193 Works

Data from: Bayesian phylogenetic estimation of clade ages supports trans-atlantic dispersal of cichlid fishes

Michael Matschiner, Zuzana Musilová, Julia M.I. Barth, Zuzana Starostová, Walter Salzburger, Mike Steel & Remco Bouckaert
Divergence-time estimation based on molecular phylogenies and the fossil record has provided insights into fundamental questions of evolutionary biology. In Bayesian node dating, phylogenies are commonly time calibrated through the specification of calibration densities on nodes representing clades with known fossil occurrences. Unfortunately, the optimal shape of these calibration densities is usually unknown and they are therefore often chosen arbitrarily, which directly impacts the reliability of the resulting age estimates. As possible solutions to this...

Data from: Disentangling structural genomic and behavioral barriers in a sea of connectivity

Julia M. I. Barth, David Villegas-Ríos, Carla Freitas, Even Moland, Bastiaan Star, Carl André, Halvor Knutsen, Ian Bradbury, Jan Dierking, Christoph Petereit, David Righton, Julian Metcalfe, Kjetill S. Jakobsen, Esben M. Olsen, Sissel Jentoft & Julia M.I. Barth
Genetic divergence among populations arises through natural selection or drift and is counteracted by connectivity and gene flow. In sympatric populations, isolating mechanisms are thus needed to limit the homogenizing effects of gene flow to allow for adaptation and speciation. Chromosomal inversions act as an important mechanism maintaining isolating barriers, yet their role in sympatric populations and divergence with gene flow is not entirely understood. Here, we revisit the question whether inversions play a role...

Data from: Despite high levels of expression in thymic epithelial cells, miR-181a1 and miR-181b1 are not required for thymic development

Heather E. Stefanski, Yan Xing, Patricia A. Taylor, Stefano Maio, Jorge Henao-Meija, Adam Williams, Richard A. Flavell, Georg A. Hollander & Bruce R. Blazar
MicroRNAs (miRNAs) have been shown to be key modulators of post-transcriptional gene silencing in many cellular processes. In previous studies designed to understand the role of miRNAs in thymic development, we globally deleted miRNA exclusively in thymic epithelial cells (TECs), which are critical in thymic selection. This resulted in the loss of stromal cells that instruct T cell lineage commitment and affect thymocyte positive selection, required for mature T cell development. Since murine miR-181 is...

Data from: Molecular evolution of key metabolic genes during transitions to C4 and CAM photosynthesis

Eric W. Goolsby, Abigail J. Moore, Lillian P. Hancock, Jurriaan M. De Vos & Erika J. Edwards
PREMISE OF THE STUDY: Next-generation sequencing facilitates rapid production of well-sampled phylogenies built from very large genetic datasets, which can then be subsequently exploited to examine the molecular evolution of the genes themselves. We present an evolutionary analysis of 83 gene families (19 containing carbon-concentrating mechanism (CCM) genes, 64 containing non-CCM genes) in the portullugo clade (Caryophyllales), a diverse lineage of mostly arid-adapted plants that contains multiple evolutionary origins of all known photosynthesis types in...

Data from: Forecasting range shifts of a cold-adapted species under climate change: are genomic and ecological diversity within species crucial for future resilience?

Spyros Theodoridis, Theofania S. Patsiou, Christophe Randin & Elena Conti
Cold-adapted taxa are experiencing severe range shifts due to climate change and are expected to suffer a significant reduction of their climatically suitable habitats in the next few decades. However, it has been proposed that taxa with sufficient standing genetic and ecologic diversity will better withstand climate change. These taxa are typically more broadly distributed in geographic and ecological niche space, therefore they are likely to endure higher levels of populations loss than more restricted,...

Data from: Intrinsic and extrinsic factors act at different spatial and temporal scales to shape population structure, distribution and speciation in Italian Barbus (Osteichthyes: Cyprinidae)

Luca Buornerba, Serena Zaccara, Giovanni B. Delmastro, Massimo Lorenzoni, Walter Salzburger, Hugo F. Gante & Luca Buonerba
Previous studies have given substantial attention to external factors that affect the distribution and diversification of freshwater fish in Europe and North America, in particular Pleistocene and Holocene glacial cycles. In the present paper we examine sequence variation at one mitochondrial and four nuclear loci (over 3 kbp) from populations sampled across several drainages of all species of Barbus known to inhabit Italian freshwaters (introduced B. barbus and native B. balcanicus, B. caninus, B. plebejus...

Data from: The temporal dynamics and infectiousness of subpatent Plasmodium falciparum infections in relation to parasite density

Hannah C. Slater, Amanda Ross, Ingrid Felger, Natalie E. Hofmann, Leanne Robinson, Jackie Cook, Bronner P. Gonçalves, Anders Björkman, Andre Lin Ouedraogo, Ulrika Morris, Mwinyi Msellem, Cristian Koepfli, Ivo Mueller, Fitsum Tadesse, Endalamaw Gadisa, Smita Das, Gonzalo Domingo, Melissa Kapulu, Janet Midega, Seth Owusu-Agyei, Cécile Nabet, Renaud Piarroux, Ogobara Doumbo, Safiatou Niare Doumbo, Kwadwo Koram … & Lucy C. Okell
Malaria infections occurring below the limit of detection of standard diagnostics are common in all endemic settings. However, key questions remain surrounding their contribution to sustaining transmission and whether they need to be detected and targeted to achieve malaria elimination. In this study we analyse a range of malaria datasets to quantify the density, detectability, course of infection and infectiousness of subpatent infections. Asymptomatically infected individuals have lower parasite densities on average in low transmission...

Data from: Quantitative genetic inheritance of morphological divergence in a lake-stream stickleback ecotype pair: implications for reproductive isolation

Daniel Berner, Renaud Kaeuffer, Anne-Catherine Grandchamp, Joost A. M. Raeymaekers, Katja Räsänen & Andrew P. Hendry
Ecological selection against hybrids between populations occupying different habitats might be an important component of reproductive isolation during the initial stages of speciation. The strength and directionality of this barrier to gene flow depends on the genetic architecture underlying divergence in ecologically relevant phenotypes. We here present line cross analyses of inheritance for two key foraging-related morphological traits involved in adaptive divergence between stickleback ecotypes residing parapatrically in lake and stream habitats within the Misty...

Data from: Structural alterations of the social brain: a comparison between schizophrenia and autism

Daniel Radeloff, Angela Ciaramidaro, Sabine Schlitt, Sven Bölte, Fritz Poustka, Daniela Hainz, Bernhard Weber, Michael Siniatchkin, Henrik Walter & Christine Margarete Freitag
Autism spectrum disorder and schizophrenia share a substantial number of etiologic and phenotypic characteristics. Still, no direct comparison of both disorders has been performed to identify differences and commonalities in brain structure. In this voxel based morphometry study, 34 patients with autism spectrum disorder, 21 patients with schizophrenia and 26 typically developed control subjects were included to identify global and regional brain volume alterations. No global gray matter or white matter differences were found between...

Data from: Comparative proteomics of stenotopic caddisfly Crunoecia irrorata identifies acclimation strategies to warming

Joshua Niklas Ebner, Danilo Ritz & Stefanie Von Fumetti
Species’ ecological preferences are often deduced from habitat characteristics thought to represent more or less optimal conditions for physiological functioning. Evolution has led to stenotopic and eurytopic species, the former having decreased niche breadths and lower tolerances to environmental variability. Species inhabiting freshwater springs are often described as being stenotopic specialists, adapted to the stable thermal conditions found in these habitats. Whether due to past local adaptation these species have evolved or have lost intra-generational...

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...

Whole genome re-sequencing of mother and offspring D. magna genotypes

Luca Cornetti
Inbreeding refers to the fusion of related individuals' gametes, with self-fertilization (selfing) being an extreme form of inbreeding—involving gametes produced by the same individual. Selfing is expected to reduce heterozygosity by an average of 50 % in one generation; however, little is known about the empirical variation on a genome level surrounding this figure, and the factors that affect variation. We selfed genotypes of the cyclic parthenogen Daphnia magna and analyzed whole genomes of mothers...

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...

Widespread intersex differentiation across the stickleback genome – the signature of sexually antagonistic selection?

Daniel Berner, Mirjam Bissegger, Telma Laurentino & Marius Roesti
Females and males within a species commonly have distinct reproductive roles, and the associated traits may be under perpetual divergent natural selection between the sexes if their sex-specific control has not yet evolved. We here explore whether such sexually antagonistic selection can be detected based on the magnitude of differentiation between the sexes across genome-wide genetic polymorphisms by whole-genome sequencing of large pools of female and male threespine stickleback fish. We find numerous autosomal genome...

GMBA Mountain Inventory v2

Mark A. Snethlage, Jonas Geschke, Eva M. Spehn, Ajay Ranipeta, Nigel G. Yocco, Christian Körner, Walter Jetz, Markus Fischer & Davnah Urbach
A standardized delineation of the worlds’ mountains has many applications in research, education, and the science-policy interface. Here we provide a new inventory of 8616 mountain ranges developed under the auspices of the Global Mountain Biodiversity Assessment (GMBA). Building on an earlier compilation, the presented geospatial database uses a further advanced and generalized mountain definition and a semi-automated method to enable globally standardized, transparent delineations of mountain ranges worldwide. The inventory is presented on EarthEnv...

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...

Data from: Genetic effects of anthropogenic habitat fragmentation on remnant animal and plant populations: a meta-analysis

Daniel R. Schlaepfer, Brigitte Braschler, Hans-Peter Rusterholz & Bruno Baur
Habitat loss and fragmentation are among the biggest threats to biodiversity. Anthropogenic habitat fragmentation leads to small and isolated remnant plant and animal populations. The combination of increased random genetic drift, inbreeding, and reduced gene flow may substantially reduce genetic variation of remnant populations. However, the magnitude of these responses may depend on several poorly understood factors including organism group, habitat type of both the fragment and the surrounding matrix, life‐history traits, and time since...

Data from: Study of morphological variation of northern Neotropical Ariidae reveals conservatism despite macrohabitat transitions

Madlen Stange, Gabriel Aguirre-Fernández, Walter Salzburger & Marcelo R. Sánchez-Villagra
Background: Morphological convergence triggered by trophic adaptations is a common pattern in adaptive radiations. The study of shape variation in an evolutionary context is usually restricted to well-studied fish models. We take advantage of the recently revised systematics of New World Ariidae and investigate skull shape evolution in six genera of northern Neotropical Ariidae. They constitute a lineage that diversified in the marine habitat but repeatedly adapted to freshwater habitats. 3D geometric morphometrics was applied...

Data from: A targeted in situ hybridization screen identifies putative seminal fluid proteins in a simultaneously hermaphroditic flatworm

Michael Weber, Julia Wunderer, Birgit Lengerer, Robert Pjeta, Marcelo Rodrigues, Lukas Schärer, Peter Ladurner & Steven A. Ramm
Background: Along with sperm, in many taxa ejaculates also contain large numbers of seminal fluid proteins (SFPs). SFPs and sperm are transferred to the mating partner, where they are thought to play key roles in mediating post-mating sexual selection. They modulate the partner's behavior and physiology in ways that influence the reproductive success of both partners, thus potentially leading to sexual conflict. Despite the presumed general functional and evolutionary significance of SFPs, their identification and...

Data from: Growth and carbon relations of mature Picea abies trees under 5 years of free-air CO2 enrichment

Tamir Klein, Martin K. F. Bader, Sebastian Leuzinger, Manuel Mildner, Patrick Schleppi, Rolf T. W. Siegwolf, Christian Koerner, Martin K.-F. Bader & Rolf T.W. Siegwolf
Are mature forests carbon limited? To explore this question, we exposed ca. 110-year-old, 40-m tall Picea abies trees to a 550-ppm CO2 concentration in a mixed lowland forest in NW Switzerland. The site receives substantial soluble nitrogen (N) via atmospheric deposition, and thus, trees are unlikely N-limited. We used a construction crane to operate the free-air CO2 release system and for canopy access. Here, we summarize the major results for growth and carbon (C) fluxes....

Data from: Blood-stage parasitaemia and age determine Plasmodium falciparum and P. vivax gametocytaemia in Papua New Guinea

Cristian Koepfli, Leanne J. Robinson, Patricia Rarau, Mary Salib, Naomi Sambale, Rahel Wampfler, Inoni Betuela, Wang Nuitragool, Alyssa E. Barry, Peter Siba, Ingrid Felger & Ivo Mueller
A better understanding of human-to-mosquito transmission is crucial to control malaria. In order to assess factors associated with gametocyte carriage, 2083 samples were collected in a cross-sectional survey in Papua New Guinea. Plasmodium species were detected by light microscopy and qPCR and gametocytes by detection of pfs25 and pvs25 mRNA transcripts by reverse-transcriptase PCR (qRT-PCR). The parasite prevalence by PCR was 18.5% for Plasmodium falciparum and 13.0% for P. vivax. 52.5% of all infections were...

Data from: Strategies for understanding and reducing the Plasmodium vivax and Plasmodium ovale hypnozoite reservoir in Papua New Guinean children: a randomised placebo-controlled trial and mathematical model

Leanne J. Robinson, Rahel Wampfler, Inoni Betuela, Stephan Karl, Michael T. White, Connie S. N. Li Wai Suen, Natalie E. Hofmann, Benson Kiniboro, Andreea Waltmann, Jessica Brewster, Lina Lorry, Nandao Tarongka, Lornah Samol, Mariabeth Silkey, Quique Bassat, Peter M. Siba, Louis Schofield, Ingrid Felger, Ivo Mueller & Benson Kinboro
Background: The undetectable hypnozoite reservoir for relapsing Plasmodium vivax and P. ovale malarias presents a major challenge for malaria control and elimination in endemic countries. This study aims to directly determine the contribution of relapses to the burden of P. vivax and P. ovale infection, illness, and transmission in Papua New Guinean children. Methods and Findings: From 17 August 2009 to 20 May 2010, 524 children aged 5–10 y from East Sepik Province in Papua...

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