139 Works

Data from: Molecular palaeontology illuminates the evolution of ecdysozoan vision

James F. Fleming, Reinhardt M. Kristensen, Martin V. Sørensen, Tae-Yoon S. Park, Kazuharu Arakawa, Mark Blaxter, Lorena Rebecchi, Roberto Guidetti, Tom A. Williams, Nicholas W. Roberts, Jakob Vinther & Davide Pisani
Colour vision is known to have arisen only twice – once in Vertebrata and once within the Ecdysozoa, in Arthropoda. However, the evolutionary history of ecdysozoan vision is unclear. At the molecular level, visual pigments, composed of a chromophore and a protein belonging to the opsin family, have different spectral sensitivities and these mediate colour vision. At the morphological level, ecdysozoan vision is conveyed by eyes of variable levels of complexity; from the simple ocelli...

Data from: Persistence, impacts and environmental drivers of covert infections in invertebrate hosts

Inês Fontes, Hanna Hartikainen, Chris Williams & Beth Okamura
Background: Persistent covert infections of the myxozoan, Tetracapsuloides bryosalmonae, in primary invertebrate hosts (the freshwater bryozoan, Fredericella sultana) have been proposed to represent a reservoir for proliferative kidney disease in secondary fish hosts. However, we have limited understanding of how covert infections persist and vary in bryozoan populations over time and space and how they may impact these populations. In addition, previous studies have likely underestimated covert infection prevalence. To improve our understanding of the...

Data from: Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics

Debora P. Paula, Benjamin Linard, David A. Andow, Edison R. Sujii, Carmen S. S. Pires & Alfried P. Vogler
DNA methods are useful to identify ingested prey items from the gut of predators, but reliable detection is hampered by low amounts of degraded DNA. PCR-based methods can retrieve minute amounts of starting material but suffer from amplification biases and cross-reactions with the predator and related species genomes. Here, we use PCR-free direct shotgun sequencing of total DNA isolated from the gut of the harlequin ladybird Harmonia axyridis at five time points after feeding on...

Data from: Lessons from genome skimming of arthropod-preserving ethanol

Benjamin Linard, Paula Arribas, Carmelo Andújar, Alex Crampton-Platt & Alfried P. Vogler
Field-collected specimens of invertebrates are regularly killed and preserved in ethanol, prior to DNA extraction from the specimens, while the ethanol fraction is usually discarded. However, DNA may be released from the specimens into the ethanol, which can potentially be exploited to study species diversity in the sample without the need for DNA extraction from tissue. We used shallow shotgun sequencing of the total DNA to characterize the preservative ethanol from two pools of insects...

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: Lake sediment multi-taxon DNA from North Greenland records early post-glacial appearance of vascular plants and accurately tracks environmental changes

Laura S. Epp, Galina Gussarova, Sanne Boessenkool, Jesper Olsen, James Haile, Audun Schrøder-Nielsen, Anna Ludikova, Kristian Hassel, Hans K. Stenøien, Svend V. Funder, Eske Willerslev, Kurt Kjær & Christian Brochmann
High Arctic environments are particularly sensitive to climate changes, but retrieval of paleoecological data is challenging due to low productivity and biomass. At the same time, Arctic soils and sediments have proven exceptional for long-term DNA preservation due to their constantly low temperatures. Lake sediments contain DNA paleorecords of the surrounding ecosystems and can be used to retrieve a variety of organismal groups from a single sample. In this study, we analyzed vascular plant, bryophyte,...

Data from: Metabarcoding and mitochondrial metagenomics of endogean arthropods to unveil the mesofauna of the soil

Paula Arribas, Carmelo Andújar, Kevin Hopkins, Matthew Shepherd & Alfried P. Vogler
Biological communities inhabiting the soil are among the most diversified, complex and yet most poorly studied terrestrial ecosystems. The greatest knowledge gaps apply to the arthropod mesofauna (0·1–2 mm body size) because conventional morphological and molecular approaches are in many cases insufficient for the characterisation of these complex communities. The development of high-throughput sequencing (HTS) methodologies is required to solve current impediments and to further advance our understanding of below-ground biodiversity. We propose a flotation–Berlese–flotation...

Data from: Time for a rethink: time sub-sampling methods in disparity-through-time analyses

Thomas Guillerme & Natalie Cooper
Disparity-through-time analyses can be used to determine how morphological diversity changes in response to mass extinctions, and to investigate the drivers of morphological change. These analyses are routinely applied to palaeobiological datasets, yet although there is much discussion about how to best calculate disparity, there has been little consideration of how taxa should be sub-sampled through time. Standard practice is to group taxa into discrete time bins, often based on stratigraphic periods. However, this can...

Data from: Phylogeny of Anophelinae using mitochondrial protein coding genes

Peter G. Foster, Tatiane M.P. De Oliveira, Eduardo S. Bergo, Jan E. Conn, Denise C. Sant'Ana, Sandra S. Nagaki, Silvio Nihei, Carlos E. Lamas, Christian González, Caio C. Moreira & Maria-Anice M. Sallum
Malaria is a vector-borne disease that is a great burden on the poorest and most marginalized communities of the tropical and subtropical world. About 41 species of Anopheline mosquitoes can effectively spread species of Plasmodium parasites that cause human malaria. Proposing a natural classification for the subfamily Anophelinae has been a continuous effort, addressed using both morphology and DNA sequence data. Monophyly of the genus Anopheles, and phylogenetic placement of the genus Bironella, subgenera Kerteszia,...

Data from: Body mass estimates of an exceptionally complete Stegosaurus (Ornithischia: Thyreophora): comparing volumetric and linear bivariate mass estimation methods

Charlotte A. Brassey, Susannah Maidment, Paul Barrett & P. M. Barrett
Body mass is a key biological variable, but difficult to assess from fossils. Various techniques exist for estimating body mass from skeletal parameters, but few studies have compared outputs from different methods. Here, we apply several mass estimation methods to an exceptionally complete skeleton of the dinosaur Stegosaurus. Applying a volumetric convex-hulling technique to a digital model of Stegosaurus, we estimate a mass of 1560 kg (95% prediction interval 1082–2256 kg) for this individual. By...

Data from: A phylogenetic backbone for Bivalvia: an RNA-seq approach

Vanessa L. González, Sónia C. S. Andrade, Rüdiger Bieler, Timothy M. Collins, Casey W. Dunn, Paula M. Mikkelsen, John D. Taylor, Gonzalo Giribet & V. L. Gonzalez
Bivalves are an ancient and ubiquitous group of aquatic invertebrates with an estimated 10 000–20 000 living species. They are economically significant as a human food source, and ecologically important given their biomass and effects on communities. Their phylogenetic relationships have been studied for decades, and their unparalleled fossil record extends from the Cambrian to the Recent. Nevertheless, a robustly supported phylogeny of the deepest nodes, needed to fully exploit the bivalves as a model...

Data from: Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill

Carmelo Andujar, Paula Arribas, Clare Gray, Katherine Bruce, Guy Woodward, Douglas W. Yu & Alfried P. Vogler
Biomonitoring underpins the environmental assessment of freshwater ecosystems and guides management and conservation. Current methodology for surveys of (macro)invertebrates uses coarse taxonomic identification where species-level resolution is difficult to obtain. Next-generation sequencing of entire assemblages (metabarcoding) provides a new approach for species detection, but requires further validation. We used metabarcoding of invertebrate assemblages with two fragments of the cox1 "barcode" and partial nuclear ribosomal (SSU) genes, to assess the effects of a pesticide spill in...

Data from: Microbial-tubeworm associations in a 440 million year old hydrothermal vent community

Magdalena N. Georgieva, Crispin T.S. Little, Russell J. Bailey, Alexander D. Ball, Adrian G. Glover & Crispin T. S. Little
Microorganisms are the chief primary producers within present-day deep-sea hydrothermal vent ecosystems, and play a fundamental role in shaping the ecology of these environments. However, very little is known about the microbes that occurred within, and structured ancient vent communities. The evolutionary history, diversity, and the nature of interactions between ancient vent microorganisms and hydrothermal vent animals are largely undetermined. The oldest known hydrothermal vent community that includes metazoans is preserved within the Ordovician-early Silurian...

Data from: Trilobite evolutionary rates constrain the duration of the Cambrian explosion

John R. Paterson, Gregory D. Edgecombe & Michael S. Y. Lee
Trilobites are often considered exemplary for understanding the Cambrian explosion of animal life, due to their unsurpassed diversity and abundance. These biomineralized arthropods appear abruptly in the fossil record with an established diversity, phylogenetic disparity, and provincialism at the beginning of Cambrian Series 2 (~521 Ma), suggesting a protracted but cryptic earlier history that possibly extends into the Precambrian. However, recent analyses indicate elevated rates of phenotypic and genomic evolution for arthropods during the early...

Data from: Phylogeny, palaeontology, and primates: do incomplete fossils bias the tree of life?

David J. Pattinson, Richard S. Thompson, Aleks K. Piotrowski & Robert J. Asher
Paleontological systematics relies heavily on morphological data that have undergone decay and fossilization. Here, we apply a heuristic means to assess how a fossil's incompleteness detracts from inferring its phylogenetic relationships. We compiled a phylogenetic matrix for primates and simulated the extinction of living species by deleting an extant taxon's molecular data and keeping only those morphological characters present in actual fossils. The choice of characters present in a given living taxon (the subject) was...

Data from: Speciation below ground: tempo and mode of diversification in a radiation of endogean ground beetles

Carmelo Andújar, Sergio Pérez-González, Paula Arribas, Juan P. Zaballos, Alfried P. Vogler & Ignacio Ribera
Dispersal is a critical factor determining the spatial scale of speciation, which is constrained by the ecological characteristics and distribution of a species' habitat and the intrinsic traits of species. Endogean taxa are strongly affected by the unique qualities of the below-ground environment and its effect on dispersal, and contrasting reports indicate either high dispersal capabilities favoured by small body size and mediated by passive mechanisms, or low dispersal due to restricted movement and confinement...

Eye size and investment in frogs and toads correlate with adult habitat, activity pattern and breeding ecology

Kate N. Thomas, David J. Gower, Rayna C. Bell, Matthew K. Fujita, Ryan K. Schott & Jeffrey W. Streicher
Frogs and toads (Amphibia: Anura) display diverse ecologies and behaviours, which are often correlated with visual capacity in other vertebrates. Additionally, anurans exhibit a broad range of relative eye sizes, which have not previously been linked to ecological factors in this group. We measured relative investment in eye size and corneal size for 220 species of anurans representing all 55 currently recognized families and tested whether they were correlated with six natural history traits hypothesized...

Data from: Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

Jenni Harmoinen, Alina Von Thaden, Jouni Aspi, Laura Kvist, Berardino Cocchiararo, Anne Jarausch, Andrea Gazzola, Teodora Sin, Hannes Lohi, Marjo Hytönen, Ilpo Kojola, Astrid Vik Stronen, Romolo Caniglia, Federica Mattucci, Marco Galaverni, Raquel Godinho, Aritz Ruiz-González, Ettore Randi, Violeta Muñoz-Fuentes & Carsten Nowak
Background: Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due to the low number of markers showing distinctive allele frequencies between wolves and dogs. Moreover, calibration across laboratories is time-consuming and costly. In this study, we selected...

Data from: Hurricane effects on Neotropical lizards span geographic and phylogenetic scales

Colin Donihue, Alex Kowaleski, Jonathan Losos, Adam Algar, Simon Baeckens, Robert Buchkowski, Anne-Claire Fabre, Hannah Frank, Anthony Geneva, Graham Reynolds, James Stroud, Julián Velasco, Jason Kolbe, Luke Mahler & Anthony Herrel
Extreme climate events such as droughts, cold snaps, and hurricanes can be powerful agents of natural selection, producing acute selective pressures very different from the everyday pressures acting on organisms. However, it remains unknown whether these infrequent but severe disruptions are quickly erased by quotidian selective forces, or whether they have the potential to durably shape biodiversity patterns across regions and clades. Here, we show that hurricanes have enduring evolutionary impacts on the morphology of...

Termite abundance and ecosystem processes in Maliau Basin, 2015-2016

L.A. Ashton, H.M. Griffiths, C.L. Parr, T.A. Evans & P. Eggleton
This dataset consists of invertebrate abundance data and associated ecosystem measurements (Including leaf litter depth and mass, seedlings, soil moisture and nutrients, and rainfall) measured within an area of lowland, old growth dipterocarp rainforest in the Maliau Basin Conservation Area, Sabah, Malaysia between 2015 and 2016. Data were collected during a collaborative project which was included in the NERC Human-modified tropical forest (HMTF) programme.

Data from: The phylogenetic conundrum of Lutzia (Diptera: Culicidae: Culicini): a cautionary account of conflict and support

Ian J. Kitching, C. Lorna Culverwell & Ralph E. Harbach
Lutzia Theobald was reduced to a subgenus of Culex in 1932 and was treated as such until it was restored to its original generic status in 2003, based mainly on modifications of the larvae for predation. Previous phylogenetic studies based on morphological and molecular data have provided conflicting support for the generic status of Lutzia: analyses of morphological data support the generic status whereas analyses based on DNA sequences do not. Our previous phylogenetic analyses...

Data from: Australian spiny mountain crayfish and their temnocephalan ectosymbionts: an ancient association on the edge of coextinction?

Jennifer F. Hoyal Cuthill, Kim B. Sewell, Lester R. G. Cannon, Michael A. Charleston, Susan Lawler, D. Timothy J. Littlewood, Peter D. Olson & David Blair
Australian spiny mountain crayfish (Euastacus, Parastacidae) and their ecotosymbiotic temnocephalan flatworms (Temnocephalida, Platyhelminthes) may have co-occurred and interacted through deep time, during a period of major environmental change. Therefore, reconstructing the history of their association is of evolutionary, ecological, and conservation significance. Here, time-calibrated Bayesian phylogenies of Euastacus species and their temnocephalans (Temnohaswellia and Temnosewellia) indicate near-synchronous diversifications from the Cretaceous. Statistically significant cophylogeny correlations between associated clades suggest linked evolutionary histories. However, there is...

Data from: Morphometric discrimination of two allozymically diagnosed sibling species of the Echinorhynchus gadi Zoega in Muller complex (Acanthocephala) in the North Sea.

Matthew T. Wayland, David I. Gibson & Christina Sommerville
Allozyme electrophoresis was used to detect biological species of the E. gadi complex from gadids from the northern North Sea. A fixed difference at one of nine enzyme loci surveyed confirmed the existence of two reproductively isolated, sympatric species. Mixed infections of two E. gadi spp. (termed A and B) were observed in Gadus morhua and Pollachius virens. E. gadi sp. B was also found in Melanogrammus aeglefinus and Merlangius merlangus. The presence of gravid...

Data from: Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the Mesozoic Marine Revolution

Alastair R. Tanner, Dirk Fuchs, Inger E. Winkelmann, Thomas P. Gilbert, M. Sabrina Pankey, Angela M. Ribeiro, Kevin M. Kocot, Kenneth M. Halanych, Todd H. Oakley, Rute R. Da Fonseca, Davide Pisani, Jakob Vinther & M. Thomas P. Gilbert
Coleoid cephalopod molluscs comprise squid, cuttlefish and octopuses, and represent nearly the entire diversity of modern cephalopods. Sophisticated adaptations such as the use of colour for camouflage and communication, jet propulsion and the ink sac highlight the unique nature of the group. Despite these striking adaptations, there are clear parallels in ecology between coleoids and bony fishes. The coleoid fossil record is limited, however, hindering confident analysis of the tempo and pattern of their evolution....

Data from: Computer simulations show that Neanderthal facial morphology represents adaptation to cold and high energy demands, but not heavy biting

Stephen Wroe, William C.H. Parr, Justin A. Ledogar, Jason Bourke, Samuel P. Evans, Luca Fiorenza, Stefano Benazzi, Jean-Jacques Hublin, Chris Stringer, Ottmar Kullmer, Michael Curry, Todd C. Rae, Todd R. Yokley & William C. H. Parr
Three adaptive hypotheses have been forwarded to explain the distinctive Neanderthal face: 1) an improved ability to accommodate high anterior bite forces, 2) more effective conditioning of cold and/or dry air, and, 3) adaptation to facilitate greater ventilatory demands. We test these hypotheses using three-dimensional models of Neanderthals, modern humans, and a close outgroup (H. heidelbergensis), applying finite element analysis (FEA) and computational fluid dynamics (CFD). This is the most comprehensive application of either approach...

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  • Natural History Museum
  • Imperial College London
  • University College London
  • University of Oxford
  • University of Bristol
  • University of Cambridge
  • Royal Botanic Gardens
  • Field Museum of Natural History
  • University of Otago
  • University of Manchester