96 Works

Data from: Postglacial expansion and not human persecution best explains the population structure in the endangered kea (Nestor notabilis)

Nick Dussex, D. Wegmann & B. C. Robertson
Inferring past demography is a central question in evolutionary and conservation biology. It is however sometimes challenging to infer the processes that shaped the current patterns of genetic variation in endangered species. Population sub-structuring can occur as a result of survival in several isolated refugia and subsequent recolonization processes or via genetic drift following a population decline. The kea (Nestor notabilis) is an endemic parrot widely distributed in the mountains of the South Island of...

Data from: Including community composition in biodiversity-productivity models

Nadine Sandau, Rudolf P. Rohr, Russell E. Naisbit, Yvonne Fabian, Odile T. Bruggisser, Patrik Kehrli, Alexandre Aebi & Louis-Félix Bersier
1. Studies on biodiversity and ecosystem functioning (BEF) have elicited debate over the interpretation of the positive relationship between species richness and plant productivity. Manipulating richness cannot be achieved without affecting composition; it is thus essential to consider the latter in statistical models. 2. We firstly review existing approaches that use species richness as an explanatory variable and propose modifications to improve their performance. We use an original dataset to illustrate the analyses. The classical...

Data from: Genomics of the divergence continuum in an African plant biodiversity hotspot, I: drivers of population divergence in Restio capensis (Restionaceae)

Christian Lexer, Rafael O. Wüest, Sofia Mangili, Myriam Heuertz, Kai N. Stolting, Peter B. Pearman, Felix Forest, Nicolas Salamin, Niklaus E. Zimmermann & Eligio Bossolini
Understanding the drivers of population divergence, speciation and species persistence is of great interest to molecular ecology, especially for species-rich radiations inhabiting the world’s biodiversity hotspots. The toolbox of population genomics holds great promise for addressing these key issues, especially if genomic data are analyzed within a spatially and ecologically explicit context. We have studied the earliest stages of the divergence continuum in the Restionaceae, a species-rich and ecologically important plant family of the Cape...

Data from: Selection against recombinant hybrids maintains reproductive isolation in hybridizing Populus species despite F1 fertility and recurrent gene flow

Camille Christie, Kai N. Stölting, Luisa Bresadola, Barbara Fussi, Berthold Heinze, Daniel Wegmann, Christian Lexer & Camille Christe
Natural hybrid zones have proven to be precious tools for understanding the origin and maintenance of reproductive isolation (RI) and therefore species. Most available genomic studies of hybrid zones using whole- or partial-genome resequencing approaches have focused on comparisons of the parental source populations involved in genome admixture, rather than exploring fine-scale patterns of chromosomal ancestry across the full admixture gradient present between hybridizing species. We have studied three well-known European ‘replicate’ hybrid zones of...

Data from: HDAC1/2-dependent P0 expression maintains paranodal and nodal integrity independently of myelin stability through interactions with neurofascins

Valérie Brügger, Stefanie Engler, Jorge A. Pereira, Sophie Ruff, Michael Horn, Hans Welzl, Emmanuelle Münger, Adrien Vaquié, Páris N. M. Sidiropoulos, Boris Egger, Peter Yotovski, Luis Filgueira, Christian Somandin, Tessa C. Lühmann, Maurizio D’Antonio, Teppei Yamaguchi, Patrick Matthias, Ueli Suter & Claire Jacob
The pathogenesis of peripheral neuropathies in adults is linked to maintenance mechanisms that are not well understood. Here, we elucidate a novel critical maintenance mechanism for Schwann cell (SC)–axon interaction. Using mouse genetics, ablation of the transcriptional regulators histone deacetylases 1 and 2 (HDAC1/2) in adult SCs severely affected paranodal and nodal integrity and led to demyelination/remyelination. Expression levels of the HDAC1/2 target gene myelin protein zero (P0) were reduced by half, accompanied by altered...

Data from: Genes mirror geography in Daphnia magna

Peter D. Fields, Céline Reisser, Marinela Dukić, Christoph R. Haag & Dieter Ebert
Identifying the presence and magnitude of population genetic structure remains a major consideration in evolutionary biology as doing so allows one to understand the demographic history of a species as well as make predictions of how the evolutionary process will proceed. Next-generation sequencing methods allow us to reconsider previous ideas and conclusions concerning the distribution of genetic variation, and what this distribution implies about a given species evolutionary history. A previous phylogeographic study of the...

Data from: Reorganization of interaction networks modulates the persistence of species in late successional stages

Serguei Saavedra, Simone Cenci, Ek Del-Val, Karina Boege & Rudolf P. Rohr
1.Ecological interaction networks constantly reorganize as interspecific interactions change across successional stages and environmental gradients. This reorganization can also be associated with the extent to which species change their preference for types of niches available in their local sites. Despite the pervasiveness of these interaction changes, previous studies have revealed that network reorganizations have a minimal or insignificant effect on global descriptors of network architecture, such as: connectance, modularity, and nestedness. However, little is known...

Distal and proximal hypoxia response elements cooperate to regulate organ-specific erythropoietin gene expression

Roland Wenger, Ilaria M.C. Orlando, Véronique N. Lafleur, Federica Storti, Patrick Spielmann, Lisa Crowther, Sara Santambrogio, Johannes Schödel, David Hoogewijs & David R. Mole
While it is well-established that distal hypoxia response elements (HREs) regulate hypoxia-inducible factor (HIF) target genes such as erythropoietin (Epo), an interplay between multiple distal and proximal (promoter) HREs has not been described so far. Hepatic Epo expression is regulated by a HRE located downstream of the EPO gene, but this 3' HRE is dispensable for renal EPO gene expression. We previously identified a 5' HRE and could show that both HREs direct exogenous reporter...

Data from: Genome assembly of the ragweed leaf beetle, a step forward to better predict rapid evolution of a weed biocontrol agent to environmental novelties

Sarah Bouchemousse, Laurent Falquet & Heinz Müller-Schärer
Rapid evolution of weed biological control agents (BCAs) to new biotic and abiotic conditions is poorly understood and so far, only little considered both in pre-release and post-release studies, despite potential major negative or positive implications for risks of non-targeted attacks or for colonizing yet unsuitable habitats, respectively. Provision of genetic resources, such as assembled and annotated genomes, is essential to assess potential adaptive processes by identifying underlying genetic mechanisms. Here, we provide the first...

Data from: Thin-film structural coloration from simple fused scales in moths

Cédric Kilchoer, Ullrich Steiner & Bodo D. Wilts
The metallic coloration of insects often originates from diverse nanostructures ranging from simple thin films to complex three-dimensional photonic crystals. In Lepidoptera, structural coloration is widely present and seems to be abundant in extant species. However, even some basal moths exhibit metallic coloration. Here, we have investigated the origin of the vivid metallic colours of the wing scales of the basal moth Micropterix aureatella by spectrophotometry and scanning electron microscopy. The metallic gold-, bronze- and...

Data from: Diversification dynamics of Cheilostome Bryozoa based on a Bayesian analysis of the fossil record

Farideh Moharrek, Paul Taylor, Daniele Silvestro, Helen Jenkins, Dennis Gordon & Andrea Waeschenbach
Cheilostomata is the most diverse and ecologically dominant order of bryozoans living today. We apply a Bayesian framework to estimate macroevolutionary rates of cheilostomes since the Late Jurassic across four datasets: I) manually curated genus ranges, II) published text-mined genus ranges, III) non-revised Paleobiology Database (PBDB) records, IV) revised and augmented PBDB records. All datasets revealed increased origination rates in the Albian, and a twin K-Pg and Danian extinction rate peak. High origination rates in...

Data from: The diversity of population responses to environmental change

Fernando Colchero, Owen R. Jones, Dalia A. Conde, Dave Hodgson, Felix Zajitschek, Benedikt R. Schmidt, Aurelio F. Malo, Susan C. Alberts, Peter H. Becker, Sandra Bouwhuis, Anne M. Bronikowski, Kristel M. De Vleeschouwer, Richard J. Delahay, Stefan Dummermuth, Eduardo Fernández-Duque, John Frisenvænge, Martin Hesselsøe, Sam Larson, Jean-Francois Lemaitre, Jennifer McDonald, David A.W. Miller, Colin O'Donnell, Craig Packer, Becky E. Raboy, Christopher J. Reading … & Chris J. Reading
The current extinction and climate change crises pressure us to predict population dynamics with ever-greater accuracy. Although predictions rest on the well-advanced theory of age-structured populations, two key issues remain poorly-explored. Specifically, how the age-dependency in demographic rates and the year-to-year interactions between survival and fecundity affect stochastic population growth rates. We use inference, simulations, and mathematical derivations to explore how environmental perturbations determine population growth rates for populations with different age-specific demographic rates and...

Data from: Feeding habits of the Middle Triassic pseudosuchian Batrachotomus kupferzellensis from Germany and palaeoecological implications for archosaurs

Eudald Mujal, Eudald Mujal, Christian Foth, Erin Maxwell, Dieter Seegis & Rainer Schoch
Bite traces on fossil bones are key to deciphering feeding ecology and trophic interactions of vertebrate past ecosystems. However, similarities between traces produced by different carnivorous taxa with similar dentitions and misidentifications due to equifinality hinder confident identifications of the bite makers. Here, we correlate bite traces with macroscopic wear and microanatomy of the teeth of the pseudosuchian archosaur Batrachotomus kupferzellensis from the Triassic Lower Keuper fossil lagerstätten (southern Germany), untangling its feeding habits and...

Additional file 1 of Deeper genomic insights into tomato CLE genes repertoire identify new active peptides

Samy Carbonnel, Laurent Falquet & Ora Hazak
Additional file 1.

Additional file 2 of Deeper genomic insights into tomato CLE genes repertoire identify new active peptides

Samy Carbonnel, Laurent Falquet & Ora Hazak
Additional file 2.

Assessing the effects of survey-inherent disturbance on primate detectability: Recommendations for line transect distance sampling. Dataset

Mattia Bessone, Hjalmar Kühl, Ilka Herbinger, Kouame Paul N'Goran, Papy Asanzi, Barros Pedro Da Costa, Violette Dérozier, Dadis Bush Ernest Fotsing, Beka Bernard Ikembelo, Mpongo Dieumerci Iyomi, Iyomi Bernard Iyatshi, Pierre Kafando, Mbangi Augistin Kambere, Dissondet Baudelaire Moundzoho, Kako Loving Musubaho & Barbara Fruth
Habitat destruction and over-hunting are increasingly threatening the arboreal primates of Central Africa. To establish effective conservation strategies, accurate assessments of primate density, abundance and spatial distribution are required. To date, the method of choice for primate density estimation is line transect distance sampling. However, primates fleeing human observers violate methodological assumptions, biasing the accuracy of resulting estimates. In this study, we used line transect distance sampling to study 5 primate species along 378 km...

Swiss Glacier Volume Change (release 2022)

The comparison of digital elevation models derived from aerial remote sensing allows the computation of glacier ice volume changes over periods of years to decades. Ice volume changes have been converted to geodetic mass balances assuming a density of volume change of 850 kg m-3. The dataset contains all available observations for the most important Swiss glaciers up to present and is delivered as a .csv file.

Deeper genomic insights into tomato CLE genes repertoire identify new active peptides

Samy Carbonnel, Laurent Falquet & Ora Hazak
Abstract Background In eukaryotes, cell-to-cell communication relies on the activity of small signaling peptides. In plant genomes, many hundreds of genes encode for such short peptide signals. However, only few of them are functionally characterized and due to the small gene size and high sequence variability, the comprehensive identification of such peptide-encoded genes is challenging. The CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION-RELATED (CLE) gene family encodes for short peptides that have a role in plant meristem maintenance,...

Pitfalls in methods to study colocalization of nanoparticles in mouse macrophage lysosomes

Aura Maria Moreno-Echeverri, Eva Susnik, Dimitri Vanhecke, Patricia Taladriz-Blanco, Sandor Balog, Alke Petri-Fink & Barbara Rothen-Rutishauser
Abstract Background In the field of nanoscience there is an increasing interest to follow dynamics of nanoparticles (NP) in cells with an emphasis on endo-lysosomal pathways and long-term NP fate. During our research on this topic, we encountered several pitfalls, which can bias the experimental outcome. We address some of these pitfalls and suggest possible solutions. The accuracy of fluorescence microscopy methods has an important role in obtaining insights into NP interactions with lysosomes at...

Depositional and diagenetic processes in carbonate systems

Anneleen Foubert, Chelsea Pederson & Lars Reuning
Modern carbonate systems such as reefs provide livelihood and ecosystem services, such as coastal protection and food security, for hundreds of millions of people. Fossil carbonate systems are important archives of environmental change and form a valuable resource for renewable energy exploration and exploitation such as geothermal heat but also for CO2 sequestration. Over the past decades, our understanding of carbonate systems has improved by the combination of traditional fieldwork with new techniques such as...

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