156 Works

Data from: Molecular phylogenetics of Gobioidei and phylogenetic placement of European gobies

Ainhoa Agorreta, Diego San Mauro, Ulrich Schliewen, James L. Van Tassell, Marcelo Kovačić, Rafael Zardoya & Lukas Rüber
Gobioidei is one of the largest suborders of teleost fishes, with nearly 2000 extant species currently recognized. They have a worldwide distribution and show a spectacular variety in morphology, ecology, and behavior. Despite their importance, phylogenetic relationships among many groups of gobioids (including some of the major lineages) still remain poorly understood. In this study, we analyze sequence data of five molecular markers (two mitochondrial and three nuclear) averaging 6000 bp for 222 species of...

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: Experimental design in phylogenetics: testing predictions from expected information

Diego San Mauro, David J. Gower, James A. Cotton, Rafael Zardoya, Mark Wilkinson & Tim Massingham
Taxon and character sampling is central to phylogenetic experimental design yet we lack general rules. Goldman introduced a method to construct efficient sampling designs in phylogenetics, based on the calculation of expected Fisher information given a probabilistic model of sequence evolution. The considerable potential of this approach remains largely unexplored. In an earlier study, we applied Goldman’s method to a problem in the phylogenetics of caecilian amphibians and made an a priori evaluation and testable...

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: Phylogeny and new taxonomy of the Booted Eagles (Accipitriformes: Aquilinae)

Heather R. L. Lerner, Les Christidis, Anita Gamauf, Carole Griffiths, Elisabeth Haring, Christopher J. Huddleston, Sonia Kabra, Annett Kocum, Meade Krosby, Kirsti Kvaloy, David Mindell, Pamela Rasmussen, Nils Rov, Rachel Wadleigh, Michael Wink & Jan Ove Gjershaug
We present a phylogeny of all booted eagles (38 extant and one extinct species) based on analysis of published sequences from seven loci. We find molecular support for five major clades within the booted eagles: Nisaetus (10 species), Spizaetus (4 species), Clanga (3 species), Hieraaetus (6 species) and Aquila (11 species), requiring generic changes for 14 taxa. Additionally, we recommend that the Long-crested Eagle (Lophaetus occipitalis) and the Black Eagle (Ictinaetus malaiensis) remain in their...

Data from: Uncovering cryptic parasitoid diversity in Horismenus (Chalcidoidea, Eulophidae)

Sarah G. Kenyon, Sven Buerki, Christer Hansson, Nadir Alvarez & Betty Benrey
Horismenus parasitoids are an abundant and understudied group of eulophid wasps found mainly in the New World. Recent surveys based on morphological analyses in Costa Rica have quadrupled the number of named taxa, with more than 400 species described so far. This recent revision suggests that there is still a vast number of unknown species to be identified. As Horismenus wasps have been widely described as parasitoids of insect pests associated with crop plants, it...

Data from: Beyond neutral and forbidden links: morphological matches and the assembly of mutualistic hawkmoth-plant networks

Federico D. Sazatornil, Marcela Moré, Santiago Benitez-Vieyra, Andrea A. Cocucci, Ian J. Kitching, Boris O. Schlumpberger, Paulo E. Oliveira, Marlies Sazima & Felipe W. Amorim
A major challenge in evolutionary ecology is to understand how co-evolutionary processes shape patterns of interactions between species at community level. Pollination of flowers with long corolla tubes by long-tongued hawkmoths has been invoked as a showcase model of co-evolution. Recently, optimal foraging models have predicted that there might be a close association between mouthparts' length and the corolla depth of the visited flowers, thus favouring trait convergence and specialization at community level. Here, we...

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: 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: Implementing and testing Bayesian and Maximum likelihood supertree methods in phylogenetics

Wasiu A. Akanni, Mark Wilkinson, Peter G. Foster, Christopher J. Creevey & Davide Pisani
Since their advent, supertrees have been increasingly used in large-scale evolutionary studies requiring a phylogenetic framework and substantial efforts have been devoted to developing a wide variety of supertree methods (SMs). Recent advances in supertree theory have allowed the implementation of maximum likelihood (ML) and Bayesian SMs, based on using an exponential distribution to model incongruence between input trees and the supertree. Such approaches are expected to have advantages over commonly used non-parametric SMs, e.g....

Data from: Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages

Carola Gómez-Rodríguez, Alex Crampton-Platt, Martijn J. T. N. Timmermans, Andrés Baselga & Alfried P. Vogler
1. The biodiversity of mixed-species samples of arthropods can be characterized by shotgun sequencing of bulk genomic DNA and subsequent bioinformatics assembly of mitochondrial genomes. Here, we tested the power of mitochondrial metagenomics by conducting Illumina sequencing on mixtures of >2600 individuals of leaf beetles (Chrysomelidae) from 10 communities. 2. Patterns of species richness, community dissimilarity and biomass were assessed from matches of reads against three reference databases, including (i) a custom set of mitogenomes...

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: Transition in sexual system and sex chromosome evolution in the tadpole shrimp Triops cancriformis

Thomas C. Mathers, Robert L. Hammond, Ronald A. Jenner, Bernd Hänfling, Jennifer Atkins & Africa Gómez
Transitions in sexual system and reproductive mode may affect the course of sex chromosome evolution, for instance by altering the strength of sexually antagonistic selection. However, there have been few studies of sex chromosomes in systems where such transitions have been documented. The European tadpole shrimp, Triops cancriformis, has undergone a transition from dioecy to androdioecy (a sexual system where hermaphrodites and males coexist), offering an excellent opportunity to test the impact of this transition...

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: Global decline of bumblebees is phylogenetically structured and inversely related to species range size and pathogen incidence

Marina P. Arbetman, Gabriela Gleiser, Carolina L. Morales, Paul Williams & Marcelo A. Aizen
Conservation biology can profit greatly from incorporating a phylogenetic perspective into analyses of patterns and drivers of species extinction risk. We applied such an approach to analyse patterns of bumblebee (Bombus) decline. We assembled a database representing approximately 43% of the circa 260 globally known species, which included species extinction risk assessments following the International Union fo Conservation of Nature Red List categories and criteria, and information on species traits presumably associated with bumblebee decline....

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....

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: Size, weapons and armor as predictors of competitive outcomes in fossil and contemporary marine communities

Lee Hsiang Liow, Trond Reitan, Kjetil Voje, Paul Taylor & Emanuela Di Martino
Inter- and intraspecific competition are usually observed over a few generations but their patterns and consequences are seldom tractable in natural systems over longer timescales relevant to macroevolutionary change. Here, we use win-draw-lose competitive overgrowths for a marine benthic community of encrusting bryozoans that have evolved together in New Zealand for at least 2.3 million years to investigate battles for substrate space, a resource that is limiting for these colonial organisms. Using more than 6000...

Data from: Strong but taxon-specific responses of termites and wood-nesting ants to forest regeneration in Borneo

Annie Kimber & Paul Eggleton
Land use change is accelerating globally at the expense of biodiversity and ecosystem functioning. Invertebrates are numerically dominant and functionally important in old growth tropical rain forests but highly susceptible to the adverse effects of forest degradation and fragmentation. Ants (Formicidae) and termites (Blattodea: Termitoidae) perform crucial ecosystem services. Here, the potential effects of anthropogenic disturbance on ant and termite communities in dead wood are investigated. Community composition, generic richness, and occupancy rates of ants...

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...

Data from: The evolutionary history of dogs in the Americas

Máire Ní Leathlobhair, Angela R. Perri, Evan K. Irving-Pease, Kelsey E. Witt, Anna Linderholm, James Haile, Ophelie Lebrasseur, Carly Ameen, Jeffrey Blick, Adam R. Boyko, Selina Brace, Yahaira Nunes Cortes, Susan J. Crockford, Alison Devault, Evangelos A. Dimopoulos, Morley Eldridge, Jacob Enk, Shyam Gopalakrishnan, Kevin Gori, Vaughan Grimes, Eric Guiry, Anders J. Hansen, Ardern Hulme-Beaman, John Johnson, Andrew Kitchen … & Laurent A. F. Frantz
Dogs were present in the Americas prior to the arrival of European colonists, but the origin and fate of these pre-contact dogs are largely unknown. We sequenced 71 mitochondrial and seven nuclear genomes from ancient North American and Siberian dogs spanning ~9,000 years. Our analysis indicates that American dogs were not domesticated from North American wolves. Instead, American dogs form a monophyletic lineage that likely originated in Siberia and dispersed into the Americas alongside people....

Data from: Lepidosaurian diversity in the Mesozoic–Paleogene: the potential roles of sampling biases and environmental drivers

Terri J. Cleary, Roger B.J. Benson, Susan E. Evans, Paul M. Barrett & Roger B. J. Benson
Lepidosauria is a speciose clade with a long evolutionary history, but there have been few attempts to explore its taxon-richness through time. Here we estimate patterns of terrestrial lepidosaur genus diversity for the Triassic–Paleogene (252–23 Ma), and compare observed and sampling-corrected richness curves generated using Shareholder Quorum Subsampling and classical rarefaction. Generalized least-squares regression (GLS) is used to investigate the relationships between richness, sampling and environmental proxies. We found low levels of richness from the...

Data from: The chemical basis of a signal of individual identity: Shell pigment concentrations track the unique appearance of Common Murre eggs

Mark E Hauber, Alexander L Bond, Amy-Lee Kouwenberg, Gregory J Robertson, Erpur S Hansen, Mande Holford, Miri Dainson, Alec Luro & James Dale
In group-living species with parental care, the accurate recognition of one’s own young is critical to fitness. Because discriminating offspring within a large colonial group may be challenging, progeny of colonial breeders often display familial or individual identity signals to elicit and receive costly parental provisions from their own parents. For instance, the Common Murre (or Common Guillemot: Uria aalge) is a colonially breeding seabird that does not build a nest and lays and incubates...

Data from: REvoSim: organism-level simulation of macro and microevolution

Russell J. Garwood, Alan R. T. Spencer & Mark D. Sutton
Macroevolutionary processes dictate the generation and loss of biodiversity. Understanding them is a key challenge when interrogating the earth-life system in deep time. Model-based approaches can reveal important macroevolutionary patterns, and generate hypotheses on the underlying processes. Here we present and document a novel model called REvoSim (Rapid Evolutionary Simulator) coupled with a software implementation of this model. The latter is available here as both source code (C++/Qt, GNU General Public License), and as distributables...

Data from: Acherontiscus caledoniae, the earliest heterodont and durophagous tetrapod

Jennifer Clack, Marcello Ruta, Andrew Milner, John Marshall, Timothy Smithson & Keturah Smithson
The enigmatic tetrapod Acherontiscus caledoniae from the Pendleian stage of the Early Carboniferous shows heterodontous and durophagous teeth, representing the earliest known examples of significant adaptations in tetrapod dental morphology. Tetrapods of the Late Devonian and Early Carboniferous (Mississippian), now known in some depth, are generally conservative in their dentition and body morphologies. Their teeth are simple and uniform, being cone-like and sometimes recurved at the tip. Modifications such as keels occur for the first...

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