355 Works

Data from: Multi-trait single-step genomic prediction accounting for heterogeneous (co)variances over the genome

Emre Karaman, Mogens S. Lund & Guosheng Su
Widely used genomic prediction models may not properly account for heterogeneous (co)variance structure across the genome. Models such as BayesA and BayesB assume locus-specific variance, which are highly influenced by the prior for (co)variance of single nucleotide polymorphism (SNP) effect, regardless of the size of data. Models such as BayesC or GBLUP assume a common (co)variance for a proportion (BayesC) or all (GBLUP) of the SNP effects. In this study, we propose a multi-trait Bayesian...

Data from: Consequences of past and present harvest management in a declining flyway population of common eiders Somateria mollissima

Rune Tjørnløv, Roger Pradel, Remi Choquet, Thomas Kjær Christensen & Morten Frederiksen
1. Harvested species population dynamics are shaped by the relative contribution of natural and harvest mortality. Natural mortality is usually not under management control, so managers must continuously adjust harvest rates to prevent overexploitation. Ideally, this requires regular assessment of the contribution of harvest to total mortality and how this affects population dynamics. 2. To assess the impact of hunting mortality on the dynamics of the rapidly declining Baltic/Wadden Sea population of common eiders Somateria...

Genome-scale target capture of mitochondrial and nuclear environmental DNA from water samples

Mads Reinholdt Jensen & Philip Francis Thomsen
Environmental DNA (eDNA) provides a promising supplement to traditional sampling methods for population genetic inferences, but current studies have almost entirely focused on short mitochondrial markers. Here, we develop one mitochondrial and one nuclear set of target capture probes for the whale shark (Rhincodon typus) and test them on seawater samples collected in Qatar to investigate the potential of target capture for eDNA-based population studies. The mitochondrial target capture successfully retrieved ~235x (90x-352x per base...

Using vertebrate environmental DNA from seawater in biomonitoring of marine habitats

Eva Egelyng Sigsgaard, Felipe Torquato, Tobias Guldberg Frøslev, Alec B. M. Moore, Johan Mølgård Sørensen, Pedro Range, Radhouane Ben Hamadou, Steffen Sanvig Bach, Peter Rask Møller & Philip Francis Thomsen
Conservation and management of marine biodiversity depends on biomonitoring of marine habitats, but current approaches are resource-intensive and require different approaches for different organisms. Environmental DNA (eDNA) extracted from water samples is an efficient and versatile approach to detecting aquatic animals. In the ocean, eDNA composition reflects local fauna at fine spatial scales, but little is known about the effectiveness of eDNA-based monitoring of marine communities at larger scales. We investigated the potential of eDNA...

Data from: Vessel noise levels drive behavioural responses of humpback whales with implications for whale-watching

Kate Sprogis
Disturbance from whale-watching can cause significant behavioural changes with fitness consequences for targeted whale populations. However, the sensory stimuli triggering these responses are unknown, preventing effective mitigation. Here, we test the hypothesis that vessel noise level is a driver of disturbance, using humpback whales (Megaptera novaeangliae) as a model species. We conducted controlled exposure experiments (n= 42) on resting mother-calf pairs on a resting ground off Australia, by simulating whale-watch scenarios with a research vessel...

Data from : Historical legacies and ecological determinants of grass naturalizations worldwide

Anne-Christine Monnet, Maria S. Vorontsova, Rafaël H. A. Govaerts, Jens-Christian Svenning & Brody Sandel
The global distribution of exotic species is the result of abiotic, biotic and dispersal filtering processes that shape the movement and success of species outside their native range. In this study we aim to understand how these filtering processes drive the fluxes of grass species among regions, the factors that influence which species establish outside of their native range, and where they do so. We used national and subnational checklists of native and introduced grass...

Data from: Vessel noise levels drive behavioural responses of humpback whales with implications for whale-watching

Kate Sprogis
Disturbance from whale-watching can cause significant behavioural changes with fitness consequences for targeted whale populations. However, the sensory stimuli triggering these responses are unknown, preventing effective mitigation. Here, we test the hypothesis that vessel noise level is a driver of disturbance, using humpback whales (Megaptera novaeangliae) as a model species. We conducted controlled exposure experiments (n= 42) on resting mother-calf pairs on a resting ground off Australia, by simulating whale-watch scenarios with a research vessel...

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: 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: 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: 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: 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: Efficacy of psychosocial interventions for psychological and pregnancy outcomes in infertile women and men: a systematic review and meta-analysis

Yoon Frederiksen, Ingeborg Farver-Vestergaard, Ninna Skovgård, Hans Jakob Ingerslev & Robert Zachariae
Objective: To evaluate the evidence on the efficacy of psychosocial interventions for improving pregnancy rates and reducing distress for couples in treatment with assisted reproductive technology (ART). Design: Systematic review and meta-analysis. Data sources PsycINFO, PubMed, Embase, CINAHL, Web of Science and The Cochrane Library between 1978 and April 2014. Study selection Studies were considered eligible if they evaluated the effect of any psychosocial intervention on clinical pregnancy and/or distress in infertile participants, used a...

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: 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: Competitor relatedness, indirect soil effects and plant co-existence

Bodil K. Ehlers, Patrice David, Christian F. Damgaard & Thomas Lenormand
How species co-exist is a central question in ecology. Niche differentiation can prevent two species from excluding each other by competition. However, this interaction can vary in space because of internal factors such as intraspecific genetic variation, or external ones such as the presence of a third species. While these effects have been repeatedly observed, their joint effect on the outcome of competition has rarely been considered. We experimentally investigated how a dominant ecosystem engineer...

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: Mowing exacerbates the loss of ecosystem stability under nitrogen enrichment in a temperate grassland

Yunhai Zhang, Michel Loreau, Nianpeng He, Guangming Zhang & Xingguo Han
Summary: 1. Global reactive nitrogen (N) is projected to further increase in the coming years. Previous studies have demonstrated that N enrichment weakens the temporal stability of ecosystem primary productivity through decreased biodiversity and species asynchrony. Mowing is a globally common practice in grasslands; and infrequent mowing can maintain or increase plant diversity under N enrichment conditions. However, it is unclear how infrequent mowing affects ecosystem stability in the face of N enrichment. 2. By...

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: Plant community composition and species richness in the High Arctic tundra: from the present to the future

Jacob Nabe-Nielsen, Signe Normand, Francis K. C. Hui, Lærke Stewart, Christian Bay, Louise I. Nabe-Nielsen, Niels Martin Schmidt & Laerke Stewart
Arctic plant communities are altered by climate changes. The magnitude of these alterations depends on whether species distributions are determined by macroclimatic conditions, by factors related to local topography, or by biotic interactions. Our current understanding of the relative importance of these conditions is limited due to the scarcity of studies, especially in the High Arctic. We investigated variations in vascular plant community composition and species richness based on 288 plots distributed on three sites...

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: The shield effect: nuptial gifts protect males against precopulatory sexual cannibalism

Søren Toft & Maria Jose Albo
Several not mutually exclusive functions have been ascribed to nuptial gifts across different taxa. Although the idea that a nuptial prey gift may protect the male from pre-copulatory sexual cannibalism is attractive, it has previously been considered of no importance based on indirect evidence and rejected by experimental tests. We reinvestigated whether nuptial gifts may function as a shield against female attacks during mating encounters in the spider Pisaura mirabilis and whether female hunger influences...

Data from: Species richness change across spatial scales

Jonathan M. Chase, Brian J. McGill, Patrick L. Thompson, Laura H. Antão, Amanda E. Bates, Shane A. Blowes, Maria Dornelas, Andrew Gonzalez, Anne E. Magurran, Sarah R. Supp, Marten Winter, Anne D. Bjorkmann, Helge Bruelheide, Jarrett E.K. Byrnes, Juliano Sarmento Cabral, Robin Ehali, Catalina Gomez, Hector M. Guzman, Forest Isbell, Isla H. Myers-Smith, Holly P. Jones, Jessica Hines, Mark Vellend, Conor Waldock & Mary O'Connor
Humans have elevated global extinction rates and thus lowered global-scale species richness. However, there is no a priori reason to expect that losses of global species richness should always, or even often, trickle down to losses of species richness at regional and local scales, even though this relationship is often assumed. Here, we show that scale can modulate our estimates of species richness change through time in the face of anthropogenic pressures, but not in...

Data from: Conservation genetics of the pond bat (Myotis dasycneme) with special focus on the populations in northwestern Germany and Jutland, Denmark

Liselotte Wesley Andersen, Ronja Dirksen, Elena A. Nikulina, Hans J. Baagøe, Gunars Petersons, Péter Estók, Oleg L. Orlov, Maria V. Orlova, Florian Gloza-Rausch, Matthias Göttsche, Esben Fjederholt, Frauke Krüger & Morten Elmeros
Conservation genetics is important in the management of endangered species, helping to understand their connectivity and long-term viability, thus identifying populations of importance for conservation. The pond bat (Myotis dasycneme) is a rare species classified as ‘Near threatened’ with a wide but patchy Palearctic distribution. A total of 277 samples representing populations in Denmark, Germany, Latvia, Hungary and Russia were used in the genetic analyses; 224 samples representing Denmark, Germany and Russia were analysed at...

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