Data from: Influence of parameter settings in automated scoring of AFLPs on population genetic analysisMarc Herrmann, Rolf Holderegger & Maarten J. Van Strien
The use of procedures for the automated scoring of AFLP fragments has recently increased. Corresponding software does not only automatically score the presence or absence of AFLP fragments, but also allows an evaluation of how different settings of scoring parameters influence subsequent population genetic analyses. In this study, we used the automated scoring package RAWGENO to evaluate how five scoring parameters influence the number of polymorphic bins and estimates of pairwise genetic differentiation between populations...
Data from: European phylogeography of the epiphytic lichen fungus Lobaria pulmonaria and its green algal symbiontIvo Widmer, Francesco Dal Grande, Laurent Excoffier, Rolf Holderegger, Christine Keller, Vladimir S. Mikryukov & Christoph Scheidegger
In lichen symbiosis, fungal and algal partners form close associations, often co-dispersed by vegetative propagules. Due to the particular interdependence, processes such as colonization, dispersal or genetic drift are expected to result in congruent patterns of genetic structure in the symbionts. To study the population structure of an obligate symbiotic system in Europe, we genotyped the fungal and algal symbionts of the epiphytic lichen Lobaria pulmonaria at eight and seven microsatellite loci, respectively, and analyzed...
Data from: Genetic diversity in widespread species is not congruent with species richness in alpine plant communitiesPierre Taberlet, Niklaus E. Zimmermann, Thorsten Englisch, Andreas Tribsch, Rolf Holderegger, Nadir Alvarez, Harald Niklfeld, Zbigniew Mirek, Atte Moilanen, Wolfgang Ahlmer, Paolo Ajmone Marsan, Enzo Bona, Maurizio Bovio, Philippe Choler, Elżbieta Cieślak, Gheorghe Coldea, Licia Colli, Vasile Cristea, Jean-Pierre Dalmas, Božo Frajman, Luc Garraud, Myriam Gaudeul, Ludovic Gielly, Walter Gutermann, Nejc Jogan … & Karol Marhold
The Convention on Biological Diversity (CBD) aims at the conservation of all three levels of biodiversity, i.e. ecosystems, species and genes. Genetic diversity represents evolutionary potential and is important for ecosystem functioning. Unfortunately, genetic diversity in natural populations is hardly considered in conservation strategies because it is difficult to measure and has been hypothesized to co-vary with species richness. This means that species richness is taken as a surrogate of genetic diversity in conservation planning,...
Data from: Scale-dependent adaptive evolution and morphological convergence to climatic niche in Californian eriogonoids (Polygonaceae)Anna Kostikova, Nicolas Salamin, Peter B. Pearman, Glenn Litsios, Sarah Burgy & Laura Milani
Aim: Macroevolutionary patterns and processes change substantially depending on levels of taxonomic and ecological organization, and the resolution of environmental and spatial variability. In comparative methods, the resolution of environmental and spatial variability often defines the number of selective regimes used to test whether phenotypic characteristics are adaptively correlated with the environment. Here, we examine how investigator choice of the number of selective regimes, determined by varying the resolution of among-species variability in the species...
Data from: Retracing the routes of introduction of invasive species: the case of the Sirex noctilio woodwasp.Emilie Boissin, Brett Hurley, Michael J. Wingfield, Rimvydas Vasaitis, Jan Stenlid, Chuck Davis, Peter De Groot, Rodrigo Ahumeda, Angus Carnegie, Arturo Goldarazena, Paula Klasmer, Beat Wermelinger & Bernard Slippers
Understanding the evolutionary histories of invasive species is critical to adopt appropriate management strategies, but this process can be exceedingly complex to unravel. As illustrated in this study of the worldwide invasion of the woodwasp Sirex noctilio, population genetic analyses using coalescent-based scenario testing together with Bayesian clustering and historical records provide opportunities to address this problem. The pest spread from its native Eurasian range to the Southern Hemisphere in the 1900’s and recently to...
Data from: Lessons learned from microsatellite development for non-model organisms using 454 pyrosequencingCorine Schoebel, Sabine Brodbeck, Dominique Buehler, Carolina Cornejo, Jyoti Gajurel, Hanna Hartikainen, Daniela Keller, Marie Leys, Štěpánka Říčanová, Gernot Segelbacher, Silke Werth, Daniela Csencsics & C. N. Schoebel
Microsatellites, also known as simple sequence repeats (SSRs), are among the most commonly used marker types in evolutionary and ecological studies. Next Generation Sequencing techniques such as 454 pyrosequencing allow the rapid development of microsatellite markers in nonmodel organisms. 454 pyrosequencing is a straightforward approach to develop a high number of microsatellite markers. Therefore, developing microsatellites using 454 pyrosequencing has become the method of choice for marker development. Here, we describe a user friendly way...
Data from: Are adaptive loci transferable across genomes of related species? Outlier and environmental association analyses in Alpine Brassicaceae speciesDeborah Zulliger, Elvira Schnyder & Felix Gugerli
Local adaptation is one possible response of organisms to survive in a changing environment. However, the genetic basis of adaptation is not well understood, especially in nonmodel species. To infer recurrent patterns of local adaptation, we investigated whether the same putative adaptive loci reoccur in related species. We performed genome scans using amplified fragment length polymorphism (AFLP) markers on populations of five Alpine Brassicaceae species sampled across a wide range of environmental conditions. To identify...
Data from: Tales of the unexpected: Phylogeography of the arctic-alpine model plant Saxifraga oppositifolia (Saxifragaceae) revisitedManuela Winkler, Andreas Tribsch, Gerald M. Schneeweiss, Sabine Brodbeck, Felix Gugerli, Rolf Holderegger, Richard J. Abbott & Peter Schönswetter
Arctic-alpine biota occupy enormous areas in the Arctic and the northern hemisphere mountain ranges, and have undergone major range shifts during their comparatively short history. The origins of individual arctic-alpine species remain largely unknown. In the case of the Purple saxifrage, Saxifraga oppositifolia, an important model for arctic-alpine plants, phylogeographic studies have remained inconclusive about early stages of the species’ spatiotemporal diversification, but have provided evidence for long-range colonization out of a presumed Beringian origin...
Data from: Forecasting changes in population genetic structure of alpine plants in response to global warmingFlora Jay, Stéphanie Manel, Nadir Alvarez, Eric Y. Durand, Wilfried Thuiller, Rolf Holderegger, Pierre Taberlet & Olivier François
Species range shifts in response to climate and land use change are commonly forecasted with species distribution models based on species occurrence or abundance data. Although appealing, these models ignore the genetic structure of species, and the fact that different populations might respond in different ways due to adaptation to their environment. Here, we introduced ancestry distribution models, i.e., statistical models of the spatial distribution of ancestry proportions, for forecasting intra-specific changes based on genetic...
Lichens are widespread symbioses and play important roles in many terrestrial ecosystems. The genetic structure of lichens is the result of the association between fungal and algal populations constituting the lichen thallus. Using eight fungus- and seven alga-specific highly variable microsatellite markers on within-population spatial genetic data from 62 replicate populations across Europe, North America, Asia and Africa, we investigated the contributions of vertical and horizontal transmission of the photobiont to the genetic structure of...
Data from: A new analytical approach to landscape genetic modeling: least-cost transect analysis and linear mixed modelsMaarten J. Van Strien, Daniela Keller & Rolf Holderegger
Landscape genetics aims to assess the effect of the landscape on intraspecific genetic structure. To quantify interdeme landscape structure, landscape genetics mostly uses landscape resistance surfaces and least-cost paths or straight-line transects. However, both approaches have drawbacks. Parameterization of resistance surfaces is a subjective process, and least-cost paths represent a single migration route. A transect-based approach might oversimplify migration patterns by assuming rectilinear migration. To overcome these limitations, we combined these two methods in a...
Swiss Federal Institute for Forest, Snow and Landscape Research11
University of Lausanne2
University of Vienna2
University of the Basque Country1
Swiss Institute of Bioinformatics1
University of Pretoria1
Swiss Federal Institute of Aquatic Science and Technology1
University of Neuchâtel1
University of California, Berkeley1
Polish Academy of Sciences1