382 Works

Nutrient digestibility and balance studies

Sadjad Danesh Mesgaran, Björn Kuhla, René Baumont, Gonzalo Cantalapiedra-Hijar, Pierre Noziére, Peter Lund, David Humphries & Jan Dijkstra
The nutritional value of a feed for cattle depends on its nutrient and energy contents, the extent of rumen fermentation and degradation, and the post-ruminal digestibility. Efficiency of digestion depends on different factors, for example, the apparent digestibility (estimated by subtracting the nutrients contained in faeces from the nutrients contained in dietary intake – unlike true digestibility where the endogenous and microbial amount is taken into account and corrected in final outcome) usually decreases when...

Data from: The REporting of studies Conducted using Observational Routinely-collected health Data (RECORD) statement: methods for arriving at consensus and developing reporting guidelines

Stuart G. Nicholls, Pauline Quach, Erik Von Elm, Astrid Guttmann, David Moher, Irene Petersen, Henrik T. Sørensen, Liam Smeeth, Sinéad M. Langan & Eric I. Benchimol
Objective: Routinely collected health data, collected for administrative and clinical purposes, without specific a priori research questions, are increasingly used for observational, comparative effectiveness, health services research, and clinical trials. The rapid evolution and availability of routinely collected data for research has brought to light specific issues not addressed by existing reporting guidelines. The aim of the present project was to determine the priorities of stakeholders in order to guide the development of the REporting...

Data from: Resource availability determines the importance of niche-based vs. stochastic community assembly in grasslands

Timo Conradi, Vicky M. Temperton & Johannes Kollmann
Niche-based selection and stochastic processes can operate simultaneously to generate spatial and temporal variation in species composition. Yet, the conditions under which ecological dynamics are dominated by niche-based vs. stochastic processes are poorly understood. Using a field experiment in early-successional temperate grassland and null models of beta diversity, this study investigates the effects of soil nutrient supply on the relative importance of niche-based selection vs. stochastic dynamics for variation in species composition among sites. Nutrient...

Data from: Individual, unit, and vocal clan level identity cues in sperm whale codas

Shane Gero, Hal Whitehead & Luke Rendell
The ‘social complexity hypothesis’ suggests that complex social structure is a driver of diversity in animal communication systems. Sperm whales have a hierarchically structured society in which the largest affiliative structures, the vocal clans, are marked on ocean-basin scales by culturally transmitted dialects of acoustic signals known as ‘codas’. We examined variation in coda repertoires among both individual whales and social units—the basic element of sperm whale society—using data from nine Caribbean social units across...

Data from: Interannual variations in needle and sapwood traits of Pinus edulis branches under an experimental drought

Marceau Guerin, Dario Martin-Benito, Georg Von Arx, Laia Andreu Hayles, Kevin L. Griffin, Rayann Hamdan, Nate G. McDowell, Robert Muscarella, Will Pockman, Pierre Gentine, William Pockman & Laia Andreu-Hayles
1) In the Southwest United States, recent large-scale die-offs of conifers raise the question of their resilience and mortality under droughts. To date, little is known about the interannual structural response to droughts. 2) We hypothesized that piñon pines (Pinus edulis) respond to drought by reducing the drop of leaf water potential in branches from year to year through needle morphological adjustments. We tested our hypothesis using a seven-year experiment in central New Mexico with...

Data from: PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data

Shenglin Liu & Michael M. Hansen
The pairwise sequentially Markovian coalescent (PSMC) method uses the genome sequence of a single individual to estimate demographic history covering a time span of thousands of generations. Although originally designed for whole-genome data, we here use simulations to investigate its applicability to reference genome-aligned restriction site associated DNA (RAD) data. We find that RAD data can potentially be used for PSMC analysis, but at present with limitations. The key factor is the proportion (p) of...

Data from: Linear reaction norms of thermal limits in Drosophila: predictable plasticity in cold but not in heat tolerance

Mads Fristrup Schou, Marie Brandt Mouridsen, Jesper Givskov Sørensen & Volker Loeschcke
1. Thermal limits of ectotherms have been studied extensively and are believed to be evolutionary constrained, leaving ectotherms at risk under future climate change. Phenotypic plasticity may extend the thermal limits, but we lack detailed characterizations of thermal limit reaction norms as well as an understanding of the interspecific variation of these reaction norms. 2. Here we investigated the interspecific variation in phenotypic plasticity of thermal limits in 13 Drosophila species. We obtained high-resolution reaction...

Data from: A replicated climate change field experiment reveals rapid evolutionary response in an ecologically important soil invertebrate

Thomas Bataillon, Nicolas Galtier, Aurelien Bernard, Nicolai Cryer, Nicolas Faivre, Sylvain Santoni, Dany Severac, Theis N. Mikkelsen, Klaus S. Larsen, Claus Beier, Jesper G. Sørensen, Martin Holmstrup, Bodil Ehlers, Bodil K. Ehlers & Teis N. Mikkelsen
Whether species can respond evolutionarily to current climate change is crucial for the persistence of many species. Yet, very few studies have examined genetic responses to climate change in manipulated experiments carried out in natural field conditions. We examined the evolutionary response to climate change in a common annelid worm using a controlled replicated experiment where climatic conditions were manipulated in a natural setting. Analyzing the transcribed genome of 15 local populations, we found that...

Data from: Sex-specific, inverted rhythms of breeding-site attendance in an Arctic seabird

Nicholas Per Huffeldt & Flemming R. Merkel
In contrast to daily rhythms that are common in the presence of the geophysical light–dark cycle, organisms at polar latitudes exhibit many diel activity patterns during natural periods of continuous solar light or darkness (polar day and night, respectively), from 24 h rhythms to arrhythmicity. In Arctic Greenland (73.7° N, 56.6° W) during polar day, we observed breeding-site attendance rhythms of thick-billed murres (Uria lomvia; n = 21 pairs), a charadriiform seabird, which provide biparental...

Data from: Environmental gradients and the evolution of successional habitat specialization: a test case with 14 Neotropical forest sites

Susan G. Letcher, Jesse R. Lasky, Robin L. Chazdon, Natalia Norden, S. Joseph Wright, Jorge A. Meave, Eduardo A. Pérez-García, Rodrigo Muñoz, Eunice Romero-Pérez, Ana Andrade, José Luis Andrade, Patricia Balvanera, Justin M. Becknell, Tony V. Bentos, Radika Bhaskar, Frans Bongers, Vanessa Boukili, Pedro H. S. Brancalion, Ricardo G. César, Deborah A. Clark, David B. Clark, Dylan Craven, Alexander DeFrancesco, Juan M. Dupuy, Bryan Finegan … & G. Bruce Williamson
1. Successional gradients are ubiquitous in nature, yet few studies have systematically examined the evolutionary origins of taxa that specialize at different successional stages. Here we quantify successional habitat specialization in Neotropical forest trees and evaluate its evolutionary lability along a precipitation gradient. Theoretically, successional habitat specialization should be more evolutionarily conserved in wet forests than in dry forests due to more extreme microenvironmental differentiation between early and late successional stages in wet forest. 2....

Data from: Environment not dispersal limitation drives clonal composition of arctic Daphnia in a recently deglaciated area

Tsegazeabe Hadush Haileselasie, Joachim Mergeay, Lawrence J. Weider, Ruben Sommaruga, Thomas A. Davidson, Mariana Meerhoff, Hartmut Arndt, Klaus Jürgens, Erik Jeppesen & Luc De Meester
One of the most prominent manifestations of the ongoing climate warming is the retreat of glaciers and ice sheets around the world. Retreating glaciers result in the formation of new ponds and lakes, which are available for colonization. The gradual appearance of these new habitat patches allows us to determine to what extent the composition of asexual Daphnia (water flea) populations is affected by environmental drivers versus dispersal limitation. Here we used a landscape genetics...

Data from: Identifying drivers of parallel evolution: a regression model approach

Susan F Bailey, Qianyun Guo & Thomas Bataillon
Parallel evolution, defined as identical changes arising in independent populations, is often attributed to similar selective pressures favoring the fixation of identical genetic changes. However, some level of parallel evolution is also expected if mutation rates are heterogeneous across regions of the genome. Theory suggests that mutation and selection can have equal impacts on patterns of parallel evolution; however empirical studies have yet to jointly quantify the importance of these two processes. Here, we introduce...

Data from: Asgard archaea illuminate the origin of eukaryotic cellular complexity

Katarzyna Zaremba-Niedzwiedzka, Eva F. Caceres, Jimmy H. Saw, Disa Bäckström, Lina Juzokaite, Emmelien Vancaester, Kiley W. Seitz, Karthik Anantharaman, Piotr Starnawski, Kasper U. Kjeldsen, Matthew B. Stott, Takuro Nunoura, Jillian F. Banfield, Andreas Schramm, Brett J. Baker, Anja Spang & Thijs J. G. Ettema
The origin and cellular complexity of eukaryotes represent a major enigma in biology. Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell. The host cell is related to Lokiarchaeota, an archaeal phylum with many eukaryotic features. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. Here we describe the ‘Asgard’ superphylum, a group of uncultivated archaea that, as...

Data from: Using museum specimens to track morphological shifts through climate change

Heidi J. MacLean, Matthew E. Nielsen, Joel G. Kingsolver & Lauren B. Buckley
Museum specimens offer a largely untapped resource for detecting morphological shifts in response to climate change. However, morphological shifts can be obscured by shifts in phenology or distribution or sampling biases. Additionally, interpreting phenotypic shifts requires distinguishing whether they result from plastic or genetic changes. Previous studies using collections have documented consistent historical size changes, but the limited studies of other morphological traits have often failed to support, or even test, hypotheses. We explore the...

Data from: Global transcriptome changes in perennial ryegrass during early infection by pink snow mould

Mallikarjuna Rao Kovi, Mohamed Abdelhalim, Anil Kunapareddy, Åshild Ergon, Anne Marte Tronsmo, May Bente Brurberg, Ingerd Skow Hofgaard, Torben Asp & Odd Arne Rognli
Lack of resistance to pink snow mould (Microdochium nivale) is a major constraint for adaptation of perennial ryegrass (Lolium perenne L.) to continental regions with long-lasting snow cover at higher latitudes. Almost all investigations of genetic variation in resistance have been performed using cold acclimated plants. However, there may be variation in resistance mechanisms that are functioning independently of cold acclimation. In this study our aim was to identify candidate genes involved in such resistance...

Data from: The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: threespine sticklebacks in divergent environments

Anne-Laure Ferchaud & Michael M. Hansen
Heterogeneous genomic divergence between populations may reflect selection, but should also be seen in conjunction with gene flow and drift, particularly population bottlenecks. Marine and freshwater threespine stickleback (Gasterosteus aculeatus) populations often exhibit different lateral armor plate morphs. Moreover, strikingly parallel genomic footprints across different marine-freshwater population pairs are interpreted as parallel evolution and gene reuse. Nevertheless, in some geographic regions like the North Sea and Baltic Sea different patterns are observed. Freshwater populations in...

Data from: An evolutionary modelling approach to understanding the factors behind plant invasiveness and community susceptibility to invasion

John Warren, Chris J Topping & Penri James
Ecologists have had limited success in understanding which introduced species may become invasive. An evolutionary model is used to investigate which traits are associated with invasiveness. Translocation experiments were simulated in which species were moved into similar but evolutionary younger communities. The main findings were that species that had previously been the most abundant in their original communities have significantly higher rates of establishment than did species that had previously occurred at low abundance in...

Data from: Impact of disease on diversity and productivity of plant populations

Henry E. Creissen, Tove H. Jorgensen & James K. M. Brown
Experiments were conducted on the role of intra- and inter-genotypic competition in ecological processes operating at the population scale in diseased plant populations. Combinations of Arabidopsis thaliana genotypes showing variation for phenotypic traits relating to competitive ability and pathogen compatibility were infected with the oomycete Hyaloperonospora arabidopsidis and Turnip yellows virus in separate experiments. Plant fitness and competitive ability were estimated from phenotypic measurements. Pathogen-induced reduction in competitive ability for susceptible genotypes increased the competitive...

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: Field metabolic rates of teleost fishes are recorded in otolith carbonate

Ming-Tsung Chung, Clive N. Trueman, Jane A. Godiksen, Mathias Engell Holmstrup & Peter Grønkjær
Field metabolic rate (FMR) is key to understanding individual and population-level responses to environmental changes, but is challenging to measure in field conditions, particularly in aquatic environments. Here we show that FMR can be estimated directly from the isotopic composition of carbon in fish otoliths (δ13Coto). We describe the relationship between δ13Coto values and oxygen consumption rate, and report results from laboratory experiments relating individual-level measurements of oxygen consumption rates to δ13Coto values in Atlantic...

Data from: Molecular and pollen-based vegetation analysis in lake sediments from central Scandinavia

Laura Parducci, Irina Matetovici, Sonia L. Fontana, Keith D. Bennett, Yoshihisa Suyama, James Haile, Kurt H. Kjær, Nicolaj K. Larsen, Andreas D. Drouzas, Eske Willerslev & Kurt H. Kjaer
Plant and animal biodiversity can be studied by obtaining DNA directly from the environment. This new approach in combination with the use of generic barcoding primers (metabarcoding) has been suggested as complementary or alternative to traditional biodiversity monitoring in ancient soil sediments. However, the extent to which metabarcoding truly reflects plant composition remains unclear, as does its power to identify species with no pollen or macrofossil evidence. Here, we compared pollen-based and metabarcoding approaches to...

Data from: Effects of food abundance and early clutch predation on reproductive timing in a high Arctic shorebird exposed to advancements in arthropod abundance

Jeroen Reneerkens, Niels Martin Schmidt, Olivier Gilg, Jannik Hansen, Lars Holst Hansen, Jérôme Moreau & Theunis Piersma
Climate change may influence the phenology of organisms unequally across trophic levels and thus lead to phenological mismatches between predators and prey. In cases where prey availability peaks before reproducing predators reach maximal prey demand, any negative fitness consequences would selectively favor resynchronization by earlier starts of the reproductive activities of the predators. At a study site in northeast Greenland, over a period of 17 years, the median emergence of the invertebrate prey of Sanderling...

Data from: Eelgrass (Zostera marina) food web structure in different environmental settings

Jonas Thormar, Harald Hasler-Sheetal, Susanne Baden, Christoffer Boström, Kevin Kuhlmann Clausen, Dorte Krause-Jensen, Birgit Olesen, Jonas Ribergaard Rasmussen, Carl Johan Svensson & Marianne Holmer
This study compares the structure of eelgrass (Zostera marina L.) meadows and associated food webs in two eelgrass habitats in Denmark, differing in exposure, connection to the open sea, nutrient enrichment and water transparency. Meadow structure strongly reflected the environmental conditions in each habitat. The eutrophicated, protected site had higher biomass of filamentous algae, lower eelgrass biomass and shoot density, longer and narrower leaves, and higher above to below ground biomass ratio compared to the...

Data from: Congruent signals of population history but radically different patterns of genetic diversity between mitochondrial and nuclear markers in a mountain lizard

Anne-Laure Ferchaud, Rémy Eudeline, Véronique Arnal, Marc Cheylan, Gilles Pottier, Raphaël Leblois & Pierre-Andre Crochet
Historical factors, current population size, population connectivity and selective processes at linked loci contribute to shaping contemporary patterns of neutral genetic diversity. It is now widely acknowledged that nuclear and mitochondrial markers react differently to current demography as well as to past history, so the use of both types of markers is often advocated to gain insight on both historical and contemporary processes. We used 12 microsatellite loci genotyped in 13 populations of a mountain...

Data from: Cultural turnover among Galápagos sperm whales

Mauricio Cantor, Hal Whitehead, Shane Gero & Luke Rendell
While populations may wax and wane, it is rare for an entire population to be replaced by a completely different set of individuals. We document the large-scale relocation of cultural groups of sperm whale off the Galápagos Islands, in which two sympatric vocal clans were entirely replaced by two different ones. Between 1985 and 1999, whales from two clans (called Regular and Plus-One) defined by cultural dialects in coda vocalizations were repeatedly photo-identified off Galápagos....

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