13 Works

Data from: Genome-wide signatures of local selection in the panmictic European eel

Jose Martin Pujolar, Magnus W. Jacobsen, Thomas D. Als, Jane Frydenberg, Kasper Munch, Bjarni Jónsson, Jianbo B. Jian, Ling Cheng, Gregory E. Maes, Louis Bernatchez & Michael M. Hansen
Next-generation sequencing and the collection of genome-wide data allow identifying adaptive variation and footprints of directional selection. Using a large SNP data set from 259 RAD-sequenced European eel individuals (glass eels) from eight locations between 34 and 64oN, we examined the patterns of genome-wide genetic diversity across locations. We tested for local selection by searching for increased population differentiation using FST-based outlier tests and by testing for significant associations between allele frequencies and environmental variables....

Data from: Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography

Filip Bielejec, Philippe Lemey, Guy Baele, Andrew Rambaut & Marc A. Suchard
Molecular phylogenetic and phylogeographic reconstructions generally assume time-homogeneous substitution processes. Motivated by computational convenience, this assumption sacrifices biological realism and offers little opportunity to uncover the temporal dynamics in evolutionary histories. Here, we propose an evolutionary approach that explicitly relaxes the time-homogeneity assumption by allowing the specification of different infinitesimal substitution rate matrices across different time intervals, called epochs, along the evolutionary history. We focus on an epoch model implementation in a Bayesian inference framework...

Data from: Unravelling the effects of contemporary and historical range expansion on the distribution of genetic diversity in the damselfly Coenagrion scitulum

Janne Swaegers, Joachim Mergeay, Lieven Therry, Dries Bonte, Maarten H. D. Larmuseau & Robby Stoks
Although genetic diversity provides the basic substrate for evolution, there are a limited number of studies that assess the impact of recent climate change on intraspecific genetic variation. This study aims to unravel the degree to which historical and contemporary factors shape genetic diversity and structure across a large part of the range of the range-expanding damselfly Coenagrion scitulum (Rambur, 1842). A total of 525 individuals from 31 populations were genotyped at nine microsatellites, and...

Data from: Diet quality determines interspecific parasite interactions in host populations

Benjamin Lange, Max Reuter, Dieter Ebert, Koenraad Muylaert & Ellen Decaestecker
The widespread occurrence of multiple infections and the often vast range of nutritional resources for their hosts allow that interspecific parasite interactions in natural host populations might be determined by host diet quality. Nevertheless, the role of diet quality with respect to multispecies parasite interactions on host population level is not clear. We here tested the effect of host population diet quality on the parasite community in an experimental study using Daphnia populations. We studied...

Data from: Local and regional founder effects in lake zooplankton persist after thousands of years despite high dispersal potential

Marc Ventura, Adam Petrusek, Alexandre Miró, Eva Hamrová, Danilo Buñay, Luc De Meester & Joachim Mergeay
We reconstructed the genetic structure of a planktonic crustacean Daphnia longispina living in high mountain lakes and ponds in the Pyrenees to investigate whether it was shaped by persistent founder effects originating shortly after the last glacial maximum or by ongoing dispersal and effective migration (gene flow). We found that the genetic structure can largely be explained by a single colonization event following gradual deglaciation of the Pyrenees c. 10-15 000 years ago. Nuclear genetic...

Data from: Integrating influenza antigenic dynamics with molecular evolution

Trevor Bedford, Marc A. Suchard, Philippe Lemey, Gytis Dudas, Victoria Gregory, Alan J. Hay, John W. McCauley, Colin A. Russell, Derek J. Smith & Andrew Rambaut
Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between influenza strains using the hemagglutination inhibition (HI) assay. Here, we extend previous approaches to antigenic cartography, and simultaneously characterize antigenic and genetic evolution by modeling the diffusion of antigenic phenotype over a shared virus phylogeny. Using HI data from influenza lineages A/H3N2, A/H1N1, B/Victoria and B/Yamagata,...

Data from: Temperature- and latitude-specific individual growth rates shape the vulnerability of damselfly larvae to a widespread pesticide

Khuong Dinh Van, Lizanne Janssens, Sara Debecker & Robby Stoks
1. Freshwater ecosystems are especially vulnerable to climate change and pollution. One key challenge for aquatic toxicology is to determine and manage the combined effects of temperature increase and contaminants across species' ranges. 2. We tested how thermal adaptation and life-history evolution along a natural temperature gradient influence the vulnerability of an aquatic insect to a pesticide under global warming. We applied a space-for-time substitution approach to study the effect of warming on the vulnerability...

Data from: Inbreeding within human Schistosoma mansoni: do host- specific factors shape the genetic composition of parasite populations?

Frederik Van Den Broeck, Lynn Meurs, Joost A. M. Raeymaekers, Nele Boon, Tandakha N. Dieye, Filip A. M. Volckaert, Katja Polman & Tine Huyse
The size, structure and distribution of host populations are key determinants of the genetic composition of parasite populations. Despite the evolutionary and epidemiological merits, there has been little consideration of how host heterogeneities affect the evolutionary trajectories of parasite populations. We assessed the genetic composition of natural populations of the parasite Schistosoma mansoni in northern Senegal. A total of 1346 parasites were collected from 14 snail and 57 human hosts within three villages and individually...

Data from: Long-term experimental warming alters community composition of ascomycetes in Alaskan moist and dry arctic tundra

Tatiana A. Semenova, Luis N. Morgado, Jeffrey M. Welker, Marilyn D. Walker, Erik Smets & József Geml
Arctic tundra regions have been responding to global warming with visible changes in plant community composition, including expansion of shrubs and declines in lichens and bryophytes. Even though it is well-known that the majority of arctic plants are associated with their symbiotic fungi, how fungal community composition will be different with climate warming remains largely unknown. In this study, we addressed the effects of long-term (18 years) experimental warming on the community composition and taxonomic...

Data from: Landscape genomics and a common garden trial reveal adaptive differentiation to temperature across Europe in the tree species Alnus glutinosa

Hanne De Kort, Katrien Vandepitte, Hans Henrik Bruun, Déborah Closset-Kopp, Olivier Honnay & Joachim Mergeay
The adaptive potential of tree species to cope with climate change has important ecological and economic implications. Many temperate tree species experience a wide range of environmental conditions, suggesting high adaptability to new environmental conditions. We investigated adaptation to regional climate in the drought-sensitive tree species Alnus glutinosa (Black alder), using a complementary approach that integrates genomic, phenotypic and landscape data. A total of 24 European populations were studied in a common garden and through...

Data from: Ontogenetic changes in genetic variances of age-dependent plasticity along a latitudinal gradient

Viktor Nilsson-Örtman, Bjorn Rogell, Robby Stoks & Frank Johansson
The expression of phenotypic plasticity may differ among life stages of the same organism. Age-dependent plasticity can be important for adaptation to heterogeneous environments, but this has only recently been recognized. Whether age-dependent plasticity is a common outcome of local adaptation and whether populations harbor genetic variation in this respect remains largely unknown. To answer these questions, we estimated levels of additive genetic variation in age-dependent plasticity in six species of damselflies sampled from 18...

Data from: An SNP-based second-generation genetic map of Daphnia magna and its application to QTL analysis of phenotypic traits

Jarkko Routtu, Matthew D. Hall, Brian Albere, Christian Beisel, R. Daniel Bergeron, Anurag Chaturvedi, Jeong-Hyeon Choi, John Colbourne, Luc De Meester, Melissa T. Stephens, Claus-Peter Stelzer, Eleanne Solorzano, W. Kelley Thomas, Michael E. Pfrender & Dieter Ebert
Background: Although Daphnia is increasingly recognized as a model for ecological genomics and biomedical research, there is, as of yet, no high-resolution genetic map for the genus. Such a map would provide an important tool for mapping phenotypes and assembling the genome. Here we estimate the genome size of Daphnia magna and describe the construction of an SNP array based linkage map. We then test the suitability of the map for life history and behavioural...

Data from: Rapid genetic adaptation precedes the spread of an exotic plant species

Katrien Vandepitte, Tim De Meyer, Kenny Helsen, Kasper Van Acker, Isabel Roldán-Ruiz, Joachim Mergeay & Olivier Honnay
Human activities have increasingly introduced plant species far outside their native ranges under environmental conditions that can strongly differ from those originally met. Therefore, before spreading, and potentially causing ecological and economical damage, non native species may rapidly evolve. Evidence of genetically based adaptation during the process of becoming invasive is very scant however, which is due to the lack of knowledge regarding the historical genetic makeup of the introduced populations and the lack of...

Registration Year

  • 2014

Resource Types

  • Dataset


  • KU Leuven
  • Research Institute for Nature and Forest
  • University of Basel
  • Ghent University
  • National Institutes of Health
  • University of Edinburgh
  • University of California Los Angeles
  • David Geffen School of Medicine at UCLA
  • Augusta University
  • University of Cambridge