73 Works

Data from: Temporal variation in antibiotic environments slows down resistance evolution in pathogenic Pseudomonas aeruginosa

Roderich Roemhild, Camilo Barbosa, Robert E. Beardmore, Gunther Jansen & Hinrich Schulenburg
Antibiotic resistance is a growing concern to public health. New treatment strategies may alleviate the situation by slowing down the evolution of resistance. Here, we evaluated sequential treatment protocols using two fully independent laboratory-controlled evolution experiments with the human pathogen Pseudomonas aeruginosa PA14 and two pairs of clinically relevant antibiotics (doripenem/ciprofloxacin and cefsulodin/gentamicin). Our results consistently show that the sequential application of two antibiotics decelerates resistance evolution relative to monotherapy. Sequential treatment enhanced population extinction...

Experimental data for Pseudomonas aeruginosa from experimental evolution under different bottleneck sizes and antibiotic selection pressures

Hinrich Schulenburg
We here combined evolution experiments with genomic and genetic analyses to assess whether bottleneck size and antibiotic-induced selection influences the evolutionary path to resistance in pathogenic Pseudomonas aeruginosa, one of the most problematic opportunistic human pathogens. Two sets of evolution experiments were performed across 16 transfers, in which either the aminoglycoside gentamicin or the fluoroquinolone ciprofloxacin were used as antibiotic. The evolutionary response was studied using counts of bacterial cells at the end of each...

Data from: Association mapping of morphological traits in wild and captive zebra finches: reliable within but not between populations

Ulrich Knief, Holger Schielzeth, Niclas Backstrom, Georg Hemmrich-Stanisak, Michael Wittig, Andre Franke, Simon C. Griffith, Hans Ellegren, Bart Kempenaers & Wolfgang Forstmeier
Identifying causal genetic variants underlying heritable phenotypic variation is a longstanding goal in evolutionary genetics. We previously identified several quantitative trait loci (QTL) for five morphological traits in a captive population of zebra finches (Taeniopygia guttata) by whole-genome linkage mapping. We here follow up on these studies with the aim to narrow down on the quantitative trait variants (QTN) in one wild and three captive populations. First, we performed an association study using 672 single...

Data from: Conservation genetics of the pond bat (Myotis dasycneme) with special focus on the populations in northwestern Germany and Jutland, Denmark

Liselotte Wesley Andersen, Ronja Dirksen, Elena A. Nikulina, Hans J. Baagøe, Gunars Petersons, Péter Estók, Oleg L. Orlov, Maria V. Orlova, Florian Gloza-Rausch, Matthias Göttsche, Esben Fjederholt, Frauke Krüger & Morten Elmeros
Conservation genetics is important in the management of endangered species, helping to understand their connectivity and long-term viability, thus identifying populations of importance for conservation. The pond bat (Myotis dasycneme) is a rare species classified as ‘Near threatened’ with a wide but patchy Palearctic distribution. A total of 277 samples representing populations in Denmark, Germany, Latvia, Hungary and Russia were used in the genetic analyses; 224 samples representing Denmark, Germany and Russia were analysed at...

Data from: Multiple sequence alignment averaging improves phylogeny reconstruction

Haim Ashkenazy, Itamar Sela, Eli Levy Karin, Giddy Landan & Tal Pupko
The classic methodology of inferring a phylogenetic tree from sequence data is composed of two steps. First, a multiple sequence alignment (MSA) is computed. Then, a tree is reconstructed assuming the MSA is correct. Yet, inferred MSAs were shown to be inaccurate and alignment errors reduce tree inference accuracy. It was previously proposed that filtering unreliable alignment regions can increase the accuracy of tree inference. However, it was also demonstrated that the benefit of this...

Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history

Dilan Sarange Rajapaksha Patiranage, Elodie Rey, Nazgol Emrani, Gordon Wellman, Karl Schmid, Sandra Schmöckel, Mark Tester & Christian Jung
Quinoa germplasm preserves useful and substantial genetic variation, yet it remains untapped due to a lack of implementation of modern breeding tools. We have integrated field and sequence data to characterize a large diversity panel of quinoa. Whole-genome sequencing of 310 accessions revealed 2.9 million polymorphic high confidence SNP loci. Highland and Lowland quinoa were clustered into two main groups, with FST divergence of 0.36 and fast LD decay of 6.5 and 49.8 Kb, respectively....

Neutral processes related to regional bee commonness and dispersal distances are important predictors of plant-pollinator networks along gradients of climate and landscape conditions

Markus Arne Sydenham, Zander Venter, Stein Moe, Katrine Eldegard, Michael Kuhlmann, Trond Reitan, Claus Rasmussen, Robert Paxton, Yoko Dupont, Astrid Skrindo, Megan Nowell, Stein Hegland, Anders Nielsen, Jens Olesen & Graciela Rusch
Understanding how niche-based and neutral processes contribute to the spatial variation in plant-pollinator interactions is central to designing effective pollination conservation schemes. Such schemes are needed to reverse declines of wild bees and other pollinating insects and to promote pollination services to wild and cultivated plants. We used data on wild bee interactions with plants belonging to the four tribes Loteae, Trifolieae, Anthemideae, and either spring- or summer-flowering Cichorieae, sampled systematically along a 682km latitudinal...

Additional file 1 of A correlation map of genome-wide DNA methylation patterns between paired human brain and buccal samples

Yasmine Sommerer, Olena Ohlei, Valerija Dobricic, Derek H. Oakley, Tanja Wesse, Sanaz Sedghpour Sabet, Ilja Demuth, Andre Franke, Bradley T. Hyman, Christina M. Lill & Lars Bertram
Additional file 1. Supplementary Tables.

Cellular bicarbonate accumulation and vesicular proton transport promote calcification in the sea urchin larva

Marian Hu, Marian Hu, Inga Petersen, William Chang, Christine Blurton & Meike Stumpp
The sea urchin embryo develops a calcitic endoskeleton through intracellular formation of amorphous calcium carbonate (ACC). Intracellular precipitation of ACC, requires HCO3-/CO32- concentrating as well as proton export mechanisms to promote calcification. These processes are of fundamental importance in biological mineralization, but remain largely unexplored. Here we demonstrate that the calcifying primary mesenchyme cells (PMCs) utilize Na+/H+- exchange (NHE) mechanisms to control cellular pH homeostasis during maintenance of the skeleton. During skeleton re-calcification, pHi of...

Data from: Plasticity and epistasis strongly affect bacterial fitness after losing multiple metabolic genes

Glen D’Souza, Silvio Waschina, Christoph Kaleta, Christian Kost & Glen D'Souza
Many bacterial lineages lack seemingly essential metabolic genes. Previous work suggested selective benefits could drive the loss of biosynthetic functions from bacterial genomes when the corresponding metabolites are sufficiently available in the environment. However, the factors that govern this ‘genome streamlining’ remain poorly understood. Here we determine the effect of plasticity and epistasis on the fitness of Escherichia coli genotypes from whose genome biosynthetic genes for one, two, or three different amino acids have been...

Data from: Climate and fishing steer ecosystem regeneration to uncertain economic futures

Thorsten Blenckner, Marcos Llope, Christian Möllmann, Rudi Voss, Martin F. Quaas, Michele Casini, Martin Lindegren, Carl Folke, Nils Chr. Stenseth & C. Mollmann
Overfishing of large predatory fish populations has resulted in lasting restructurings of entire marine food webs worldwide, with serious socio-economic consequences. Fortunately, some degraded ecosystems show signs of recovery. A key challenge for ecosystem management is to anticipate the degree to which recovery is possible. By applying a statistical food-web model, using the Baltic Sea as a case study, we show that under current temperature and salinity conditions, complete recovery of this heavily altered ecosystem...

Data from: Population genomics of local adaptation versus speciation in coral reef fishes (Hypoplectrus spp, Serranidae)

Sophie Picq, Owen McMillan, Oscar Puebla & W. Owen McMillan
Are the population genomic patterns underlying local adaptation and the early stages of speciation similar? Addressing this question requires a system in which i. local adaptation and the early stages of speciation can be clearly identified and distinguished, ii. the amount of genetic divergence driven by the two processes is similar, and iii. comparisons can be repeated both taxonomically (for local adaptation) and geographically (for speciation). Here, we report just such a situation in the...

Data from: Phylogeographic differentiation versus transcriptomic adaptation to warm temperatures in Zostera marina, a globally important seagrass

Alexander Jueterbock, Susanne U. Franssen, Nina Bergmann, Jenny Gu, James A. Coyer, Thorsten B. H. Reusch, Erich Bornberg-Bauer & Jeanine L. Olsen
Populations distributed across a broad thermal cline are instrumental in addressing adaptation to increasing temperatures under global warming. Using a space-for-time substitution design, we tested for parallel adaptation to warm temperatures along two independent thermal clines in Zostera marina, the most widely distributed seagrass in the temperate Northern Hemisphere. A North–South pair of populations was sampled along the European and North American coasts and exposed to a simulated heatwave in a common-garden mesocosm. Transcriptomic responses...

Data from: Patterns and thresholds of grazing-induced changes in community structure and ecosystem functioning: species-level responses and the critical role of species traits

Wenhuai Li, Fengwei Xu, Shuxia Zheng, Friedhelm Taube & Yongfei Bai
Overgrazing has resulted in widespread decline in biodiversity and ecosystem functioning in grasslands worldwide in recent decades. However, few studies have examined the patterns and thresholds of grazing-induced changes in community structure and ecosystem functioning along a grazing gradient and based on species-level responses and plant functional traits. To identify the thresholds of grazing intensity at both species and community levels, we conducted a grazing manipulation experiment with seven levels of grazing intensity (0–9 sheep...

Data from: Adhesion forces and mechanics in mannose-mediated acanthamoeba interactions

Steven Huth, Julia F. Reverey, Matthias Leippe & Christine Selhuber‐Unkel
The human pathogenic amoeba Acanthamoeba castellanii (A. castellanii) causes severe diseases, including acanthamoeba keratitis and encephalitis. Pathogenicity arises from the killing of target-cells by an extracellular killing mechanism, where the crucial first step is the formation of a close contact between A. castellanii and the target-cell. This process is mediated by the glycocalix of the target-cell and mannose has been identified as key mediator. The aim of the present study was to carry out a...

Data from: Connectivity increases trophic subsidies in fragmented landscapes

Christine L. Hawn, John D. Herrmann, Sean R. Griffin & Nick M. Haddad
Landscape corridors mitigate the negative effects of habitat fragmentation by increasing dispersal. Corridors also increase biodiversity in connected habitat fragments, suggestive of metacommunity dynamics. What is unknown in this case is the mechanisms through which metacommunity dynamics act. Working in a large-scale fragmentation experiment, we tested the effect of corridors on the movement of prey species and subsequent effects on predator nutrition (which we call trophic subsidies). We enriched plants of central patches with 15N,...

Data from: Inter-chromosomal coupling between vision and pigmentation genes during genomic divergence

Kosmas Hench, Marta Vargas, Marc P. Höppner, W. Owen McMillan & Oscar Puebla
Recombination between loci underlying mate choice and ecological traits is a major evolutionary force acting against speciation with gene flow. The evolution of linkage disequilibrium between such loci is therefore a fundamental step in the origin of species. Here, we show that this process can take place in the absence of physical linkage in hamlets—a group of closely related reef fishes from the wider Caribbean that differ essentially in colour pattern and are reproductively isolated...

Data from: Exotic plant species are locally adapted but not to high UV‐B radiation: a reciprocal multi‐species experiment

Maria Hock, Rainer W. Hofmann, Caroline Müller & Alexandra Erfmeier
Ultraviolet (UV) radiation intensities differ among global regions, with significantly higher levels in the southern hemisphere. UV-B may act as an environmental filter during plant invasions, which might particularly apply to plant species from Europe introduced to New Zealand. Just like for any other abiotic or biotic filter, successful invaders can cope with novel environmental conditions via plastic responses and/or through rapid adaptation by natural selection in the exotic range. We conducted a multi-species experiment...

Data from: A multi-taxa assessment of the effectiveness of agri-environmental schemes for biodiversity management

Fabian A. Boetzl, Jochen Krauss, Jonathan Heinze, Hannes Hoffmann, Jan Juffa, Sebastian König, Elena Krimmer, Maren Prante, Emily A. Martin, Andrea Holzschuh & Ingolf Steffan-Dewenter
Agri-environmental schemes (AES) aim to restore biodiversity and biodiversity-mediated ecosystem services in landscapes impoverished by modern agriculture. However, a systematic, empirical evaluation of different AES types across multiple taxa and functional groups is missing. Within one orthogonal design, we studied sown flowering AES types with different temporal continuity, size, and landscape context and used calcareous grasslands as semi-natural reference habitat. We measured species richness of twelve taxonomic groups (vascular plants, cicadas, orthopterans, bees, butterflies, moths,...

Breaking force Spekia

Wencke Krings, Alexander Kovalev & Stanislav N. Gorb
One molluscan autapomorphy is the radula, the organ used for feeding. Here, for the first time, the performance and failure of taenioglossan radular teeth were tested in a biomechanical experiment which in turn allowed building hypotheses about tooth functionalities. Shear load was applied to tooth cusps with a force transducer until structural failure occurred, the broken area was measured, and finally breaking stress was calculated. These experiments were carried out under dry and wet conditions....

Pollinator community predicts trait-matching between oil-producing flowers and a guild of oil-collecting bees

Hilke Hollens-Kuhr, Timotheüs Van Der Niet, Ruth Cozien & Michael Kuhlmann
The impact of pollinator community diversity on trait-matching in plant-pollinator interactions is poorly studied, even though many mutualisms involve multiple interaction partners. We studied ten communities in which one to three species of oil-collecting Rediviva bee pollinate the long-spurred, oil-producing flowers of Diascia ‘floribunda’ to examine how pollinator diversity affects covariation of functional traits across sites and trait-matching within sites. Floral spur-length was significantly correlated with weighted grand mean foreleg length of the local bee...

Rewetting does not return drained fen peatlands to their old selves

Juergen Kreyling, Franziska Tanneberger, Florian Jansen, Sebastian Van Der Linden, Camiel Aggenbach, Volker Blüml, John Couwenberg, Willem-Jan Emsens, Hans Joosten, Agatha Klimkowska, Wiktor Kotowski, Lukasz Kozub, Bernd Lennartz, Yvonne Liczner, Haojie Liu, Dierk Michaelis, Claudia Oehmke, Karsten Parakenings, Elisabeth Pleyl, Arne Poyda, Stefanie Raabe, Markus Röhl, Kirsten Rücker, Anett Schneider, Joachim Schrautzer … & Gerald Jurasinski
Peatlands, in particular groundwater-fed fens of the temperate zone, have been drained for agriculture, forestry and peat extraction for a long time and on a large scale. Drainage turns peatlands from a carbon and nutrient sink into a respective source, diminishes water regulation capacity at the landscape scale, causes continuous surface height loss and destroys their typical biodiversity. Over the last decades, drained peatlands have been rewetted for biodiversity restoration and, as it strongly decreases...

Data from: Timing of spring departure of long distance migrants correlates with previous year's conditions at their breeding site

Françoise Amélineau, Nicolas Delbart, Philipp Schwemmer, Riho Marja, Jérôme Fort, Stefan Garthe, Jaanus Elts, Philippe Delaporte, Pierre Rousseau, Françoise Duraffour & Pierrick Bocher
Precise timing of the migration is crucial for animals targeting seasonal resources at locations encountered across their annual cycle. Upon departure, long distance migrants need to anticipate unknown environmental conditions at their arrival site, and they do zkzdsxso with their internal annual clock. Here, we tested the hypothesis that long distance migrants synchronize their circannual clock according to the phenology of their environment during the breeding season, and therefore adjust their spring departure date according...

Environment regimes play an important role in structuring trait- and taxonomy-based temporal beta diversity of riverine diatoms

Naicheng Wu, Yaochun Wang, Yixia Wang, Xiuming Sun, Claas Faber & Nicola Fohrer
This dataset is from the manuscript 'Environment regimes play an important role in structuring trait-and taxonomy-based temporal beta diversity of riverine diatoms' whereby daily riverine diatom data, flow, nutrients and metal ions data were used to examine i) the relative roles of turnover and nestedness components to trait- and taxonomy-based temporal beta diversity of riverine diatoms; ii) whether trait-based temporal beta diversity provides complementary information to taxonomy-based temporal beta diversity; iii) the relative roles of...

Data from: Diet of the insectivorous bat Pipistrellus nathusii during autumn migration and summer residence

Frauke Krüger, Elizabeth L. Clare, William O. C. Symondson, Oskars Keišs & Gunārs Pētersons
Migration is widespread among vertebrates. Yet bat migration has received little attention and only in the recent decades knowledge of it has been gained. Migration can cause significant changes in behaviour and physiology, due to increasing energy demands and aerodynamic constraints. Dietary shifts, for examples, have been shown to occur in birds before onset of migration. For bats it is not known if a change in diet occurs during migration, although especially breeding season related...

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