351 Works

Immune challenges increase network centrality in a queenless ant

Giacomo Alciatore, Line V. Ugelvig, Erik Frank, Jérémie Bidaux, Asaf Gal, Thomas Schmitt, Daniel J.C. Kronauer & Yuko Ulrich
Social animals display a wide range of behavioural defences against infectious diseases, some of which inherently increase social contacts with infectious individuals (e.g., mutual grooming), while others decrease them (e.g., social exclusion). These defences often rely on the detection of infectious individuals, but this can be achieved in several ways that are difficult to differentiate. Here, we combine non-pathogenic immune challenges with automated tracking in colonies of the clonal raider ant to ask whether ants...

Plasticity in leakiness

John Pannell
In dioecious plants, males and females frequently show ‘leaky’ sex expression, with individuals occasionally producing flowers of the opposite sex. This leaky sex expression may have enabled the colonization of oceanic islands by dioecious plant species, and it is likely to represent the sort of variation upon which selection acts to bring about evolutionary transitions from dioecy to hermaphroditism. Although leakiness is commonly reported for dioecious species, it is not known whether it has plastic...

Data from: Four myriapod relatives – but who are sisters? No end to debates on relationships among the four major myriapod subgroups

Nikolaus U. Szucsich, Daniela Bartel, Alexander Blanke, Alexander Böhm, Alexander Donath, Makiko Fukui, Simon Grove, Shanlin Liu, Oliver Macek, Ryuichiro Machida, Bernhard Misof, Yasutaka Nakagaki, Lars Podsiadlowski, Kaoru Sekiya, Shigekazu Tomizuka, Björn M. Von Reumont, Robert M. Waterhouse, Manfred Walzl, Guanliang Meng, Xin Zhou, Günther Pass & Karen Meusemann
Background: Phylogenetic relationships among the myriapod subgroups Chilopoda, Diplopoda, Symphyla and Pauropoda are still not robustly resolved. The first phylogenomic study covering all subgroups resolved phylogenetic relationships congruently to morphological evidence but is in conflict with most previously published phylogenetic trees based on diverse molecular data. Outgroup choice and long-branch attraction effects were stated as possible explanations for these incongruencies. In this study, we addressed these issues by extending the myriapod and outgroup taxon sampling...

BayesW time-to-event analysis posterior outputs and summary statistics

Sven Erik Ojavee & Matthew Robinson
Here, we develop a Bayesian approach (BayesW) that provides probabilistic inference of the genetic architecture of age-at-onset phenotypes in a hybrid-parallel sampling scheme that facilitates Bayesian time-to-event large-scale biobank analyses. We show in extensive simulation work that BayesW achieves a greater number of discoveries, better model performance and improved genomic prediction as compared to other approaches. In the UK Biobank, we find many thousands of common genomic regions underlying the age-at-onset of high blood pressure...

Input files of various genomic analyses used to unravel the domestication history of Cannabis

Guangpeng Ren & Luca Fumagalli
Cannabis sativa has long been an important source of fiber extracted from hemp and both medicinal and recreational drugs based on cannabinoid compounds. Here, we investigated its poorly known domestication history using whole-genome resequencing of 110 accessions from worldwide origins. We show that C. sativa was first domesticated in early Neolithic times in East Asia and that all current hemp and drug cultivars diverged from an ancestral gene pool currently represented by feral plants and...

Population abundance data and species range maps

Mathieu Chevalier, Olivier Broennimann & Antoine Guisan
Aim – The abundant-center hypothesis (ACH) predicts a negative relationship between species abundance and the distance to geographic range center. Since its formulation, empirical tests of the ACH have involved different settings (e.g. the distance to the ecological niche or to the geographic range center), but studies found contrasting support for this hypothesis. Here, we evaluate whether these discrepancies might stem from differences regarding the context in which the ACH is tested (geographical or environmental),...

Data from: European common frog (Rana temporaria) recolonised Switzerland from multiple glacial refugia in northern Italy via trans- and circum-Alpine routes

Alexandra Jansen Van Rensburg, Mathieu Robin, Barret Phillips & Josh Van Buskirk
The high mountain ranges of western Europe had a profound effect on the biotic recolonisation of Europe from glacial refugia. The Alps present a particularly interesting case because they form an absolute barrier to dispersal for most taxa, obstructing recolonisation from multiple refugia in northern Italy. Here we investigate the effect of the European Alps on the phylogeographic history of the European common frog Rana temporaria. Based on partial cytochrome b and COXI sequences from...

Data from: Predicting species occurrences with habitat network models

Damian Omar Ortiz-Rodríguez, Antoine Guisan, Rolf Holderegger & Maarten Van Strien
1. Biodiversity conservation requires modelling tools capable of predicting the presence or absence (i.e. occurrence-state) of species in habitat patches. Local habitat characteristics of a patch (lh), the cost of traversing the landscape matrix between patches (weighted connectivity; (wc), and the position of the patch in the habitat network topology (nt) all influence occurrence-state. Existing models are data demanding or consider only local habitat characteristics. We address these shortcomings and present a network-based modelling approach,...

Data from: How to evaluate community predictions without thresholding?

Daniel Scherrer, Heidi Mod & Antoine Guisan
Stacked species distribution models (S-SDM) provide a tool to make spatial predictions about communities by first modelling individual species and then stacking the modelled predictions to form assemblages. The evaluation of the predictive performance is usually based on a comparison of the observed and predicted community properties (e.g., species richness, composition). However, the most available and widely used evaluation metrics require the thresholding of single species’ predicted probabilities of occurrence to obtain binary outcomes (i.e.,...

Low adaptive potential for tolerance to ethynylestradiol, but also low toxicity, in a grayling population (Thymallus thymallus)

Lucas Marques Da Cunha, Diane Maitre & Claus Wedekind
Background: The presence of a novel pollutant can induce rapid evolution if there is additive genetic variance for the tolerance to the stressor. Continuous selection over some generations can then reduce the toxicity of the pollutant but also deplete the additive genetic variance for the tolerance and thereby slow down adaptation. One common pollutant that has been ecologically relevant for some time is 17alpha-ethynyestradiol (EE2), a synthetic compound of oral contraceptives since their market launch...

Adaptation to a bacterial pathogen in Drosophila melanogaster is not aided by sexual selection

Sakshi Sharda, Tadeusz Kawecki & Brian Hollis
Theory predicts that sexual selection should aid adaptation to novel environments, but empirical support for this idea is limited. Pathogens are a major driver of host evolution and, unlike abiotic selection pressures, undergo epidemiological and co-evolutionary cycles with the host involving adaptation and counteradaptation. Because of this, populations harbor ample genetic variation underlying immunity and the opportunity for sexual selection based on condition-dependent “good genes” is expected to be large. In this study, we evolved...

Inbreeding and kinship coefficients of parents of sperm competition experiment with lake char (Lake Geneva 2017/18)

Christian De Guttry, David Nusbaumer, Laura Garaud, Laurie Ançay & Claus Wedekind
A total of 14 lake char (Salvelinus umbla) were genotyped in the same library using ddRADsequencing. The data includes 14 gzipped .fastq files generated using 2 lanes of sequencing on an Illumina HIseq 2500 and the final dataset with the final estimates of kinship and inbreeding. For each individual, the fastq files of the 2 sequencings lanes were merged after demultiplexing using process_radtags (Stacks 1.48). We provide the bash and R scripts that we used....

Moths and butterflies on alien shores – global biogeography of non-native Lepidoptera

Richard Mally, Rebecca M. Turner, Rachael E. Blake, Gyda Fenn-Moltu, Cleo Bertelsmeier, Eckehard G. Brockerhoff, Robert J. B. Hoare, Helen F. Nahrung, Alain Roques, Deepa S. Pureswaran, Takehiko Yamanaka & Andrew M. Liebhold
Lepidoptera is a highly diverse, predominantly herbivorous insect order, with species transported to outside their native range largely facilitated by the global trade of plants and plant-based goods. Analogous to island disharmony, we examine invasion disharmony, where species filtering during invasions increases systematic compositional differences between native and non-native species assemblages, and test whether some families are more successful at establishing in non-native regions than others. We compared numbers of non-native, unintentionally introduced Lepidoptera species...

Data from: Systematics of snow voles (Chionomys, Arvicolinae) revisited

Glenn Yannic, Reto Burri, Vladimir G. Malikov & Peter Vogel
To elucidate the evolutionary history of snow voles, genus Chionomys, we studied the phylogeography of Chionomys nivalis across its range and investigated its relationships with two congeneric species, C. gud and C. roberti, using independent molecular markers. Analyses were based on mitochondrial (~940 bp cyt b) and Y-chromosomal (~2020 bp from three introns) genetic variation. Our data provide conclusive evidence for a Caucasian and Middle Eastern origin for the three species and a subsequent westward...

Data from: Reconstructing the origins of high-alpine niches and cushion life form in the genus Androsace s.l. (Primulaceae)

Florian Boucher, Wilfried Thuiller, Cristina Roquet, Rolland Douzet, Serge Aubert, Nadir Alvarez & Sébastien Lavergne
Relatively few species have been able to colonize extremely cold alpine environments. We investigate the role played by the cushion life form in the evolution of climatic niches in the plant genus Androsace s.l., which spreads across the mountain ranges of the Northern Hemisphere. Using robust methods that account for phylogenetic uncertainty, intraspecific variability of climatic requirements and different life history evolution scenarios, we show that climatic niches of Androsace s.l. exhibit low phylogenetic signal...

Data from: Ecology and life history affect different aspects of the population structure of 27 high-alpine plants

Patrick G. Meirmans, Jerome Goudet, IntraBioDiv Consortium & Oscar E. Gaggiotti
A plant species' genetic population structure is the result of a complex combination of its life history, ecological preferences, position in the ecosystem, and historical factors. As a result, many different statistical methods exist that measure different aspects of species’ genetic structure. However, little is known about how these methods are interrelated and how they are related to a species’ ecology and life history. In this study, we used the IntraBioDiv AFLP-dataset from 27 high-alpine...

Data from: Evidence for morphological and adaptive genetic divergence between lake and stream habitats in European minnows (Phoxinus phoxinus, Cyprinidae)

Hélène Collin & Luca Fumagalli
Natural selection drives local adaptation, potentially even at small temporal and spatial scales. As a result, adaptive genetic and phenotypic divergence can occur among populations living in different habitats. We investigated patterns of differentiation between contrasting lake and stream habitats in the cyprinid fish European minnow (Phoxinus phoxinus) at both the morphological and genomic level using geometric morphometrics and AFLP markers, respectively. We also used a spatial correlative approach to identify AFLP loci associated with...

Data from: Scale-specific sex-biased dispersal in the Valais shrew unveiled by genetic variation on the Y chromosome, autosomes, and mitochondrial DNA

Glenn Yannic, Patrick Basset, Lucie Büchi, Jacques Hausser & Thomas Broquet
We investigated sex-specificities in the evolutionary processes shaping Y chromosome, autosomes and mitochondrial DNA patterns of genetic structure in the Valais shrew (Sorex antinorii), a mountain dwelling species with a hierarchical distribution. Both hierarchical analyses of variance and isolation-by-distance analyses revealed patterns of population structure that were not consistent across maternal, paternal and bi-parentally inherited markers. Differentiation on a Y microsatellite was lower than expected from the comparison with autosomal microsatellites and mtDNA, and it...

Data from: Reduced genetic diversity, increased isolation and multiple introductions of invasive giant hogweed in the western Swiss Alps

Philippe Henry, Gwenaëlle Le Lay, Jerome Goudet, Antoine Guisan, Sarka Jahodova & Guillaume Besnard
The Giant Hogweed (Heracleum mantegazzianum) has successfully invaded 19 European countries as well as parts of North America. It has become a problematic species due to its ability to displace native flora and to cause public health hazards. Applying population genetics to species invasion can help reconstruct invasion history and may promote more efficient management practice. We thus analyzed levels of genetic variation and population genetic structure of H. mantegazzianum in an invaded area of...

Data from: Nonspecific PCR amplification by high-fidelity polymerases: implications for next-generation sequencing of AFLP markers.

Alan Brelsford, Hélène Collin, Nicolas Perrin & Luca Fumagalli
High-fidelity “proofreading” polymerases are often used in library construction for next-generation sequencing projects, in an effort to minimize errors in the resulting sequence data. The increased template fidelity of these polymerases can come at the cost of reduced template specificity, and library preparation methods based on the AFLP technique may be particularly susceptible. Here, we compare AFLP profiles generated with standard Taq and two versions of a high-fidelity polymerase. We find that Taq produces fewer...

Data from: Genetic components to caste allocation in a multiple-queen ant species

Romain Libbrecht, Tanja Schwander & Laurent Keller
Reproductive division of labor and the coexistence of distinct castes are hallmarks of insect societies. In social insect species with multiple queens per colony, the fitness of nestmate queens directly depends on the process of caste allocation (i.e., the relative investment in queen, sterile worker and male production). The aim of this study is to investigate the genetic components to the process of caste allocation in a multiple-queen ant species. We conducted controlled crosses in...

Data from: Multiple refugia and barriers explain the phylogeography of the Valais shrew, Sorex antinorii (Mammalia: Soricomorpha)

Glenn Yannic, Loïc Pellissier, Sylvain Dubey, Rodrigo Vega, Patrick Basset, Stefano Mazzotti, Elena Pecchioli, Cristiano Vernesi, Heidi C. Hauffe, Jeremy B. Searle & Jacques Hausser
The aim of the present study was to investigate the genetic structure of the Valais shrew (Sorex antinorii) by a combined phylogeographical and landscape genetic approach, and thereby to infer the locations of glacial refugia and establish the influence of geographical barriers. We sequenced part of the mitochondrial cytochrome b (cyt b) gene of 179 individuals of S. antinorii sampled across the entire species' range. Six specimens attributed to S. arunchi were included in the...

Data from: Plastic and evolutionary responses of cell size and number to larval malnutrition in Drosophila melanogaster

Roshan K Vijendravarma, Sunitha Narasimha & Tadeusz J Kawecki
Both development and evolution under chronic malnutrition lead to reduced adult size in Drosophila. We studied the contribution of changes in size vs. number of epidermal cells to plastic and evolutionary reduction of wing size in response to poor larval food. We used flies from six populations selected for tolerance to larval malnutrition and from six unselected control populations, raised either under standard conditions or under larval malnutrition. In the control populations, phenotypic plasticity of...

Data from: Group-size diversity in public goods games

Jorge Peña
Public goods games are models of social dilemmas where cooperators pay a cost for the production of a public good while defectors free ride on the contributions of cooperators. In the traditional framework of evolutionary game theory, the payoffs of cooperators and defectors result from interactions in groups formed by binomial sampling from an infinite population. Despite empirical evidence showing that group-size distributions in nature are highly heterogeneous, most models of social evolution assume that...

Data from: Chromosomal rearrangements do not seem to affect the gene flow in hybrid zones between karyotypic races of the common shrew (Sorex araneus)

Agnès Horn
Chromosomal rearrangements are proposed to promote genetic differentiation between chromosomally differentiated taxa and therefore promote speciation. Due to their remarkable karyotypic polymorphism, the shrews of the Sorex araneus group were used to investigate the impact of chromosomal rearrangements on gene flow. Five intraspecific chromosomal hybrid zones characterized by different levels of karyotypic complexity were studied using 16 microsatellites markers. We observed low levels of genetic differentiation even in the hybrid zones with the highest karyotypic...

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