102 Works

Data from: Patterns of linkage disequilibrium and long range hitchhiking in evolving experimental Drosophila melanogaster populations

Susanne U. Franssen, Viola Nolte, Ray Tobler & Christian Schlötterer
Whole genome re-sequencing of experimental populations evolving under a specific selection regime has become a popular approach to determine genotype-phenotype maps and understand adaptation to new environments. Despite its conceptual appeal and success in identifying some causative genes, it has become apparent that many studies suffer from an excess of candidate loci. Several explanations have been proposed for this phenomenon, but it is clear that information about the linkage structure during such experiments is needed....

Data from: Recovery of large carnivores in Europe’s modern human-dominated landscapes

Guillaume Chapron, Petra Kaczensky, John D. C. Linnell, Manuela Von Arx, Djuro Huber, Henrik Andrén, José Vicente López-Bao, Michal Adamec, Francisco Álvares, Ole Anders, Linas Balčiauskas, Vaidas Balys, Péter Bedő, Ferdinand Bego, Juan Carlos Blanco, Urs Breitenmoser, Henrik Brøseth, Luděk Bufka, Raimonda Bunikyte, Paolo Ciucci, Alexander Dutsov, Thomas Engleder, Christian Fuxjäger, Claudio Groff, Katja Holmala … & Luigi Boitani
The conservation of large carnivores is a formidable challenge for biodiversity conservation. Using a data set on the past and current status of brown bears (Ursus arctos), Eurasian lynx (Lynx lynx), gray wolves (Canis lupus), and wolverines (Gulo gulo) in European countries, we show that roughly one-third of mainland Europe hosts at least one large carnivore species, with stable or increasing abundance in most cases in 21st-century records. The reasons for this overall conservation success...

Data from: Genome assembly and annotation of a Drosophila simulans strain from Madagascar

Nicola Palmieri, Viola Nolte, Jun Chen & Christian Schlötterer
Drosophila simulans is a closely relative of the genetic model D. melanogaster. In an effort to improve the genomic resources for D. simulans, we assembled and annotated the genome of a strain originating from Madagascar (M252), the ancestral range of D. simulans. The comparison of the M252 genome to other available D. simulans assemblies confirmed its high quality, but also highlighted genomic regions that are difficult to assemble with NGS data. The annotation of M252...

Data from: Re-visiting the phylogeography and demography of European badgers (Meles meles) based on broad sampling, multiple markers and simulations

Alain C. Frantz, Allan D. McDevitt, Lisa C. Pope, Joanna Kochan, John Davison, Chris F. Clements, Morten Elmeros, Guillem Molina-Vacas, Aritz Ruiz-Gonzalez, Alessandro Balestrieri, Koen Van Den Berge, Peter Breyne, Emmanuel Do Linh San, Erik O. Ågren, Franz Suchentrunk, Laurent Schley, Rafał Kowalczyk, Berit I. Kostka, Dusko Ćirović, Nikica Šprem, Marc Colyn, Marco Ghirardi, Venislava Racheva, Christophe Braun, Rita Oliveira … & Terry Burke
Although the phylogeography of European mammals has been extensively investigated since the 1990s, many studies were limited in terms of sampling distribution, the number of molecular markers used and the analytical techniques employed, frequently leading to incomplete postglacial recolonisation scenarios. The broad-scale genetic structure of the European badger (Meles meles) is of interest as it may result from historic restriction to glacial refugia and/or recent anthropogenic impact. However, previous studies were based mostly on samples...

Data from: Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles

Pablo Orozco-TerWengel, Martin Kapun, Viola Nolte, Robert Kofler, Thomas Flatt & Christian Schlötterer
The genomic basis of adaptation to novel environments is a fundamental problem in evolutionary biology that has gained additional importance in the light of the recent global change discussion. Here, we combined laboratory natural selection (experimental evolution) in Drosophila melanogaster with genome-wide next generation sequencing of DNA pools (Pool-Seq) to identify alleles that are favourable in a novel laboratory environment and traced their trajectories during the adaptive process. Already after 15 generations, we identified a...

Data from: Evidence for complex selection on four-fold degenerate sites in Drosophila melanogaster

Florian Clemente & Claus Vogl
We considered genome-wide four-fold degenerate sites from an African Drosophila melanogaster population and compared them to short introns. To include divergence and to polarize the data, we used its close relatives Drosophila simulans, Drosophila sechellia, Drosophila erecta and Drosophila yakuba as outgroups. In D. melanogaster, the GC content at four-fold degenerate sites is higher than in short introns; compared to its relatives, more AT than GC is fixed. The former has been explained by codon...

Data from: Selection for brain size impairs innate, but not adaptive immune responses

Alexander Kotrschal, Niclas Kolm & Dustin J. Penn
The brain and the immune system are both energetically demanding organs, and when natural selection favors increased investment into one, then the size or performance of the other should be reduced. While comparative analyses have attempted to test this potential evolutionary trade-off, the results remain inconclusive. To test this hypothesis, we compared the tissue graft rejection (an assay for measuring innate and acquired immune responses) in guppies (Poecilia reticulata) artificially selected for large and small...

Data from: Chironomus riparius (Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence

Ann-Marie Oppold, Hanno Schmidt, Marcel Rose, Sören Lukas Hellman, Florian Dolze, Fabian Ripp, Bettina Weich, Urs Schmidt-Ott, Erwin Schmidt, Robert Kofler, Thomas Hankeln & Markus Pfenninger
Active transposable elements (TEs) may result in divergent genomic insertion and abundance patterns among conspecific populations. Upon secondary contact, such divergent genetic backgrounds can theoretically give rise to classical Dobzhansky-Muller incompatibilities (DMI), thus contributing to the evolution of endogenous genetic barriers and eventually cause population divergence. We investigated differential TE abundance among conspecific populations of the non-biting midge Chironomus riparius and evaluated their potential role in causing endogenous genetic incompatibilities between these populations. We focussed...

Data from: The genetics of egg retention and fertilization success in Drosophila: one step closer to understanding the transition from facultative to obligate viviparity

Barbara Horváth & Alex T. Kalinka
Oviparous, facultative egg retention enables Drosophila females to withhold fertilized eggs in their reproductive tracts until circumstances favor oviposition. The propensity to retain fertilized eggs varies greatly between species, and is correlated with other reproductive traits, such as egg size and ovariole number. While previous studies have described the phenomenon, no study to date has characterized within-species variation or the genetic basis of the trait. Here, we develop a novel microscope-based method for measuring egg...

Fitness effects for Ace insecticide resistance mutations are determined by ambient temperature

Anna Maria Langmüller, Viola Nolte, Ruwansha Galagedara, Rodolphe Poupardin, Marlies Dolezal & Christian Schlötterer
Background Insect pest control programs often use periods of insecticide treatment with intermittent breaks, to prevent fixing of mutations conferring insecticide resistance. Such mutations are typically costly in an insecticide free environment, and their frequency is determined by the balance between insecticide treatment and cost of resistance. Ace, a key gene in neuronal signaling, is a prominent target of many insecticides and across several species three amino acid replacements (I161V, G265A and F330Y) provide resistance...

Data from: Genetic redundancy fuels polygenic adaptation in Drosophila

Neda Barghi, Raymond Tobler, Viola Nolte, Ana Marija Jakšić, François Mallard, Kathrin Anna Otte, Marlies Dolezal, Thomas Taus, Robert Kofler & Christian Schlötterer
The genetic architecture of adaptive traits is of key importance to predict evolutionary responses. Most adaptive traits are polygenic—i.e., result from selection on a large number of genetic loci—but most molecularly characterized traits have a simple genetic basis. This discrepancy is best explained by the difficulty in detecting small allele frequency changes (AFCs) across many contributing loci. To resolve this, we use laboratory natural selection to detect signatures for selective sweeps and polygenic adaptation. We...

Early life growth and telomere length in wild boar piglets 2018

Magdalena Spießberger, Franz Hoelzl, Steve Smith, Sebastian Vetter & Julia Nowack
Life history theory predicts a trade-off between growth rates and lifespan, which is reflected by telomere length, a biomarker of somatic state. We investigated the correlation between telomere length and early life growth of wild boar piglets, Sus scrofa, kept under semi-natural conditions with high food availability to examine our hypothesis that increased pre-and post-natal growth will lead to telomere length attrition but that a high supply of nutrient may provide the possibility to compensate...

Data from: Wild Goffin’s cockatoos flexibly manufacture and use tool sets

Mark O'Hara, Berenika Mioduszewska, Roger Mundry, , Tri Haryoko, Rini Rachmatika, Dewi Malia Prawiradilaga, Ludwig Huber & Alice Marie Isabel Auersperg
The use of different tools to achieve a single goal is considered unique to human and primate technology. To unravel the origins of such complex behaviors, it is crucial to investigate tool use that does not occur species wide. These cases can be assumed to have emerged innovatively and be applied flexibly, thus emphasizing creativity and intelligence. However, it is intrinsically challenging to record tool innovations in natural settings that do not occur species-wide. Here...

Data from: Through the eye of a Gobi khulan – application of camera collars for ecological research of far-ranging species in remote and highly variable ecosystems

Petra Kaczensky, Sanchir Khaliun, John Payne, Bazartseren Boldgiv, Bayarbaatar Buuveibaatar & Chris Walzer
The Mongolian Gobi-Eastern Steppe Ecosystem is one of the largest remaining natural drylands and home to a unique assemblage of migratory ungulates. Connectivity and integrity of this ecosystem are at risk if increasing human activities are not carefully planned and regulated. The Gobi part supports the largest remaining population of the Asiatic wild ass (Equus hemionus; locally called “khulan”). Individual khulan roam over areas of thousands of square kilometers and the scale of their movements...

Past, present and future of chamois science

Luca Corlatti, Laura Iacolina, Toni Safner, Marco Apollonio, Elena Buzan, Francesco Ferretti, Sabine Hammer, Juan Herrero, Luca Rossi, Emmanuel Serrano, Mari Cruz Arnal, Francesca Brivio, Roberta Chirichella, Antonella Cotza, Barbara Crestanello, Johan Espunyes, Daniel Fernández De Luco, Saskia Friedrich, Dragan Gačić, Laura Grassi, Stefano Grignolio, Heidi Hauffe, Kresmir Kavčić, Andreas Kinser, Francesca Lioce … & Nikica Šprem
The chamois Rupicapra spp. is the most abundant mountain ungulate of Europe and the Near East, where it occurs as two species, the Northern chamois R. rupicapra and the Southern chamois R. pyrenaica. Here, we provide a state-of-the-art overview of research trends and the most challenging issues in chamois research and conservation, focusing on taxonomy and systematics, genetics, life history, ecology and behavior, physiology and disease, management, and conservation. Research on Rupicapra has a longstanding...

Species, signalment, origin, pathological findings, and ISH results

Christiane Weissenbacher-Lang
Raw data of the study "Detection of Pneumocystis and morphological description of fungal distribution and severity of infection in eight mammal orders"; the file contains order, suborder, family, species and breed, age, sex origin, main pathomorphological diagnosis, co-infections and concomitant diseases, and results of in situ hybridization and histopathology of 845 animals

Genomic insights into evolution and control of Wohlfahrtia magnifica, a widely distributed myiasis-causing fly of warm-blooded vertebrates

Zhipeng Jia, Surong Hasi, Claus Vogl & Pamela Burger
Wohlfahrtia magnifica is a pest fly species, invading livestock in many European, African and Asian countries, and causing heavy agro-economic losses. In the life cycle of this obligatory parasite, adult flies infect the host by depositing the first-stage larvae into body cavities or open wounds. The feeding larvae cause severe (skin) tissue damage and potentially fatal infections if untreated. Despite serious health detriments and agro-economic concerns, genomic resources for understanding the biology of W. magnifica...

Dogs take into account the actions of a human partner in a cooperative task

Mayte Martinez, Lauren M. Robinson, Sarah F. Brosnan & Friederike Range
Humans stand out for their capacity to flexibly cooperate, possibly because they understand their partners’ role. Researchers have explored if such understanding is unique to humans by assessing whether non-human species wait to manipulate a cooperative apparatus until a delayed partner arrives. If animals do wait, then it is assumed that they recognize the need for a partner. However, success in these tasks may be the result of social facilitation, while failure may be due...

Data from: Pan-European phylogeography of the European roe deer (Capreolus capreolus)

Kamila Plis, Magdalena Niedziałkowska, Tomasz Borowik, Johannes Lang, Mike Heddergott, Juha Tiainen, Aleksey Bunevich, Nikica Šprem, Ladislav Paule, Aleksey Danilkin, Marina Kholodova, Elena Zvychaynaya, Nadezhda Kashinina, Boštjan Pokorny, Katarina Flajšman, Algimantas Paulauskas, Mihajla Djan, Zoran Ristić, Luboš Novák, Szilvia Kusza, Christine Miller, Dimitris Tsaparis, Stoyan Stoyanov, Maryna Shkvyria, Franz Suchentrunk … & Bogumiła Jędrzejewska
To provide the most comprehensive picture of species phylogeny and phylogeography of European roe deer (Capreolus capreolus), we analysed mtDNA control region (610 bp) of 1469 samples of roe deer from Central and Eastern Europe and included in the analyses an additional 1,541 mtDNA sequences from GenBank from other regions of the continent. We detected two mtDNA lineages of the species: European and Siberian (an introgression of C. pygargus mtDNA into C. capreolus). The Siberian...

Data from: Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds

Yoshan Moodley, Juan F. Masello, Gopi K. Munimanda, Theresa L. Cole, Marco R. Thali, Rachael Alderman, Richard J. Cuthbert, Manuel Marin, Melanie Massaro, Joan Navarro, Richard A. Phillips, Peter G. Ryan, Cristián G. Suazo, Yves Cherel, Henri Weimerskirch, Petra Quillfeldt & Luciano Calderon
Microsatellite loci are ideal for testing hypotheses relating to genetic segregation at fine spatio-temporal scales. They are also conserved among closely related species, making them potentially useful for clarifying interspecific relationships between recently diverged taxa. However, mutations at primer binding sites may lead to increased nonamplification, or disruptions that may result in decreased polymorphism in nontarget species. Furthermore, high mutation rates and constraints on allele size may also with evolutionary time, promote an increase in...

Data from: Reproductive and post-reproductive life history of wild-caught Drosophila melanogaster under laboratory conditions

Peter Klepsatel, Martina Gáliková, Nicola De Maio, Sara Ricci, Christian Schlötterer & Thomas Flatt
The life history of the fruit fly (Drosophila melanogaster) is well understood, but fitness components are rarely measured by following single individuals over their lifetime, thereby limiting insights into lifetime reproductive success, reproductive senescence and post-reproductive lifespan. Moreover, most studies have examined long-established laboratory strains rather than freshly caught individuals and may thus be confounded by adaptation to laboratory culture, inbreeding or mutation accumulation. Here, we have followed the life histories of individual females from...

Data from: Density triggers maternal hormones that increase adaptive offspring growth in a wild mammal

Ben Dantzer, Amy E. M. Newman, Rudy Boonstra, Rupert Palme, Stan Boutin, Murray M. Humphries & Andrew G. McAdam
Spruce cone and squirrel density dataData used to investigate how previous year spruce cones and food-supplementation affected red squirrel density. All data collected in Kluane, Yukon, Canada.Spruce cone and density data.csvTable S2 Results - neonate mass and growth rateData used for results shown in Table 2. Only neonate mass and offspring growth data. All data collected in Kluane, Yukon, Canada.Table S2 - neonate mass and growth rate.csvTable S2-S3 ResultsData for results shown in Table S2...

Data from: Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster

Alan O. Bergland, Ray Tobler, Josefa Gonzalez, Paul Schmidt, Dimitri A. Petrov & Dmitri Petrov
Populations arrayed along broad latitudinal gradients often show patterns of clinal variation in phenotype and genotype. Such population differentiation can be generated and maintained by both historical demographic events and local adaptation. These evolutionary forces are not mutually exclusive and can in some cases produce nearly identical patterns of genetic differentiation among populations. Here, we investigate the evolutionary forces that generated and maintain clinal variation genome-wide among populations of Drosophila melanogaster sampled in North America...

Data from: Seeking signatures of reinforcement at the genetic level: a hitchhiking mapping and candidate gene approach in the house mouse

Carole M. Smadja, Etienne Loire, Pierre Caminade, Marios Thoma, Yasmin Latour, Camille Roux, Michaela Thoss, Dustin J. Penn, Gulia Ganem & Pierre Boursot
Reinforcement is the process by which prezygotic isolation is strengthened as a response to selection against hybridization. Most empirical support for reinforcement comes from the observation of its possible phenotypic signature: an accentuated degree of prezygotic isolation in the hybrid zone as compared to allopatry. Here, we implemented a novel approach to this question by seeking for the signature of reinforcement at the genetic level. In the house mouse, selection against hybrids and enhanced olfactory-based...

Data from: The impact of library preparation protocols on the accuracy of allele frequency estimates in Pool-Seq data

Robert Kofler, Viola Nolte & Christian Schlötterer
Sequencing pools of individuals (Pool-Seq) is a cost-effective method to determine genome-wide allele frequency estimates. Given the importance of meta-analyses combining data sets, we determined the influence of different genomic library preparation protocols on the consistency of allele frequency estimates. We found that typically no more than 1% of the variation in allele frequency estimates could be attributed to differences in library preparation. Also read length had only a minor effect on the consistency of...

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  • University of Veterinary Medicine Vienna
  • University of Vienna
  • Norwegian Institute for Nature Research
  • University of Zagreb
  • French National Centre for Scientific Research
  • University of Porto
  • University of Pennsylvania
  • University of Lausanne
  • University of Lisbon
  • University of Belgrade