the next five years. It will allow researchers to more easily study the London collection. It would even make it possible for someone to "print" their own blue whale skeleton. The NHM wants the cetacean to be a new kind of emblem. The museum expects the skeleton's display in Hintze Hall to increase the wow factor for visitors. It also hopes the whale can convey better all the cutting-edge science it does on a daily basis. But for fans of Dippy, the NHM is keen to stress the dinosaur will not be sidelined. Indeed, on its return to London the Diplodocus is likely still to enjoy star billing. The museum plans to renovate and re-model the gardens that surround its buildings. Dippy is set to be re-cast in bronze and be the first thing visitors see as they approach the institution from South Kensington tube station. "In many ways, Dippy and the whale are tied together; I feel passionately about both of them," said Lorraine Cornish. "They do different things but they are both part of our strategy to get people interested and excited about science, the natural world and the challenges we face." BBC TV's Horizon programme is following the whale's preparation for its re-suspension in the NHM's front entrance. The episode will be broadcast next year around the time of the public unveiling. Jonathan.Amos-INTERNET@bbc.co.uk and follow me on Twitter: @BBCAmos
Bocak L.,NHM |
Barton C.,NHM |
Barton C.,Imperial College London |
Crampton-Platt A.,NHM |
And 5 more authors.
Systematic Entomology | Year: 2014
The species representation of public databases is growing rapidly and permits increasingly detailed phylogenetic inferences. We present a supermatrix based on all gene sequences of Coleoptera available in Genbank for two nuclear (18S and 28S rRNA) and two mitochondrial (rrnL and cox1) genes. After filtering for unique species names and the addition of ̃2000 unpublished sequences for cox1 and 18S rRNA, the resulting data matrix included 8441 species-level terminals and 6600 aligned nucleotide positions. The concatenated matrix represents the equivalent of 2.17% of the 390000 described species of Coleoptera and includes 152 beetle families. The remaining 29 families constitute small lineages with ̃250 known species in total. Taxonomic coverage remains low for several major lineages, including Buprestidae (0.16% of described species), Staphylinidae (1.03%), Tenebrionidae (0.90%) and Cerambycidae (0.58%). The current taxon sampling was strongly biased towards the Northern Hemisphere. Phylogenetic trees obtained from the supermatrix were in very good agreement with the Linnaean classification, in particular at the family level, but lower for the subfamily and lowest for the genus level. The topology supports the basal split of Derodontidae and Scirtoidea from the remaining Polyphaga, and the broad paraphyly of Cucujoidea. The data extraction pipeline and detailed tree provide a framework for placement of any new sequences, including environmental samples, into a DNA-based classification system of Coleoptera. © 2013 The Royal Entomological Society.