268 Works

Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species

Matheus Bianconi, Luke Dunning, Emma Curran, Oriane Hidalgo, Robyn Powell, Sahr Mian, Ilia Leitch, Marjorie Lundgren, Sophie Manzi, Maria Vorontsova, Guillaume Besnard, Colin Osborne, Jill Olofsson & Pascal-Antoine Christin
C4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C4 and non-C4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during, and after photosynthetic divergence in A. semialata. We further analyse the genome composition of individuals with varied ploidy...

Historical isolation facilitates species radiation by sexual selection: insights from Chorthippus grasshoppers

Zachary Nolen, Burcin Yildirim, Iker Irisarri, Shanlin Liu, Clara Groot Crego, Daniel Amby, Frieder Mayer, M. Gilbert & Ricardo Pereira
Theoretical and empirical studies have shown that species radiations are facilitated when a trait under divergent natural selection is also involved in sexual selection. It is yet unclear how quick and effective radiations are where assortative mating is unrelated to the ecological environment and primarily results from sexual selection. We address this question using sympatric grasshopper species of the genus Chorthippus, which have evolved strong behavioral isolation while lacking noticeable eco-morphological divergence. Mitochondrial genomes suggest...

Evolution of putative barrier loci at an intermediate stage of speciation with gene flow in campions (Silene)

Xiaodong Liu, Xiaodong Liu, Sylvain Glemin & Sophie Karrenberg
Understanding the origin of new species is a central goal in evolutionary biology. Diverging lineages often evolve highly heterogeneous patterns of genetic differentiation; however, the underlying mechanisms are not well understood. We investigated evolutionary processes governing genetic differentiation between the hybridizing campions Silene dioica (L.) Clairv. and S. latifolia Poiret. Demographic modeling indicated that the two species diverged with gene flow. The best-supported scenario with heterogeneity in both migration rate and effective population size suggested...

The evolution of virulence in Pseudomonas aeruginosa during chronic wound infection

Jelly Vanderwoude, Derek Fleming, Sheyda Azimi, Urvish Trivedi, Kendra Rumbaugh & Stephen Diggle
Opportunistic pathogens are associated with a number of chronic human infections, yet the evolution of virulence in these organisms during chronic infection remains poorly understood. Here, we tested the evolution of virulence in the human opportunistic pathogen Pseudomonas aeruginosa in a murine chronic wound model using a two-part serial passage and sepsis experiment, and found that virulence evolved in different directions in each line of evolution. We also assessed P. aeruginosa adaptation to a chronic...

Using vertebrate environmental DNA from seawater in biomonitoring of marine habitats

Eva Egelyng Sigsgaard, Felipe Torquato, Tobias Guldberg Frøslev, Alec B. M. Moore, Johan Mølgård Sørensen, Pedro Range, Radhouane Ben Hamadou, Steffen Sanvig Bach, Peter Rask Møller & Philip Francis Thomsen
Conservation and management of marine biodiversity depends on biomonitoring of marine habitats, but current approaches are resource-intensive and require different approaches for different organisms. Environmental DNA (eDNA) extracted from water samples is an efficient and versatile approach to detecting aquatic animals. In the ocean, eDNA composition reflects local fauna at fine spatial scales, but little is known about the effectiveness of eDNA-based monitoring of marine communities at larger scales. We investigated the potential of eDNA...

Data from: Shotgun microbial profiling of fossil remains

Clio Der Sarkissian, Luca Ermini, Hákon Jónsson, Anatoly N. Alekseev, Éric Crubézy, Beth Shapiro & Ludovic Orlando
Millions to billions of DNA sequences can now be generated from ancient skeletal remains thanks to the massive throughput of next-generation sequencing platforms. Except in cases of exceptional endogenous DNA preservation, most of the sequences isolated from fossil material do not originate from the specimen of interest, but instead reflect environmental organisms that colonized the specimen after death. Here, we characterize the microbial diversity recovered from seven ca. 200-13,000 year old horse bones collected from...

Data from: Third wave cognitive therapy versus mentalization-based treatment for major depressive disorder: a randomised clinical trial

Janus Christian Jakobsen, Christian Gluud, Mickey Kongerslev, Kirsten Aaskov Larsen, Per Sørensen, Per Winkel, Theis Lange, Ulf Søgaard & Erik Simonsen
Objective: To compare the benefits and harms of third-wave cognitive therapy versus mentalisation-based therapy in a small sample of depressed participants. Setting: The trial was conducted at an outpatient psychiatric clinic for non-psychotic patients in Roskilde, Denmark. Participants: 44 consecutive adult participants diagnosed with major depressive disorder. Interventions: 18 weeks of third-wave cognitive therapy (n=22) versus 18 weeks of mentalisation-based treatment (n=22). Outcomes: The primary outcome was the Hamilton Rating Scale for Depression (HDRS) at...

Data from: Ancient DNA microsatellite analyses of the extinct New Zealand giant moa (Dinornis robustus) identify relatives within a single fossil site

Morten E. Allentoft, Rasmus Heller, Richard N. Holdaway & Michael Bunce
By analysing ancient DNA (aDNA) from 74 14C-dated individuals of the extinct South Island giant moa (Dinornis robustus) of New Zealand, we identified four dyads of closely related adult females. Although our total sample included bones from four fossil deposits located within a 10 km radius, these eight individuals had all been excavated from the same locality. Indications of kinship were based on high pairwise genetic relatedness (rXY) in six microsatellite markers genotyped from aDNA,...

Data from: Anthropogenic hybridization between endangered migratory and commercially harvested stationary whitefish taxa (Coregonus spp.)

Jan Dierking, Luke Phelps, Kim Præbel, Gesine Ramm, Enno Prigge, Jost Borcherding, Matthias Brunke & Christophe Eizaguirre
Natural hybridization plays a key role in the process of speciation. However, anthropogenic (human induced) hybridization of historically isolated taxa raises conservation issues. Due to weak barriers to gene flow and the presence of endangered taxa, the whitefish species complex is an excellent study system to investigate the consequences of hybridization in conservation. We focused on three naturally reproductively isolated whitefish taxa in Germany: the endangered, anadromous North Sea houting (NSH) and Baltic houting (BH),...

Data from: Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance

Michael D. Martin, Elizabeth A. Zimmer, Morten T. Olsen, Andrew D. Foote, M. Thomas P. Gilbert & Grace S. Brush
Invasive plants provide ample opportunity to study evolutionary shifts that occur after introduction to novel environments. However, although genetic characters pre-dating introduction can be important determinants of later success, large-scale investigations of historical genetic structure have not been feasible. Common ragweed (Ambrosia artemisiifolia L.) is an invasive weed native to North America that is known for its allergenic pollen. Palynological records from sediment cores indicate that this species was uncommon before European colonization of North...

Data from: Relative impacts of environmental variation and evolutionary history on the nestedness and modularity of tree-herbivore networks.

Kathryn M. Robinson, Céline Hauzy, Nicolas Loeuille & Benedicte R. Albrectsen
Nestedness and modularity are measures of ecological networks whose causative effects are little understood. We analyzed antagonistic plant–herbivore bipartite networks using common gardens in two contrasting environments comprised of aspen trees with differing evolutionary histories of defence against herbivores. These networks were tightly connected owing to a high level of specialization of arthropod herbivores that spend a large proportion of the life cycle on aspen. The gardens were separated by ten degrees of latitude with...

Data from: Chronic Trichuris muris Infection Decreases Diversity of the Intestinal Microbiota and Concomitantly Increases the Abundance of Lactobacilli

Jacob Bak Holm, Daniel Sorobetea, Pia Kiilerich, Yuliaxis Ramayo-Caldas, Jordi Estellé, Tao Ma, Lise Madsen, Karsten Kristiansen & Marcus Svensson-Frej
The intestinal microbiota is vital for shaping the local intestinal environment as well as host immunity and metabolism. At the same time, epidemiological and experimental evidence suggest an important role for parasitic worm infections in maintaining the inflammatory and regulatory balance of the immune system. In line with this, the prevalence of persistent worm infections is inversely correlated with the incidence of immune-associated diseases, prompting the use of controlled parasite infections for therapeutic purposes. Despite...

Data from: Is there a causal link between knee loading and knee osteoarthritis progression? A systematic review and meta-analysis of cohort studies and randomised trials

Marius Henriksen, Mark W. Creaby, Hans Lund, Carsten Juhl & Robin Christensen
Objective: We performed a systematic review, meta-analysis and assessed the evidence supporting a causal link between knee joint loading during walking and structural knee osteoarthritis (OA) progression. Design: Systematic review, meta-analysis and application of Bradford Hill's considerations on causation. Data sources: We searched MEDLINE, Scopus, AMED, CINAHL and SportsDiscus for prospective cohort studies and randomised controlled trials (RCTs) from 1950 through October 2013. Study eligibility criteria: We selected cohort studies and RCTs in which estimates...

Data from: Fifty thousand years of arctic vegetation and megafaunal diet

Eske Willerslev, John Davison, Mari Moora, Martin Zobel, Eric Coissac, Mary E. Edwards, Eline D. Lorenzen, Mette Vestergård, Galina Gussarova, James Haile, Joseph Craine, Gaddy Bergmann, Ludovic Gielly, Sanne Boessenkool, Laura S. Epp, Peter B. Pearman, Rachid Cheddadi, David Murray, Karri Anne Bråthen, Nigel Yoccoz, Heather Binney, Corinne Cruaud, Patrick Wincker, Tomasz Goslar, Inger Greve Alsos … & Pierre Taberlet
Although it is generally agreed that the arctic flora is among the youngest and least diverse on Earth, the processes that shaped it are poorly understood. Here we present 50 thousand years (kyr) of arctic vegetation history, derived from the first large-scale ancient DNA metabarcoding study of circumpolar plant diversity. For this interval we additionally explore nematode diversity as a proxy for modelling vegetation cover and soil quality, and diets of herbivorous megafaunal mammals, many...

Data from: A century-long genetic record reveals that protist effective population sizes are comparable to those of macroscopic species

Phillip C. Watts, Nina Lundholm, Sofia Ribeiro & Marianne Ellegaard
Effective population size (Ne) determines the rate of genetic drift and the relative influence of selection over random genetic changes. While free-living protist populations characteristically consist of huge numbers of cells (N), the absence of any estimates of contemporary Ne raises the question whether protist effective population sizes are comparably large. Using microsatellite genotype data of strains derived from revived cysts of the marine dinoflagellate Pentapharsodinum dalei from sections of a sediment record that spanned...

Data from: Dramatic niche shifts and morphological change in two insular bird species

Per Alström, Jon Fjeldså, Knud Andreas Jønsson, Anders Ödeen, Per G. P. Ericson, Martin Irestedt, J. Fjeldsa, K. A. Jonsson, P. Alstrom & A. Odeen
Colonizations of islands are often associated with rapid morphological divergence. We present two previously unrecognized cases of dramatic morphological change and niche shifts in connection with colonization of tropical forest-covered islands. These evolutionary changes have concealed the fact that the passerine birds madanga, Madanga ruficollis, from Buru, Indonesia, and São Tomé shorttail, Amaurocichla bocagii, from São Tomé, Gulf of Guinea, are forest-adapted members of the family Motacillidae (pipits and wagtails). We show that Madanga has...

Data from: Natural genetic variation in Arabidopsis thaliana defense metabolism genes modulate field fitness

Rachel Kerwin, Julie Feusier, Jason Corwin, Matthew Rubin, Catherine Lin, Alise Muok, Brandon Larson, Baohua Li, Bindu Joseph, Marta Francisco, Daniel Copeland, Cynthia Weinig & Daniel J. Kliebenstein
Natural populations persist in complex environments, where biotic stressors, such as pathogen and insect communities, fluctuate temporally and spatially. These shifting biotic pressures generate heterogeneous selective forces that can maintain standing natural variation within a species. To directly test if genes containing causal variation for the Arabidopsis thaliana defensive compounds, glucosinolates (GSL) control field fitness and are therefore subject to natural selection, we conducted a multi-year field trial using lines that vary in only specific...

Data from: Effects of elevation and nitrogen and phosphorus fertilization on plant defence compounds in subarctic tundra heath vegetation

Jonathan R. De Long, Maja K. Sundqvist, Michael J. Gundale, Reiner Giesler & David A. Wardle
1. Plant chemical and structural defence compounds are well known to impact upon herbivory of fresh leaves and influence decomposition rates after leaf senescence. A number of theories predict that alleviating nutrient limitation and reducing other environmental stressors will result in decreased production of plant chemical defences. 2. In this study, we measured plant defence properties [total polyphenols (TP), condensed tannins (CT) and lignin concentrations, and protein complexation capacity (PCC)] in both fresh and senesced...

Data from: A replicated climate change field experiment reveals rapid evolutionary response in an ecologically important soil invertebrate

Thomas Bataillon, Nicolas Galtier, Aurelien Bernard, Nicolai Cryer, Nicolas Faivre, Sylvain Santoni, Dany Severac, Theis N. Mikkelsen, Klaus S. Larsen, Claus Beier, Jesper G. Sørensen, Martin Holmstrup, Bodil Ehlers, Bodil K. Ehlers & Teis N. Mikkelsen
Whether species can respond evolutionarily to current climate change is crucial for the persistence of many species. Yet, very few studies have examined genetic responses to climate change in manipulated experiments carried out in natural field conditions. We examined the evolutionary response to climate change in a common annelid worm using a controlled replicated experiment where climatic conditions were manipulated in a natural setting. Analyzing the transcribed genome of 15 local populations, we found that...

Data from: Computing the local field potential (LFP) from integrate-and-fire network models

Alberto Mazzoni, Henrik Anders Lindén, Hermann Cuntz, Anders Lansner, Stefano Panzeri, Gaute Tomas Einevoll & Henrik Lindén
Leaky integrate-and-fire (LIF) network models are commonly used to study how the spiking dynamics of neural networks changes with stimuli, tasks or dynamic network states. However, neurophysiological studies in vivo often rather measure the mass activity of neuronal microcircuits with the local field potential (LFP). Given that LFPs are generated by spatially separated currents across the neuronal membrane, they cannot be computed directly from quantities defined in models of point-like LIF neurons. Here, we explore...

Data from: Seawater environmental DNA reflects seasonality of a coastal fish community

Eva Egelyng Sigsgaard, Ida Broman Nielsen, Henrik Carl, Marcus Anders Krag, Steen Wilhelm Knudsen, Yingchun Xing, Tore Hejl Holm-Hansen, Peter Rask Møller & Philip Francis Thomsen
Coastal marine fish populations are in decline due to overfishing, habitat destruction, climate change and invasive species. Seasonal monitoring is important for detecting temporal changes in the composition of fish communities, but current monitoring is often non-existent or limited to annual or semi-annual surveys. In the present study, we investigate the potential of using environmental DNA (eDNA) metabarcoding of seawater samples to detect the seasonal changes in a coastal marine fish community. Water sampling and...

Data from: Identifying the most surprising victims of mass extinction events: an example using Late Ordovician brachiopods

Seth Finnegan, Christian M. Ø. Rasmussen & David A. T. Harper
Mass extinction events are recognized by increases in extinction rate and magnitude and, often, by changes in the selectivity of extinction. When considering the selective fingerprint of a particular event, not all taxon extinctions are equally informative: some would be expected even under a ‘background’ selectivity regime, whereas others would not and thus require special explanation. When evaluating possible drivers for the extinction event, the latter group is of particular interest. Here, we introduce a...

Data from: The genus Gennadas (Benthesicymidae: Decapoda): morphology of copulatory characters, phylogeny and coevolution of genital structures

Alexander L. Vereshchaka, Anastasia A. Lunina & Jørgen Olesen
Species within Gennadas differ from each other largely only in male (petasma) and female (thelycum) copulatory characters, which were restudied in scanning electron microscopy and used as a basis for phylogenetic analyses. Twenty-six petasma characters and 49 thelycum characters were identified. All sixteen recognized species of Gennadas and Aristaeomorpha foliacea (outgroup) were included as terminals. Four robust monophyletic clades were retrieved, described and diagnosed as new species groups. The thelycum characters had greater impact on...

Data from: Isotopic methods for non-destructive assessment of carbon dynamics in shrublands under long-term climate change manipulation

Louise C. Andresen, Maria T. Dominguez, Sabine Reinsch, Andy R. Smith, Inger Kappel Schmidt, Per Ambus, Claus Beier, Pascal Boeckx, Roland Bol, Giovanbattista De Dato, Bridget A. Emmett, Marc Estiarte, Mark H. Garnett, György Kröel-Dulay, Sharon L. Mason, Cecilie S. Nielsen, Josep Penuelas, Albert Tietema & Andrew R. Smith
1.Long-term climate change experiments are extremely valuable for studying ecosystem responses to environmental change. Examination of the vegetation and the soil should be non-destructive to guarantee long-term research. In this paper, we review field methods using isotope techniques for assessing carbon dynamics in the plant-soil-air continuum, based on recent field experience and examples from a European climate change manipulation network. 2.Eight European semi-natural shrubland ecosystems were exposed to warming and drought manipulations. One field site...

Data from: Explaining European fungal fruiting phenology with climate variability

Carrie Andrew, Einar Heegaard, Klaus Høiland, Beatrice Senn-Irlet, Thomas W. Kuyper, Irmgard Krisai-Greilhuber, Paul M. Kirk, Jacob Heilmann-Clausen, Alan C. Gange, Simon Egli, Claus Bässler, Ulf Büntgen, Lynne Boddy & Håvard Kauserud
Here we assess the impact of geographically dependent (latitude, longitude and altitude) changes in bioclimatic (temperature, precipitation and primary productivity) variability on fungal fruiting phenology across Europe. Two main nutritional guilds of fungi, saprotrophic and ectomycorrhizal, were further separated into spring and autumn fruiters. We used a path‐analysis to investigate how biogeographic patterns in fungal fruiting phenology coincided with seasonal changes in climate and primary production. Across central to northern Europe, mean fruiting varied by...

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  • University of Copenhagen
  • Aarhus University
  • University of Cambridge
  • Swedish University of Agricultural Sciences
  • Uppsala University
  • University of Oxford
  • Natural History Museum
  • University of Helsinki
  • Lund University
  • University of Oslo