51 Works

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: 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: 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...

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...

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...

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: To remain or leave: dispersal variation and its genetic consequences in benthic freshwater invertebrates

Paolo Ruggeri, Ellen Pasternack & Beth Okamura
Variation in dispersal capacity may influence population genetic variation and relatedness of freshwater animals and hence provide insights on patterns and processes that influence biodiversity. The majority of studies addressing this issue have focused on dispersal variation in in fish inhabiting riverine systems whose dendritic nature and upstream/downstream gradients facilitate characterizing populations along networks. We undertook extensive, large-scale investigations of two freshwater bryozoans species whose dispersive propagules (statoblasts) are either attached to surfaces (Fredericella sultana)...

Early Silurian chondrichthyans from the Tarim Basin (Xinjiang, China)

Plamen Andreev, Wenjin Zhao, Nian-Zhong Wang, Moya Smith, Li Qiang, Xindong Cui, Min Zhu & Ivan Sansom
The Sinacanthida ordo nov. and Mongolepidida are spine- and scale-based taxa whose remains encompass some of the earliest reported fossils of chondrichthyan fish. Investigation of fragmentary material from the Early Silurian Tataertag and Ymogantau Formations of the Tarim Basin (Xinjiang Uygur Autonomous Region, China) has revealed a diverse mongolepidid and sinacanthid fauna dominated by mongolepids and sinacanthids in association with abundant dermoskeletal elements of the endemic ‘armoured’ agnathans known as galeaspids. Micro-computed tomography, scanning electron...

Data from: Phylogenetic response of naraoiid arthropods to early - middle Cambrian environmental change

Andrew Bond & Greg Edgecombe
The Cambrian Period, primarily known for animal life diversifying, experienced global extinctions. Pulses of extinction in Cambrian Series 2 are exemplified by the disappearance of archaeocyath sponges and olenelline and redlichiid trilobites. However, the effect of such extinctions on outer shelf organisms, as typify Burgess Shale-type (BST) deposits, remains relatively unknown. The phylogeny of naraoiid arthropods, represented in BST deposits globally, has consequently been reconstructed from either side of the Series 2–Miaolingian extinction event to...

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: 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...

Data from: A nonstationary Markov model detects directional evolution in hymenopteran morphology

Seraina Klopfstein, Lars Vilhelmsen & Fredrik Ronquist
Directional evolution has played an important role in shaping the morphological, ecological, and molecular diversity of life. However, standard substitution models assume stationarity of the evolutionary process over the time scale examined, thus impeding the study of directionality. Here we explore a simple, nonstationary model of evolution for discrete data, which assumes that the state frequencies at the root differ from the equilibrium frequencies of the homogeneous evolutionary process along the rest of the tree...

Data from: Identifying the most surprising victims of mass extinction events: an example using Late Ordovician brachiopods

Seth Finnegan, Christian M. Ø. Rasmussen & David A. T. Harper
Mass extinction events are recognized by increases in extinction rate and magnitude and, often, by changes in the selectivity of extinction. When considering the selective fingerprint of a particular event, not all taxon extinctions are equally informative: some would be expected even under a ‘background’ selectivity regime, whereas others would not and thus require special explanation. When evaluating possible drivers for the extinction event, the latter group is of particular interest. Here, we introduce a...

Data from: The genus Gennadas (Benthesicymidae: Decapoda): morphology of copulatory characters, phylogeny and coevolution of genital structures

Alexander L. Vereshchaka, Anastasia A. Lunina & Jørgen Olesen
Species within Gennadas differ from each other largely only in male (petasma) and female (thelycum) copulatory characters, which were restudied in scanning electron microscopy and used as a basis for phylogenetic analyses. Twenty-six petasma characters and 49 thelycum characters were identified. All sixteen recognized species of Gennadas and Aristaeomorpha foliacea (outgroup) were included as terminals. Four robust monophyletic clades were retrieved, described and diagnosed as new species groups. The thelycum characters had greater impact on...

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: 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: 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: 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: 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: 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: 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...

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...

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