323 Works

Skeleton 1000

Canan Çakirlar

Data from: Dynamics of deep soil carbon - insights from 14C time series across a climatic gradient

Tessa Sophia Van Der Voort, Utsav Mannu, Frank Hagedorn, Cameron McIntyre, Lorenz Walthert, Patrick Schleppi, Negar Haghipour & Timothy I. Eglinton
Quantitative constraints on soil organic matter (SOM) dynamics are essential for comprehensive understanding of the terrestrial carbon cycle. Deep soil carbon is of particular interest, as it represents large stocks and its turnover times remain highly uncertain. In this study, SOM dynamics in both the top and deep soil across a climatic (average temperature ~1-9 °C) gradient are determined using time-series (~20 years) 14C data from bulk soil and water-extractable organic carbon (WEOC). Analytical measurements...

Hawksbill turtle ddRAD raw sequencing data

Jurjan Van Der Zee, Marjolijn Christianen, Mabel Nava, Sietske Van Der Wal, Jessica Berkel, Tadzio Bervoets, Melanie Meijer Zu Schlochtern, Martine Bérubé, Leontine Becking & Per Palsbøll
Pleistocene environmental changes are generally assumed to have dramatically affected species’ demography via changes in habitat availability, but this is challenging to investigate due to our limited knowledge of how Pleistocene ecosystems changed through time. Here, we tracked changes in shallow marine habitat availability resulting from Pleistocene sea level fluctuations throughout the last glacial cycle (120 – 14 thousand years ago; kya) and assessed correlations with past changes in genetic diversity inferred from genome-wide SNPs,...

Data for: Telomere dynamics in relation to experimentally increased locomotion costs and fitness in great tits

Simon Verhulst, Els Atema & Arie J. Van Noordwijk
Evidence that telomere length (TL) and dynamics can be interpreted as proxy for ‘life stress’ experienced by individuals stems largely from correlational studies. We tested for effects of an experimental increase of workload on telomere dynamics by equipping male great tits (Parus major) with a 0.9 gram backpack for a full year. In addition, we analysed associations between natural life-history variation, TL and TL dynamics. Carrying 5% extra weight for a year did not significantly...

Large herbivores facilitate a dominant grassland plant via multiple indirect effects

Zhiwei Zhong, Xiaofei Li, Christian Smit, Tianyun Li, Ling Wang, Valeria Aschero, Diego Vázquez, Mark Ritchie, Hall Cushman & Deli Wang
While large herbivores are critically important components of terrestrial ecosystems and can have pronounced top-down effects on plants, our understanding of the underlying mechanisms driving these effects remains incomplete. Large herbivores can alter plant growth, reproduction and abundance through direct effects (predominantly consumption) and through indirect effects via altered interactions with abiotic factors and other species. We know considerably less about these indirect effects than the direct effects. Here, we integrate medium- and small-scale field...

A molecular view on the escape of lipoplexed DNA from the endosome (no trajectories)

Bart Bruininks, Paulo De Souza, Helgi Ingolffson & Siewert Marrink
The use of non-viral vectors for in vivo gene therapy could drastically increase safety, whilst reducing the cost of preparing the vectors. A promising approach to non-viral vectors makes use of DNA/cationic liposome complexes (lipoplexes) to deliver the genetic material. Here we use coarse-grained molecular dynamics simulations to investigate the molecular mechanism underlying efficient DNA transfer from lipoplexes. Our computational fusion experiments of lipoplexes with endosomal membrane models show two distinct modes of transfection: parallel...

High-arctic family planning: earlier spring onset advances age at first reproduction in barnacle geese

Kate Layton-Matthews, Mari Aas Fjelldal, Aline Magdalena Lee, Vidar Grøtan, Maarten J.J.E. Loonen & Brage Bremset Hansen
Quantifying how key life-history traits respond to climatic change is fundamental in understanding and predicting long-term population prospects. Age at first reproduction, which affects fitness and population dynamics, may be influenced by environmental stochasticity but has rarely been directly linked to climate change. Here, we use a case study from the highly seasonal and stochastic environment in high-arctic Svalbard, with strong temporal trends in breeding conditions, to test whether rapid climate warming may induce changes...

Data from: Reciprocal facilitation between annual plants and burrowing crabs: implications for the restoration of degraded salt marshes

Dongdong Qiu, Baoshan Cui, Xu Ma, Jiaguo Yan, Yanzi Cai, Tian Xie, Fang Gao, Fangfang Wang, Haochen Sui, Junhong Bai, Johan Van De Koppel & Han Olff
​​​​​​Increasing evidence shows that facilitative interactions between species play an essential role in coastal wetland ecosystems. However, there is a lack of understanding of how such interactions can be used for restoration purposes in salt marsh ecosystems. We, therefore, studied the mechanisms of reciprocal facilitative interactions between native annual plants, Suaeda salsa, and burrowing crabs, Helice tientsinensis, in a middle-elevation salt marsh (with generally high plant density and moderate tides) in the Yellow River Delta...

Datasets used for the publication: State-dependence explains individual variation in nest defence behaviour in a long-lived bird

Margje E. De Jong, Marion Nicolaus, Rienk W. Fokkema & Maarten J.J.E. Loonen
The uploaded datasets were used to test if variation in states predicts nest defence behaviour (a ‘risky’ behaviour) in a long-lived species, the barnacle goose (Branta leucopsis). Repeated measures of nest defence towards a human intruder (flight initiation distance or FID) of females of known age were collected during 15 breeding seasons. Increasing values of FID represent increasing shyness. Adaptive models have predicted that an individual’s residual reproductive value or ‘asset’ is an important state...

Density-dependent individual variation in male attractiveness in a wild field cricket

Petri Niemelä, Stefano Tiso & Niels Dingemanse
Social environments modify a male’s ability to attract females and thus affect its fitness. Theory implies that an individual’s fitness should trade-off with its ability to cope with competition. Individuals are expected to solve this trade-off differently: some males should be more attractive at low but others instead at high density. This prediction has rarely been tested in the wild. We used an automated RFID-surveillance system to quantify for each hour of the day, over...

Timing of increased temperature sensitivity coincides with nervous system development in winter moth embryos

Natalie Van Dis, Maurijn Van Der Zee, Roelof Hut, Bregje Wertheim & Marcel Visser
Climate change is rapidly altering the environment and many species will need to genetically adapt their seasonal timing to keep up with these changes. Insect development rate is largely influenced by temperature, but we know little about the mechanisms underlying temperature sensitivity of development. Here we investigate seasonal timing of egg hatching in the winter moth, one of the few species which has been found to genetically adapt to climate change, likely through selection on...

Data from: Body shrinkage due to Arctic warming reduces red knot fitness in tropical wintering range

Jan A. Van Gils, Simeon Lisovski, Tamar Lok, Włodzimierz Meissner, Agnieszka Ożarowska, Jimmy De Fouw, Eldar Rakhiemberdiev, Mikhail Y. Soloviev, Theunis Piersma & Marcel Klaassen
Reductions in body size are increasingly being identified as a response to climate warming. Here we present evidence for a case of such body shrinkage, potentially due to malnutrition in early life. We show that an avian long-distance migrant (red knot, Calidris canutus canutus), which is experiencing globally unrivaled warming rates at its high-Arctic breeding grounds, produces smaller offspring with shorter bills during summers with early snowmelt. This has consequences half a world away at...

Data from: Climate impacts on trans-ocean dispersal and habitat in gray whales from the Pleistocene to 2100

S. Elizabeth Alter, Matthias Meyer, Klaas Post, Paul Czechowski, Peter Gravlund, Cork Gaines, Howard C. Rosenbaum, Kristin Kaschner, Samuel T. Turvey, Johannes Van Der Plicht, Beth Shapiro & Michael Hofreiter
Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is...

Data from: Mediation analysis demonstrates that trans-eQTLs are often explained by cis-mediation: a genome-wide analysis among 1,800 South Asians

Brandon L. Pierce, Lin Tong, Lin S. Chen, Ronald Rahaman, Maria Argos, Farzana Jasmine, Shantanu Roy, Rachelle Paul-Brutus, Harm-Jan Westra, Lude Franke, Tonu Esko, Rakibuz Zaman, Tariqul Islam, Mahfuzar Rahman, John A. Baron, Muhammad G. Kibriya & Habibul Ahsan
A large fraction of human genes are regulated by genetic variation near the transcribed sequence (cis-eQTL, expression quantitative trait locus), and many cis-eQTLs have implications for human disease. Less is known regarding the effects of genetic variation on expression of distant genes (trans-eQTLs) and their biological mechanisms. In this work, we use genome-wide data on SNPs and array-based expression measures from mononuclear cells obtained from a population-based cohort of 1,799 Bangladeshi individuals to characterize cis-...

Data from: Social conformity and propagation of information in collective u-turns of fish schools

Valentin Lecheval, Li Jiang, Pierre Tichit, Clément Sire, Charlotte K. Hemelrijk & Guy Theraulaz
Moving animal groups such as schools of fish or flocks of birds often undergo sudden collective changes of their travelling direction as a consequence of stochastic fluctuations in heading of the individuals. However, the mechanisms by which these behavioural fluctuations arise at the individual level and propagate within a group are still unclear. In the present study, we combine an experimental and theoretical approach to investigate spontaneous collective U-turns in groups of rummy-nose tetra (Hemigrammus...

Data from: Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient

Sean F. Ryan, Michaël C. Fontaine, J. Mark Scriber, Michael E. Pfrender, Shawn T. O'Neil & Jessica J. Hellmann
Hybrid zones are a valuable tool for studying the process of speciation and for identifying the genomic regions undergoing divergence and the ecological (extrinsic) and non-ecological (intrinsic) factors involved. Here, we explored the genomic and geographic landscape of divergence in a hybrid zone between Papilio glaucus and Papilio canadensis. Using a genome scan of 28,417 ddRAD SNPs, we identified genomic regions under possible selection and examined their distribution in the context of previously identified candidate...

Data from: Reproduction and dispersal in an ant-associated root aphid community

Aniek B. F. Ivens, Daniel J. C. Kronauer, Ido Pen, Franz J. Weissing & Jacobus J. Boomsma
Clonal organisms with occasional sex are important for our general understanding of the costs and benefits that maintain sexual reproduction. Cyclically parthenogenetic aphids are highly variable in their frequency of sexual reproduction and studies have mostly focused on free-living aphids above ground, whereas dispersal constraints and dependence on ant-tending may differentially affect the costs and benefits of sex in subterranean aphids. Here, we studied reproductive mode and dispersal in a community of root aphids that...

Data from: Exposing the structure of an Arctic food web

Eero J. Vesterinen, Helena K. Wirta, Peter A. Hambäck, Elisabeth Weingartner, Claus Rasmussen, Jeroen Reneerkens, Niels M. Schmidt, Olivier Gilg & Tomas Roslin
How food webs are structured has major implications for their stability and dynamics. While poorly studied to date, arctic food webs are commonly assumed to be simple in structure, with few links per species. If this is the case, then different parts of the web may be weakly connected to each other, with populations and species united by only a low number of links. We provide the first highly resolved description of trophic link structure...

Data from: Genetic consequences of breaking migratory traditions in barnacle geese Branta leucopsis

Rudy M. Jonker, Robert H. S. Kraus, Qiong Zhang, Pim Van Hooft, Kjell Larsson, Henk P. Van Der Jeugd, Ralf H. J. M. Kurvers, Sip E. Van Wieren, Maarten J. J. M. Loonen, Richard P. M. A. Crooijmans, Ronald C. Ydenberg, Martien A. M. Groenen, Herbert H. T. Prins & M. J. J. E. Loonen
Cultural transmission of migratory traditions enables species to deal with their environment based on experiences from earlier generations. Also, it allows a more adequate and rapid response to rapidly changing environments. When individuals break with their migratory traditions, new population structures can emerge that may affect gene flow. Recently, the migratory traditions of the Barnacle Goose Branta leucopsis changed, and new populations differing in migratory distance emerged. Here, we investigate the population genetic structure of...

Data from: The impact of translocations on neutral and functional genetic diversity within and among populations of the Seychelles warbler

David J. Wright, Lewis G. Spurgin, Nigel J. Collar, Jan Komdeur, Terry Burke & David S. Richardson
Translocations are an increasingly common tool in conservation. The maintenance of genetic diversity through translocation is critical for both the short and long term persistence of populations and species. However, the relative spatio-temporal impacts of translocations on neutral and functional genetic diversity and how this affects genetic structure among the conserved populations overall has received little investigation. We compared the impact of translocating different numbers of founders on both microsatellite and major histocompatibility complex (MHC)...

Data from: Moving on with foraging theory: incorporating movement decisions into the functional response of a gregarious shorebird

Jan A. Van Gils, Matthijs Van Der Geest, Brecht De Meulenaer, Hanneke Gillis, Theunis Piersma & Eelke O. Folmer
1. Models relating intake rate to food abundance and competitor densities (generalized functional response models) can predict forager distributions and movements between patches, but we lack understanding of how distributions and small-scale movements by the foragers themselves affect intake rates. 2. Using a state-of-the-art approach based on continuous-time Markov chain dynamics, we add realism to classic functional response models by acknowledging that the chances to encounter food and competitors are influenced by movement decisions, and,...

Data from: Independence among physiological traits suggests flexibility in the face of ecological demands on phenotypes

Deborah M. Buehler, Francois Vézina, Wolfgang Goymann, Ingrid Schwabl, Maaike Versteegh, B. Irene Tieleman & Theunis Piersma
Phenotypic flexibility allows animals to adjust their physiology to diverse environmental conditions encountered over the year. Examining how these varying traits covary gives insights into potential constraints or freedoms that may shape evolutionary trajectories. In this study we examined relationships among hematocrit, baseline corticosterone concentration, constitutive immune function and basal metabolic rate in red knot Calidris canutus islandica individuals subjected to experimentally manipulated temperature treatments over an entire annual cycle. If covariation among traits is...

Data from: Behavioural isolation may facilitate homoploid hybrid speciation in cichlid fish

Oliver M. Selz, Rahel Thommen, Martine E. Maan & Ole Seehausen
Hybrid speciation is constrained by the homogenizing effects of gene flow from the parental species. In the absence of post-mating isolation due to structural changes in the genome, or temporal or spatial premating isolation, another form of reproductive isolation would be needed for homoploid hybrid speciation to occur. Here, we investigate the potential of behavioural mate choice to generate assortative mating among hybrids and parental species. We made three-first-generation hybrid crosses between different species of...

Data from: No fitness benefits of early molt in a fairy-wren: relaxed sexual selection under genetic monogamy?

Marie Fan, Michelle L. Hall, Sjouke A. Kingma, Lisa M. Mandeltort, Nataly Hidalgo Aranzamendi, Kaspar Delhey & Anne Peters
The evolution of male ornamentation has long been the focus of sexual selection studies. However, evidence is accumulating that sexually selected traits can also be lost, although the process is ill-understood. In male fairy-wrens (Malurus spp.), early molt into the seasonal breeding plumage is critical for obtaining extra-pair paternity (EPP), which reaches very high levels in these socially monogamous songbirds. A notable exception is the purple-crowned fairy-wren, Malurus coronatus, which, like its congeners, breeds cooperatively,...

Data from: Baseline immune activity is associated with date rather than with moult stage in the Arctic-breeding barnacle goose (Branta leucopsis)

Cecilia A. M. Sandström, Jouke Prop, H Van Der Jeugd & Maarten J. J. E. Loonen
Variation in immune defence in birds is often explained either by external factors such as food availability and disease pressure or by internal factors such as moult and reproductive effort. We explored these factors together in one sampling design by measuring immune activity over the time frame of the moulting period of Arctic-breeding barnacle geese (Branta leucopsis). We assessed baseline innate immunity by measuring levels of complement-mediated lysis and natural antibody-mediated agglutination together with total...

Registration Year

  • 2022
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Resource Types

  • Dataset


  • University of Groningen
  • University of Sheffield
  • University of East Anglia
  • Nederlands Instituut voor Ecologie
  • Royal Netherlands Institute for Sea Research
  • Wageningen University & Research
  • University Medical Center Groningen
  • VU University Amsterdam
  • Institute of Avian Research
  • University of Oxford