94 Works

Dogs’ looking times and pupil dilation response reveal expectations about contact causality

Christoph Völter & Ludwig Huber
Contact causality is one of the fundamental principles allowing us to make sense of our physical environment. From an early age, humans perceive spatiotemporally contiguous launching events as causal. Surprisingly little is known about causal perception in nonhuman animals, particularly outside the primate order. Violation-of-expectation paradigms in combination with eye-tracking and pupillometry have been used to study physical expectations in human infants. In the current study, we establish this approach for dogs (Canis familiaris). We...

Hidden treasure of the Gobi: understanding how water limits range use of khulan in the Mongolian Gobi

John C. Payne, Bayarbaatar Buuveibaatar, Diana E. Bowler, Kirk A. Olson, Chris Walzer & Petra Kaczensky
Most large herbivores in arid landscapes need to drink which constrains their movements and makes them vulnerable to disturbance. Asiatic wild ass or khulan (Equus hemionus) were widespread and abundant throughout the arid landscapes of Central Asia and Mongolia, but have undergone dramatic population declines and range constrictions; denying khulan access to water is believed to have played a major role. Mongolia’s South Gobi Region now houses the world largest remaining khulan population, but is...

Detecting selected haplotype blocks in evolve and resequence experiments

Kathrin A. Otte & Christian Schlötterer
Shifting from the analysis of single nucleotide polymorphisms to the reconstruction of selected haplotypes greatly facilitates the interpretation of Evolve and Resequence (E&R) experiments. Merging highly correlated hitchhiker SNPs into haplotype blocks reduces thousands of candidates to few selected regions. Current methods of haplotype reconstruction from Pool-Seq data need a variety of data-specific parameters that are typically defined ad hoc and require haplotype sequences for validation. Here, we introduce haplovalidate, a tool which detects selected...

Data from: Stable isotopes reveal diet shift from pre-extinction to reintroduced Przewalski’s horses

Petra Kaczensky, Martina Burnik Šturm, Mikhail V. Sablin, Christian Voigt, Steve Smith, Oyunsaikhan Ganbaatar, Boglarka Balint, Chris Walzer & Natalia N. Spasskaya
The Przewalski’s horse (Equus ferus przewalskii), the only remaining wild horse within the equid family, is one of only a handful of species worldwide that went extinct in the wild, was saved by captive breeding, and has been successfully returned to the wild. However, concerns remain that after multiple generations in captivity the ecology of the Przewalski’s horse and / or the ecological conditions in its former range have changed in a way compromising the...

Data from: Stress in biological invasions: introduced invasive grey squirrels increase physiological stress in native Eurasian red squirrels

Francesca Santicchia, Ben Dantzer, Freya Van Kesteren, Rupert Palme, Adriano Martinoli, Nicola Ferrari & Lucas Armand Wauters
1. Invasive alien species can cause extinction of native species through processes including predation, interspecific competition for resources, or disease-mediated competition. Increases in stress hormones in vertebrates may be associated with these processes and contribute to the decline in survival or reproduction of the native species. 2. Eurasian red squirrels (Sciurus vulgaris) have gone extinct across much of the British Isles and parts of Northern Italy following the introduction of North American invasive grey squirrels...

Data from: Extinctions, genetic erosion and conservation options for the black rhinoceros (Diceros bicornis)

Yoshan Moodley, Isa-Rita M. Russo, Desiré L. Dalton, Antoinette Kotzé, Shadrack Muya, Patricia Haubensak, Boglárka Bálint, Gopi K. Munimanda, Caroline Deimel, Andrea Setzer, Kara Dicks, Barbara Herzig-Straschil, Daniela C. Kalthoff, Hans R. Siegismund, Jan Robovský, Paul O’Donoghue & Michael W. Bruford
The black rhinoceros is again on the verge of extinction due to unsustainable poaching in its native range. Despite a wide historic distribution, the black rhinoceros was traditionally thought of as depauperate in genetic variation, and with very little known about its evolutionary history. This knowledge gap has hampered conservation efforts because hunting has dramatically reduced the species’ once continuous distribution, leaving five surviving gene pools of unknown genetic affinity. Here we examined the range-wide...

Data from: Drosophila simulans: a species with improved resolution in evolve and resequence studies

Neda Barghi, Raymond Tobler, Viola Nolte & Christian Schlötterer
The combination of experimental evolution with high-throughput sequencing of pooled individuals—i.e., evolve and resequence (E&R)—is a powerful approach to study adaptation from standing genetic variation under controlled, replicated conditions. Nevertheless, E&R studies in Drosophila melanogaster have frequently resulted in inordinate numbers of candidate SNPs, particularly for complex traits. Here, we contrast the genomic signature of adaptation following ∼60 generations in a novel hot environment for D. melanogaster and D. simulans. For D. simulans, the regions...

Data from: Inference of chromosomal inversion dynamics from Pool-Seq data in natural and laboratory populations of Drosophila melanogaster

Martin Kapun, Hester Van Schalkwyk, Bryant McAllister, Thomas Flatt & Christian Schlötterer
Sequencing of pools of individuals (Pool-Seq) represents a reliable and cost-effective approach for estimating genome-wide SNP and transposable element insertion frequencies. However, Pool-Seq does not provide direct information on haplotypes so that for example obtaining inversion frequencies has not been possible until now. Here, we have developed a new set of diagnostic marker SNPs for 7 cosmopolitan inversions in Drosophila melanogaster that can be used to infer inversion frequencies from Pool-Seq data. We applied our...

Data from: Unexpected high genetic diversity in small populations suggests maintenance by associative overdominance

Mads F. Schou, Volker Loeschcke, Jesper Bechsgaard, Christian Schlötterer & Torsten N. Kristensen
The effective population size (Ne) is a central factor in determining maintenance of genetic variation. The neutral theory predicts that loss of variation depends on Ne, with less genetic drift in larger populations. We monitored genetic drift in 42 Drosophila melanogaster populations of different adult census population sizes (10, 50 or 500) using pooled RAD sequencing. In small populations, variation was lost at a substantially lower rate than expected. This observation was consistent across two...

Data from: Pathologic evaluation of type 2 porcine reproductive and respiratory syndrome virus infection at the maternal-fetal interface of late gestation pregnant gilts

Predrag Novakovic, John C.S. Harding, Ahmad N. Al-Dissi, Andrea Ladinig, Susan E. Detmer & John C. S. Harding
The pathogenesis of fetal death caused by reproductive porcine reproductive and respiratory syndrome virus (PRRSV) remains unclear. The objective of this study was to improve our understanding of the pathogenesis by assessing potential relationships between specific histopathological lesions and PRRSV RNA concentration in the fetuses and the maternal-fetal interface. Pregnant gilts were inoculated with PRRSV (n=114) or sham inoculated (n=19) at 85±1 days of gestation. Dams and their litters were humanely euthanized and necropsied 21...

Data from: DNA motifs are not general predictors of recombination in two Drosophila sister species.

James M. Howie, Rupert Mazzucco, Thomas Taus, Viola Nolte & Christian Schlötterer
Meiotic recombination is crucial for chromosomal segregation, and facilitates the spread of beneficial and removal of deleterious mutations. Recombination rates frequently vary along chromosomes and Drosophila melanogaster exhibits a remarkable pattern. Recombination rates gradually decrease towards centromeres and telomeres, with a dramatic impact on levels of variation in natural populations. Two close sister species, D. simulans and D. mauritiana do not only have higher recombination rates, but also exhibit a much more homogeneous recombination rate...

Horizontal gene transfer is the main driver of antimicrobial resistance in broiler chicks infected with Salmonella enterica serovar Heidelberg

Adelumola Oladeinde, Zaid Abdo, Maximilian Press, Kimberly Cook, Nelson Cox, Benjamin Zwirzitz, Reed Woyda, Steven Lakin, , Torey Looft, Douglas Cosby, , Jean Guard, Eric Line, Michael Rothrock, Mark Berrang, Kyler Herrington, Gregory Zock, Jodie Plumblee Lawrence, Denice Cudnik, Sandra House, Kimberly Ingram, Leah Lariscy, Robert Wagner, Samuel Aggrey … & Casey Ritz
Overuse and misuse of antibiotics in clinical settings and in food production have been linked to the increased prevalence and spread of antimicrobial resistance (AR). Consequently, public health and consumer concerns have resulted in a remarkable reduction in antibiotics used for food animal production. However, there are no data on the effectiveness of antibiotic removal in reducing AR shared through horizontal gene transfer (HGT). In this study, we used neonatal broiler chicks and Salmonella enterica...

Hunting suitability model - a new tool for managing wild ungulates

Paul Griesberger, Leopold Obermair, Josef Zandl, Gabrielle Stalder, Walter Arnold & Klaus Hackländer
Rising numbers of wild ungulates in human-dominated landscapes of Europe can induce negative effects like damages to forests. Therefore, effective wildlife management, including harvesting through hunting is becoming increasingly important. However, current hunting practices often fail to diminish those negative effects, as many ungulate species retreat to areas unsuitable for hunting. This predator-avoidance behaviour makes it difficult to fulfill the demand of reducing population numbers. Thus, there is an urgent need for innovative and effective...

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: 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: 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...

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: 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: Broad geographic sampling reveals predictable, pervasive, and strong seasonal adaptation in Drosophila

Heather E. Machado, Alan O. Bergland, Ryan Taylor, Susanne Tilk, Emily Behrman, Kelly Dyer, Daniel K. Fabian, Thomas Flatt, Josefa González, Talia L. Karasov, Iryna Kozeretska, Brian P. Lazzaro, Thomas JS Merritt, John E. Pool, Katherine O’Brien, Subhash Rajpurohit, Paula R. Roy, Stephen W. Schaeffer, Svitlana Serga, Paul Schmidt, Dmitri Petrov & Bernard Kim
To advance our understanding of adaptation to temporally varying selection pressures, we identified signatures of seasonal adaptation occurring in parallel among Drosophila melanogaster populations. Specifically, we estimated allele frequencies genome-wide from flies sampled early and late in the growing season from 20 widely dispersed populations. We identified parallel seasonal allele frequency shifts across North America and Europe, demonstrating that seasonal adaptation is a general phenomenon of temperate fly populations. Seasonally fluctuating polymorphisms are enriched at...

Data from: Ancestral population reconstitution from isofemale lines as a tool for experimental evolution

Pierre Nouhaud, Ray Tobler, Viola Nolte & Christian Schlötterer
Experimental evolution is a powerful tool to study adaptation under controlled conditions. Laboratory natural selection experiments mimic adaptation in the wild with better-adapted genotypes having more offspring. Because the selected traits are frequently not known, adaptation is typically measured as fitness increase by comparing evolved populations against an unselected reference population maintained in a laboratory environment. With adaptation to the laboratory conditions and genetic drift, however, it is not clear to what extent such comparisons...

Data from: A Drosophila laboratory evolution experiment points to low evolutionary potential under increased temperatures likely to be experienced in the future

Mads F. Schou, Torsten N. Kristensen, Vanessa Kellermann, Christian Schlötterer & Volker Loeschcke
The ability to respond evolutionarily to increasing temperatures is important for survival of ectotherms in a changing climate. Recent studies suggest that upper thermal limits may be evolutionary constrained. We address this hypothesis in a laboratory evolution experiment, encompassing ecologically relevant thermal regimes. To examine the potential for species to respond to climate change, we exposed replicate populations of Drosophila melanogaster to increasing temperatures (0.3 °C every generation) for 20 generations, whereas corresponding replicate control...

Data from: Uncovering the genetic signature of quantitative trait evolution with replicated time series data

Susanne U. Franssen, Robert Kofler & Christian Schloetterer
The genetic architecture of adaptation in natural populations has not yet been resolved: it is not clear to what extent the spread of beneficial mutations (selective sweeps) or the response of many quantitative trait loci drive adaptation to environmental changes. Although much attention has been given to the genomic footprint of selective sweeps, the importance of selection on quantitative traits is still not well studied, as the associated genomic signature is extremely difficult to detect....

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: Evolution of longevity improves immunity in Drosophila

Daniel K. Fabian, Kathrin Garschall, Peter Klepsatel, Gonçalo Santos-Matos, Élio Sucena, Martin Kapun, Bruno Lemaitre, Robert Arking, Christian Schloetterer & Thomas Flatt
Much has been learned about the genetics of aging from studies in model organisms, but still little is known about naturally occurring alleles that contribute to variation in longevity. For example, analysis of mutants and transgenes has identified insulin signaling as a major regulator of longevity, yet whether standing variation in this pathway underlies microevolutionary changes in lifespan and correlated fitness traits remains largely unclear. Here we have analyzed the genomes of a set of...

Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies

Jean Elbers, Sara Lado, Mark Rogers, José Melo-Ferreira, Jukka Corander, Petr Horin, Pamela Burger & Adiya Yadamsuren
Background Immune-response (IR) genes have an important role in the defense against highly variable pathogens, and therefore, genetic diversity in these genomic regions is essential for species’ survival and adaptation. Although current genome assemblies from Old World camelids are very useful for investigating genome-wide diversity, demography and population structure, they have inconsistencies and gaps that limit analyses at local genomic scales. Improved and more accurate genome assemblies and annotations are needed to study complex genomic...

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