64 Works

Data from: Tracing the patterns of non-marine turtle richness from Triassic–Palaeogene: from origin through global spread

Terri Cleary, Roger Benson, Patricia Holroyd & Paul Barrett
Turtles are key components of modern vertebrate faunas and it is predicted that their diversity and distributions will be affected by anthropogenic climate change. Despite this, few studies have attempted to provide baseline data on turtle taxonomic richness through time or assess their past responses to global environmental change. We used the extensive Triassic–Palaeogene (252–23 Ma) fossil record of terrestrial and freshwater turtles to investigate diversity patterns, finding substantial variation in richness through time and...

Support for the habitat amount hypothesis from a global synthesis of species density studies

James Watling, Víctor Arroyo-Rodríguez, Marion Pfeifer, Lander Baeten, Cristina Banks-Leite, Laura Cisneros, Rebecca Fang, Caroli Hamel-Leigue, Thibault Lachat, Inara Leal, Luc Lens, Hugh Possingham, Dinarzarde Raheem, Danilo Ribeiro, Eleanor Slade, Nicolas Urbina-Cardona, Eric Wood & Lenore Fahrig
Decades of research suggest that species richness depends on spatial characteristics of habitat patches, especially their size and isolation. In contrast, the habitat amount hypothesis predicts that: 1) species richness in plots of fixed size (species density) is more strongly and positively related to the amount of habitat around the plot than to patch size or isolation; 2) habitat amount better predicts species density than patch size and isolation combined, 3) there is no effect...

Linking micro and macroevolution of head shape in an island radiation

Maxime Taverne, Hugo Dutel, Michael Fagan, Anamaria Štambuk, Duje Lisičić, Zoran Tadić, Anne-Claire Fabre & Anthony Herrel
Phenotypic traits have been shown to evolve in response to variation in the environment. However, the evolutionary processes underlying the emergence of phenotypic diversity can typically only be understood at the population level. Consequently, how subtle phenotypic differences at the intraspecific level can give rise to larger-scale changes in performance and ecology remains poorly understood. We here tested for the covariation between ecology, bite force, jaw muscle architecture, and the three-dimensional shape of the cranium...

Towards a stable global Noctuidae (Lepidoptera) taxonomy

Kevin Keegan, Jadranka Rota, Reza Zahiri, Alberto Zilli, Niklas Wahlberg, B. Christian Schmidt, J. Donald Lafontaine, Paul Goldstein & David Wagner
The family Noctuidae is one of the world’s most diverse, ecologically successful, and economically important animal lineages; with over 12,000 species in ~1150 genera. We inferred a phylogeny based on eight protein-coding genes (>6,400 base pairs) for the global fauna, greatly expanding upon previous attempts to stabilize the higher classification of Noctuidae by sampling 70 of the 76 widely recognized family-group taxa: 20 of the 21 subfamilies, 32 of the 35 tribes, and 18 of...

Feeding in the Devonian antiarch placoderm fishes: a study based upon morpho-functional analysis of jaws

Zerina Johanson, Oleg Lebedev, Alexander Kuznetsov, Aleksey Tsessarsky, Kate Trinajstic & Farkhad Isakhodzayev
Antiarch placoderm fishes were an abundant component of the Middle Paleozoic vertebrate assemblages. Despite a large number of known taxa and specimens, the morphology and function of the skeletal elements of their jaws is inadequately known. Because of this, questions regarding their feeding modes and their roles in the trophic webs remains open. We present a skeleto-muscular model of the antiarch jaw apparatus with an attempt to reconstruct its potential biomechanical function. The position of...

Data from: Phylogenomics and the evolution of hemipteroid insects

Kevin P. Johnson, Christopher H. Dietrich, Frank Friedrich, Rolf G. Beutel, Benjamin Wipfler, Ralph S. Peters, Julie M. Allen, Malte Petersen, Alexander Donath, Kimberly K. O. Walden, Alexey M. Kozlov, Lars Podsiadlowski, Christoph Mayer, Karen Meusemann, Alexandros Vasilikopoulos, Robert M. Waterhouse, Stephen L. Cameron, Christiane Weirauch, Daniel R. Swanson, Diana M. Percy, Nate B. Hardy, Irene Terry, Shanlin Liu, Xin Zhou, Bernhard Misof … & Kazunori Yoshizawa
Hemipteroid insects (Paraneoptera), with over 10% of all known insect diversity, are a major component of terrestrial and aquatic ecosystems. Previous phylogenetic analyses have not consistently resolved the relationships among major hemipteroid lineages. We provide maximum likelihood-based phylogenomic analyses of a taxonomically comprehensive dataset comprising sequences of 2,395 single-copy, protein-coding genes for 193 samples of hemipteroid insects and outgroups. These analyses yield a well-supported phylogeny for hemipteroid insects. Monophyly of each of the three hemipteroid...

Data from: Global distribution of Chelonid fibropapilloma-associated herpesvirus among clinically healthy sea turtles

Alonzo Alfaro-Núñez, Mads Frost Bertelsen, Anders Miki Bojesen, Isabel Rasmussen, Lisandra Zepeda-Mendoza, Morten Tange Olsen & Marcus Thomas Pius Gilbert
Background: Fibropapillomatosis (FP) is a neoplastic disease characterized by cutaneous tumours that has been documented to infect all sea turtle species. Chelonid fibropapilloma-associated herpesvirus (CFPHV) is believed to be the aetiological agent of FP, based principally on consistent PCR-based detection of herpesvirus DNA sequences from FP tumours. We used a recently described PCR-based assay that targets 3 conserved CFPHV genes, to survey 208 green turtles (Chelonia mydas). This included both FP tumour exhibiting, and clinically...

Data from: The influence of wing morphology upon the dispersal, geographical distributions and diversification of the Corvides (Aves; Passeriformes)

Jonathan D. Kennedy, Michael K. Borregaard, Knud Andreas Jønsson, Petter Z. Marki, Jon Fjeldså & Carsten Rahbek
New species are sometimes known to arise as a consequence of the dispersal and establishment of populations in new areas. It has nevertheless been difficult to demonstrate an empirical link between rates of dispersal and diversification, partly because dispersal abilities are challenging to quantify. Here, using wing morphology as a proxy for dispersal ability, we assess this relationship among the global radiation of corvoid birds. We found that species distributions are associated with wing shape....

Data from: Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

Tobias Guldberg Frøslev, Rasmus Kjøller, Hans Henrik Bruun, Rasmus Ejrnæs, Ane Kirstine Brunbjerg, Carlotta Pietroni & Anders Johannes Hansen
DNA metabarcoding is promising for cost-effective biodiversity monitoring, but reliable diversity estimates are difficult to achieve and validate. Here we present and validate a method, called LULU, for removing erroneous molecular operational taxonomic units (OTUs) from community data derived by high-throughput sequencing of amplified marker genes. LULU identifies errors by combining sequence similarity and co-occurrence patterns. To validate the LULU method, we use a unique data set of high quality survey data of vascular plants...

Precision mapping of snail habitat provides a powerful indicator of human schistosomiasis transmission

Chelsea Wood, Susanne Sokolow, Isabel Jones, Andrew Chamberlin, Kevin Lafferty, Armand Kuris, Merlijn Jocque, Skylar Hopkins, Grant Adams, Julia Buck, Andrea Lund, Ana Garcia-Vedrenne, Evan Fiorenza, Jason Rohr, Fiona Allan, Bonnie Webster, Muriel Rabone, Joanne Webster, Lydie Bandagny, Raphael Ndione, Simon Senghor, Anne-Marie Schacht, Nicolas Jouanard, Gilles Riveau & Giulio De Leo
Recently, the World Health Organization recognized that efforts to interrupt schistosomiasis transmission through mass drug administration have been ineffective in some regions; one of their new recommended strategies for global schistosomiasis control emphasizes targeting the freshwater snails that transmit schistosome parasites. We sought to identify robust indicators that would enable precision targeting of these snails. At the site of the world’s largest recorded schistosomiasis epidemic—the Lower Senegal River Basin in Senegal—intensive sampling revealed positive relationships...

Origin and adaptive radiation of the exceptional and threatened bembidiine beetle fauna of St Helena (Coleoptera: Carabidae)

David Maddison, John Sproul & Howard Mendel
The central peaks of the isolated island of St Helena (in the south Atlantic Ocean) are home to an extraordinary set of ground beetles of the tribe Bembidiini, and belong to three endemic genus-group taxa. These beetles are strikingly different in overall body form from the many bembidiines found elsewhere in the world. At least some of the St Helena species are likely extinct, and all are threatened by habitat destruction and invasive species. Through...

Data from: Cranial evolution in the extinct Rodrigues Island owl Otus murivorus (Strigidae), associated with unexpected ecological adaptations

Antoine Louchart, Anaïs Duhamel, Julian Hume, Pauline Guenser & Céline Salaviale
Island birds that were victim of anthropic extinctions were often more specialist species, having evolved their most distinctive features in isolation. Here we studied a fossil cranium of the ‘giant’ extinct scops owl Otus murivorus from Rodrigues Island (Mascarene Islands, southwestern Indian Ocean), to determine any potential unique characters. The fossil and extant strigids were imaged through x-ray microtomography, providing 3D views of external and internal (endocast, inner ear) cranial structures. Geometric morphometrics and analyses...

Data from: Telenomus nizwaensis (Hymenoptera: Scelionidae), an important egg parasitoid of the pomegranate butterfly Deudorix livia Klug (Lepidoptera: Lycaenidae) in Oman

A. Polaszek, A. Al-Riyami, Z. Lahey, S. A. Al-Khatri, R. H. Al-Shidi & I. C. W. Hardy
The pomegranate butterfly Deudorix (=Virachola) livia is the major pest of pomegranate, a crop of economic importance, in Oman. A species of parasitoid wasp in the hymenopteran family Scelionidae is responsible for high levels of mortality of its eggs. This wasp is described herein as Telenomus nizwaensis Polaszek sp. n. based on morphology and DNA sequence data. Telenomus nizwaensis is currently known only from D. livia, which is also a pest of economic importance on...

Data from: Paradoxical escape responses by narwhals (Monodon monoceros)

Terrie M. Williams, Susanna B. Blackwell, Beau Richter, Mikkel-Holger S. Sinding & Mads Peter Heide-Jørgensen
Until recent declines in Arctic sea ice levels, narwhals (Monodon monoceros) have lived in relative isolation from human perturbation and sustained predation pressures. The resulting naïvety has made this cryptic, deep-diving cetacean highly susceptible to disturbance, although quantifiable effects have been lacking. We deployed a submersible, animal-borne electrocardiograph-accelerometer-depth recorder to monitor physiological and behavioral responses of East Greenland narwhals after release from net entanglement and stranding. Escaping narwhals displayed a paradoxical cardiovascular down-regulation (extreme bradycardia...

Data from: Geographic and temporal dynamics of a global radiation and diversification in the killer whale

Phillip A. Morin, Kim M. Parsons, Frederick I. Archer, María C. Ávila-Arcos, Lance G. Barrett-Lennard, Luciano Dalla Rosa, Sebastián Duchêne, John W. Durban, Graeme M. Ellis, Steven H. Ferguson, John K. Ford, Michael J. Ford, Cristina Gabrilao, M. Thomas P. Gilbert, Kristin Kaschner, Craig O. Matkin, Stephen D. Petersen, Kelly M. Robertson, Ingrid N. Visser, Paul R. Wade, Simon Y. W. Ho & Andrew D. Foote
Global climate change during the Late Pleistocene periodically encroached and then released habitat during the glacial cycles, causing range expansions and contractions in some species. These dynamics have played a major role in geographic radiations, diversification and speciation. We investigate these dynamics in the most widely distributed of marine mammals, the killer whale (Orcinus orca), using a global data set of over 450 samples. This marine top predator inhabits coastal and pelagic ecosystems ranging from...

Data from: Recent diversification of a marine genus (Tursiops spp.) tracks habitat preference and environmental change

Andre E. Moura, Sandra C. A. Nielsen, Julia T. Vilstrup, Jose Victor Moreno-Mayar, Marcus Thomas P. Gilbert, Howard Gray, Ada Natoli, Luciana Möller, Alan Rus Hoelzel & Howard W. I. Gray
Understanding the evolution of diversity and the resulting systematics in marine systems is confounded by the lack of clear boundaries in oceanic habitats, especially for highly mobile species like marine mammals. Dolphin populations and sibling species often show differentiation between coastal and offshore habitats, similar to the pelagic/littoral or benthic differentiation seen for some species of fish. Here we test the hypothesis that lineages within the polytypic genus Tursiops track past changes in the environment...

Data from: Ancient genomes revisit the ancestry of domestic and Przewalski’s horses

Charleen Gaunitz, Antoine Fages, Kristian Hanghøj, Anders Albrechtsen, Naveed Khan, Mikkel Schubert, Andaine Seguin-Orlando, Ivy J. Owens, Sabine Felkel, Olivier Bignon-Lau, Peter De Barros Damgaard, Alissa Mittnik, Azadeh F. Mohaseb, Hossein Davoudi, Saleh Alquraishi, Ahmed H. Alfarhan, Khaled A. S. Al-Rasheid, Eric Crubézy, Norbert Benecke, Sandra Olsen, Dorcas Brown, David Anthony, Ken Massy, Vladimir Pitulko, Aleksei Kasparov … & Ludovic Orlando
The Eneolithic Botai culture of the Central Asian steppes provides the earliest archaeological evidence for horse husbandry, ~5500 years ago, but the exact nature of early horse domestication remains controversial. We generated 42 ancient-horse genomes, including 20 from Botai. Compared to 46 published ancient- and modern-horse genomes, our data indicate that Przewalski’s horses are the feral descendants of horses herded at Botai and not truly wild horses. All domestic horses dated from ~4000 years ago...

Data from: Multi-proxy evidence highlights a complex evolutionary legacy of maize in South America

Logan Kistler, S. Yoshi Maezumi, Jonas Gregorio De Souza, Natalia A. S. Przelomska, Flaviane Malaquias Costa, Oliver Smith, Hope Loiselle, Jazmín Ramos-Madrigal, Nathan Wales, Eduardo Rivail Ribeiro, Ryan R. Morrison, Claudia Grimaldo, Andre P. Prous, Bernardo Arriaza, M. Thomas P. Gilbert, Fabio De Oliveira Freitas & Robin G. Allaby
Domesticated maize evolved from wild teosinte under human influences in Mexico beginning around 9,000 BP, traversed Central America by ~7,500 BP, and spread into South America by ~6,500 BP. Landrace and archaeological maize genomes from South America suggest that the ancestral population to South American maize was brought out of the domestication center in Mexico and became isolated from the wild teosinte gene pool before traits of domesticated maize were fixed. Deeply structured lineages then...

Data from: Time-calibrated molecular phylogeny of pteropods

Alice K. Burridge, Christine Hörnlein, Arie W. Janssen, Martin Hughes, Stephanie L. Bush, Ferdinand Marlétaz, Rebeca Gasca, Annelies C. Pierrot-Bults, Ellinor Michel, Jonathan A. Todd, Jeremy R. Young, Karen J. Osborn, Steph B.J. Menken, Katja T.C.A. Peijnenburg, Katja T. C. A. Peijnenburg & Steph B. J. Menken
Pteropods are a widespread group of holoplanktonic gastropod molluscs and are uniquely suitable for study of long-term evolutionary processes in the open ocean because they are the only living metazoan plankton with a good fossil record. Pteropods have been proposed as bioindicators to monitor the impacts of ocean acidification and in consequence have attracted considerable research interest, however, a robust evolutionary framework for the group is still lacking. Here we reconstruct their phylogenetic relationships and...

Data from: Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA

Eva Egelyng Sigsgaard, Ida Broman Nielsen, Steffen Sanvig Bach, Eline D. Lorenzen, David Philip Robinson, Steen Wilhelm Knudsen, Mikkel Winther Pedersen, Mohammed Al Jaidah, Ludovic Orlando, Eske Willerslev, Peter Rask Møller & Philip Francis Thomsen
Population genetics is essential for understanding and managing marine ecosystems, but sampling remains challenging. We demonstrate that high-throughput sequencing of seawater environmental DNA can provide useful estimates of genetic diversity in a whale shark (Rhincodon typus) aggregation. We recover similar mitochondrial haplotype frequencies in seawater compared to tissue samples, reliably placing the studied aggregation in a global genetic context and expanding the applications of environmental DNA to encompass population genetics of aquatic organisms.

Data from: Identification of transcription factor genes involved in anthocyanin biosynthesis in carrot (Daucus carota L.) using RNA-Seq

Miyako Kodama, Henrik Brinch-Pedersen, Shrikant Sharma, Inger Bæksted Holme, Bjarne Joernsgaard, Tsaneta Dzhanfezova, Daniel Buchvaldt Amby, Filipe Garrett Vieira, Shanlin Liu & M. Thomas P. Gilbert
Background Anthocyanins are water-soluble colored flavonoids present in multiple organs of various plant species including flowers, fruits, leaves, stems and roots. DNA-binding R2R3-MYB transcription factors, basic helix–loop–helix (bHLH) transcription factors, and WD40 repeat proteins are known to form MYB-bHLH-WD repeat (MBW) complexes, which activates the transcription of structural genes in the anthocyanin pathway. Although black cultivars of carrots (Daucus carota L.) can accumulate large quantities of anthocyanin in their storage roots, the regulatory genes responsible...

Data from: Arthropod diversity in a tropical forest

Yves Basset, Lukas Cizek, Philippe Cuénoud, Raphael K. Didham, François Guilhaumon, Olivier Missa, Vojtech Novotny, Frode Ødegaard, Tomas Roslin, Jürgen Schmidl, Alexey K. Tishechkin, Neville N. Winchester, David W. Roubik, Henri-Pierre Aberlenc, Johannes Bail, Héctor Barrios, Jon R. Bridle, Gabriela Castaño-Meneses, Bruno Corbara, Gianfranco Curletti, Wesley Duarte Da Rocha, Domir De Bakker, Jacques H. C. Delabie, Alain Dejean, Laura L. Fagan … & Maurice Leponce
Most eukaryotic organisms are arthropods. Yet, their diversity in rich terrestrial ecosystems is still unknown. Here we produce tangible estimates of the total species richness of arthropods in a tropical rainforest. Using a comprehensive range of structured protocols, we sampled the phylogenetic breadth of arthropod taxa from the soil to the forest canopy in the San Lorenzo forest, Panama. We collected 6,144 arthropod species from 0.48 ha and extrapolated total species richness to larger areas...

Data from: Gene flow and population structure of a common agricultural wild species (Microtus agrestis) under different land management regimes

Chiara Marchi, Liselotte W. Andersen, Christian Damgaard, Kent Olsen, Thomas S. Jensen & Volker Loeschcke
The impact of landscape structure and land management on dispersal of populations of wild species inhabiting the agricultural landscape was investigated focusing on the field vole (Microtus agrestis) in three different areas in Denmark using molecular genetic markers. The main hypotheses were the following: (i) organic farms act as genetic sources and diversity reservoirs for species living in agricultural areas and (ii) gene flow and genetic structure in the agricultural landscape are influenced by the...

Data from: Is diagnosability an indicator of speciation? Response to ‘Why one century of phenetics is enough’

Rasmus Heller, Peter Frandsen, Eline Dierdre Lorenzen, Hans R. Siegismund & Eline Deirdre Lorenzen
Recently (Heller et al. 2013; H&A), we commented on a revision of the bovid taxonomy, which proposes a doubling in the number of recognized species (Groves and Grubb 2011; G&G). The subsequent response by Cotterill et al. (2014; C&A) contains a number of misunderstandings and leaves much of the critique voiced in our paper unanswered, focusing instead on species ontologies and taxonomic history. C&A argue strongly against phenetics, morphospecies and taxonomic conservatism, ascribing us views...

Online Supplementary Data: Deep-time biodiversity patterns and the dinosaurian fossil record of the Late Cretaceous Western Interior, USA

Susannah Maidment
In order for palaeontological data to be informative to ecologists seeking to understand the causes of today’s diversity patterns, palaeontologists must demonstrate that actual biodiversity patterns are preserved in our reconstructions of past ecosystems. During the Late Cretaceous, North America was divided into two landmasses, Laramidia and Appalachia. Previous work has suggested strong faunal provinciality on Laramidia at this time, but these arguments are almost entirely qualitative. We quantitatively investigated faunal provinciality in ceratopsid and...

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