61 Works

Data from: Tracking individuals shows spatial fidelity is a key regulator of ant social organization

Danielle P. Mersch, Alessandro Crespi & Laurent Keller
Ants live in organized societies with a marked division of labor among workers, but little is known about how this is generated. We use a tracking system to continuously monitor individually-tagged workers in six colonies of the ant Camponotus fellah over 41 days. Network analyses of over 9 million interactions revealed three distinct groups that differ in behavioral repertoires. Each group represents a functional behavioral unit with workers moving from one group to the next...

Data from: Demographic stochasticity and resource autocorrelation control biological invasions in heterogeneous landscapes

Andrea Giometto, Florian Altermatt & Andrea Rinaldo
Mounting theoretical evidence suggests that demographic stochasticity, environmental heterogeneity and biased movement of organisms individually affect the dynamics of biological invasions and range expansions. Studies of species spread in heterogeneous landscapes have traditionally characterized invasion velocities as functions of the mean resource density throughout the landscape, thus neglecting higher-order moments of the spatial resource distribution. Here, we show theoretically that different spatial arrangements of resources lead to different spread velocities even if the mean resource...

Data from: Signatures of selection and environmental adaptation across the goat genome post-domestication

Licia Colli, Marco Milanesi, Andrea Talenti, Francesca Bertolini, Minhui Chen, Alessandra Crisà, Kevin Daly, Marcello Del Corvo, Bernt Guldbrandtsen, Johannes A. Lenstra, Ben D. Rosen, Elia Vajana, Gennaro Catillo, Stéphane Joost, Ezequiel Luis Nicolazzi, Estelle Rochat, Max F. Rothschild, Bertrand Servin, Tad S. Sonstegard, Roberto Steri, Curtis P. Van Tassel, Paolo Ajmone-Marsan, Paola Crepaldi, Alessandra Stella & AdaptMap Consortium
Background: Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we...

Data from: Contrasting leaf trait responses of conifer and broadleaved seedlings to altered resource availability are linked to resource strategies

Barbara Moser, Yan-Li Zhang, Mai-He Li, Thomas Wohlgemuth, Jing-Pin Lei & Christoph Bachofen
(1) Understanding tree seedling responses to water, nutrient and light availability is crucial to precisely predict potential shifts in composition and structure of forest communities under future climatic conditions. (2) We exposed seedlings of widespread central European tree species with contrasting leaf habit, deciduous broadleaves (DB) and evergreen conifers (EC), to factorial combinations of manipulated precipitation (100% and 50% of ambient), shade (40% and 60% of full sunlight) and nutrient availability (low and high NPK),...

Seek and learn: automated identification of microevents in animal behaviour using envelopes of acceleration data and machine learning

Pritish Chakravarty, Gabriele Cozzi, Hooman Dejnabadi, Pierre-Alexandre Léziart, Marta Manser, Arpat Ozgul & Kamiar Aminian
1. Animal-borne accelerometers have been used across more than 120 species to infer biologically significant information such as energy expenditure and broad behavioural categories. While the accelerometer’s high sensitivity to movement and fast response times present the unprecedented opportunity to resolve fine-scale behaviour, leveraging this opportunity will require overcoming the challenge of developing general, automated methods to analyse the nonstationary signals generated by nonlinear processes governing erratic, impulsive movement characteristic of fine-scale behaviour. 2. We...

Quantification of Bone Marrow Compartments in Histological Sections

Josefine Tratwal & Olaia Naveiras
Away from the Mouse H&E quantification, the current version of MarrowQuant was tested on a small set of H&E bone marrow biopsies from anonymised patients. The tool performs in a comparable way as compared to the gold standard (Pathologists’ scorings), but it needs many optimisations before validating at the level of the human bone marrow biopsies quantifications and in clinical context.

Diversity, equity, and inclusion in engineering education: an exploration of European higher education institutions’ strategic frameworks, resources, and initiatives

I. Direito, Shannon Chance, L. Clemmensen, S. Craps, S.B. Economides, S.R. Isaac, A.M. Jolly, F.R. Truscott & N. Wint

The permeability of granite deformed in the brittle regime to large strains: Implications for the permeability of fractured geothermal reservoirs

Michael Heap , Hugo Duwiquet , Luke Griffiths , Laurent Guillou-Frottier , Patrick Baud & Marie Violay
Efficient fluid flow and circulation are important for an economically viable geothermal reservoir. One type of underexplored reservoir for high-temperature geothermal exploitation is a crustal fault zone, where hot fluids from depths corresponding to the brittle-ductile transition are brought to the surface via crustal-scale, permeable fault zones. To better understand the evolving permeability of reservoir rock during deformation in the brittle regime—fault formation and sliding on the fault—we performed triaxial experiments on samples of well-characterised...

Data from: Peatland vascular plant functional types affect methane dynamics by altering microbial community structure

Bjorn J. M. Robroek, Vincent E. J. Jassey, Martine A. R. Kox, Roeland L. Berendsen, Robert T. E. Mills, Lauric Cécillon, Jéremy Puissant, Marion Meima–Franke, Peter A. H. M. Bakker, Paul L. E. Bodelier & Marion Meima-Franke
1. Peatlands are natural sources of atmospheric methane (CH4), an important greenhouse gas. It is established that peatland methane dynamics are controlled by both biotic and abiotic conditions, yet the interactive effect of these drivers is less studied and consequently poorly understood. 2. Climate change affects the distribution of vascular plant functional types (PFTs) in peatlands. By removing specific PFTs, we assessed their effects on peat organic matter chemistry, microbial community composition and on potential...

Data from: Diffusion tensor imaging in patients with glioblastoma multiforme using the supertoroidal model

Choukri Mekkaoui, Philippe Metellus, William J. Kostis, Roberto Martuzzi, Fabricio R. Pereira, Jean-Paul Beregi, Timothy G. Reese, Todd R. Constable & Marcel P. Jackowski
Purpose: Diffusion Tensor Imaging (DTI) is a powerful imaging technique that has led to improvements in the diagnosis and prognosis of cerebral lesions and neurosurgical guidance for tumor resection. Traditional tensor modeling, however, has difficulties in differentiating tumor-infiltrated regions and peritumoral edema. Here, we describe the supertoroidal model, which incorporates an increase in surface genus and a continuum of toroidal shapes to improve upon the characterization of Glioblastoma multiforme (GBM). Materials and Methods: DTI brain...

Data from: On the (un)predictability of a large intragenic fitness landscape

Claudia Bank, Sebastian Matuszewski, Ryan T. Hietpas & Jeffrey D. Jensen
The study of fitness landscapes, which aims at mapping genotypes to fitness, is receiving ever-increasing attention. Novel experimental approaches combined with next-generation sequencing (NGS) methods enable accurate and extensive studies of the fitness effects of mutations, allowing us to test theoretical predictions and improve our understanding of the shape of the true underlying fitness landscape and its implications for the predictability and repeatability of evolution. Here, we present a uniquely large multiallelic fitness landscape comprising...

Data from: The telomeric DNA damage response occurs in the absence of chromatin decompaction

Aleksandra Vancevska, Kyle M. Douglass, Verena Pfeiffer, Suliana Manley & Joachim Lingner
Telomeres are specialized nucleoprotein structures that protect chromosome ends from DNA damage response (DDR) and DNA rearrangements. The telomeric shelterin protein TRF2 suppresses the DDR, and this function has been attributed to its abilities to trigger t-loop formation or prevent massive decompaction and loss of density of telomeric chromatin. Here, we applied stochastic optical reconstruction microscopy (STORM) to measure the sizes and shapes of functional human telomeres of different lengths and dysfunctional telomeres that elicit...

Data from: Genome-wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae)

Aude Rogivue, Rimjhim Roy Choudhury, Stefan Zoller, Stéphane Joost, Francois Felber, Michel Kasser, Christian Parisod & Felix Gugerli
Advances in high-throughput sequencing have promoted the collection of reference genomes and genome-wide diversity. However, the assessment of genomic variation among populations has hitherto mainly been surveyed through single-nucleotide polymorphisms (SNPs) and largely ignored the often major fraction of genomes represented by transposable elements (TEs). Despite accumulating evidence supporting the evolutionary significance of TEs, comprehensive surveys remain scarce. Here, we sequenced the full genomes of 304 individuals of Arabis alpina sampled from four nearby natural...

Data from: Linking a mutation to survival in wild mice

Rowan D. H. Barrett, Stefan Laurent, Ricardo Mallarino, Susanne P. Pfeifer, Charles C. Y. Xu, Matthieu Foll, Kazumasa Wakamatsu, Jonathan S. Duke-Cohan, Jeffrey D. Jensen & Hopi E. Hoekstra
Adaptive evolution in new or changing environments can be difficult to predict because the functional connections between genotype, phenotype, and fitness are complex. Here, we make these explicit connections by combining field and laboratory experiments in wild mice. We first directly estimate natural selection on pigmentation traits and an underlying pigment locus, Agouti, by using experimental enclosures of mice on different soil colors. Next, we show how a mutation in Agouti associated with survival causes...

Data from: Combining landscape genomics and ecological modelling to investigate local adaptation of indigenous Ugandan cattle to East Coast fever

Elia Vajana, Mario Barbato, Licia Colli, Marco Milanesi, Estelle Rochat, Enrico Fabrizi, Christopher Mukasa, Marcello Del Corvo, Charles Masembe, Vincent B. Muwanika, Fredrick Kabi, Tad Stewart Sonstegard, Heather Jay Huson, Riccardo Negrini, NextGen Consortium, Stéphane Joost & Paolo Ajmone-Marsan
East Coast fever (ECF) is a fatal sickness affecting cattle populations of eastern, central, and southern Africa. The disease is transmitted by the tick Rhipicephalus appendiculatus, and caused by the protozoan Theileria parva parva, which invades host lymphocytes and promotes their clonal expansion. Importantly, indigenous cattle show tolerance to infection in ECF-endemically stable areas. Here, the putative genetic bases underlying ECF-tolerance were investigated using molecular data and epidemiological information from 823 indigenous cattle from Uganda....

Data from: Seasonal variability of groundwater level effects on the growth of Carex cinerascens in lake wetlands

Wenjuan Feng, Pierre Mariotte, Xu Ligang, Alexandre Buttler, Luca Bragazza, Jiahu Jiang & Mathieu Santonja
Groundwater level is crucial for wetland plant growth and reproduction, but the extent of its effect on plant growth can vary along with changed precipitation and temperature at different seasons. In this context, we investigated the effect of two groundwater levels (10 cm vs. 20 cm depth) on growth and reproductive parameters of Carex cinerascens, a dominant plant species in the Poyang Lake wetland, during three seasons (spring, summer and autumn) and during two consecutive...

Dataset: A multi-site, year-round turbulence microstructure atlas for the deep perialpine Lake Garda

Sebastiano Piccolroaz, Bieito Fernández Castro, Marco Toffolon & Henk Dijkstra
This repository includes the dataset described in "A multi-site, year-round turbulence microstructure atlas for the deep perialpine Lake Garda", Scientific Reports, 2021, DOI: 10.1038/s41597-021-00965-0 A multi-site, year-round dataset comprising a total of 606 high-resolution turbulence microstructure profiles of shear and temperature gradient in the upper 100 m depth is made available for Lake Garda (Italy). Concurrent meteorological data were measured from the fieldwork boat at the location of the turbulence measurements. During the fieldwork campaign...

Phenotypic plasticity versus ecotypic differentiation under recurrent summer drought in two drought-tolerant pine species

Christoph Bachofen, Anouchka Perret-Gentil, Tom Wohlgemuth, Pierre Vollenweider & Barbara Moser
1. Despite worldwide reports of high tree mortality, growing evidence indicates that many tree species are well adapted to survive repeated dry spells. The drought resilience of trees is related to their phenotypic plasticity and ecotypic differentiation. Whether these two mechanisms act at the same organisational level of a tree and involve similar plant traits is still unknown. 2. We assessed phenotypic plasticity and ecotypic differentiation across four populations of Pinus sylvestris and Pinus nigra...

CrossLoc Benchmark Datasets

Iordan Doytchinov, Qi Yan, Jianhao Zheng, Simon Reding & Shanci Li
To study the data-scarcity mitigation for learning-based visual localization methods via sim-to-real transfer, we curate and now present the CrossLoc benchmark datasets—a multimodal aerial sim-to-real data available for flights above nature and urban terrains. Unlike the previous computer vision datasets focusing on localization in a single domain (mostly real RGB images), the provided benchmark datasets include various multimodal synthetic cues paired to all real photos. Complementary to the paired real and synthetic data, we offer...

Data from: Very high resolution digital elevation models: are multi-scale derived variables ecologically relevant?

Kevin Leempoel, Christian Parisod, Céline Geiser, Lucas Daprà, Pascal Vittoz & Stéphane Joost
Digital Elevation Models (DEMs) are often used in landscape ecology to retrieve elevation or first derivative terrain attributes such as slope or aspect in the context of species distribution modelling. However, DEM-derived variables are scale-dependent and, given the increasing availability of very high resolution (VHR) DEMs, their ecological relevance must be assessed for different spatial resolutions. In a study area located in the Swiss Western Alps, we computed VHR DEMs-derived variables related to morphometry, hydrology...

A critical literature review of spatio-temporal simulation methods for daylight glare assessment

Stephen Wasilewski, Lars Oliver Grobe, Jan Wienold & Marilyne Andersen

Carabids data of Pterostichus flavofemoratus and Carabus depressus in the Gran Paradiso National Park (2006, 2007, 2012, 2013)

Jonathan Giezendanner, Damiano Pasetto, Javier Perez-Saez, Cristiana Cerrato, Ramona Viterbi, Silvia Terzago, Elisa Palazzi & Andrea Rinaldo
Understanding risks to biodiversity requires predictions of the spatial distribution of species adapting to changing ecosystems and, to that end, earth observations integrating field surveys prove essential as they provide key figures for assessing landscape-wide biodiversity scenarios. Here, we develop, and apply to a relevant case study, a method suited to merge earth/field observations with spatially explicit stochastic metapopulation models to study the near-term ecological dynamics of target species in complex terrains. Our framework incorporates...

Drainage Canals in Southeast Asian Peatland

Nathan Dadap, Alison M Hoyt, Alexander R Cobb, Doruk Oner, Mateusz Kozinski, Pascal V Fua, Krishna Rao, Charles F Harvey & Alexandra G Konings
These images depict drainage canals and roads in peatlands in Borneo, Sumatra, and Peninsular Malaysia at 5 meter resolution. These canals were detected from July-September 2017 Planet Basemaps satellite imagery using a convolutional neural network. Please contact Nathan Dadap (ndadap@stanford.edu) with any questions.

Automated flow control of a multi-lane swimming chamber for small fishes indicates species-specific sensitivity to experimental protocols

Björn Illing, Andrea Severati, Justin Hochen, Paul Boyd, Paulin Raison, Rachel Mather, Adam T. Downie, Jodie L. Rummer, Frederieke J. Kroon & Craig Humphrey
In fishes, swimming performance is considered an important metric to measure fitness, dispersal, and migratory abilities. Swimming performance of individual larval fishes is often integrated into models to make inferences on how environmental parameters affect population-level dynamics (e.g., connectivity). However, little information exists regarding how experimental protocols affect the swimming performance of marine fish larvae. In addition, the technical setups used to measure larval fish swimming performance often lack automation and accurate control of water...

Amoebocytes facilitate efficient carbon and nitrogen assimilation in the Cassiopea Symbiodiniaceae symbiosis

Niclas Heidelberg Lyndby, Nils Rädecker, Sandrine Bessette, Louise Jensen, Stéphane Escrig, Erik Trampe, Michael Kühl & Anders Meibom
The upside-down jellyfish Cassiopea engages in symbiosis with photosynthetic microalgae that facilitate uptake and recycling of inorganic nutrients. In contrast to most other symbiotic cnidarians, algal endosymbionts in Cassiopea are not restricted to the gastroderm but are found in amoebocyte cells within the mesoglea. While symbiont-bearing amoebocytes are highly abundant, their role in nutrient uptake and cycling in Cassiopea remains unknown. By combining isotopic labelling experiments with correlated SEM and NanoSIMS imaging, we quantified the...

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Affiliations

  • École Polytechnique Fédérale de Lausanne
    59
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  • Swiss Federal Institute for Forest, Snow and Landscape Research
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  • Harvard University
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  • Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, PA 15261, USA
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