14 Works

Data from: A reliable DNA barcode reference library for the identification of the European shelf fish fauna

Thomas Knebelsberger, Gary R. Carvalho, Silke Laakmann, Michael J. Raupach, Hermann Neumann, Patrick D. Campbell, Monica Landi & Filipe O. Costa
Valid fish species identification is an essential step both for fundamental science and fisheries management. The traditional identification is mainly based on external morphological diagnostic characters, leading to inconsistent results in many cases. Here, we provide a sequence reference library based on mitochondrial cytochrome c oxidase subunit I (COI) for a valid identification of 93 North Atlantic fish species originating from the North Sea and adjacent waters, including many commercially exploited species. Neighbour-joining analysis based...

Data from: Phylogenomics resolves the timing and pattern of insect evolution

Bernhard Misof, Shanlin Liu, Karen Meusemann, Ralph S. Peters, Alexander Donath, Christoph Mayer, Paul B. Frandsen, Jessica Ware, Tomas Flouri, Rolf G. Beutel, Oliver Niehuis, Malte Petersen, Fernando Izquierdo-Carrasco, Torsten Wappler, Jes Rust, Andre J. Aberer, Ulrike Aspöck, Horst Aspöck, Daniela Bartel, Alexander Blanke, Simon Berger, Alexander Böhm, Thomas Buckley, Brett Calcott, Junqing Chen … & Xin Zhou
Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight...

Data from: Benefits and costs of ecological restoration: rapid assessment of changing ecosystem service values at a UK wetland

Francine M. R. Hughes, Kelvin S. H. Peh, Andrew Balmford, Rob H. Field, Anthony Lamb, Jennifer C. Birch, Richard B. Bradbury, Claire Brown, Stuart H. M. Butchart, Martin Lester, Ross Morrison, Isabel Sedgwick, Chris Soans, Alison J. Stattersfield, Peter A. Stroh, Ruth D. Swetnam, David H. L. Thomas, Matt Walpole, Stuart Warrington & Kelvin S.-H. Peh
Restoration of degraded land is recognized by the international community as an important way of enhancing both biodiversity and ecosystem services, but more information is needed about its costs and benefits. In Cambridgeshire, U.K., a long-term initiative to convert drained, intensively farmed arable land to a wetland habitat mosaic is driven by a desire both to prevent biodiversity loss from the nationally important Wicken Fen National Nature Reserve (Wicken Fen NNR) and to increase the...

Data from: Discovery of an unknown diversity of Leucinodes species damaging Solanaceae fruits in sub-Saharan Africa and moving in trade (Insecta, Lepidoptera, Pyraloidea)

Richard Mally, Anastasia Korycinska, David J. L. Agassiz, Jayne Hall, Jennifer Hodgetts & Matthias Nuss
The larvae of the Old World genera Leucinodes Guenée, 1854 and Sceliodes Guenée, 1854 are internal feeders in the fruits of Solanaceae, causing economic damage to cultivated plants like Solanum melongena and S. aethiopicum. In sub-Saharan Africa five nominal species of Leucinodes and one of Sceliodes occur. One of these species, the eggplant fruit and shoot borer L. orbonalis Guenée, 1854, is regarded as regularly intercepted from Africa and Asia in Europe, North and South...

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: 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: 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: Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions

Peter G. Foster, Martin Embley, Peter Civáň, Cymon J. Cox, Blaise Li & T. Martin Embley
Plants are the primary producers of the terrestrial ecosystems that dominate much of the natural environment. Occurring approximately 480 MYA (Sanderson 2003; Kenrick et. al. 2012), the evolutionary transition of plants from an aquatic to a terrestrial environment was accompanied by several major developmental innovations. The freshwater charophyte ancestors of land plants have a haplobiontic life cycle with a single haploid multicellular stage, whereas land plants, which include the bryophytes (liverworts, hornworts, and mosses) and...

Data from: A palaeoequatorial Ornithischian and new constraints on early dinosaur diversification

Paul M. Barrett, Richard J. Butler, Roland Mundil, Torsten M. Scheyer, Randall B. Irmis, Marcelo R. Sánchez-Villagra & M. R. Sanchez-Villagra
Current characterizations of early dinosaur evolution are incomplete: existing palaeobiological and phylogenetic scenarios are based on a fossil record dominated by saurischians and the implications of the early ornithischian record are often overlooked. Moreover, the timings of deep phylogenetic divergences within Dinosauria are poorly constrained owing to the absence of a rigorous chronostratigraphical framework for key Late Triassic–Early Jurassic localities. A new dinosaur from the earliest Jurassic of the Venezuelan Andes is the first basal...

Data from: The monophyly of Euparkeriidae (Reptilia: Archosauriformes) and the origins of Archosauria: a revision of Dorosuchus neoetus from the Mid-Triassic of Russia

Roland B. Sookias, Andrey G. Sennikov, David J. Gower & Richard J. Butler
Euparkeria capensis is resolved as the sister taxon to crown Archosauria in many cladistic phylogenies and provides a key outgroup which may approximate the ancestral archosaur morphology. Several other taxa have been referred to the family Euparkeriidae, but the monophyly of this taxon remains doubtful and largely untested. In order to test this monophyly, the archosauriform and putative euparkeriid Dorosuchus neoetus from the Mid-Triassic of Russia is reexamined in light of recent work on the...

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: The evolution of scarab beetles tracks the consecutive rise of angiosperms and mammals

Dirk Ahrens, Julia Schwarzer & Alfried P. Vogler
Extant terrestrial biodiversity arguably is driven by the evolutionary success of angiosperm plants, but the evolutionary mechanisms and timescales of angiosperm-dependent radiations remain poorly understood. The Scarabaeoidea is a diverse lineage of predominantly plant- and dung-feeding beetles. Here, we present a phylogenetic analysis of Scarabaeoidea based on four DNA markers for a taxonomically comprehensive set of specimens and link it to recently described fossil evidence. The phylogeny strongly supports multiple origins of coprophagy, phytophagy and...

Data from: Cranial biomechanics underpins high sauropod diversity in resource-poor environments

David J. Button, Emily J. Rayfield & Paul M. Barrett
High megaherbivore species richness is documented in both fossil and contemporary ecosystems despite their high individual energy requirements. An extreme example of this is the Late Jurassic Morrison Formation, which was dominated by sauropod dinosaurs, the largest known terrestrial vertebrates. High sauropod diversity within the resource-limited Morrison is paradoxical, but might be explicable through sophisticated resource partitioning. This hypothesis was tested through finite-element analysis of the crania of the Morrison taxa Camarasaurus andDiplodocus. Results demonstrate...

Data from: Disentangling the Pelomedusa complex using type specimens and historical DNA (Testudines: Pelomedusidae)

Uwe Fritz, Alice Petzold, Christian Kehlmaier, Carolin Kindler, Patrick Campbell, Margaretha D. Hofmeyr & William R. Branch
Recent research has shown that the helmeted terrapin (Pelomedusa subrufa), a species that occurs throughout sub-Saharan Africa, in Madagascar and the southwestern Arabian Peninsula, consists of several deeply divergent genetic lineages. Here we examine all nominal taxa currently synonymized with Pelomedusa subrufa (Bonnaterre, 1789) and provide mitochondrial DNA sequences of type specimens or topotypic material for most taxa. Lectotypes are designated for Testudo galeata Schoepff, 1792, Pentonyx capensis Duméril & Bibron, 1835, Pelomedusa nigra Gray,...

Registration Year

  • 2014
    14

Resource Types

  • Dataset
    14

Affiliations

  • Natural History Museum
    14
  • University of Birmingham
    2
  • Anglia Ruskin University
    1
  • Staffordshire University
    1
  • University of Hamburg
    1
  • University of the Western Cape
    1
  • Field Museum of Natural History
    1
  • Centre for Ecology and Hydrology
    1
  • Zoological Research Museum Alexander Koenig
    1
  • Johns Hopkins University
    1