20 Works

Drivers and dynamics of a massive adaptive radiation in cichlid fishes

Fabrizia Ronco, Michael Matschiner, Astrid Böhne, Anna Boila, Heinz H. Büscher, Athimed El Taher, Adrian Indermaur, Milan Malinsky, Virginie Ricci, Ansgar Kahmen, Sissel Jentoft & Walter Salzburger
Adaptive radiation is the likely source of much of the ecological and morphological diversity of life. How adaptive radiations proceed and what determines their extent remains elusive in most cases. Here we report the in-depth examination of the spectacular adaptive radiation of cichlid fishes in African Lake Tanganyika. Based on whole-genome phylogenetic analyses, multivariate morphological measurements of three ecologically relevant trait complexes (body shape, upper oral jaw morphology, and lower pharyngeal jaw shape), scoring of...

Secondary contact zones of closely-related Erebia butterflies overlap with narrow phenotypic and parasitic clines

Kay Lucek, Roger Butlin & Theofania Patsiou
Zones of secondary contact between closely related taxa are a common legacy of the Quaternary ice ages. Despite their abundance, the factors that keep species apart and prevent hybridisation are often unknown. Here we study a very narrow contact zone between three closely related butterfly species of the Erebia tyndarus species complex. Using genomic data, we first determined if gene flow occurs and then assessed whether it might be hampered by differences in chromosome number...

Stable species boundaries despite ten million years of hybridization in tropical eels

Julia Barth, Chrysoula Gubili, Michael Matschiner, Ole Tørresen, Shun Watanabe, Bernd Egger, Yu-San Han, Eric Feunteun, Ruben Sommaruga, Robert Jehle & Robert Schabetsberger
Genomic evidence is increasingly underpinning that hybridization between taxa is commonplace, challenging our views on the mechanisms that maintain their boundaries. Here, we focus on seven catadromous eel species (genus Anguilla), and use genome-wide sequence data from more than 450 individuals sampled across the tropical Indo-Pacific, morphological information, and three newly assembled draft genomes to compare contemporary patterns of hybridization with signatures of past gene flow across a time-calibrated phylogeny. We show that the seven...

Data from: Dissecting the genetic architecture of a stepwise infection process

Matthew D Hall, Jarkko Routtu & Dieter Ebert
How a host fights infection depends on an ordered sequence of steps, beginning with attempts to prevent a pathogen from establishing an infection, through to steps that mitigate a pathogen’s control of host resources, or minimising the damage caused during infection. Yet empirically characterising the genetic basis of these steps remains challenging. Although each step is likely to have a unique genetic and environmental signature, and may, therefore, respond to selection in a specific way,...

Heavy Metal Bricolage

Lavinia Pflugfelder
Using the term “bricolage”, this article examines the articulation of religious imagery in the visual language of extreme metal. Transgression and bricolage, which describes a specific mode of reusing elements of cultural repertoire to fashion new expressions, have their own history and tradition in heavy metal. Any implementation of its visual language relies accordingly on shared knowledge of scene traditions and patterns to decode, but disembedded religious images and religious patterns are abundant in pop...

Raw nucleotide counts for clinal Misty Lake and stream stickleback samples

Daniel Berner & Quiterie Haenel
How ecological divergence causes strong reproductive isolation between populations in close geographic contact remains poorly understood at the genomic level. We here study this question in a stickleback fish population pair adapted to contiguous, ecologically different lake and stream habitats. Clinal whole-genome sequence data reveal numerous genome regions (nearly) fixed for alternative alleles over a distance of just a few hundred meters. This strong polygenic adaptive divergence must constitute a genome-wide barrier to gene flow...

Dsuite - fast D-statistics and related admixture evidence from VCF files

Milan Malinsky, Michael Matschiner & Hannes Svardal
Patterson’s D, also known as the ABBA-BABA statistic, and related statistics such as the f4-ratio, are commonly used to assess evidence of gene flow between populations or closely related species. Currently available implementations often require custom file formats, implement only small subsets of the available statistics, and are impractical to evaluate all gene flow hypotheses across datasets with many populations or species due to computational inefficiencies. Here we present a new software package Dsuite, an...

Data from: Climatic refugia boosted allopatric diversification in Western Mediterranean vipers

Fernando Martínez-Freiría, Inês Freitas, Marco A. L. Zuffi, Philippe Golay, Sylvain Ursenbacher & Guillermo Velo-Antón
Abstract: Aim: to understand the role of climate in fostering diversification, this study reconstructs the historical biogeography of Western Mediterranean vipers Location: Western Mediterranean Basin Taxon: Vipera aspis and V. latastei-monticola complex Methods: phylogeographic analyses were performed over mitochondrial (three genes) and nuclear sequences (two genes), extensively covering species ranges. A total of 4,056 records were assigned to genetic units, using interpolations of genetic data, to test phylogenetic niche conservatism, under a 3D hypervolume approach,...

Structural manipulations of a shelter resource reveal underlying preference functions in a shell-dwelling cichlid fish

Aneesh Bose, Johannes Windorfer, Alex Böhm, Fabrizia Ronco, Adrian Indermaur, Walter Salzburger & Alex Jordan
Many animals can modify the environments in which they live, thereby changing the selection pressures they experience. A common example of such niche-construction is the use, creation, or modification of environmental resources for use as nests or shelters. Because these resources often have correlated structural elements, it can be difficult to disentangle the relative contribution of these elements to resource choice, and the preference functions underlying niche-construction behaviour remain hidden. Here, we present an experimental...

Chironomid-based temperature reconstruction from Burgäschisee, Switzerland

Alexander Bolland, Fabian Rey, Erika Gobet, Willy Tinner & Oliver Heiri
The data herein presents a new chironomid record and associated chironomid-based temperature reconstruction covering the time interval 18,000-14,000 cal. BP from the lacustrine sediments of a kettle hole lake Burgäschisee, Switzerland. Chironomid assemblages show ecological turnover beginning 1,300 years before the onset of the Oldest Dryas / Bølling transition at ca. 14,700 cal. BP and associated increases in chironomid-based temperature reconstructions. These data also include non-chironomid invertebrate remains, including Ceratopogonidae, Daphnia and Ephemeroptera as well...

Lineage-specific adaptation to climate involves flowering time in North American Arabidopsis lyrata

Nora Walden, Kay Lucek & Yvonne Willi
Adaptation to local climatic conditions is commonly found within species, but whether it involves the same intraspecific genomic variants is unknown. We studied this question in North American Arabidopsis lyrata, whose current distribution is shaped by post-glacial range expansion from two refugia, resulting in two distinct genetic clusters covering comparable climatic gradients. Using whole-genome pooled sequence data of 41 outcrossing populations, we identified loci associated with three niche-determining climatic variables in the two clusters and...

Saproxylic insects and fungi in deciduous forests along a rural–urban gradient

Sandro Meyer
Urbanisation is increasing worldwide and is regarded a major threat to biodiversity in forests. As consequences of intensive human use, the vegetation structure of naturally growing urban forests and their amount of deadwood can be reduced. Deadwood is an essential resource for various saproxylic insects and fungi. We assessed the effects of urbanisation and forest characteristics on saproxylic insects and fungi. We exposed standardized bundles consisting of each three fresh-cut beech and oak branches in...

Subpopulations of sensorless bacteria drive fitness in fluctuating environments

Thomas Julou
We use quantitative time-lapse microscopy combined with microfluidics to analyse the induction dynamics of the lac operon in single bacteria cells.

Gene expression dynamics during rapid organismal diversification of African cichlid fishes

Athimed El Taher, Astrid Böhne, Nicolas Boileau, Fabrizia Ronco, Adrian Indermaur, Lukas Widmer & Walter Salzburger
Changes in gene expression play a fundamental role in phenotypic evolution. Transcriptome evolutionary dynamics have so far mainly been compared among distantly related species and remain largely unexplored during rapid organismal diversification, in which gene regulatory changes have been suggested as particularly effective drivers of phenotypic divergence. Here, we studied gene expression evolution in a model system of adaptive radiation, the cichlid fishes of African Lake Tanganyika. By comparing gene expression profiles of six different...

Data from: Where Am I? Niche constraints due to morphological specialisation in two Tanganyikan cichlid fish species

Lukas Widmer, Adrian Indermaur, Bernd Egger & Walter Salzburger
Food resource specialisation within novel environments is considered a common axis of diversification in adaptive radiations. Feeding specialisations are often coupled with striking morphological adaptations and exemplify the relation between morphology and diet (phenotype-environment correlations), as seen in, for example, Darwin finches, Hawaiian spiders and, in particular, the cichlid radiations in East Africa. The cichlids’ potential to rapidly exploit and occupy a variety of different habitats has previously been attributed to the variability and adaptability...

Combining GWAS and FST-based approaches to identify targets of Borrelia-mediated selection in natural rodent hosts

Luca Cornetti & Barbara Tschirren
Recent advances in high-throughput sequencing technologies provide opportunities to gain novel insights into the genetic basis of phenotypic trait variation. Yet to date, progress in our understanding of genotype-phenotype associations in non-model organisms in general and natural vertebrate populations in particular has been hampered by small sample sizes typically available for wildlife populations and a resulting lack of statistical power, as well as a limited ability to control for false positive signals. Here we propose...

Comparative data for dance fly eye morphology and female ornamentation

R. Axel W. Wiberg, Rosalind L Murray, Elizabeth Herridge, Darryl T Gwynne & Luc F Bussière
These data were collected as part of a comparative study of the relationship between female ornamentation and sexual dimorphism in eye morphology. Data come from specimens collected in the field in Scotland near Loch Lomond in the summers of 2009, 2010, and 2011 as well as the summer of 2012 near Glen Williams in Ontario, Canada. The repository contains raw image files including information on magnifications at which these were taken, excel spreadsheets of morphological...

Data from: Expressed mutational load increases towards the edge of a species’ geographic range

Antoine Perrier, Dario Sanchez-Castro & Yvonne Willi
There is no general explanation for why species have restricted geographic distributions. One hypothesis posits that range expansion or increasing scarcity of suitable habitat result in accumulation of mutational load due to enhanced genetic drift, which constrains population performance towards range limits and further expansion. We tested this hypothesis in the North American plant, Arabidopsis lyrata. We experimentally assessed mutational load by crossing plants of 20 populations from across the entire species range and by...

Gene expression remodelling and immune response during adaptive divergence in an African cichlid fish

Jelena Rajkov, Athimed El Taher, Astrid Böhne, Walter Salzburger & Bernd Egger
Variation in gene expression contributes to ecological speciation by facilitating population persistence in novel environments. Likewise, immune response can be a relevant factor in speciation driven by adaptation to different environments. Previous studies examining gene expression differences between recently diverged ecotypes often relied on only one pair of populations, targeted the expression of only a subset of genes, or used wild caught-individuals. Here, we investigated the contribution of habitat-specific parasites and symbionts and the underlying...

Data from: The repeatable opportunity for selection differs between pre- and post-copulatory fitness components

Lucas Marie-Orleach, Nikolas Vellnow & Lukas Schärer
In species with multiple mating, intense sexual selection may occur both before and after copulation. However, comparing the strength of pre- and postcopulatory selection is challenging, because i) postcopulatory processes are generally difficult to observe and ii) the often-used opportunity for selection (I) metric contains both deterministic and stochastic components. Here, we quantified pre- and postcopulatory male fitness components of the simultaneously hermaphroditic flatworm, Macrostomum lignano. We did this by tracking fluorescent sperm—using transgenics—through the...

Registration Year

  • 2020

Resource Types

  • Dataset
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  • Text


  • University of Basel
  • University of Oslo
  • Zoological Research Museum Alexander Koenig
  • University of Zurich
  • University of Bern
  • Swiss Institute of Bioinformatics
  • University of Antwerp
  • University of Salford
  • Max Planck Institute of Animal Behavior
  • Sorbonne University