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: 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: 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: 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: 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: 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: Microglial activation in early Alzheimer trajectory is associated with higher grey matter volume

Grazia Daniela Femminella, Melanie Dani, Melanie Wood, Zhen Fan, Valeria Calsolaro, Rebecca Atkinson, Trudi Edginton, Rainer Hinz, David J. Brooks & Paul Edison
Objective: To investigate the influence of microglial activation in the early stages of Alzheimer’s disease trajectory, we assessed the relationship between microglial activation and grey matter volume and hippocampal volume in MCI patients. Methods: In this study, fifty-five participants (37 early stages MCI and 18 controls) underwent [11C]PBR28 PET, a marker of microglial activation; volumetric MRI to evaluate grey matter and hippocampal volumes as well as clinical and neuropsychometric evaluation. [11C]PBR28 VT (volume of distribution)...

Data from: Limited dietary overlap amongst resident Arctic herbivores in winter - complementary insights from complementary methods

Niels M. Schmidt, Jesper B. Mosbacher, Eero J. Vesterinen, Tomas Roslin & Anders Michelsen
Snow may prevent Arctic herbivores from accessing their forage in winter, forcing them to aggregate in the few patches with limited snow. In High Arctic Greenland, Arctic hare and rock ptarmigan often forage in muskox feeding craters. We therefore hypothesized that due to limited availability of forage, the dietary niches of these resident herbivores overlap considerably, and that the overlap increases as winter progresses. To test this, we analyzed fecal samples collected in early and...

Data from: Human paths have positive impacts on plant richness and diversity: a meta-analysis

Meredith Root-Bernstein & Jens-Christian Svenning
We assess the impacts of human paths, trails and roads on plant species richness and Shannon diversity. Most reviews of this topic have not considered community-level measures, and have focused on excessive tourism impacts. We found significant positive effects of paths on plant richness and diversity. The effect size for richness was highest when studies included roads (paved) or trails (unpaved). The effect size found for diversity was highest when studies were in grasslands. We...

Data from: Heaviside's dolphins (Cephalorhynchus heavisidii) relax acoustic crypsis to increase communication range

Morgan J. Martin, Tess Gridley, Simon H. Elwen & Frants H. Jensen
The costs of predation may exert significant pressure on the mode of communication used by an animal, and many species balance the benefits of communication (e.g. mate attraction) against the potential risk of predation. Four groups of toothed whales have independently evolved narrowband high-frequency (NBHF) echolocation signals. These signals help NBHF species avoid predation through acoustic crypsis by echolocating and communicating at frequencies inaudible to predators such as mammal-eating killer whales. Heaviside’s dolphins (Cephalorhynchus heavisidii)...

Data from: A widespread thermodynamic effect, but maintenance of biological rates through space across life’s major domains

Jesper G. Sørensen, Craig R. White, Grant A. Duffy & Steven L. Chown
For over a century, the hypothesis of temperature compensation, the maintenance of similar biological rates in species from different thermal environments, has remained controversial. An alternative idea, that fitness is greater at higher temperatures (the thermodynamic effect), has gained increasing traction. This alternative hypothesis is also being used to understand large-scale biodiversity responses to environmental change. Yet evidence in favour of each of these contrasting hypotheses continues to emerge. In consequence, the fundamental nature of...

Data from: A 2.6‐g sound and movement tag for studying the acoustic scene and kinematics of echolocating bats

Laura Stidsholt, Mark Johnson, Kristian Beedholm, Lasse Jakobsen, Kathrin Kugler, Signe Brinkløv, Angeles Salles, Cynthia F. Moss & Peter Teglberg Madsen
1. To study sensorimotor behaviour in wild animals, it is necessary to synchronously record the sensory inputs available to the animal, and its movements. To do this, we have developed a biologging device that can record the primary sensory information and the associated movements during foraging and navigating in echolocating bats. 2. This 2.6 -gram tag records the sonar calls and echoes from an ultrasonic microphone, while simultaneously sampling fine-scale movement in three dimensions from...

Data from: Genomic parallelism and lack thereof in contrasting systems of three‐spined sticklebacks

Shenglin Liu, Anne-Laure Ferchaud, Peter Grønkjær, Rasmus Nygaard & Michael M. Hansen
Parallel evolution and the extent to which it involves gene reuse has attracted much interest. Whereas it has theoretically been predicted under which circumstances gene reuse is expected, empirical studies that directly compare systems showing high and low parallelism are rare. Three-spine stickleback (Gasterosteus aculeatus), where freshwater populations have been independently founded by ancestral marine populations, represent prime examples of phenotypic and genomic parallelism, but cases exist where parallelism is low. Based on RAD (Restriction...

Data from: Stable coexistence of genetically divergent Atlantic cod ecotypes at multiple spatial scales

Halvor Knutsen, Per Erik Jorde, Jeffrey A. Hutchings, Jakob Hemmer-Hansen, Peter Grønkjær, Kris-Emil Mose Jørgensen, Carl Andre, Marte Sodeland, Jon Albretsen, Esben M. Olsen & Peter Grønkjaer
Coexistence in the same habitat of closely related yet genetically different populations is a phenomenon that challenges our understanding of local population structure and adaptation. Identifying the underlying mechanisms for such coexistence can yield new insight into adaptive evolution, diversification, and the potential for organisms to adapt and persist in response to a changing environment. Recent studies have documented cryptic, sympatric populations of Atlantic cod (Gadus morhua) in coastal areas. We analyzed genetic origin of...

Data from: Male spiders control offspring sex ratio through greater production of female-determining sperm

Bram Vanthournout, Mette Marie Busck, Jesper Bechsgaard, Frederik Hendrickx, Andreas Schramm & Trine Bilde
Sex allocation theory predicts that when sons and daughters have different reproductive values, parents should adjust offspring sex ratio towards the sex with the higher fitness return. Haplo-diploid species directly control offspring sex ratio, but species with chromosomal sex determination (CSD) were presumed to be constrained by Mendelian segregation. There is now increasing evidence that CSD species can adjust sex ratio strategically, but the underlying mechanism is not well understood. One hypothesis states that adaptive...

Data from: Natural selection interacts with recombination to shape the evolution of hybrid genomes

Molly Schumer, Chenling Xu, Daniel L Powell, Arun Durvasula, Laurits Skov, Chris Holland, John C Blazier, Sriram Sankararaman, Peter Andolfatto, Gil G Rosenthal & Molly Przeworski
To investigate the consequences of hybridization between species, we studied three replicate hybrid populations that formed naturally between two swordtail fish species, estimating their fine-scale genetic map and inferring ancestry along the genomes of 690 individuals. In all three populations, ancestry from the “minor” parental species is more common in regions of high recombination and where there is linkage to fewer putative targets of selection. The same patterns are apparent in a reanalysis of human...

Data from: Laboratory maintenance does not alter ecological and physiological patterns among species: a Drosophila case study

Heidi J. MacLean, Torsten Nygaard Kristensen, Jesper G. Sorensen & Johannes Overgaard
Large comparative studies in animal ecology, physiology, and evolution often use animals reared in the laboratory for many generations; however, the relevance of these studies hinges on the assumption that laboratory populations are still representative for their wild living conspecifics. In the present study, we investigate if laboratory-maintained and freshly-collected animal populations are fundamentally different and if data from laboratory-maintained animals are valid to use in large comparative investigations of ecological and physiological patterns. Here,...

Data from: Living in two worlds: evolutionary mechanisms act differently in the native and introduced ranges of an invasive plant

Wen-Yong Guo, Carla Lambertini, Petr Pyšek, Laura A. Meyerson & Hans Brix
Identifying the factors that influence spatial genetic structure among populations can provide insights into the evolution of invasive plants. In this study, we used the common reed (Phragmites australis), a grass native in Europe and invading North America, to examine the relative importance of geographic, environmental (represented by climate here) and human effects on population genetic structure and its changes during invasion. We collected samples of P. australis from both the invaded North American and...

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: 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: 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: 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,...

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: 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...

Registration Year

  • 2018
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Resource Types

  • Dataset
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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