5,864 Works

Data from: Multiple-strain infections of borrelia afzelii: a role for within-host interactions in the maintenance of antigenic diversity?

Martin Andersson, Kristin Scherman & Lars Råberg
Genetically diverse infections are common but little is known about what effects coinfecting strains have on each other in natural host-parasite systems. To explore the nature and consequences of interactions in the wild, we studied the tick-transmitted bacterium Borrelia afzelii in one of its main reservoir hosts, the bank vole Myodes glareolus. We measured overall infection intensity with quantitative polymerase chain reaction (PCR) and resolved the composition of multiple infections using strain-specific PCR assays targeting...

Data from: Multiple predator species alter prey behavior, population growth and a trophic cascade in a model estuarine food web

Pamela L. Reynolds & John F. Bruno
Predators can influence prey population dynamics by affecting prey behaviors with strong fitness consequences, with cascading effects on lower trophic levels. Here, we demonstrate that multiple predator species can nonconsumptively influence prey population growth and the strength of a trophic cascade in a model marine community. We exposed the herbivorous amphipod Ampithoe longimana to olfactory and visual cues from three common predators (pinfish, mud crabs, brown shrimp) singly and together in a multiple-predator assemblage to...

Data from: Genotype-by-genotype specificity remains robust to average temperature variation in an aphid/endosymbiont/parasitoid system

Luis Cayetano & Christoph Vorburger
Genotype-by-genotype interactions demonstrate the existence of variation upon which selection acts in host-parasite systems at respective resistance and infection loci. These interactions can potentially be modified by environmental factors, which would entail that different genotypes are selected under different environmental conditions. In the current study, we checked for a G x G x E interaction in the context of average temperature and the genotypes of asexual lines of the endoparasitoid wasp Lysiphlebus fabarum and isolates...

Data from: Differential Expression Analysis for Pathways

Winston A. Haynes, Roger Higdon, Larissa Stanberry, Dwayne Collins & Eugene Kolker
Life science technologies generate a deluge of data that hold the keys to unlocking the secrets of important biological functions and disease mechanisms. We present DEAP, Differential Expression Analysis for Pathways, which capitalizes on information about biological pathways to identify important regulatory patterns from differential expression data. DEAP makes significant improvements over existing approaches by including information about pathway structure and discovering the most differentially expressed portion of the pathway. On simulated data, DEAP significantly...

Data from: A virus responds instantly to the presence of the vector on the host and forms transmission morphs

Alexandre Martinière, Aurélie Bak, Jean-Luc Macia, Nicole Lautredou, Daniel Gargani, Juliette Doumayrou, Elisa Garzo, Aranzazu Moreno, Alberto Fereres, Stéphane Blanc & Martin Drucker
Many plant and animal viruses are spread by insect vectors. Cauliflower mosaic virus (CaMV) is aphid-transmitted, with the virus being taken up from specialized transmission bodies (TB) formed within infected plant cells. However, the precise events during TB-mediated virus acquisition by aphids are unknown. Here, we show that TBs react instantly to the presence of the vector by ultra-rapid and reversible redistribution of their key components onto microtubules throughout the cell. Enhancing or inhibiting this...

Data from: Family based guilds in the ant Pachycondyla inversa

Heikki Helanterä, Oliver Aehle, Maurice Roux, Jürgen Heinze & Patrizia D'Ettorre
High relatedness promotes the evolution of sociality because potentially costly cooperative behaviours are directed towards kin. However, societies, such as those of social insects, also benefit from genetic diversity, e.g. through enhanced disease resistance and division of labour. Effects of genetic diversity have been investigated in a few complex eusocial species. Here, we show that genetically based division of labour may also be important in ‘simple societies’, with fewer individuals and limited morphological caste differentiation....

Data from: Genetic architecture underlying morning and evening circadian phenotypes in fruit flies Drosophila melanogaster

Vijay K. Sharma, Koustubh M. Vaze & K. L. Nikhil
Circadian rhythms are perhaps among the genetically best characterised behaviours. Several mutations with drastic effects on circadian processes have been identified and models developed to explain how clock genes and their products generate self-sustained oscillations. While natural variations in circadian phenotypes have been studied extensively, the genetic basis of such adaptive variations remains largely unknown. Here we report the results of a preliminary genetic analysis of adaptive divergence of circadian phenotypes in populations of fruit...

Data from: Proximity to agriculture is correlated with pesticide tolerance: evidence for the evolution of amphibian resistance to modern pesticides

Rickey D. Cothran, Jenise M. Brown & Rick A. Relyea
Anthropogenic environmental change is a powerful and ubiquitous evolutionary force, so it is critical that we determine the extent to which organisms can evolve in response to anthropogenic environmental change and whether these evolutionary responses have associated costs. This issue is particularly relevant for species of conservation concern including many amphibians, which are experiencing global declines from many causes including widespread exposure to agrochemicals. We used a lab toxicity experiment to assess variation in sensitivity...

Data from: Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution

Richard E. Broughton, Ricardo Betancur-R., Chenhong Li, Gloria Arratia & Guillermo Orti
Over half of all vertebrates are “fishes”, which exhibit enormous diversity in morphology, physiology, behavior, reproductive biology, and ecology. Investigation of fundamental areas of vertebrate biology depend critically on a robust phylogeny of fishes, yet evolutionary relationships among the major actinopterygian and sarcopterygian lineages have not been conclusively resolved. Although a consensus phylogeny of teleosts has been emerging recently, it has been based on analyses of various subsets of actinopterygian taxa, but not on a...

Data from: Parallel tagged next-generation sequencing on pooled samples – a new approach for population genetics in ecology and conservation

Monika Zavodna, Catherine E. Grueber & Neil J. Gemmell
Next-generation sequencing (NGS) on pooled samples has already been broadly applied in human medical diagnostics and plant and animal breeding. However, thus far it has been only sparingly employed in ecology and conservation, where it may serve as a useful diagnostic tool for rapid assessment of species genetic diversity and structure at the population level. Here we undertake a comprehensive evaluation of the accuracy, practicality and limitations of parallel tagged amplicon NGS on pooled population...

Data from: The effect of collective dispersal on the genetic structure of a subdivided population

Jonathan M. Yearsley, Frédérique Viard & Thomas Broquet
Correlated dispersal paths between two or more individuals are widespread across many taxa. The population genetic implications of this collective dispersal have received relatively little attention. Here we develop two-sample coalescent theory that incorporates collective dispersal in a finite island model to predict expected coalescence times, genetic diversities and F-statistics. We show that collective dispersal reduces mixing in the system, which decreases expected coalescence times and increases FST. The effects are strongest in systems with...

Data from: Diversity dynamics of mammals in relation to tectonic and climatic history: comparison of three Neogene records from North America

Catherine Badgley & John A. Finarelli
In modern ecosystems, regions of topographic heterogeneity, when compared with nearby topographically homogeneous regions, support high species densities of mammals and other groups. This biogeographic pattern could be explained by either greater diversification rates or greater accommodation of species in topographically complex regions. In this context, we assess the hypothesis that changes in landscape history have stimulated diversification in mammals. Landscape history includes tectonic and climatic processes that influence topographic complexity at regional scales. We...

Data from: Reproductive and post-reproductive life history of wild-caught Drosophila melanogaster under laboratory conditions

Peter Klepsatel, Martina Gáliková, Nicola De Maio, Sara Ricci, Christian Schlötterer & Thomas Flatt
The life history of the fruit fly (Drosophila melanogaster) is well understood, but fitness components are rarely measured by following single individuals over their lifetime, thereby limiting insights into lifetime reproductive success, reproductive senescence and post-reproductive lifespan. Moreover, most studies have examined long-established laboratory strains rather than freshly caught individuals and may thus be confounded by adaptation to laboratory culture, inbreeding or mutation accumulation. Here, we have followed the life histories of individual females from...

Data from: Homing pigeons respond to time-compensated solar cues even in sight of the loft

Chris Armstrong, Helen Wilkinson, Jessica Meade, Dora Biro, Robin Freeman & Tim Guilford
The sun has long been thought to guide bird navigation as the second step in a two-stage process, in which determining position using a map is followed by course setting using a compass, both over unfamiliar and familiar terrain. The animal’s endogenous clock time-compensates the solar compass for the sun’s apparent movement throughout the day, and this allows predictable deflections in orientation to test for the compass’ influence using clock-shift manipulations. To examine the influence...

Data from: Low fertility of wild hybrid male flycatchers despite recent divergence

Murielle Ålund, Simone Immler, Amber M. Rice, Anna Qvarnström, M. Alund & A. Qvarnstrom
Postzygotic isolation may be important for maintaining species boundaries, particularly when premating barriers are incomplete. Little is known about the course of events leading from minor environmental mismatches affecting hybrid fitness to severe genetic incompatibilities causing sterility or inviability. We investigated whether reduced reproductive success of hybrid males was caused by suboptimal sperm traits or by more severe genetic incompatibilities in a hybrid zone of pied (Ficedula hypoleuca) and collared flycatchers (F. albicollis) on the...

Data from: Signatures of diversifying selection in European pig breeds

Samantha Wilkinson, Zen H. Lu, Hendrik-Jan Megens, Alan L. Archibald, Chris Haley, Ian J. Jackson, Martien A. M. Groenen, Richard P. M. A. Crooijmans, Rob Ogden & Pamela Wiener
Porcine_60K_Data_Wilkinsonetal2013.tarMapping and variant calling data on SSC5:98000000-99000000This file shares the same REAME as SSC11_53500000-55500000.tarSSC5_98000000-99000000.tarMapping and variant calling data on SSC5:3100000-34000000This file shares the same REAME as SSC11_53500000-55500000.tarSSC5_3100000-34000000.tarMapping and variant calling data on SSC11:53500000-55500000SSC11_53500000-55500000.tar

Data from: The early evolution of synapsids, and the influence of sampling on their fossil record

Neil Brocklehurst, Christian F. Kammerer & Jörg Fröbisch
Synapsids dominated the terrestrial realm between the late Pennsylvanian and the Triassic. Their early evolution includes some of the first amniotes to evolve large size, herbivory, and macro-predators. However, little research has focused on the changes in diversity occurring during this early phase in their evolutionary history, with more effort concentrating on later events such the Permo-Triassic extinction. Here we assess synapsid diversity, at both the species and genus levels, between the Carboniferous (Moscovian) and...

Data from: Influence of late Quaternary climate change on present patterns of genetic variation in valley oak, Quercus lobata Née

Paul F. Gugger, Makihiko Ikegami & Victoria L. Sork
Phylogeography and ecological niche models (ENMs) suggest that late Quaternary glacial cycles have played a prominent role in shaping present population genetic structure and diversity, but have not applied quantitative methods to dissect the relative contribution of past and present climate vs. other forces. We integrate multilocus phylogeography, climate-based ENMs and multivariate statistical approaches to infer the effects of late Quaternary climate change on contemporary genetic variation of valley oak (Quercus lobata Née). ENMs indicated...

Data from: Multiple global radiations in tadpole shrimps challenge the concept of ‘living fossils’

Thomas C. Mathers, Robert L. Hammond, Ronald A. Jenner, Bernd Haenfling & Africa Gomez
‘Living fossils’, a phrase first coined by Darwin, are defined as species with limited recent diversification and high morphological stasis over long periods of evolutionary time. Morphological stasis, however, can potentially lead to diversification rates being underestimated. Notostraca, or tadpole shrimps, are an ancient, globally distributed order of branchiopod crustaceans regarded as ‘living fossils’ because their rich fossil record dates back to the early Devonian and their morphology is highly conserved. Recent phylogenetic reconstructions have...

Data from: Disentangling direct and indirect fitness effects of microbial dormancy

William Croft Ratcliff, Mitchell Hoverman, Michael Travisano & R. Ford Denison
Disentangling individual selection from kin selection is one of the greatest challenges of evolutionary biology. Even solitary organisms that do not interact directly with conspecifics may interact indirectly with them through competition for resources. As a result, traits that appear to affect individual fitness alone can also modify the fitness of relatives nearby and thus may evolve partially through these cryptic indirect fitness effects. Here we develop a method to quantitatively separate direct and indirect...

Data from: Within-population polymorphism of sex-determination systems in the common frog (Rana temporaria)

Nicolas Rodrigues, Caroline Betto-Colliard, Hélène Jourdan-Pineau & Nicolas Perrin
In sharp contrast with birds and mammals, the sex chromosomes of ectothermic vertebrates are often undifferentiated, for reasons that remain debated. A linkage map was recently published for Rana temporaria (Linnaeus, 1758) from Fennoscandia (Eastern European lineage), with a proposed sex-determining role for linkage group 2 (LG2). We analysed linkage patterns in lowland and highland populations from Switzerland (Western European lineage), with special focus on LG2. Sibship analyses showed large differences from the Fennoscandian map...

Data from: Evolutionary change during experimental ocean acidification

Melissa H. Pespeni, Eric Sanford, Tessa M. Hill, Jessica D. Hosfelt, Hannah K. Jaris, Michele LaVigne, Brian Gaylord, Elizabeth A. Lenz, Ann D. Russell, Megan K. Young & Stephen R. Palumbi
Rising atmospheric carbon dioxide (CO2) conditions are driving unprecedented changes in seawater chemistry, resulting in reduced pH and carbonate ion concentrations in the Earth’s oceans. This ocean acidification has negative but variable impacts on individual performance in many marine species. However, little is known about the adaptive capacity of species to respond to an acidified ocean, and as a result, predictions regarding future ecosystem responses remain incomplete. Here we demonstrate that ocean acidification generates striking...

Data from: Lights out: the evolution of bacterial bioluminescence in Loliginidae

Frank E. Anderson, Alexis Bergman, Samantha H. Cheng, M. Sabrina Pankey & Tooraj Valinassab
Representatives of several metazoan clades engage in symbiotic interactions with bioluminescent bacteria, but the evolution and maintenance of these interactions remain poorly understood. Uroteuthis is a genus of loliginid squid (Cephalopoda: Loliginidae) characterized by paired ventral photophores (light organs) housing bioluminescent bacteria. While previous phylogenetic studies have suggested that Uroteuthis is closely related to Loliolus, a genus of non-bioluminescent species, this relationship remains unresolved. To illuminate Uroteuthis and Loliolus phylogeny and its implications for the...

Data from: Phylogeography of willow grouse (Lagopus lagopus) in the Arctic: taxonomic discordance as inferred from molecular data

Jacob Höglund, Biao Wang, Thomas Axelsson & María Quintela
Using independently segregating nuclear single nucleotide polymorphisms (SNPs) and mitochondrial control region sequences, we found an east–west division among sampled willow grouse Lagopus lagopus subspecies. This division cut across the range of the subspecies with the largest distribution (lagopus) and thus contradicted existing taxonomic classifications. Russian Lagopus lagopus lagopus tended to cluster with North American willow grouse partly classified as other subspecies. Scandinavian willow grouse (L. l. lagopus) clustered with red grouse from Britain and...

Data from: Preservation of RNA and DNA from mammal samples under field conditions

Miguel Camacho-Sanchez, Pablo Burraco, Ivan Gomez-Mestre & Jennifer A. Leonard
Ecological and conservation genetics require sampling of organisms in the wild. Appropriate preservation of the collected samples, usually by cryostorage, is key to the quality of the genetic data obtained. Nevertheless, cryopreservation in the field to ensure RNA and DNA stability is not always possible. We compared several nucleic acid preservation solutions appropriate for field sampling and tested them on rat (Rattus rattus) blood, ear and tail tip, liver, brain and muscle. We compared the...

Registration Year

  • 2013

Resource Types

  • Dataset


  • French National Centre for Scientific Research
  • University of Oxford
  • University of British Columbia
  • University of Washington
  • Uppsala University
  • University of California, Davis
  • University of Exeter
  • University of Georgia
  • University of Edinburgh
  • Yale University