574 Works

Data from: Coadapted genomes and selection on hybrids: Fisher's geometric model explains a variety of empirical patterns

Alexis Simon, Nicolas Bierne & John J. Welch
Natural selection plays a variety of roles in hybridization, speciation and admixture. Most research has focused on two extreme cases: crosses between closely-related inbred lines, where hybrids are fitter than their parents, or crosses between effectively isolated species, where hybrids suffer severe breakdown. But many natural populations must fall into intermediate regimes, with multiple types of gene interaction, and these are more difficult to study. Here, we develop a simple fitness landscape model, and show...

Data from: Bony lesions in early tetrapods and the evolution of mineralized tissue repair

Eva Herbst, Michael Doube, Timothy Smithson, Jenny Clack & John Hutchinson
Bone healing is an important survival mechanism, allowing vertebrates to recover from injury and disease. Here we describe newly recognized paleopathologies in the hindlimbs of the early tetrapods Crassigyrinus scoticus and Eoherpeton watsoni from the Early Carboniferous of Cowdenbeath, Scotland. These pathologies are among the oldest known instances of bone healing in tetrapod limb bones in the fossil record (about 325 Myr old). X-ray microtomographic imaging of the internal bone structure of these lesions shows...

Data from: 1970s and ‘Patient 0’ HIV-1 genomes illuminate early HIV/AIDS history in North America

Michael Worobey, Thomas D. Watts, Richard A. McKay, Marc A. Suchard, Timothy Granade, Dirk E. Teuwen, Beryl A. Koblin, Walid Heneine, Philippe Lemey & Harold W. Jaffe
The emergence of HIV-1 group M subtype B in North American men who have sex with men was a key turning point in the HIV/AIDS pandemic. Phylogenetic studies have suggested cryptic subtype B circulation in the United States (US) throughout the 1970s1, 2 and an even older presence in the Caribbean2. However, these temporal and geographical inferences, based upon partial HIV-1 genomes that postdate the recognition of AIDS in 1981, remain contentious3, 4 and the...

Data from: Relative advantages of dichromatic and trichromatic color vision in camouflage breaking

Jolyon Troscianko, Jared Wilson-Aggarwal, David Griffiths, Claire N. Spottiswoode & Martin Stevens
There is huge diversity in visual systems and color discrimination abilities, thought to stem from an animal’s ecology and life history. Many primate species maintain a polymorphism in color vision, whereby most individuals are dichromats but some females are trichromats, implying that selection sometimes favors dichromatic vision. Detecting camouflaged prey is thought to be a task where dichromatic individuals could have an advantage. However, previous work either has not been able to disentangle camouflage detection...

Data from: Independent and parallel evolution of new genes by gene duplication in two origins of C4 photosynthesis provides new insight into the mechanism of phloem loading in C4 species

David M. Emms, Sarah Covshoff, Julian M. Hibberd & Steven Kelly
C4 photosynthesis is considered one of the most remarkable examples of evolutionary convergence in eukaryotes. However, it is unknown whether the evolution of C4 photosynthesis required the evolution of new genes. Genome-wide gene-tree species-tree reconciliation of seven monocot species that span two origins of C4 photosynthesis revealed that there was significant parallelism in the duplication and retention of genes coincident with the evolution of C4 photosynthesis in these lineages. Specifically, 21 orthologous genes were duplicated...

Data from: Requirements and limits of anatomy-based predictions of locomotion in terrestrial arthropods with emphasis on arachnids

Tom Weihmann, Hanns Hagen Goetzke & Michael Günther
Modern computer-aided techniques foster the availability and quality of 3D visualization and reconstruction of extinct and extant species. Moreover, animated sequences of locomotion and other movements find their way into motion pictures and documentary films, but also gain attraction in science. While movement analysis is well advanced in vertebrates, particularly in mammals and birds, analyses in arthropods, with their much higher variability regarding general anatomy and size, are still in their infancies and restricted to...

Data from: Salient eyes deter conspecific nest intruders in wild jackdaws (Corvus monedula)

Gabrielle L. Davidson, Nicola S. Clayton & Alex Thornton
Animals often respond fearfully when encountering eyes or eye-like shapes. Although gaze aversion has been documented in mammals when avoiding group-member conflict, the importance of eye coloration during interactions between conspecifics has yet to be examined in non-primate species. Jackdaws (Corvus monedula) have near-white irides, which are conspicuous against their dark feathers and visible when seen from outside the cavities where they nest. Because jackdaws compete for nest sites, their conspicuous eyes may act as...

Data from: Antagonistic effect of helpers on breeding male and female survival in a cooperatively breeding bird

Matthieu Paquet, Claire Doutrelant, Ben J. Hatchwell, Claire N. Spottiswoode & Rita Covas
1. Cooperatively breeding species are typically long lived and hence, according to theory, are expected to maximize their lifetime reproductive success through maximizing survival. Under these circumstances, the presence of helpers could be used to lighten the effort of current reproduction for parents to achieve higher survival. 2. In addition, individuals of different sexes and ages may follow different strategies, but whether male and female breeders and individuals of different ages benefit differently from the...

Data from: Long-term impacts of changed grazing regimes on the vegetation of heterogeneous upland grasslands

Robin J. Pakeman, Debbie A. Fielding, Liese Everts & Nick A. Littlewood
Marginal agricultural land, which in the UK refers particularly to upland grazings, will see changes in management driven by markets, subsidies, grants and environmental change with implications for biodiversity. Using a large-scale, long-term grazing experiment in the UK uplands we assessed the impact of intensification (tripling sheep numbers), abandonment (removal of sheep) and grazer diversification (partial replacement of sheep by cattle) on vegetation composition in a heterogenous area of grassland. Species benefiting from increased grazing...

Data from: Wing patterning gene redefines the mimetic history of Heliconius butterflies

Heather M. Hines, Brian A. Counterman, Riccardo Papa, Priscila Albuquerque De Moura, Marcio Z. Cardoso, Mauricio Linares, James Mallet, Robert D. Reed, Chris D. Jiggins, Marcus R. Kronforst & W. Owen McMillan
The mimetic butterflies Heliconius erato and H. melpomene have undergone parallel radiations to form a near-identical patchwork of over 20 different wing pattern races across the Neotropics. Previous molecular phylogenetic work on these radiations has suggested that similar but geographically disjunct color patterns arose multiple times independently in each species. The neutral markers used in these studies, however, can move freely across color pattern boundaries and therefore might not represent the history of the adaptive...

Data from: Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark

Elisa G. Dierickx, Simon Yung Wa Sin, Pieter Van Veelen, M. De L. Brooke, Yang Liu, Scott V. Edwards & Simon H. Martin
Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland...

Data from: Disparity, diversity, and duplications in the Caryophyllales

Stephen A. Smith, Joseph W. Brown, Ya Yang, Riva Bruenn, Chloe P. Drummond, Samuel F. Brockington, Joseph F. Walker, Noah Last, Norman A. Douglas & Michael J. Moore
The role played by whole genome duplication (WGD) in plant evolution is actively debated. WGDs have been associated with advantages such as superior colonization, various adaptations, and increased effective population size. However, the lack of a comprehensive mapping of WGDs within a major plant clade has led to uncertainty regarding the potential association of WGDs and higher diversification rates. Using seven chloroplast and nuclear ribosomal genes, we constructed a phylogeny of 5036 species of Caryophyllales,...

Data from: Cambrian petalonamid Stromatoveris phylogenetically links Ediacaran biota to later animals

Jennifer Hoyal Cuthill, Jian Han & Jennifer F. Hoyal Cuthill
Macro-organisms of the Ediacaran period (635-541 Ma) were large and morphologically complex, with some living in aphotic habitats, presenting the possibility that they were early animals. However, ‘bizarre’ Ediacaran morphologies and mouldic preservation have frustrated comparison to later taxa. Consequently, both the positions of Ediacaran biota in the tree of life and the origins of the Metazoa have been unresolved. Here we provide phylogenetic evidence to identify Ediacaran macro-biota as animals, based on 206 new...

Data from: No correlation between multi-locus heterozygosity and fitness in the common buzzard despite heterozygote advantage for plumage colour

Martina Boerner, Joseph I. Hoffman, William Amos, Nayden Chakarov & Oliver Kruger
Correlations between heterozygosity and fitness are frequently found but rarely well understood. Fitness can be affected by single loci of large effect which correlate with neutral markers via linkage disequilibrium, or as a result of variation in genome-wide heterozygosity following inbreeding. We explored these alternatives in the common buzzard, a raptor species in which three colour morphs differ in their lifetime reproductive success. Using 18 polymorphic microsatellite loci, we evaluated potential genetic differences among the...

Data from: Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers

Nian Wang, Marian Thomson, William J. A. Bodles, Robert M. M. Crawford, Harriet V. Hunt, Alan Watson Featherstone, Jaume Pellicer & Richard J. A. Buggs
New sequencing technologies allow development of genome-wide markers for any genus of ecological interest, including plant genera such as Betula (birch) that have previously proved difficult to study due to widespread polyploidy and hybridisation. We present a de novo reference genome sequence assembly, from 67X short read coverage, of Betula nana (dwarf birch) – a diploid that is the keystone woody species of sub-arctic scrub communities but of conservation concern in Britain. We also present...

Data from: Genome-wide evidence for speciation with gene flow in Heliconius butterflies

Simon H. Martin, Kanchon K. Dasmahapatra, Nicola J. Nadeau, Camilo Salazar, James R. Walters, Fraser Simpson, Mark Blaxter, Andrea Manica, James Mallet & Chris D. Jiggins
Most speciation events probably occur gradually, without complete and immediate reproductive isolation, but the full extent of gene flow between diverging species has rarely been characterized on a genome-wide scale. Documenting the extent and timing of admixture between diverging species can clarify the role of geographic isolation in speciation. Here we use new methodology to quantify admixture at different stages of divergence in Heliconius butterflies, based on whole genome sequences of 31 individuals. Comparisons between...

Data from: Synthesis, characterization and modelling of zinc and silicate co-substituted hydroxyapatite

Robert J. Friederichs, Helen F. Chappell, David V. Shepherd & Serena M. Best
Experimental chemistry and atomic modelling studies were performed here to investigate a novel ionic co-substitution in hydroxyapatite (HA). Zinc, silicate co-substituted HA (ZnSiHA) remained phase pure after heating to 1100°C with Zn and Si amounts of 0.6 wt% and 1.2 wt%, respectively. Unique lattice expansions in ZnSiHA, silicate Fourier transform infrared peaks and changes to the hydroxyl IR stretching region suggested Zn and silicate co-substitution in ZnSiHA. Zn and silicate insertion into HA was modelled...

Data from: Seasonal variation in food availability and relative importance of dietary items in the Gambian epauletted fruit bat (Epomophorus gambianus)

Kofi Amponsah-Mensah, Andrew A. Cunningham, James L.N. Wood & Yaa Ntiamoa-Baidu
1. The Gambian epauletted fruit bat (Epomophorus gambianus) is very common across a variety of West African habitats, but very little information is available on its feeding ecology or its contribution to ecosystem function. 2. We investigated seasonal variation in food availability and the relative importance of dietary items used by this species in a forest-savannah transitional ecosystem. Dietary items were identified from 1,470 samples of faecal and ejecta pellets which had been collected under...

Data from: Macrobenthic assemblage structure in a cool-temperate intertidal dwarf-eelgrass bed in comparison to those in lower latitudes.

Richard S. K. Barnes & M. D. Farnon Ellwood
The evolution and ecology of latitudinal patterns in marine macrofaunal biodiversity and assemblage structure are contentious. With the aim of investigating the occurrence of such patterns in intertidal dwarf-eelgrass beds (Nanozostera spp.), those at cool-temperate Scolt Head Island, UK (latitude 52°N), were examined and compared to equivalent systems in warm-temperate Knysna, South Africa (34°S), and subtropical Moreton Bay, Australia (27°S); systems that had earlier been examined using identical methodology. The Scolt Head bed supported the...

Data from: On heels and toes: how ants climb with adhesive pads and tarsal friction hair arrays

Thomas Endlein & Walter Federle
Ants are able to climb effortlessly on vertical and inverted smooth surfaces. When climbing, their feet touch the substrate not only with their pretarsal adhesive pads but also with dense arrays of fine hairs on the ventral side of the 3rd and 4th tarsal segments. To understand what role these different attachment structures play during locomotion, we analysed leg kinematics and recorded single-leg ground reaction forces in Weaver ants (Oecophylla smaragdina) climbing vertically on a...

Data from: Superior discrimination for hue than for saturation and an explanation in terms of correlated neural noise

Marina V. Danilova & John D. Mollon
The precision of human colour discrimination depends on the region of colour space in which measurements are made and on the direction in which the compared colours—the discriminanda—differ. Working in a MacLeod–Boynton chromaticity diagram scaled so that thresholds at the white point were equal for the two axes, we made measurements at reference points lying on lines that passed at 45° or −45° through the white point. At a given reference chromaticity, we measured thresholds...

Data from: Does coevolution with a shared parasite drive hosts to partition their defences among species?

Eleanor M. Caves, Martin Stevens & Claire N. Spottiswoode
When mimicry imposes costs on models, selection may drive the model's phenotype to evolve away from its mimic. For example, brood parasitism often drives hosts to diversify in egg appearance among females within a species, making mimetic parasitic eggs easier to detect. However, when a single parasite species exploits multiple host species, parasitism could also drive host egg evolution away from other co-occurring hosts, to escape susceptibility to their respective mimics. This hypothesis predicts that...

Data from: Developmental plasticity for male secondary sexual traits in a group of polyphenic tropical butterflies

Andrew J. Balmer, Paul M. Brakefield, Oskar Brattström & Erik Van Bergen
Many organisms alter their investment in secondary sexual traits to optimise the fitness trade-off between reproduction and survival. Though seasonal variation in the expression of sexual traits is evident (e.g. conspicuous breeding plumage in birds), little attention has been given to short-lived organisms that inhabit relatively stable environments throughout their own lifetime but are exposed to strong environmental variation across generations. Some insects have evolved seasonal polyphenism to cope with intergenerational variation in environmental selection,...

Data from: The stable isotope ecology of mycalesine butterflies: implications for plant-insect co-evolution

Erik Van Bergen, Henry S. Barlow, Oskar Brattström, Howard Griffiths, Ullasa Kodandaramaiah, Colin P. Osborne & Paul M. Brakefield
One of the most dramatic examples of biome shifts in the geological record is the rapid replacement of C3 vegetation by C4 grasses in (sub-) tropical regions during the Late Miocene–Pliocene. Climate-driven biome shifts of this magnitude are expected to have a major impact on diversification and ecological speciation, especially in grazing taxa. Mycalesine butterflies are excellent candidates to explore the evolutionary impact of these C3/C4 shifts on insect grazer communities. Mycalesine butterflies feed on...

Data from: Decomposition of coarse woody debris in a long-term litter manipulation experiment: a focus on nutrient availability

Evan M. Gora, Emma J. Sayer, Benjamin L. Turner & Edmund V. J. Tanner
1.The majority of aboveground carbon in tropical forests is stored in wood, which is returned to the atmosphere during decomposition of coarse woody debris. However, the factors controlling wood decomposition have not been experimentally manipulated over time scales comparable to the length of this process. 2.We hypothesized that wood decomposition is limited by nutrient availability and tested this hypothesis in a long-term litter addition and removal experiment in a lowland tropical forest in Panama. Specifically,...

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