47 Works

Inter- and intraspecific selection in alien plants: how population growth, functional traits and climate responses change with residence time

Marco Brendel, Frank Schurr & Christine Sheppard
Aim: When alien species are introduced to new ranges, climate or trait mismatches may initially constrain their population growth. However, inter- and intraspecific selection in the new environment should cause population growth rates to increase with residence time. Using a species-for-time approach, we test whether with increasing residence time (a) negative effects of climatic mismatches between the species’ new and native range on population growth weaken, and (b) functional traits converge towards values that maximize...

Data from: Genomic and phenotypic differentiation of Arabidopsis thaliana along altitudinal gradients in the North Italian Alps

Torsten Günther, Christian Lampei, Ivan Barilar & Karl J. Schmid
Altitudinal gradients in mountain regions are short-range clines of different environmental parameters such as temperature or radiation. We investigated genomic and phenotypic signatures of adaptation to such gradients in five Arabidopsis thaliana populations from the North Italian Alps that originated from 580 to 2350 m altitude by resequencing pools of 19–29 individuals from each population. The sample includes two pairs of low- and high-altitude populations from two different valleys. High-altitude populations showed a lower nucleotide...

Data from: Bioclimatic variables derived from remote sensing: assessment and application for species distribution modeling

Eric Waltari, Ronny Schroeder, Kyle McDonald, Robert P. Anderson & Ana Carnaval
Remote sensing techniques offer an opportunity to improve biodiversity modeling and prediction worldwide. Yet, to date, the weather-station based WorldClim dataset has been the primary source of temperature and precipitation information used in correlative species distribution models. WorldClim consists of grids interpolated from in situ station data recorded primarily from 1960 to 1990. Those datasets suffer from uneven geographic coverage, with many areas of Earth poorly represented. Here, we compare two remote sensing data sources...

Data from: Shifts in plant functional community composition under hydrological stress strongly decelerate litter decomposition

Julia Walter, Carsten Buchmann & Frank Schurr
Litter decomposition is a key process of nutrient and carbon cycling in terrestrial ecosystems. The decomposition process will likely be altered under ongoing climate change, both through direct effects on decomposer activity, and through indirect effects caused by changes in litter quality. We studied how hydrological change indirectly affects decomposition via plant functional community restructuring caused by changes in plant species´ relative abundances (community weighted mean traits (CWM) and functional diversity). We further assessed how...

Data from: Human–wildlife conflict, benefit sharing and the survival of lions in pastoralist community-based conservancies

Sara Blackburn, J. Grant C. Hopcraft, Joseph O. Ogutu, Jason Matthiopoulos & Laurence Frank
Like many wildlife populations across Africa, recent analyses indicate that African lions are declining rapidly outside of small fenced areas. Community conservancies – privately protected areas that engage community members in conservation – may potentially maintain wildlife populations in unfenced pastoralist regions, but their effectiveness in conserving large carnivores has been largely unknown until now. We identify drivers of lion survival in community conservancies within the Masai Mara ecosystem, Kenya, applying mark–recapture analyses to continuous...

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....

Range-wide population viability analyses reveal high sensitivity to wildflower harvesting in extreme environments

Martina Treurnicht, Frank Schurr, Jasper Slingsby, Karen Esler & Joern Pagel
The ecological effects of harvesting from wild populations are often uncertain, especially since the sensitivity of populations to harvesting can vary across species’ geographical ranges. In the Cape Floristic Region (CFR, South Africa) biodiversity hotspot, wildflower harvesting is widespread and economically important, providing an income to many rural communities. However, with very few species studied to date, and without considering range-wide sensitivity to harvesting, there is limited information available to ensure the sustainability of wildflower...

Data from: Meta-analysis of Arabidopsis thaliana phospho-proteomics data reveals compartmentalization of phosphorylation motifs

Klaas J. Van Wijk, Giulia Friso, Dirk Walther & Waltraud X. Schulze
Protein (de)phosphorylation plays an important role in plants. To provide a robust foundation for subcellular phosphorylation signaling network analysis and kinase-substrate relationships, we performed a meta-analysis of 27 published and unpublished in-house mass spectrometry–based phospho-proteome data sets for Arabidopsis thaliana covering a range of processes, (non)photosynthetic tissue types, and cell cultures. This resulted in an assembly of 60,366 phospho-peptides matching to 8141 nonredundant proteins. Filtering the data for quality and consistency generated a set of...

Data from: Comparison of biometrical models for joint linkage association mapping

Wenxin Liu, Manje Gowda, Hans Peter Maurer, Sandra Fischer, Axel Schechert, Jochen C. Reif & Tobias Würschum
Joint linkage association mapping (JLAM) combines the advantages of linkage mapping and association mapping, and is a powerful tool to dissect the genetic architecture of complex traits. The main goal of this study was to use a cross-validation strategy, resample model averaging and empirical data analyses to compare seven different biometrical models for JLAM with regard to the correction for population structure and the quantitative trait loci (QTL) detection power. Three linear models and four...

The trisaccharide melezitose impacts honey bees and their intestinal microbiota

Victoria Seeburger, Paul D'Alvise, Basel Shaaban, Karsten Schweikert, Getrud Lohaus, Annette Schroeder & Martin Hasselmann
In general, honey bees (Apis mellifera L.) feed on honey produced from collected nectar. In the absence of nectar, during certain times of the year or in monocultural landscapes, honey bees forage on honeydew. Honeydew is excreted by different herbivores of the order Hemiptera that consume phloem sap of plant species. In comparison to nectar, honeydew is composed of a higher variety of sugars and additional sugars with higher molecular weight, like the trisaccharide melezitose...

Date from: Foundation species promote local adaptation and fine-scale distribution of herbaceous plants

Michael O'Brien, Elisa Carbonell, Gianalberto Losapio, Philipp Schlüter & Christian Schöb
1) Interactions among neighbors can alter demography and traits of commingled species via adaptation or plasticity in phenotypic expression and understanding these two mechanisms in diverse communities is important for determining the ecological and evolutionary consequences of plant–plant interactions. 2) We reciprocally transplanted perennial species (Arenaria armerina and Festuca indigesta) among patches of two foundation shrub species and open ground to assess whether origin microsite (defined as the spatially distinct abiotic and biotic conditions associated...

Data from: The Arabidopsis kinome: phylogeny and evolutionary insights into functional diversification

Monika Zulawski, Gunnar Schulze, Rostyslav Braginets, Stefanie Hartmann & Waltraud X. Schulze
Background: Protein kinases constitute a particularly large protein family in Arabidopsis with important functions in cellular signal transduction networks. At the same time Arabidopsis is a model plant with high frequencies of gene duplications. Here, we have conducted a systematic analysis of the Arabidopsis kinase complement, the kinome, with particular focus on gene duplication events. We matched Arabidopsis proteins to a Hidden-Markov Model of eukaryotic kinases and computed a phylogeny of 942 Arabidopsis protein kinase...

Data from: Transgenerational effects of extreme weather: perennial plant offspring show modified germination, growth and stoichiometry

Julia Walter, David E. V. Harter, Carl Beierkuhnlein & Anke Jentsch
1) Climate change is predicted to increase the frequency and magnitude of extreme climatic events. These changes will directly affect plant individuals and populations and thus modify plant community composition. Little is known, however, about transgenerational effects (i.e. the influence of the parental environment on offspring phenotype and performance beyond the effects of transmitted genes) of climate extremes and community composition. Perennial plants have been particularly neglected. This impedes projections on species adaptations and population...

Data from: The genomes of two key bumblebee species with primitive eusocial organisation

Ben M. Sadd, Seth M. Barribeau, Guy Bloch, Dirk C. De Graaf, Peter Dearden, Christine Elsik, Jurgen Gadau, Cornelius Grimmelikhuijzen, Martin Hasselmann, Jeffrey Lozier, Hugh Robertson, Guy Smagghe, Eckart Stolle, Matthias Van Vaerenbergh, Robert Waterhouse, Erich Bornberg-Bauer, Steffan Klasberg, Anna Bennett, Francisco Camara, Roderic Guigo, Katharina Hoff, Marco Mariotti, Monica Munos-Torres, Terence Murphy, Didac Santesmasses … & Kim C. Worley
Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome...

Data from: Phenotypic landscapes: phenological patterns in wild and cultivated barley

Sariel Hübner, Eyal Bdolach, Shachaf Ein-Gedy, Karl J. Schmid, Abraham Korol & Eyal Fridman
Phenotypic variation in natural populations is the outcome of the joint effects of environmentally induced adaptations and neutral processes on the genetic architecture of quantitative traits. In this study we examined the role of adaptation in shaping wild barley phenotypic variation along different environmental gradients. Detailed phenotyping of 164 wild barley (Hordeum spontaneum) accessions from Israel (of the Barley1K collection), and 18 cultivated barley (H. vulgare) varieties, was conducted in common garden field trials. Cluster...

Diversification in evolutionary arenas – assessment and synthesis

Nicolai M. Nürk, H. Peter Linder, Renske E. Onstein, Matthew J. Larcombe, Colin E. Hughes, Laura Piñeiro Fernández, Philipp M. Schlüter, Luis Valente, Carl Beierkuhnlein, Vanessa Cutts, Michael J. Donoghue, Erika J. Edwards, Richard Field, Suzette G.A. Flantua, Steven I. Higgins, Anke Jentsch, Sigrid Liede-Schumann & Michael D. Pirie
Understanding how and why rates of evolutionary diversification vary is a central issue in evolutionary biology, ecology and biogeography. The concept of adaptive radiation has attracted much interest, but is metaphorical and verbal in nature, making it difficult to quantitatively compare different evolutionary lineages or geographic regions. In addition, the causes of evolutionary stasis are relatively neglected. Here we review the central concepts in the evolutionary diversification literature and bring these together by proposing a...

Data from: Biomass–density relationships of plant communities deviate from the self‐thinning rule due to age structure and abiotic stress

Maximiliane Herberich, Sebastian Gayler, Madhur Anand, Katja Tielbörger & Maximiliane Marion Herberich
A pertinent debate in plant ecology centers around the generality of the self-thinning rule. However, studies focused on highly simplified settings such as even-aged monospecific populations or optimal conditions. This neglects the fact that most natural communities, to which the classical self-thinning slope is often applied, are age-structured, composed of multiple species and exposed to various types of abiotic stress. With the help of an individual-based model, we relax these simplified assumptions and systematically test...

Data from: Multiple simultaneous treatments change plant response from adaptive parental effects to within-generation plasticity, in Arabidopsis thaliana

Christian Lampei
In general, studies on plant phenotypic plasticity concentrate on plant responses to different levels of a single environmental factor. Under natural conditions, however, multiple environmental factors often vary simultaneously. I studied the consequences for lifetime fitness caused by single treatments or treatment combinations by investigating patterns of phenotypic plasticity within and between generations. The parental plants (3 genotypes of the annual plant Arabidopsis thaliana) received zero, one or two stress treatments at an early life-stage....

Data from: RNA-Seq analysis identifies genes associated with differential reproductive success under drought-stress in accessions of wild barley Hordeum spontaneum

Sariel Hübner, Abraham B. Korol & Karl J. Schmid
Background: The evolutionary basis of reproductive success in different environments is of major interest in the study of plant adaptation. Since the reproductive stage is particularly sensitive to drought, genes affecting reproductive success during this stage are key players in the evolution of adaptive mechanisms. We used an ecological genomics approach to investigate the reproductive response of drought-tolerant and sensitive wild barley accessions originating from different habitats in the Levant. Results: We sequenced mRNA extracted...

Environmental heterogeneity predicts global species richness patterns better than area

Kristy Udy, Matthias Fritsch, Katrin Meyer, Ingo Grass, Sebastian Hanß, Florian Hartig, Thomas Kneib, Hoger Kreft, Collins Kukuna, Guy Pe'er, Hannah Reininghaus, Britta Tietjen, Clara-Sophie Van Waveren, Kerstin Wiegand & Teja Tscharntke
Aim: It is widely accepted that biodiversity can be determined by niche-relate processes and by pure area effects from local to global scales. Their relative importance, however, is still disputed, and empirical tests are still surprisingly scarce at the global scale. We compare the explanatory power of area and environmental heterogeneity as a proxy for niche-related processes as drivers of native mammal species richnessworldwide and with biogeographical regions. Location: Global Time Period: Data was collated...

Data from: QTL detection power of multi-parental RIL populations in Arabidopsis thaliana

Jonas R. Klasen, Hans-Peter Piepho, Benjamin Stich & H-P Piepho
A major goal of today's biology is to understand the genetic basis of quantitative traits. This can be achieved by statistical methods that evaluate the association between molecular marker variation and phenotypic variation in different types of mapping populations. The objective of this work was to evaluate the statistical power of QTL detection of various multi-parental mating designs as well as to assess the reasons for the observed differences. Our study was based on empirical...

Data from: N balance and cycling of Inner Mongolia typical steppe - a comprehensive case study of grazing effects

Marcus Giese, Holger Brueck, Yingzhi Gao, Shan Lin, Markus Steffens, Ingrid Kögel-Knabner, Thomas Glindemann, Andreas Susenbeth, Friedhelm Taube, Klaus Butterbach-Bahl, Xunhua Zheng, Carsten Hoffmann, Yongfei Bai & Xingguo Han
Increasing grazing pressure and climate change affect nitrogen (N) dynamics of grassland ecosystems in the Eurasian Steppe belt with unclear consequences for future delivery of essential services such as forage production, C sequestration, and diversity conservation. The identification of key processes responsive to grazing is crucial to optimize grassland management. In this comprehensive case study of a Chinese typical steppe, we present an in-depth analysis of grazing effects on N dynamics including the balance of...

Data from: Relatedness severely impacts accuracy of marker- assisted selection for disease resistance in hybrid wheat

Jochen C. Reif, Yusheng Zhao, Manje Gowda, Tobias Würschum, C. Friedrich H. Longin, Thomas Miedaner, Erhard Ebmeyer, Ralf Schachschneider, Johannes Schacht, Jean-Pierre Martinant, Michael F. Mette & Ebrahim Kazmann
The accuracy of genomic selection depends on the relatedness between the members of the set in which marker effects are estimated based on evaluation data and the types for which performance is predicted. Here, we investigate the impact of relatedness on the performance of marker-assisted selection for fungal disease resistance in hybrid wheat. A large and diverse mapping population of 1,739 elite European winter wheat inbred lines and hybrids was evaluated for powdery mildew, leaf...

Data from: Targeted re-sequencing of five Douglas-fir provenances reveals population structure and putative target genes of positive selection

Thomas Müller, Fabian Freund, Henning Wildhagen & Karl J. Schmid
Douglas-fir (Pseudotsuga menziesii) occurs in a coastal and an interior variety that differ in drought tolerance and other adaptive traits. To characterize genome-wide levels of genetic diversity in coding regions and to identify genes involved in local adaptation, we used targeted sequence capture to re-sequence 72 trees representing one interior and four coastal provenances. A custom NimbleGen sequence capture array was designed from 57,110 putative unique transcripts (PUTs) to enrich genomic sequencing libraries for these...

Data from: Genomic and phenotypic evidence for an incomplete domestication of South American grain amaranth (Amaranthus caudatus)

Markus G. Stetter, Thomas Mueller & Karl J. Schmid
The domestication syndrome comprises phenotypic changes that differentiate crops from their wild ancestors. We compared the genomic variation and phenotypic differentiation of the two putative domestication traits seed size and seed colour of the grain amaranth Amaranthus caudatus, which is an ancient crop of South America, and its two close wild relatives and putative ancestors A. hybridus and A. quitensis. Genotyping 119 accessions of the three species from the Andean region using genotyping by sequencing...

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Resource Types

  • Dataset


  • University of Hohenheim
  • University of Göttingen
  • University of Bayreuth
  • German Center for Integrative Biodiversity Research
  • University of Adelaide
  • University of Glasgow
  • Max Planck Institute for Molecular Plant Physiology
  • University of Otago
  • United States Department of Agriculture
  • University of Haifa