49 Works

Data from: Introgression of Chinese haplotypes contributed to the improvement of Danish Duroc pigs

Minhui Chen, Guosheng Su, Jinluan Fu, Aiguo Wang, Jian-Feng Liu, Mogens S. Lund & Bernt Guldbrandtsen
The distribution of Asian ancestry in the genome of Danish Duroc pigs was investigated using whole-genome sequencing data from European wild boars, Danish Duroc, Chinese Meishan and Bamaxiang pigs. Asian haplotypes deriving from Meishan and Bamaxiang occur widely across the genome. Signatures of selection on Asian haplotypes are common in the genome, but few of these haplotypes have been fixed. By defining 50 kb windows with more than 50% Chinese ancestry, which did not exhibit...

Data from: Global patterns of the double mutualism phenomenon

Francisco Fuster, Christopher Kaiser-Bunbury, Jens M. Olesen & Anna Traveset
A double mutualism (DM) occurs when two interacting species benefit each other in two different functions, e.g. when an animal species acts both as pollinator and seed disperser of the same plant. Besides the double benefit, a DM also imposes a larger risk to both functions if the performance of one partner declines. We conducted the first global review of DMs involving pollinators and seed dispersers, aiming to: (1) assess their prevalence across ecosystems and...

Data from: Overestimation of the adaptive substitution rate in fluctuating populations

Marjolaine Rousselle, Maeva Mollion, Benoit Nabholz, Thomas Bataillon & Nicolas Galtier
Estimating the proportion of adaptive substitutions (α) is of primary importance to uncover the determinants of adaptation in comparative genomic studies. Several methods have been proposed to estimate α from patterns polymorphism and divergence in coding sequences. However, estimators of α can be biased when the underlying assumptions are not met. Here we focus on a potential source of bias, i.e., variation through time in the long term population size (N) of the considered species....

Data from: Predation and nutrients drive population declines in breeding waders

Anders P. Møller, Ole Thorup & Karsten Laursen
Allee effects are defined as a decline in per capita fitness at low population density. We hypothesized that predation reduces population size of breeding waders and thereby the efficiency of predator deterrence, while total nitrogen through its effects on primary and secondary productivity increases population size. Therefore, nest predation could have negative consequences for population size because nest failure generally results in breeding dispersal and hence reduced local population density. To test these predictions we...

Data from: Functional diversity of Collembola is reduced in soils subjected to short-term, but not long-term, geothermal warming

Martin Holmstrup, Bodil K. Ehlers, Stine Slotsbo, Krassimira Ilieva-Makulec, Bjarni Diðrik Sigurðsson, Niki I. Leblans, Jacintha Ellers, Matty P. Berg, Niki I. W. Leblans & Bjarni D. Sigurdsson
1. Human activities have caused global changes of atmospheric chemistry resulting in increased temperature especially in the colder regions of the northern hemisphere. Since warming of the environment can have drastic effects on terrestrial ecosystems it is important to experimentally evaluate the extent of such effects in long-term field-based experiments. In the present study we make use of both recent (short-term) and long-term geothermal warming of Icelandic soils to examine the responses of Collembola, an...

Data from: Nationwide prevalence and incidence study of neuromyelitis optica spectrum disorder in Denmark

Viktoria Papp, Zsolt Illes, Melinda Magyari, Nils Koch-Henriksen, Matthias Kant, Claudia Christina Pfleger, Shanu Faerch Roemer, Michael Broksgaard Jensen, Annett Evelyn Petersen, Helle Hvilsted Nielsen, Lene Rosendahl, Zsolt Mezei, Tove Christensen, Kristina Svendsen, Poul Erik Hyldgaard Jensen, Magnus Christian Lydolph, Niels Heegaard, Jette Lautrup Frederiksen, Finn Thorup Sellebjerg, Egon Stenager & Thor Petersen
Objectives: To estimate the nationwide population-based incidence, prevalence, and geographical distribution of neuromyelitis optica spectrum disorder in Denmark based on the 2015 International Panel for NMO Diagnosis (IPND) criteria Methods: We conducted a multicentre, historically prospective study. Data were sourced from the Danish National Patient Registry, the Danish Multiple Sclerosis Registry, departments of neurology and laboratories providing aquaporin 4 (AQP4) antibody test. Cases were selected based on the 2006 Wingerchuk and the 2015 IPND criteria...

Data from: PHYLACINE 1.2: The Phylogenetic Atlas of Mammal Macroecology

Søren Faurby, Matt Davis, Rasmus Østergaard Pedersen, Simon D. Schowanek, Alexandre Antonelli & Jens-Christian Svenning
Data needed for macroecological analyses are difficult to compile and often hidden away in supplementary material under non-standardized formats. Phylogenies, range data, and trait data often use conflicting taxonomies and require ad hoc decisions to synonymize species or fill in large amounts of missing data. Furthermore, most available data sets ignore the large impact that humans have had on species ranges and diversity. Ignoring these impacts can lead to drastic differences in diversity patterns and...

Data from: High resistance towards herbivore-induced habitat change in a high arctic arthropod community

Niels M. Schmidt, Jesper B. Mosbacher, Bernhard Eitzinger, Eero J. Vesterinen & Tomas Roslin
Mammal herbivores may exert strong impacts on plant communities, and are often key drivers of vegetation composition and diversity. We tested whether such mammal-induced changes to a high Arctic plant community are reflected in the structure of other trophic levels. Specifically, we tested whether substantial vegetation changes following the experimental exclusion of muskoxen (Ovibos moschatus) altered the composition of the arthropod community and the predator-prey interactions therein. Overall, we found no impact of muskox-exclusion on...

Data from: Plasticity for desiccation tolerance across Drosophila species is affected by phylogeny and climate in complex ways

Vanessa Kellermann, Ary A. Hoffmann, Johannes Overgaard, Volker Loeschcke & Carla M. Sgró
Comparative analyses of ectotherm susceptibility to climate change often focus on thermal extremes, yet responses to aridity may be equally important. Here we focus on plasticity in desiccation resistance, a key trait shaping distributions of Drosophila species and other small ectotherms. We examined the extent to which 32 Drosophila species, varying in their distribution, could increase their desiccation resistance via phenotypic plasticity involving hardening, linking these responses to environment, phylogeny and basal resistance. We found...

Data from: Frequently mated males have higher protein preference in German cockroaches

Kim Jensen & Jules Silverman
Protein is an abundant nutrient in sperm, and males therefore expend protein every time they mate. In addition, many males provide the female with a nitrogen-rich nuptial gift during mating, which often increases female fertility by supplementing her pool of limiting nutrients. However, it is unknown whether males compensate for the nitrogen cost of mating by increasing their preference for protein, which would facilitate the production of new sperm and nuptial gift material. Using artificial...

Data from: Plant demographic and functional responses to management intensification: a long-term study in a Mediterranean rangeland

Eric Garnier, Adeline Fayolle, Marie-Laure Navas, Christian Damgaard, Pablo Cruz, Daniel Hubert, Jean Richarte, Paul Autran, Corentin Leurent & Cyrille Violle
1. Understanding how functional traits, which are key for plant functioning, relate to demographic parameters of populations is central to tackle pending issues in plant ecology such as the forecast of the fate of populations and communities in a changing world, the quantification of community assembly processes or the improvement of species distribution models. We addressed this question in the case of species from a Mediterranean rangeland of southern France. 2. Changes in species abundance...

Data from: Implications of survey effort on estimating demographic parameters of a long-lived marine top predator

John Symons, Kate R. Sprogis & Lars Bejder
Effective management of wildlife populations rely on knowledge of their abundance, survival and reproductive rates. Maintaining long-term studies capable of estimating demographic parameters for long-lived, slow reproducing species is challenging. Insights into effects of research intensity on the statistical power to estimate demographic parameters is limited. Here, we investigate implications of survey effort on estimating abundance, home range sizes and reproductive output of Indo-Pacific bottlenose dolphins (Tursiops aduncus), using a three-year sub-sample of a long-term,...

Data from: Prolonged fasting-induced metabolic signatures in human skeletal muscle of lean and obese men

Ann Mosegaard Bak, Mikkel Holm Vendelbo, Britt Christensen, Rikke Viggers, Bo Martin Bibby, Jørgen Rungby, Jens Otto Jørgensen, Niels Møller, Niels Jessen & Jens Otto Lunde Jørgensen
Insulin resistance is a well-known physiological adaptation to prolonged fasting in healthy skeletal muscle. Obesity is associated with insulin resistance and metabolic inflexibility in skeletal muscle, and a pronounced increase in the risk of metabolic complications. Under the hypothesis that the metabolic traits of insulin resistance associated with prolonged fasting are different from insulin resistance associated with obesity, we examined nine obese and nine lean participants during 12 and 72h of fasting, respectively. Insulin resistance...

Data from: Environmental and evolutionary drivers of diversity patterns in the tea family (Theaceae s.s.) across China

Mide Rao, Manuel J. Steinbauer, Xiaoguo Xiang, Minggang Zhang, Xiangcheng Mi, Jin-Tun Zhang, Keping Ma, Jens-Christian Svenning & Jintun Zhang
Subtropical forest is recognized as an important global vegetation type with high levels of plant species richness. However, the mechanisms underlying its diversity remain poorly understood. Here, we assessed the roles of environmental drivers and evolutionary dynamics (time-for-speciation and diversification rate) in shaping species richness patterns across China for a major subtropical plant group, the tea family (Theaceae s.s.) (145 species), at several taxonomic scales. To this end, we assessed the relationships between species richness,...

Data from: Disentangling the effects of multiple environmental drivers on population changes within communities

Diana E. Bowler, Henning Heldbjerg, Anthony D. Fox, Robert B. O'Hara & Katrin Böhning-Gaese
1. The effects of different environmental drivers on the changes in species’ population abundances can be difficult to disentangle since they often act simultaneously. Researchers have built statistical models that include environmental variables (such as annual temperature), or species attributes (such as a species’ temperature preference), which are assumed to detect the impacts of specific drivers (such as climate change). However, these approaches are often applied separately or, if combined, not explicitly compared. 2. We...

Data from: Vascular plant species richness and bioindication predict multi‐taxon species richness

Ane Kirstine Brunbjerg, Hans Henrik Bruun, Lars Dalby, Camilla Fløjgaard, Tobias Guldbjerg Frøslev, Toke Thomas Høye, Irina Goldberg, Thomas Læssøe, Morten D. D. Hansen, Lars Brøndum, Lars Skipper, Kåre Fog & Rasmus Ejrnæs
Plants regulate soils and microclimate, provide substrate for heterotrophic taxa, are easy to observe and identify and have a stable taxonomy, which strongly justifies their use as indicators in monitoring and conservation. However, there is no consensus as to whether plants are strong predictors of total multi‐taxon species richness. In this study, we investigate if general terrestrial species richness can be predicted by vascular plant richness and bioindication. To answer this question, we collected an...

Data from: How much starvation, desiccation and oxygen depletion can Drosophila melanogaster tolerate before its upper thermal limits are affected?

Tommaso Manenti, Tomás Rocha Cunha, Jesper Givskov Sørensen & Volker Loeschcke
Heat tolerance is commonly assessed as the critical thermal maximum (CTmax) using the dynamic method exposing organisms to a gradually increasing (ramping) temperature until organisms fall into a coma. The CTmax estimate is dependent on the ramping rate, with decreased rates leading to longer treatments and ultimately lower CTmax estimates. There is a current discussion surrounding the physiological dynamics of the effect of the time of exposure by temperature interaction on these estimates. Besides temperature...

Data from: Legume abundance along successional and rainfall gradients in neotropical forests

Maga Gei, Danaë M. A. Rozendaal, Lourens Poorter, Frans Bongers, Janet I. Sprent, Mira D. Garner, T. Mitchell Aide, José Luis Andrade, Patricia Balvanera, Justin M. Becknell, Pedro H.S. Brancalion, George A. L. Cabral, Ricardo Gomes César, Robin L. Chazdon, Rebecca J. Cole, Gabriel Dalla Colletta, Ben De Jong, Julie S. Denslow, Daisy H. Dent, Saara J. DeWalt, Juan Manuel Dupuy, Sandra M. Durán, Mário Marcos Do Espírito Santo, G. Wilson Fernandes, Yule Roberta Ferreira Nunes … & Jennifer S. Powers
The nutrient demands of regrowing tropical forests are partly satisfied by nitrogen (N)-fixing legume trees, but our understanding of the abundance of those species is biased towards wet tropical regions. Here we show how the abundance of Leguminosae is affected by both recovery from disturbance and large-scale rainfall gradients through a synthesis of forest-inventory plots from a network of 42 Neotropical forest chronosequences. During the first three decades of natural forest regeneration, legume basal area...

Data from: Genotype-by-sex-by-diet interactions for nutritional preference, dietary consumption and lipid deposition in a field cricket

James Rapkin, Kim Jensen, Clarissa M. House, Alastair J. Wilson & John Hunt
Changes in feeding behaviour, especially the over-consumption of calories, has led to a rise in the rates of obesity, diabetes and other associated disorders in humans and a range of animals inhabiting human-influenced environments. However, understanding the relative contribution of genes, the nutritional environment and their interaction to dietary intake and lipid deposition in the sexes still remains a major challenge. By combining nutritional geometry with quantitative genetics, we determined the effect of genes, the...

Data from: Kinship influences sperm whale social organization within, but generally not among, social units

Christine M. Konrad, Shane Gero, Timothy Frasier & Hal Whitehead
Sperm whales have a multi-level social structure based upon long-term, cooperative social units. What role kinship plays in structuring this society is poorly understood. We combined extensive association data (518 days, during 2005-2016) and genetic data (18 microsatellites and 346bp mtDNA control region sequences) for 65 individuals from 12 social units from the Eastern Caribbean to examine patterns of kinship and social behaviour. Social units were clearly matrilineally-based, evidenced by greater relatedness within social units...

Data from: A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering

Matthew G. Johnson, Lisa Pokorny, Steven Dodsworth, Laura R. Botigue, Robyn S. Cowan, Alison Devault, Wolf L. Eiserhardt, Niroshini Epitawalage, Félix Forest, Jan T. Kim, James Leebens-Mack, Ilia J. Leitch, Olivier Maurin, Doug Soltis, Pamela S. Soltis, Gane Ka-Shu Wong, William J. Baker & Norman Wickett
Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost of developing targeted sequencing approaches is associated with the generation of preliminary data needed for the identification of orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole-genome duplication events, especially in the angiosperms (flowering plants). We used...

Data from: The fitness landscape of the codon space across environments

Inês Fragata, Sebastian Matuszweski, Mark A. Schmitz, Thomas Bataillon, Jeffrey D. Jensen & Claudia Bank
Fitness landscapes map the relationship between genotypes and fitness. However, most fitness landscape studies ignore the genetic architecture imposed by the codon table and thereby neglect the potential role of synonymous mutations. To quantify the fitness effects of synonymous mutations and their potential impact on adaptation on a fitness landscape, we use a new software based on Bayesian Monte Carlo Markov Chain methods and re-estimate selection coefficients of all possible codon mutations across 9 amino-acid...

Data from: Identification of transcription factor genes involved in anthocyanin biosynthesis in carrot (Daucus carota L.) using RNA-Seq

Miyako Kodama, Henrik Brinch-Pedersen, Shrikant Sharma, Inger Bæksted Holme, Bjarne Joernsgaard, Tsaneta Dzhanfezova, Daniel Buchvaldt Amby, Filipe Garrett Vieira, Shanlin Liu & M. Thomas P. Gilbert
Background Anthocyanins are water-soluble colored flavonoids present in multiple organs of various plant species including flowers, fruits, leaves, stems and roots. DNA-binding R2R3-MYB transcription factors, basic helix–loop–helix (bHLH) transcription factors, and WD40 repeat proteins are known to form MYB-bHLH-WD repeat (MBW) complexes, which activates the transcription of structural genes in the anthocyanin pathway. Although black cultivars of carrots (Daucus carota L.) can accumulate large quantities of anthocyanin in their storage roots, the regulatory genes responsible...

Data from: Kin selection and allocare in sperm whales

Christine M. Konrad, Timothy R. Frasier, Hal Whitehead & Shane Gero
Cooperative care and defense of young are hypothesized to be foundational to the societies of several species, including the sperm whale (Physeter macrocephalus). However, the extent of allocare among sperm whales and the mechanisms driving it have not been well-characterized. Sperm whale social units are matrilineally-based, making kin selection a likely key driver of allocare, but the relationship between kinship and calf care is essentially unknown. We investigate calf care in the context of kinship,...

Registration Year

  • 2018
    49

Resource Types

  • Dataset
    49

Affiliations

  • Aarhus University
    49
  • University of Copenhagen
    4
  • University of Alberta
    3
  • Swedish University of Agricultural Sciences
    3
  • University of Pretoria
    2
  • Columbia University
    2
  • Princeton University
    2
  • Université Paul-Valéry Montpellier
    2
  • University of Toulouse
    2
  • University of California, Berkeley
    2