Data from: Whole genome-sequencing and phylogenetic analysis of a historical collection of Bacillus anthracis strains from Danish cattleSylviane Derzelle, Guillaume Girault, Branko Kokotvic, Øystein Angen & Branko Kokotovic
Bacillus anthracis, the causative agent of anthrax, is known as one of the most genetically monomorphic species. Canonical single-nucleotide polymorphism (SNP) typing and whole-genome sequencing were used to investigate the molecular diversity of eleven B. anthracis strains isolated from cattle in Denmark between 1935 and 1988. Danish strains were assigned into five canSNP groups or lineages, i.e. A.Br.001/002 (n = 4), A.Br.Ames (n = 2), A.Br.008/011 (n = 2), A.Br.005/006 (n = 2) and A.Br.Aust94...
Data from: Enhanced computational methods for quantifying the effect of geographic and environmental isolation on genetic differentiationGilles Guillot, Filippo Botta, Capser Eriksen & Michaël C. Fontaine
1. In a recent paper, Bradburd et al. (Evolution, 67, 2013, 3258) proposed a model to quantify the relative effect of geographic and environmental distance on genetic differentiation. Here, we enhance this method in several ways. 2. We modify the covariance model so as to fit better with mainstream geostatistical models and avoid mathematically ill-behaved covariance functions. We extend the model – initially implemented only for co-dominant bi-allelic markers such as single nucleotide polymorphisms –...
Data from: Shape up or ship out: migratory behaviour predicts morphology across spatial scale in a freshwater fishBen B. Chapman, Kaj Hulthén, Christer Brönmark, Anders P. Nilsson, Christian Skov, Lars-Anders Hansson & Jakob Brodersen
1. Migration is a widespread phenomenon, with powerful ecological and evolutionary consequences. Morphological adaptations to reduce the energetic costs associated with migratory transport are commonly documented for migratory species. However, few studies have investigated whether variation in body morphology can be explained by variation in migratory strategy within a species. 2. We address this question in roach Rutilus rutilus, a partially migratory freshwater fish that migrates from lakes into streams during winter. We both compare...
Data from: Performance assessment of two whole-lake acoustic positional telemetry systems - is reality mining of free-ranging aquatic animals technologically possible?Henrik Baktoft, Petr Zajicek, Thomas Klefoth, Jon Christian Svendsen, Lene Jacobsen, Martin Wæver Pedersen, David March Morla, Christian Skov, Shinnosuke Nakayama & Robert Arlinghaus
Acoustic positional telemetry systems (APTs) represent a novel approach to study the behaviour of free ranging aquatic animals in the wild at unprecedented detail. System manufactures promise remarkably high temporal and spatial resolution. However, the performance of APTs has rarely been rigorously tested at the level of entire ecosystems. Moreover, the effect of habitat structure on system performance has only been poorly documented. Two APTs were deployed to cover two small lakes and a series...
Data from: Pre-adapting parasitic phages to a pathogen leads to increased pathogen clearance and lowered resistance evolution with Pseudomonas aeruginosa cystic fibrosis bacterial isolatesVille-Petri Friman, V-P. Friman, D. Soanes-Brown, P. Sierocinski, A. Buckling, H. K. Johansen, S. Molin & M. Merabishvili
Recent years have seen renewed interest in phage therapy - the use of viruses to specifically kill disease-causing bacteria – because of the alarming rise in antibiotic resistance. However, a major limitation of phage therapy is the ease at with bacteria can evolve resistance to phages. Here we determined if in vitro experimental coevolution can increase the efficiency of phage therapy by limiting the resistance evolution of intermittent and chronic cystic fibrosis Pseudomonas aeruginosa lung...
Terrestrial plants and mammals, although separated by a great evolutionary distance, have each arrived at a highly conserved body plan in which universal allometric scaling relationships govern the anatomy of vascular networks and key functional metabolic traits. The universality of allometric scaling suggests that these phyla have each evolved an ‘optimal’ transport strategy that has been overwhelmingly adopted by extant species. To truly evaluate the dominance and universality of vascular optimization, however, it is critical...
Overfishing of large predatory fish populations has resulted in lasting restructurings of entire marine food webs worldwide, with serious socio-economic consequences. Fortunately, some degraded ecosystems show signs of recovery. A key challenge for ecosystem management is to anticipate the degree to which recovery is possible. By applying a statistical food-web model, using the Baltic Sea as a case study, we show that under current temperature and salinity conditions, complete recovery of this heavily altered ecosystem...
Data from: How little data is enough? Phase-diagram analysis of sparsity-regularized X-ray computed tomographyJakob S. Jørgensen, Emil Y. Sidky & J. S. Jorgensen
We introduce phase-diagram analysis, a standard tool in compressed sensing (CS), to the X-ray computed tomography (CT) community as a systematic method for determining how few projections suffice for accurate sparsity-regularized reconstruction. In CS, a phase diagram is a convenient way to study and express certain theoretical relations between sparsity and sufficient sampling. We adapt phase-diagram analysis for empirical use in X-ray CT for which the same theoretical results do not hold. We demonstrate in...
Data from: A genomewide catalogue of single nucleotide polymorphisms in white-beaked and Atlantic white-sided dolphinsRuth Fernández, Mikkel Schubert, A. M. Vargas-Velázquez, Andrew Brownlow, Gisli A. Víkingsson, Ursula Siebert, Lasse Fast Jensen, Nils Øien, Dave Wall, Emer Rogan, Bjarni Mikkelsen, Willy Dabin, Gilles Guillot, Ludovic Orlando, A. H. Alfarhan, S. A. Alquraishi & K. A. S. Al-Rasheid
The field of population genetics is rapidly moving into population genomics as the quantity of data generated by high-throughput sequencing platforms increases. In this study, we used restriction-site-associated DNA sequencing (RADSeq) to recover genomewide genotypes from 70 white-beaked (Lagenorhynchus albirostris) and 43 Atlantic white-sided dolphins (L. acutus) gathered throughout their north-east Atlantic distribution range. Both species are at a high risk of being negatively affected by climate change. Here, we provide a resource of 38...
Data from: Signatures of natural selection between life cycle stages separated by metamorphosis in European eelJose Martin Pujolar, Magnus W. Jacobsen, Dorte Bekkevold, Javier Lobón-Cervia, Bjarni Jónsson, Louis Bernatchez & Michael M. Hansen
Background: Species showing complex life cycles provide excellent opportunities to study the genetic associations between life cycle stages, as selective pressures may differ before and after metamorphosis. The European eel presents a complex life cycle with two metamorphoses, a first metamorphosis from larvae into glass eels (juvenile stage) and a second metamorphosis into silver eels (adult stage). We tested the hypothesis that different genes and gene pathways will be under selection at different life stages...
Although migratory plasticity is increasingly documented, the ecological drivers of plasticity are not well understood. Predation risk can influence migratory dynamics, but whether seasonal migrants can adjust their migratory behaviour according to perceived risk is unknown. We used electronic tags to record the migration of individual roach (Rutilus rutilus), a partially migratory fish, in the wild following exposure to manipulation of direct (predator presence/absence) and indirect (high/low roach density) perceived predation risk in experimental mesocosms....
Data from: Linkage mapping reveals strong chiasma interference in sockeye salmon: implications for interpreting genomic dataMorten T. Limborg, Ryan K. Waples, Fred W. Allendorf & James E. Seeb
Meiotic recombination is fundamental for generating new genetic variation and for securing proper disjunction. Further, recombination plays an essential role during the rediploidization process of polyploid-origin genomes because crossovers between pairs of homeologous chromosomes retain duplicated regions. A better understanding of how recombination affects genome evolution is crucial for interpreting genomic data; unfortunately, current knowledge mainly originates from a few model species. Salmonid fishes provide a valuable system for studying the effects of recombination in...
Technical University of Denmark12
Swiss Federal Institute of Aquatic Science and Technology2
University of Montana1
University of Washington1
George Eliava Institute of Bacteriophage, Microbiology and Virology1
Spanish Institute of Oceanography1
University of Hamburg1
Royal Swedish Academy of Sciences1