124 Works

Data from: Human-facilitated metapopulation dynamics in an emerging pest species, Cimex lectularius

Toby Fountain, Gavin Horsburgh, Ludovic Duvaux, Klaus Reinhardt & Roger K. Butlin
The number and demographic history of colonists can have dramatic consequences for the way in which genetic diversity is distributed and maintained in a metapopulation. The bed bug (Cimex lectularius) is a re-emerging pest species whose close association with humans has led to frequent local extinction and colonisation, i.e. to metapopulation dynamics. Pest control limits the lifespan of sub-populations, causing frequent local extinctions, and human-facilitated dispersal allows the colonisation of empty patches. Founder events often...

Data from: Sequence co-evolution gives 3D contacts and structures of protein complexes

Thomas A. Hopf, Charlotta P. I. Schärfe, João P. G. L. M. Rodrigues, Anna G. Green, Chris Sander, Alexandre M. J. J. Bonvin, Debora S. Marks & Oliver Kohlbacher
Protein-protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of...

Data from: Contemporary evolution during invasion: evidence for differentiation, natural selection, and local adaptation

Robert I. Colautti & Jennifer A. Lau
Biological invasions are ‘natural’ experiments that can improve our understanding of contemporary evolution. We evaluate evidence for population differentiation, natural selection and adaptive evolution of invading plants and animals at two nested spatial scales: (i) among introduced populations (ii) between native and introduced genotypes. Evolution during invasion is frequently inferred, but rarely confirmed as adaptive. In common garden studies, quantitative trait differentiation is only marginally lower (~3.5%) among introduced relative to native populations, despite genetic...

Data from: Outbreeding effects in an inbreeding insect, Cimex lectularius

Toby Fountain, Roger K. Butlin, Klaus Reinhardt & Oliver Otti
In some species, populations with few founding individuals can be resilient to extreme inbreeding. Inbreeding seems to be the norm in the common bed bug, Cimex lectularius, a flightless insect that, nevertheless, can reach large deme sizes and persist successfully. However, bed bugs can also be dispersed passively by humans, exposing inbred populations to gene flow from genetically distant populations. The introduction of genetic variation through this outbreeding could lead to increased fitness (heterosis) or...

Data from: The noise egg: a cheap and simple device to produce low-frequency underwater noise for laboratory and field experiments

Karen De Jong, Gregor Schulte & Katja U. Heubel
Studying the effect of anthropogenic noise on animal behaviour and physiology is a field of growing scientific and management interest. Anthropogenic noise is internationally seen as major environmental concern, but knowledge of the response of animals to noise and its ecological and evolutionary consequences is disparate. Even though fish and invertebrates form the majority of aquatic taxa, the effects of noise on these taxa are largely understudied. Especially the consequences of noise for short-range communication...

Data from: Identification of habitat-specific biomes of aquatic fungal communities using a comprehensive nearly full-length 18S rRNA dataset enriched with contextual data

Katrin Panzer, Pelin Yilmaz, Michael Weiß, Lothar Reich, Michael Richter, Jutta Wiese, Rolf Schmaljohann, Antje Labes, Johannes F. Imhoff, Frank Oliver Glöckner & Marlis Reich
Molecular diversity surveys have demonstrated that aquatic fungi are highly diverse, and that they play fundamental ecological roles in aquatic systems. Unfortunately, comparative studies of aquatic fungal communities are few and far between, due to the scarcity of adequate datasets. We combined all publicly available fungal 18S ribosomal RNA (rRNA) gene sequences with new sequence data from a marine fungi culture collection. We further enriched this dataset by adding validated contextual data. Specifically, we included...

Data from: Alternative splicing substantially diversifies the transcriptome during early photomorphogenesis and correlates with the energy availability in Arabidopsis

Lisa Hartmann, Philipp Drewe-Boß, Theresa Wießner, Gabriele Wagner, Sascha Geue, Hsin-Chieh Lee, Dominik M. Obermüller, André Kahles, Jonas Behr, Fabian H. Sinz, Gunnar Rätsch & Andreas Wachter
Plants use light as source of energy and information to detect diurnal rhythms and seasonal changes. Sensing changing light conditions is critical to adjust plant metabolism and to initiate developmental transitions. Here we analyzed transcriptome-wide alterations in gene expression and alternative splicing (AS) of etiolated seedlings undergoing photomorphogenesis upon exposure to blue, red, or white light. Our analysis revealed massive transcriptome reprograming as reflected by differential expression of ~20% of all genes and changes in...

Data from: Hybrid EEG/EOG-based brain/neural hand exoskeleton restores fully independent daily living activities after quadriplegia

Surjo R. Soekadar, Matthias Witkowski, Jürgen Mellinger, Marius Nann, Cristina Gómez, Eloy Opisso, Josep Medina, Mario Cortese, Marco Cempini, Maria Chiara Carrozza, Leonardo G. Cohen, Niels Birbaumer & Nicola Vitiello
Direct brain control of advanced robotic systems promises substantial improvements in health care, for example, to restore intuitive control of hand movements required for activities of daily living in quadriplegics, like holding a cup and drinking, eating with cutlery, or manipulating different objects. However, such integrated, brain- or neural-controlled robotic systems have yet to enter broader clinical use or daily life environments. We demonstrate full restoration of independent daily living activities, such as eating and...

Data from: Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets

Mary E. Prendergast, Michael Buckley, Alison Crowther, Heidi Eager, Laurent Frantz, Ophélie Lebrasseur, Rainer Hutterer, Ardern Hulme-Beaman, Wim Van Neer, Katerina Douka, Margaret-Ashley Veall, Eréndira M. Quintana Morales, Verena J. Schuenemann, Ella Reiter, Richard Allen, Evangelos A. Dimopoulos, Richard M. Helm, Ceri Shipton, Ogeto Mwebi, Christiane Denys, Mark C. Horton, Stephanie Wynne-Jones, Jeffrey Fleisher, Chantal Radimilahy, Henry Wright … & Mark Horton
Human-mediated biological exchange has had global social and ecological impacts. In sub-Saharan Africa, several domestic and commensal animals were introduced from Asia in the pre-modern period; however, the timing and nature of these introductions remain contentious. One model supports introduction to the eastern African coast after the mid-first millennium CE, while another posits introduction dating back to 3000 BCE. These distinct scenarios have implications for understanding the emergence of long-distance maritime connectivity, and the ecological...

Data from: Impacts of species richness on productivity in a large-scale subtropical forest experiment

Yuanyuan Huang, Yuxin Chen, Nadia Castro-Izaguirre, Martin Baruffol, Matteo Brezzi, Anne Lang, Ying Li, Werner Härdtle, Werner Von Oheimb, Xuefeu Yang, Xiaojuan Liu, Kequan Pei, Sabine Both, Bo Yang, David Eichenberg, Thorsten Assmann, Jürgen Bauhus, Thorsten Behrens, François Buscot, Xiao-Yong Chen, Douglas Chester, Bing-Yang Ding, Walter Durka, Alexandra Erfmeier, Jingyun Fang … & Bernhard Schmid
Biodiversity experiments have shown that species loss reduces ecosystem functioning in grassland. To test whether this result can be extrapolated to forests, the main contributors to terrestrial primary productivity, requires large-scale experiments. We manipulated tree species richness by planting more than 150,000 trees in plots with 1 to 16 species. Simulating multiple extinction scenarios, we found that richness strongly increased stand-level productivity. After 8 years, 16-species mixtures had accumulated over twice the amount of carbon...

Data from: Visual modelling supports the potential for prey detection by means of diurnal active photolocation in a small cryptobenthic fish

Pierre-Paul Bitton, Sebastian Alejandro Yun Christmann, Matteo Santon, Ulrike K. Harant & Nico K. Michiels
Active sensing has been well documented in animals that use echolocation and electrolocation. Active photolocation, or active sensing using light, has received much less attention, and only in bioluminescent nocturnal species. However, evidence has suggested the diurnal triplefin Tripterygion delaisi uses controlled iris radiance, termed ocular sparks, for prey detection. While this form of diurnal active photolocation was behaviourally described, a study exploring the physical process would provide compelling support for this mechanism. In this...

Data from: Bobbing and fin-flicking in a small benthic fish

Matteo Santon, Felix Deiss, Bitton Pierre-Paul & Nico K. Michiels
Most anti-predator strategies increase survival of individuals by signalling to predators, by reducing the chances of being recognised as prey, or by bewildering a predator's perception. In fish, bobbing and fin-flicking are commonly considered as pursuit‑deterrent behaviours that signal a predator that it has been detected and thus lost its surprise-attack advantage. Yet, very few studies assessed whether such behavioural traits are restricted to the visual presence of a predator. In this study, we used...

Data from: Evolution of flexible biting in hyperdiverse parasitoid wasps

Thomas Van De Kamp, István Mikó, Arnold H. Staniczek, Benjamin Eggs, Daria Bajerlein, Tomáš Faragó, Lea Hagelstein, Elias Hamann, Rebecca Spiecker, Tilo Baumbach, Petr Janšta & Lars Krogmann
One key event in insect evolution was the development of mandibles with two joints, which allowed powerful biting, but restricted their movement to a single degree of freedom. These mandibles define the Dicondylia, which constitute over 99 percent of all extant insect species. It was common doctrine that the dicondylic articulation of chewing mandibles remained unaltered for more than 400 million years. We report highly modified mandibles overcoming the restrictions of a single degree of...

High plasticity in marmoset monkey vocal development from infancy to adulthood

Steffen Hage, Yasemin Gultekin, Kurt Hammerschmidt & David Hildebrand
The vocal behavior of human infants undergoes dramatic changes across their first year, while becoming increasingly speech-like. Surprisingly, vocal development in nonhuman primates has been assumed to be largely predetermined and completed within the first postnatal months. Contradicting this assumption, we found a dichotomy between the development of call features and vocal sequences in marmoset monkeys suggestive of a role for experience. While changes in call features were related to physical maturation, sequences of and...

Divergent natural selection alters male sperm competition success in Drosophila melanogaster

Biz Turnell, Klaus Reinhardt, Ralph Dobler, Marc Charette & Katrin Kaplan
Sexually selected traits may also be subject to non-sexual selection. If optimal trait values depend on environmental conditions, then “narrow sense” (i.e., non-sexual) natural selection can lead to local adaptation, with fitness in a certain environment being highest among individuals selected under that environment. Such adaptation can in turn drive ecological speciation via sexual selection. To date, most research on the effect of narrow-sense natural selection on sexually selected traits has focused on precopulatory measures...

Long-term (1901-2017) phenology data of 20 forest understory herbs in Europe, collected from herbaria and GBIF, used in: \"Forest wildflowers bloom earlier as Europe warms: Lessons from herbaria and spatial modeling\", New Phytologist

Franziska Merle Willems
Today plants often flower earlier due to climate warming, and the collection dates of herbarium specimens can provide proof of this.
To test for such fingerprints of climate change in Europe, we compiled a long-term (1901-2017) dataset from 6131 herbarium specimens of 20 early-flowering European forest understory herbs. The data were collected in the herbaria of Jena (JE), Stuttgart (STU) and Tübingen (TUB), and were complemented with herbarium data from the database GBIF.
The final data file...

Data from: The outcome of shared pollination services is affected by the density and spatial pattern of an attractive neighbour

Merav Seifan, Eva-Maria Hoch, Sven Hanoteaux & Katja Tielbörger
Interactions among neighbouring plants are often mediated by foraging choices of pollinators. For example, the presence of a conspicuous species may increase the number of pollinators attracted to its vicinity, indirectly increasing visitation rates also to neighbouring plants. Because pollinator choices are frequently density dependent, the presence of a conspicuous species at high densities may also increase competition for pollination services. Additionally, models predict that plant density will interact with spatial distribution in manipulating the...

Data from: Best practices for justifying fossil calibrations

James F. Parham, Philip C. J. Donoghue, Christopher J. Bell, Tyler D. Calway, Jason J. Head, Patricia A. Holroyd, Jun G. Inoue, Randall B. Irmis, Walter G. Joyce, Daniel T. Ksepka, José S. L. Patané, Nathan D. Smith, James E. Tarver, Marcel Van Tuinen, Ziheng Yang, Kenneth D. Angielczyk, Jenny M. Greenwood, Christy A. Hipsley, Jacobs Louis, Peter J. Makovicky, Johannes Müller, Krister T. Smith, Jessica M. Theodor, Rachel C. M. Warnock, Michael J. Benton … & Louis Jacobs
Our ability to correlate biological evolution with climate change, geological evolution, and other historical patterns is essential to understanding the processes that shape biodiversity. Combining data from the fossil record with molecular phylogenetics represents an exciting synthetic approach to this challenge. The first molecular divergence dating analysis (Zuckerkandl and Pauling 1962) was based on a measure of the amino acid differences in the hemoglobin molecule; with replacement rates established (calibrated) using inaccurate paleontological age estimates...

Data from: Nonsense-mediated decay of alternative pre-mRNA splicing variants is a major determinant of the Arabidopsis steady state transcriptome

Gabriele Drechsel, André Kahles, Anil K. Kesarwani, Eva Stauffer, Jonas Behr, Philipp Drewe, Gunnar Rätsch & Andreas Wachter
The nonsense-mediated decay (NMD) surveillance pathway can recognize erroneous transcripts and physiological mRNAs, such as precursor mRNA alternative splicing (AS) variants. Currently, information on the global extent of coupled AS and NMD remains scarce and even absent for any plant species. To address this, we conducted transcriptome-wide splicing studies using Arabidopsis thaliana mutants in the NMD factor homologs UP FRAMESHIFT1 (UPF1) and UPF3 as well as wild-type samples treated with the translation inhibitor cycloheximide. Our...

Data from: Range-dependent flexibility in the acoustic field of view of echolocating porpoises (Phocoena phocoena)

Danuta M. Wisniewska, John M. Ratcliffe, Kristian Beedholm, Christian B. Christensen, Mark Johnson, Jens C. Koblitz, Magnus Wahlberg & Peter M. Madsen
Toothed whales use sonar to detect, locate, and track prey. They adjust emitted sound intensity, auditory sensitivity and click rate to target range, and terminate prey pursuits with high-repetition-rate, low-intensity buzzes. However, their narrow acoustic field of view (FOV) is considered stable throughout target approach, which could facilitate prey escape at close-range. Here, we show that, like some bats, harbour porpoises can broaden their biosonar beam during the terminal phase of attack but, unlike bats,...

Data from: Stronger neural modulation by visual motion intensity in autism spectrum disorders

Ina Peiker, Till R. Schneider, Elizabeth Milne, Daniel Schöttle, Kai Vogeley, Alexander Münchau, Odette Schunke, Markus Siegel, Andreas K. Engel & Nicole David
Theories of autism spectrum disorders (ASD) have focused on altered perceptual integration of sensory features as a possible core deficit. Yet, there is little understanding of the neuronal processing of elementary sensory features in ASD. For typically developed individuals, we previously established a direct link between frequency-specific neural activity and the intensity of a specific sensory feature: Gamma-band activity in the visual cortex increased approximately linearly with the strength of visual motion. Using magnetoencephalography (MEG),...

Data from: Diabetes mellitus and prediabetes on kidney transplant waiting list- prevalence, metabolic phenotyping and risk stratification approach

Martina Guthoff, Dorothea Vosseler, Julia Langanke, Silvio Nadalin, Alfred Königsrainer, Hans-Ulrich Häring, Andreas Fritsche & Nils Heyne
Background: Despite a significant prognostic impact, little is known about disturbances in glucose metabolism among kidney transplant candidates. We assess the prevalence of diabetes mellitus (DM) and prediabetes on kidney transplant waiting list, its underlying pathophysiology and propose an approach for individual risk stratification. Methods: All patients on active kidney transplant waiting list of a large European university hospital transplant center were metabolically phenotyped. Results: Of 138 patients, 76 (55%) had disturbances in glucose metabolism....

Data from: Transcriptomic data from panarthropods shed new light on the evolution of insulator binding proteins in insects

Thomas Pauli, Lucia Vedder, Daniel Dowling, Malte Petersen, Karen Meusemann, Alexander Donath, Ralph S. Peters, Lars Podsiadlowski, Christoph Mayer, Shanlin Liu, Xin Zhou, Peter Heger, Thomas Wiehe, Lars Hering, Georg Mayer, Bernhard Misof & Oliver Niehuis
Background Body plan development in multi-cellular organisms is largely determined by homeotic genes. Expression of homeotic genes, in turn, is partially regulated by insulator binding proteins (IBPs). While only a few enhancer blocking IBPs have been identified in vertebrates, the common fruit fly Drosophila melanogaster harbors at least twelve different enhancer blocking IBPs. We screened recently compiled insect transcriptomes from the 1KITE project and genomic and transcriptomic data from public databases, aiming to trace the...

Data from: Regionalization of surface lipids in insects

Yiwen Wang, Zhitao Yu, Jianzhen Zhang & Bernard Moussian
Cuticular hydrocarbons (CHCs) play a critical role in the establishment of the waterproof barrier that prevents dehydration and wetting in insects. While rich data are available on CHC composition in different species, we know little about their distribution and organization. Here, we report on our studies of the surface barrier of the fruit fly Drosophila melanogaster applying a newly developed Eosin Y staining method. The inert Eosin Y penetrates different regions of the adult body...

Data from: Inhibition decorrelates visual feature representations in the inner retina

Katrin Franke, Philipp Berens, Timm Schubert, Matthias Bethge, Thomas Euler & Tom Baden
The retina extracts visual features for transmission to the brain. Different types of bipolar cell split the photoreceptor input into parallel channels and provide the excitatory drive for downstream visual circuits. Mouse bipolar cell types have been described at great anatomical and genetic detail, but a similarly deep understanding of their functional diversity is lacking. Here, by imaging light-driven glutamate release from more than 13,000 bipolar cell axon terminals in the intact retina, we show...

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