473 Works

Data from: Replicated high-density genetic maps of two great tit populations reveal fine-scale genomic departures from sex-equal recombination rates

Kees Van Oers, Anna W. Santure, Isabelle De Cauwer, Nikkie E. M. Van Bers, Richard P. M. A. Crooijmans, Ben C. Sheldon, Marcel E. Visser, Jon Slate & Martien A. M. Groenen
Linking variation in quantitative traits to variation in the genome is an important, but challenging task in the study of life-history evolution. Linkage maps provide a valuable tool for the unravelling of such trait-gene associations. Moreover, they give insight into recombination landscapes and between- species karyotype evolution. Here we used genotype data, generated from a 10k SNP-chip, of over 2000 individuals to produce high-density linkage maps of the great tit (Parus major), a passerine bird,...

Data from: Do plant traits explain tree seedling survival in bogs?

Juul Limpens, Emily Van Egmond, Bingxi Li & Milena Holmgren
Moss-dominated peat bogs store approximately 30% of global soil carbon. A climate induced shift from current moss-dominated conditions to tree-dominated states is expected to strongly affect their functioning and carbon sequestration capacity. Consequently, unraveling the mechanisms that may explain successful tree seedling establishment in these ecosystems is highly relevant. To assess the role of drought on early tree seedling establishment and the relative importance of plant traits in tree seedling survival, we conducted a factorial...

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: Inferring the origin of populations introduced from a genetically structured native range by approximate Bayesian computation: case study of the invasive ladybird Harmonia axyridis

Eric Lombaert, Thomas Guillemaud, Cathleen E. Thomas, Lori J. Lawson Handley, Jiahui Li, Su Wang, Hong Pang, Irina Goryacheva, Ilya A. Zakharov, Emmanuelle Jousselin, Remy L. Poland, Alain Migeon, Joop Van Lenteren, Patrick De Clercq, Nick Berkvens, Walker Jones & Arnaud Estoup
Correct identification of the source population of an invasive species is a prerequisite for testing hypotheses concerning the factors responsible for biological invasions. The native area of invasive species may be large, poorly known and/or genetically structured. Because the actual source population may not have been sampled, studies based on molecular markers may generate incorrect conclusions about the origin of introduced populations. In this study, we characterized the genetic structure of the invasive ladybird Harmonia...

Data from: Hysteresis in an experimental phytoplankton population

Elisabeth J. Faassen, Annelies J. Veraart, Egbert H. Van Nes, Vasilis Dakos, Miquel Lürling & Marten Scheffer
The road to recovery of a deteriorated system is often different, and fraught with more barriers, than the path to the system's deterioration. This phenomenon is called hysteresis, and is inherent to systems presenting alternative stable states. In such systems, the stability of a given state is the product of positive feedback loops. A broad range of natural systems have been predicted to show hysteretic behaviour, but hysteresis has so far only been unambiguously demonstrated...

Data from: Plant species richness promotes soil carbon and nitrogen stocks in grasslands without legumes

Wen-Feng Cong, Jasper Van Ruijven, Liesje Mommer, Gerlinde De Deyn, Frank Berendse, Ellis Hoffland & Gerlinde B. De Deyn
1. The storage of carbon (C) and nitrogen (N) in soil are important ecosystem functions. Grassland biodiversity experiments have shown a positive effect of plant diversity on soil C and N storage. However, these experiments all included legumes, which constitute an important N input through N2-fixation. Indeed, the results of these experiments suggest that N2-fixation by legumes is a major driver of soil C and N storage. 2. We studied whether plant diversity affects soil...

Data from: Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men

Anne Salonen, Leo Lahti, Jarkko Salojärvi, Grietje Holtrop, Katri Korpela, Sylvia H. Duncan, Priya Date, Freda Farquharson, Alexandra M. Johnstone, Gerald E. Lobley, Petra Louis, Harry J. Flint & Willem M. De Vos
There is growing interest in understanding how diet affects the intestinal microbiota, including its possible associations with systemic diseases such as metabolic syndrome. Here we report a comprehensive and deep microbiota analysis of fourteen obese males consuming fully controlled diets supplemented with resistant starch (RS) or non-starch polysaccharides (NSP), and a weight-loss diet (WL). We analyzed the composition, diversity and dynamics of the faecal microbiota on each dietary regime by phylogenetic microarray and quantitative PCR...

Data from: How body torque and Strouhal number change with swimming speed and developmental stage in larval zebrafish

Johan L. Van Leeuwen, Cees J. Voesenek & Ulrike K. Muller
Small undulatory swimmers such as larval zebrafish experience both inertial and viscous forces, the relative importance of which is indicated by the Reynolds number (Re). Re is proportional to swimming speed (vswim) and body length; faster swimming reduces the relative effect of viscous forces. Compared with adults, larval fish experience relatively high (mainly viscous) drag during cyclic swimming. To enhance thrust to an equally high level, they must employ a high product of tail-beat frequency...

Data from: Dispersal versus environmental filtering in a dynamic system: drivers of vegetation patterns and diversity along stream riparian gradients

Rob G. A. Fraaije, Cajo J. F. Ter Braak, Betty Verduyn, Jos T. A. Verhoeven & Merel B. Soons
1. Both environmental filtering and dispersal filtering are known to influence plant species distribution patterns and biodiversity. Particularly in dynamic habitats, however, it remains unclear whether environmental filtering (stimulated by stressful conditions) or dispersal filtering (during re-colonization events) dominates in community assembly, or how they interact. Such a fundamental understanding of community assembly is critical to the design of biodiversity conservation and restoration strategies. 2. Stream riparian zones are species-rich dynamic habitats. They are characterized...

Data from: Early plant recruitment stages set the template for the development of vegetation patterns along a hydrological gradient

Rob G. A. Fraaije, Cajo J. F. Ter Braak, Betty Verduyn, Leonieke B. S. Breeman, Jos T. A. Verhoeven & Merel B. Soons
1. Recruitment processes are critical components of a plant's life cycle. However, in comparison with later stages in the plant life cycle (e.g. competition among adults), relatively little is known about their contribution to the regulation of plant species distribution. Particularly little is known about the individual contributions of the three main recruitment processes—germination, seedling survival, and seedling growth—to community assembly, while quantitative information on these contributions is essential for a more mechanistic understanding of...

Data from: The role of social and ecological processes in structuring animal populations: a case study from automated tracking of wild birds

Damien R. Farine, Joshua Firth, Lucy M. Aplin, Ross A. Crates, Antica Culina, Colin J. Garroway, Lindall R. Kidd, Nicole D. Milligan, Ioannis Psorakis, Reinder Radersma, Brecht Verhelst, Bernhard Voelkl, Ben C. Sheldon, C. A. Hinde & J. A. Firth
Both social and ecological factors influence population process and structure, with resultant consequences for phenotypic selection on individuals. Understanding the scale and relative contribution of these two factors is thus a central aim in evolutionary ecology. In this study, we develop a framework using null models to identify the social and spatial patterns that contribute to phenotypic structure in a wild population of songbirds. We used automated technologies to track 1053 individuals that formed 73...

Data from: Regular bottlenecks and restrictions to somatic fusion prevent the accumulation of mitochondrial defects in Neurospora

Eric Bastiaans, Duur K. Aanen, Afons J. M. Debets, Rolf F. Hoekstra, Bram Lestrade & Marc F. P. M. Maas
The replication and segregation of the multi-copy mitochondrial DNA (mtDNA) are not under strict control of the nuclear DNA. Within-cell selection may thus favour variants with an intracellular selective advantage but a detrimental effect on cell fitness. High relatedness among the mtDNA variants of an individual is predicted to disfavour such deleterious selfish genetic elements, but experimental evidence for this hypothesis is scarce. We studied the effect of mtDNA relatedness on the opportunities for suppressive...

Data from: Influence of land use and climate on recent forest expansion: a case study in the Eurosiberian-Mediterranean limit of northwest Spain

Jose Manuel Álvarez-Martínez, Susana Suárez-Seoane, Jetse J. Stoorvogel & Estanisao De Luis Calabuig
1. In Mediterranean mountainous areas, forests have expanded in recent decades because traditional management practices have been abandoned or reduced. However, understanding the ecological mechanism behind landscape change is a complex undertaking as the effects of land use may be influenced (reinforced or constrained) by other factors such as climate. 2. We used orthorectified aerial photographs to monitor changes in forest distribution in a set of 20 head-water basins (located in the Cantabrian Mountains of...

Data from: Compatible and incompatible pathogen-plant interactions differentially affect plant volatile emissions and the attraction of parasitoid wasps

Camille Ponzio, Berhane T. Weldegergis, Marcel Dicke & Rieta Gols
The effects of multiple insect attacks on herbivore-induced plant volatiles and carnivorous arthropods are increasingly studied. Phytopathogens also represent an important threat to plants, and plant defense strategies against pathogens and insects are strongly interconnected, yet the potential impact of pathogens on insect-induced volatiles has been largely overlooked, and degree of pathogenicity rarely considered. We investigated how pathogen challenge, with virulent and avirulent strains of Xanthomonas campestris either alone or with simultaneous Pieris brassicae caterpillar...

Data from: Modification of plant-induced responses by an insect ecosystem engineer influences the colonization behaviour of subsequent shelter-users

Akane Uesugi, Kimberly Morrell, Erik H. Poelman, Ciska E. Raaijmakers & André Kessler
Herbivores that modify plant morphology, such as gall forming insects, can disproportionately impact arthropod community on their host plants by providing novel habitats and shelters from biotic and abiotic stresses. These ecosystem engineers could also modify plant chemical properties, but how such changes in plant quality affect the behaviour of subsequent colonizers has rarely been investigated. We explored how an initial infestation of the tall goldenrod (Solidago altissima) by an ecosystem engineer, the rosette gall-midge...

Data from: Adaptation to abiotic conditions drives local adaptation in bacteria and viruses coevolving in heterogeneous environments

Florien A. Gorter, Pauline D. Scanlan & Angus Buckling
Parasite local adaptation, the greater performance of parasites on their local compared with foreign hosts, has important consequences for the maintenance of diversity and epidemiology. While the abiotic environment may significantly affect local adaptation, most studies to date have failed either to incorporate the effects of the abiotic environment, or to separate them from those of the biotic environment. Here, we tease apart biotic and abiotic components of local adaptation using the bacterium Pseudomonas fluorescens...

Data from: Fine-scale spatial genetic structure in the frankincense tree Boswellia papyrifera (Del.) Hochst. and implications for conservation

A. B. Addisalem, Jérôme Duminil, Doret Wouters, Frans Bongers & Marinus J. M. Smulders
The fine-scale genetic structure and how it varies between generations depends on the spatial scale of gene dispersal and other fundamental aspects of species’ biology, such as the mating system. Such knowledge is crucial for the design of genetic conservation strategies. This is particularly relevant for species that are increasingly fragmented such as Boswellia papyrifera. This species occurs in dry tropical forests from Ethiopia, Eritrea and Sudan and is an important source of frankincense, a...

Data from: Spatial patterns of self-recruitment of a coral reef fish in relation to island-scale retention mechanisms

Ricardo Beldade, Sally J. Holbrook, Russell J. Schmitt, Serge Planes & Giacomo Bernardi
Oceanographic features influence the transport and delivery of marine larvae, and physical retention mechanisms, such as eddies, can enhance self-recruitment (i.e. the return of larvae to their natal population). Knowledge of exact locations of hatching (origin) and settlement (arrival) of larvae of reef animals provides a means to compare observed patterns of self-recruitment ‘connectivity’ with those expected from water circulation patterns. Using parentage inference based on multiple sampling years in Moorea, French Polynesia, we describe...

Data from: Cascading effects of defaunation on the coexistence of two specialized insect seed predators

Guille Peguero, Helene C. Muller-Landau, Patrick A. Jansen & S. Joseph Wright
Identification of the mechanisms enabling stable coexistence of species with similar resource requirements is a central challenge in ecology. Such coexistence can be facilitated by species at higher trophic levels through complex multi-trophic interactions, a mechanism that could be compromised by ongoing defaunation. We investigated cascading effects of defaunation on Pachymerus cardo and Speciomerus giganteus, the specialized insect seed predators of the Neotropical palm Attalea butyracea, testing the hypothesis that vertebrate frugivores and granivores facilitate...

Data from: Aboveground mammal and invertebrate exclusions cause consistent changes in soil food webs of two subalpine grassland types, but mechanisms are system-specific

Martijn L. Vandegehuchte, Wim H. Van Der Putten, Henk Duyts, Martin Schütz & Anita C. Risch
Ungulates, smaller mammals, and invertebrates can each affect soil biota through their influence on vegetation and soil characteristics. However, direct and indirect effects of the aboveground biota on soil food webs remain to be unraveled. We assessed effects of progressively excluding aboveground large-, medium- and small-sized mammals as well as invertebrates on soil nematode diversity and feeding type abundances in two subalpine grassland types: short- and tall-grass vegetation. We explored pathways that link exclusions of...

Data from: Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing

Nathalie Smitz, Pim Van Hooft, Rasmus Heller, Daniel Cornélis, Philippe Chardonnet, Robert Kraus, Ben J. Greyling, Richard Crooijmans, Martien Groenen, Johan Michaux & Ben Greyling
This study aimed to develop a set of SNP markers with high resolution and accuracy within the African buffalo. Such a set can be used, among others, to depict subtle population genetic structure for a better understanding of buffalo population dynamics. In total, 18.5 million DNA sequences of 76 bp were generated by next generation sequencing on an Illumina Genome Analyzer II from a reduced representation library using DNA from a panel of 13 African...

Data from: De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens

Daniel Blande, Pauliina Halimaa, Arja I. Tervahauta, Mark G. M. Aarts & Sirpa O. Kärenlampi
Noccaea caerulescens of the Brassicaceae family has become the key model plant among the metal hyperaccumulator plants. Populations/accessions of N. caerulescens from geographic locations with different soil metal concentrations differ in their ability to hyperaccumulate and hypertolerate metals. Comparison of transcriptomes in several accessions provides candidates for detailed exploration of the mechanisms of metal accumulation and tolerance and local adaptation. This can have implications in the development of plants for phytoremediation and improved mineral nutrition....

Data from: Species interactions increase the temporal stability of community productivity in Pinus sylvestris-Fagus sylvatica mixtures across Europe

Miren Del Río, Hans Pretzsch, Ricardo Ruiz-Peinado, Evy Ampoorter, Peter Annighöfer, Ignacio Barbeito, Kamil Bielak, Gediminas Brazaitis, Lluis Coll, Lars össler, Marek Fabrika, David I. Forrester, Michael Heym, Václav Hurt, Viktor Kurylyak, Magnus Löf, Fabio Lombardi, Ekaterina Makrickiene, Bratislav Matovic, Frits Mohren, Renzo Motta, Jan Den Ouden, Maciej Pach, Quentin Ponette, Gerhard Schütze … & Lars Drössler
1.There is increasing evidence that species diversity enhances the temporal stability of community productivity in different ecosystems, although its effect at population and tree levels seems to be negative or neutral. Asynchrony in species responses to environmental conditions was found to be one of the main drivers of this stabilizing process. However, the effect of species mixing on the stability of productivity, and the relative importance of the associated mechanisms, remain poorly understood in forest...

Data from: Unequal contribution of widespread and narrow-ranged species to botanical diversity patterns

Andre S. J. Van Proosdij, Niels Raes, Jan J. Wieringa & Marc S. M. Sosef
In conservation studies, solely widespread species are often used as indicators of diversity patterns, but narrow-ranged species can show different patterns. Here, we assess how well subsets of narrow-ranged, widespread or randomly selected plant species represent patterns of species richness and weighted endemism in Gabon, tropical Africa. Specifically, we assess the effect of using different definitions of widespread and narrow-ranged and of the information content of the subsets. Finally, we test if narrow-ranged species are...

Data from: Genetic variation of loci potentially under selection confounds species-genetic diversity correlations in a fragmented habitat

Angeline Bertin, Nicolas Gouin, Alex Baumel, Ernesto Gianoli, Juan Serratosa, Rodomiro Osorio & Stéphanie Manel
Positive species-genetic diversity correlations (SGDCs) are often thought to result from the parallel influence of neutral processes on genetic and species diversity. Yet, confounding effects of non-neutral mechanisms have not been explored. Here, we investigate the impact of non-neutral genetic diversity on SGDCs in high Andean wetlands. We compare correlations between plant species diversity (SD) and genetic diversity (GD) calculated with and without loci potentially under selection (outlier loci). The study system includes 2188 specimens...

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