44 Works

Data from: Peptidomics-based phylogeny and biogeography of Mantophasmatodea (Hexapoda)

Reinhard Predel, Susanne Neupert, Wolf Huetteroth, Jörg Kahnt, Dietmar Waidelich & Steffen Roth
The insect order Mantophasmatodea was described in 2002. Prior to that time, several generations of entomologists had assumed that all major insect taxa were known; thus, its description was a sensation for zoologists. Since then, a surprising abundance and species diversity of this taxon have been found, particularly in the winter rainfall region of South Africa. To learn more about the evolutionary lineages, speciation, and biogeography of Mantophasmatodea, we applied an unusual peptidomics approach. We...

Data from: Evolutionary advantage of small populations on complex fitness landscapes

Kavita Jain, Joachim Krug & Su-Chan Park
Recent experimental and theoretical studies have shown that small asexual populations evolving on complex fitness landscapes may achieve a higher fitness than large ones due to the increased heterogeneity of adaptive trajectories. Here we introduce a class of haploid three-locus fitness landscapes that allow the investigation of this scenario in a precise and quantitative way. Our main result derived analytically shows how the probability of choosing the path of the largest initial fitness increase grows...

Data from: Zinc supplementation inhibits complement activation in age-related macular degeneration

Dzenita Smailhodzic, Freekje Van Asten, Anna M. Blom, Frida C. Mohlin, Anneke I. Den Hollander, Johannes P. H. Van De Ven, Ramon A. C. Van Huet, Joannes M. M. Groenewoud, Yuan Tian, Tos T. J. M. Berendschot, Yara T. E. Lechanteur, Sascha Fauser, Chris De Bruijn, Mohamed R. Daha, Gert Jan Van Der Wilt, Carel B. Hoyng & B. Jeroen Klevering
Age-related macular degeneration (AMD) is the leading cause of blindness in the Western world. AMD is a multifactorial disorder but complement-mediated inflammation at the level of the retina plays a pivotal role. Oral zinc supplementation can reduce the progression of AMD but the precise mechanism of this protective effect is as yet unclear. We investigated whether zinc supplementation directly affects the degree of complement activation in AMD and whether there is a relation between serum...

Detecting selection using extended haplotype homozygosity (EHH)-based statistics in unphased or unpolarized data

Alexander Klassmann & Mathieu Gautier
Analysis of population genetic data often includes the search for genomic regions with signs of recent positive selection. One of the approaches involves the concept of Extended Haplotype Homozygosity (EHH) and its associated statistics. These statistics typically need phased haplotypes and, some of them, polarized variants. Here, we unify and extend previously proposed modifications to loosen these requirements. We compare the modified versions with the original ones by measuring the False Discovery Rate in simulated...

Phenotype pictures of Arabidopsis thaliana in high light and low light conditions

Benedict Wieters & Juliette De Meaux
The rate at which plants grow is a major functional trait in plant ecology. However, little is known about its evolution in natural populations. Here, we investigate evolutionary and environmental factors shaping variation in the growth rate of Arabidopsis thaliana. We used plant diameter as a proxy to monitor plant growth over time in environments that mimicked latitudinal differences in the intensity of natural light radiation, across a set of 278 genotypes sampled within four...

Data from: Bacterial diversity amplifies nutrient-based plant-soil feedbacks

Simone Weidner, Robert Koller, Ellen Latz, George Kowalchuk, Michael Bonkowski, Stefan Scheu & Alexandre Jousset
Plants foster diverse assemblages of bacteria in the rhizosphere serving important functions which may result in enhanced plant growth. Microbial diversity is increasingly recognized to shape the functionality of microbial communities. This leads to the assumption that there is a positive relationship between rhizosphere diversity and plant growth. Here we investigate how bacterial diversity affects the mineralization of organic matter and plant nutrient acquisition. We hypothesized that altered bacterial diversity will affect nitrogen mineralisation, uptake...

Data from: Competition is crucial for social comparison processes in long-tailed macaques

Stefanie Keupp, Rowan Titchener, Thomas Bugnyar, Thomas Mussweiler & Julia Fischer
Humans modulate their self-evaluations and behaviour as a function of conspecific presence and performance. In this study we tested for the presence of human-like social comparison effects in long-tailed macaques (Macaca fascicularis). The monkeys’ task was to extract food from an apparatus by pulling drawers within reach and we measured latency between drawer-pulls. Subjects either worked on the task with a partner who could access the apparatus from an adjacent cage, worked in the absence...

Macrobenthic Cumacea collected by epibenthic sledge from the Amundsen Sea in March 2008 and from the Prince Gustav Channel and Duse Bay, Eastern Antarctic Peninsula in March 2018

Katrin Linse, Laura Steib, Angelika Brandt & Davide Di Franco
In 2008 RRS James Clark Ross investigated the marine benthic biodiversity in Amundsen Sea and in 2018 the marine benthic biodiversity of the Prince Gustav Channel (PGC) area and the macrobenthic cumacean fauna (Peracarida, Crustacea) collected by epibenthic sledge (EBS) has been assessed for species richness, abundance and assemblage composition. In total 4431 cumacean specimens assigned to 58 morphospecies and 5 families were identified. To set the cumacean dataset into a wider context, published cumacean...

Toolbox for: Teaching lab for large cohorts of undergraduates: private and social information in fish

Jost Borcherding, Mike M Webster & Katja Heubel
A challenge in the Bachelor's studies in Biology, is to strive for a balance between reducing the teaching of practical scientific experiments to what is feasible in a short time, and teaching "real" science in undergraduate labs for high numbers of participants. We describe a lab in behavioural biology, with the primary focus on the student learning. However, also the underlying scientific question and the results of the experiment, namely the behaviour of the three-spined...

Data from: Reciprocity and the tragedies of maintaining and providing the commons

Simon Gächter, Felix Kölle & Simone Quercia
Social cooperation often requires collectively beneficial but individually costly restraint to maintain a public good, or it needs costly generosity to create one. Status quo effects predict that maintaining a public good is easier than providing a new one. Here, we show experimentally and with simulations that even under identical incentives, low levels of cooperation (the ‘tragedy of the commons’) are systematically more likely in maintenance than provision. Across three series of experiments, we find...

Data from: Phytochrome diversity in green plants and the origin of canonical plant phytochromes

Fay-Wei Li, Michael Melkonian, Carl J. Rothfels, Juan Carlos Villarreal, Dennis W. Stevenson, Sean W. Graham, Gane Ka-Shu Wong, Kathleen M. Pryer & Sarah Mathews
Phytochromes are red/far-red photoreceptors that play essential roles in diverse plant morphogenetic and physiological responses to light. Despite their functional significance, phytochrome diversity and evolution across photosynthetic eukaryotes remain poorly understood. Using newly available transcriptomic and genomic data we show that canonical plant phytochromes originated in a common ancestor of streptophytes (charophyte algae and land plants). Phytochromes in charophyte algae are structurally diverse, including canonical and non-canonical forms, whereas in land plants, phytochrome structure is...

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: Genome-wide patterns of transposon proliferation in an evolutionary young hybrid fish

Stefan Dennenmoser, Fritz J. Sedlazeck, Michael C. Schatz, Janine Altmüller, Matthias Zytnicki & Arne W. Nolte
Hybridization can induce transposons to jump into new genomic positions, which may result in their accumulation across the genome. Alternatively, transposon copy numbers may increase through non-allelic (ectopic) homologous recombination in highly repetitive regions of the genome. The relative contribution of transposition bursts versus recombination-based mechanisms to evolutionary processes remains unclear because studies on transposon dynamics in natural systems are rare. We assessed the genome-wide distribution of transposon insertions in a young hybrid lineage (“invasive...

RepeatModeler and RepeatMasker output files

Reuben Nowell, Christopher Wilson, Pedro Almeida, Philipp Schiffer, Diego Fontaneto, Lutz Becks, Fernando Rodriguez, Irina Arkhipova & Timothy Barraclough
Transposable elements (TEs) are selfish genomic parasites whose ability to spread autonomously is facilitated by sexual reproduction in their hosts. If hosts become obligately asexual, TE frequencies and dynamics are predicted to change dramatically, but the long-term outcome is unclear. Here, we test current theory using whole-genome sequence data from eight species of bdelloid rotifers, a class of invertebrates in which males are thus far unknown. Contrary to expectations, we find a variety of active...

Data from: The best of both worlds: a combined approach for analyzing microalgal diversity via metabarcoding and morphology-based methods

Sophie Groendahl, Maria Kahlert & Patrick Fink
An increasing number of studies use next generation sequencing (NGS) to analyze complex communities, but is the method sensitive enough when it comes to identification and quantification of species? We compared NGS with morphology-based identification methods in an analysis of microalgal (periphyton) communities. We conducted a mesocosm experiment in which we allowed two benthic grazer species to feed upon benthic biofilms, which resulted in altered periphyton communities. Morphology-based identification and 454 (Roche) pyrosequencing of the...

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: Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies

Jonas Zimmermann, Gernot Glöckner, Regine Jahn, Neela Enke & Birgit Gemeinholzer
Diatoms are frequently used for water quality assessments; however, identification to species level is difficult, time-consuming and needs in-depth knowledge of the organisms under investigation, as nonhomoplastic species-specific morphological characters are scarce. We here investigate how identification methods based on DNA (metabarcoding using NGS platforms) perform in comparison to morphological diatom identification and propose a workflow to optimize diatom fresh water quality assessments. Diatom diversity at seven different sites along the course of the river...

Data from: Diminishing-returns epistasis among random beneficial mutations in a multicellular fungus

Sijmen Schoustra, Sungmin Hwang, Joachim Krug, J. Arjan G.M. De Visser & J. Arjan G. M. De Visser
Adaptive evolution ultimately is fuelled by mutations generating novel genetic variation. Non-additivity of fitness effects of mutations (called epistasis) may affect the dynamics and repeatability of adaptation. However, understanding the importance and implications of epistasis is hampered by the observation of substantial variation in patterns of epistasis across empirical studies. Interestingly, some recent studies report increasingly smaller benefits of beneficial mutations once genotypes become better adapted (called diminishing-returns epistasis) in unicellular microbes and single genes....

Data from: Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa

Stefan Geisen, Ivo Laros, Antón Vizcaíno, Michael Bonkowski & G. Arjen De Groot
Protists, the most diverse eukaryotes, are largely considered to be free-living bacterivores, but vast numbers of taxa are known to parasitize plants or animals. High-throughput sequencing (HTS) approaches now commonly replace cultivation-based approaches in studying soil protists, but insights into common biases associated with this method are limited to aquatic taxa and samples. We created a mock community of common free-living soil protists (amoebae, flagellates, ciliates), extracted DNA and amplified it in the presence of...

Data from: Unraveling the causes of adaptive benefits of synonymous mutations in TEM-1 β-lactamase

Mark P. Zwart, Martijn F. Schenk, Sungmin Hwang, Bertha Koopmanschap, Niek De Lange, Lion Van De Pol, Tran T.T. Nga, Ivan G. Szendro, Joachim Krug & J. Arjan G.M. De Visser
While synonymous mutations were long thought to be without phenotypic consequences, there is growing evidence they can affect gene expression, protein folding and ultimately the fitness of an organism. In only a few cases have the mechanisms by which synonymous mutations affect the phenotype been elucidated. We previously identified 48 mutations in TEM-1 β-lactamase that increased resistance of Escherichia coli to cefotaxime, 10 of which were synonymous. To better understand the molecular mechanisms underlying the...

Data from: Role of pleiotropy during adaptation of TEM-1 β-lactamase to two novel antibiotics

Martijn F. Schenk, Sariette Witte, Merijn L. M. Salverda, Bertha Koopmanschap, Joachim Krug & J. Arjan G. M. De Visser
Pleiotropy is a key feature of the genotype–phenotype map, and its form and extent have many evolutionary implications, including for the dynamics of adaptation and the evolution of specialization. Similarly, pleiotropic effects of antibiotic resistance mutations may affect the evolution of antibiotic resistance in the simultaneous or fluctuating presence of different antibiotics. Here, we study the role of pleiotropy during the in vitro adaptation of the enzyme TEM-1 β-lactamase to two novel antibiotics, cefotaxime (CTX)...

Data from: The diverse dietary profiles of MIS 3 cave bears from the Romanian Carpathians: insights from stable isotope (δ13C and δ15N) analysis

Marius Robu, Jonathan G. Wynn, Ionuţ C. Mirea, Alexandru Petculescu, Marius Kenesz, Cristina M. Puşcaş, Marius Vlaicu, Erik Trinkaus & Silviu Constantin
Late Pleistocene European cave bears (Ursus spelaeus) have been considered to be largely vegetarian, although stable isotope data (δ13C and δ15N values) from the Romanian Carpathians has suggested considerable dietary variation. Here we evaluate previous and additional adult cave bear isotopic data from four Marine Isotope Stage 3 (MIS 3) sites in the Carpathians. Peştera Urşilor (N = 35), Peştera Cioclovina (N = 32), Peştera Muierilor (N = 8), and Peştera cu Oase (N =...

Data from: A new mechanistic approach for the further development of a population with established size bimodality

Lisa Heermann, Donald L. DeAngelis & Jost Borcherding
Usually, the origin of a within-cohort bimodal size distribution is assumed to be caused by initial size differences or by one discrete period of accelerated growth for one part of the population. The aim of this study was to determine if more continuous pathways exist allowing shifts from the small to the large fraction within a bimodal age-cohort. Therefore, a Eurasian perch population, which had already developed a bimodal size-distribution and had differential resource use...

Data from: A potential role for GSK3beta in glucose-driven intrauterine catch-up growth in maternal obesity

Sarah Appel, Jon Grothe, Sarah Storck, Ruth Janoschek, Inga Bae-Gartz, Maria Wohlfarth, Marion Handwerk, Eva Hucklenbruch-Rother, Alexandra Gellhaus & Jörg Dötsch
Obesity and an unhealthy nutrition are on the rise and affect also women in childbearing age and hence, during pregnancy. Despite normal or even high birth weight the offspring suffers from long term metabolic risks. We hypothesized that fetal growth is disturbed during different intrauterine phases. Underlying molecular events remain elusive. Female mice were fed either a control diet (SD) or a high fat diet (HFD) after weaning until mating and during pregnancy. Pregnant mice...

Rapid adaptive evolution to drought in a subset of plant traits in a large-scale climate change experiment

Johannes Metz, Christian Lampei, Laura Bäumler, Hervé Bocherens, Hannes Dittberner, Lorenz Henneberg, Juliette De Meaux & Katja Tielbörger
Rapid evolution of traits and of plasticity may enable adaptation to climate change, yet solid experimental evidence under natural conditions is scarce. Here, we imposed rainfall manipulations (+30%, control, -30%) for ten years on entire natural plant communities in two Eastern Mediterranean sites. Additional sites along a natural rainfall gradient and selection analyses in a greenhouse assessed whether potential responses were adaptive. In both sites, our annual target species Biscutella didyma consistently evolved earlier phenology...

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  • University of Cologne
  • Wageningen University & Research
  • Lund University
  • University of Oslo
  • University of Tübingen
  • Duke University
  • University of Alberta
  • Natural History Museum
  • University of California, Berkeley
  • University of Alaska Fairbanks