64 Works

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: 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...

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...

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...

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...

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...

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...

Accumulation of airborne, eukaryotic environmental DNA contamination: Raw sequencing data and demultiplexing info

Martin Klepke, Eva Sigsgaard, Mads Jensen, Kent Olsen & Philip Thomsen
Environmental DNA (eDNA) metabarcoding is increasingly being implemented as a non-invasive and efficient approach for biodiversity research and monitoring across ecosystems. However, accurate detection of species with eDNA requires robust experimental designs, as eDNA analysis carries a risk of contamination at every step of the fieldwork and laboratory process. Several studies focus on rigorous laboratory procedures and processing of sequencing data, but surprisingly little research investigates the process of background input of DNA in the...

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: 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: 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...

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: 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...

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...

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...

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: 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: Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA

Sanne Boessenkool, Laura S. Epp, James Haile, Eva Bellemain, Mary Edwards, Eric Coissac, Eske Willerslev & Christian Brochmann
Analyses of degraded DNA are typically hampered by contamination, especially when employing universal primers such as commonly used in environmental DNA studies. In addition to false-positive results, the amplification of contaminant DNA may cause false-negative results due to competition, or bias, during the PCR. In this study, we test the utility of human-specific blocking primers in mammal diversity analyses of ancient permafrost samples from Siberia. Using quantitative PCR (qPCR) on human and mammoth DNA we...

Data from: Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA meta-barcoding

Tina Jørgensen, Kurt H Kjær, James Haile, Morten Rasmussen, Sanne Boessenkool, Kenneth Andersen, Eric Coissac, Pierre Taberlet, Christian Brochmann, Ludovic Orlando, M. Thomas P. Gilbert & Eske Willerslev
Nunataks are isolated bedrocks protruding through ice sheets. They vary in age, but represent island environments in “oceans” of ice through which organism dispersals and replacements can be studied over time. The J.A.D. Jensen’s Nunataks at the southern Greenland ice sheet are the most isolated nunataks on the northern hemisphere - some 30 km from the nearest biological source. They constitute around 2 km2 of ice-free land that was established in the early Holocene. We...

Data from: A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability

Tina Jørgensen, James Haile, Per Möller, Andrei Andreev, Sanne Boessenkool, Morten Rasmussen, Frank Kienast, Eric Coissac, Pierre Taberlet, Christian Brochmann, Nancy H. Bigelow, Kenneth Andersen, Ludovic Orlando, M. Thomas P. Gilbert & Eske Willerslev
Although ancient DNA from sediments (sedaDNA) has been used to investigate past ecosystems, the approach has never been directly compared to the traditional methods of pollen and macrofossil analysis. We conducted a comparative survey of 18 ancient permafrost samples spanning the Late Pleistocene (46–12.5 thousand years ago), from the Taymyr Peninsula in northern Siberia. The results show that pollen, macrofossils and sedaDNA are complementary rather than overlapping, and in combination reveal more detailed information on...

Data from: Spatial heterogeneity in the Mediterranean Biodiversity Hotspot affects barcoding accuracy of its freshwater fishes

Matthias F. Geiger, Fabian Herder, Michael T. Monaghan, Vitor Almada, Roberta Barbieri, Michel Bariche, Patrick Berrebi, Jörg Bohlen, Miriam Casal-Lopez, Gaël P. J. Denys, Agnès Dettai, Ignacio Doadrio, Elena Kalogianni, Heiko Kärst, Maurice Kottelat, Marcelo Kovačić, Martin Laporte, Massimo Lorenzoni, Zoran Marčić, Müfit Özuluğ, Anabel Perdices, Silvia Perea, Henri Persat, Stefano Porcellotti, Cesare Puzzi … & G. B. Delmastro
Incomplete knowledge of biodiversity remains a stumbling block for conservation planning, and even occurs within globally important Biodiversity Hotspots. Although technical advances have boosted the power of molecular biodiversity assessments, the link between DNA sequences and species and the analytics to discriminate entities, remain crucial. Here, we present an analysis of the first DNA barcode library for the freshwater fish fauna of the Mediterranean Biodiversity Hotspot (526 spp.), with virtually complete species coverage (498 spp.,...

Data from: New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems

Laura S. Epp, Sanne Boessenkool, Eva P. Bellemain, James Haile, Alfonso Esposito, Tiayyba Riaz, Christer Erséus, Vladimir I. Gusarov, Mary E. Edwards, Arild Johnsen, Hans K. Stenøien, Kristian Hassel, Håvard Kauserud, Nigel G. Yoccoz, Kari Anne Bråthen, Eske Willerslev, Pierre Taberlet, Eric Coissac & Christian Brochmann
Metabarcoding approaches use total and typically degraded DNA from environmental samples to analyse biotic assemblages and can potentially be carried out for any kinds of organisms in an ecosystem. These analyses rely on specific markers, here called metabarcodes, which should be optimized for taxonomic resolution, minimal bias in amplification of the target organism group and short sequence length. Using bioinformatic tools, we developed metabarcodes for several groups of organisms: fungi, bryophytes, enchytraeids, beetles and birds....

Data from: A new dimension in documenting new species: high-detail imaging for myriapod taxonomy and first 3D cybertype of a new millipede species (Diplopoda, Julida, Julidae)

Nesrine Akkari, Henrik Enghoff & Brian D. Metscher
We review the state-of-the-art approaches currently applied in myriapod taxonomy, and we describe, for the first time, a new species of millipede (Ommatoiulus avatar n. sp., family Julidae) using high-resolution X-ray microtomography (microCT) as a substantive adjunct to traditional morphological examination. We present 3D models of the holotype and paratype specimens and discuss the potential of this non-destructive technique in documenting new species of millipedes and other organisms. The microCT data have been uploaded to...

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  • Natural History Museum
  • University of Copenhagen
  • University of Oslo
  • French National Centre for Scientific Research
  • Aarhus University
  • University College London
  • University of Zagreb
  • University of Kansas
  • National Museum of Natural History
  • University of Hamburg