306 Works

Mathematical chromatography deciphers the molecular fingerprints of dissolved organic matter

Urban J. Wünsch & Jeffrey A. Hawkes
High-resolution mass spectrometry (HRMS) elucidates the molecular composition of dissolved organic matter (DOM) through the unequivocal assignment of molecular formulas. When HRMS is used as a detector coupled to high performance liquid chromatography (HPLC), the molecular fingerprints of DOM are further augmented. However, the identification of eluting compounds remains impossible when DOM chromatograms consist of unresolved humps. Here, we utilized the concept of mathematical chromatography to achieve information reduction and feature extraction. Parallel Factor Analysis...

Manipulation of trait expression and pollination regime reveal the adaptive significance of spur length

Jon Ågren, Nina Sletvold & Judith Trunschke
Understanding the mechanisms of adaptive population differentiation requires that both the functional and adaptive significance of divergent traits are characterized in contrasting environments. Here, we (a) determined the effects of floral spur length on pollen removal and receipt using plants with artificial spurs representing the species-wide variation in length, and (b) quantified pollinator-mediated selection on spur length and three traits contributing to floral display in two populations each of the short-spurred and the long-spurred ecotype...

The role of low-grade inflammation in ME/CFS (Myalgic Encephalomyelitis/Chronic Fatigue Syndrome) - associations with symptoms

Anna Andreasson, Martin Jonsjö, Gunnar Olsson, Rikard K Wicksell, Kjell Alving & Linda Holmström
Background Patients with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) often present with a range of flu-like symptoms resembling sickness behavior as well as widespread pain and concentration deficits. The aim of this study was to explore the association between inflammatory markers previously shown to be related to fatigue severity in ME/CFS and common ME/CFS symptoms post-exertional fatigue, impaired cognitive processing, musculoskeletal pain and recurrent flu-like symptoms, and the moderating effect of sex on these associations. Methods...

Broad-scale patterns of the Afro-Palearctic landbird migration

Martins Briedis, Silke Bauer, Peter Adamík, José Alves, Joana Costa, Tamara Emmenegger, Lars Gustafsson, Jaroslav Koleček, Miloš Krist, Felix Liechti, Simeon Lisovski, Christoph Meier, Petr Procházka & Steffen Hahn
Aim: Animal migration strategies balance trade-offs between mortality and reproduction in seasonal environments. Knowledge of broad-scale biogeographical patterns of animal migration is important for understanding ecological drivers of migratory behaviours. Here we present a flyway-scale assessment of the spatial structure and seasonal dynamics of the Afro-Palearctic bird migration system and explore how phenology of the environment guides long-distance migration. Location: Europe and Africa. Time period: 2009–2017. Major taxa studied: Birds. Methods: We compiled an individual-based...

Data from: Parental genetic similarity and offspring performance in blue tits in relation to brood size manipulation

Aneta Arct, Szymon Drobniak, Samantha Mellinger, Lars Gustafsson & Mariusz Cichon
In birds, as in many other taxa, the level of genetic similarity between parents is an important source of variation in offspring fitness. The majority of avian studies which explore the influence of mates’ genetic similarity on offspring viability have focused on hatching success as a viability measure. Yet, viability benefits may extend into later life stages, including the nestling period and beyond. Here, we analysed data from free-living blue tits (Cyanistes caeruleus) across three...

Dietary Restriction Improves Fitness of Aging Parents But Reduces Fitness of Their Offspring in Nematodes

Brian Mautz, Martin I Lind & Alexei A Maklakov
Abstract Dietary restriction (DR) is a well-established intervention to extend lifespan across taxa. Recent studies suggest that DR-driven lifespan extension can be cost-free, calling into question a central tenant of the evolutionary theory of aging. Nevertheless, boosting parental longevity can reduce offspring fitness. Such intergenerational trade-offs are often ignored but can account for the “missing costs” of longevity. Here, we use the nematode Caenorhabditis remanei to test for effects of DR by fasting on fitness...

Data from: Stabilizing selection and adaptive evolution in a combination of two traits in an arctic ungulate

Håkon Holand, Thomas Kvalnes, Knut Røed, Øystein Holand, Bernt-Erik Sæther & Jouko Kumpula
Stabilizing selection is thought to be common in wild populations and act as one of the main evolutionary mechanisms which constrain phenotypic variation. When multiple traits interact to create a combined phenotype, correlational selection may be an important process driving adaptive evolution. Here we report on phenotypic selection and evolutionary changes in two natal traits in a semi-domestic population of reindeer (Rangifer tarandus) in northern Finland. The population has been closely monitored since 1969, and...

Intraspecific mating system evolution and its effect on complex male secondary sexual traits: does male-male competition increase selection on size or shape?

Julian Baur, Jeannine Roy, Martin A. Schäfer, Nalini Puniamoorthy, Wolf U. Blanckenhorn & Patrick T. Rohner
Sexual selection is generally held responsible for the exceptional diversity in secondary sexual traits in animals. Mating system evolution is therefore expected to profoundly affect the covariation between secondary sexual traits and mating success. While there is such evidence at the interspecific level, data within species remain scarce. We here investigate sexual selection acting on the exaggerated male fore femur and the male wing in the common and widespread dung flies Sepsis punctum and S....

Towards a comparative approach to the structure of animal personality variation

Stephen White, David Pascall & Alastair Wilson
Latent personality traits underpinning observed behavioral variation have been studied in a great many species. However, a lack of standardized behavioral assays, coupled to a common reliance on inferring personality from a single, observed, behavioral trait makes it difficult to determine if, when, and how conclusions can be directly compared across taxa. Here, we estimate the among-individual (co)variance structure (ID) for a set of four behaviors expressed in an open field trial, putatively indicative of...

A genome-wide investigation of adaptations related to to tool use behaviour in New Caledonian and Hawaiian crows

Nicolas Dussex, Verena E. Kutschera, R. Axel W. Wiberg, Darren Parker, Gavin Hunt, Russell D. Gray, Kim Rutherford, Abe Hideaki, Robert Fleischer, Christian Rutz, Michael G. Ritchie, Jochen B.W. Wolf & Neil J. Gemmell
GFF3 file with protein-coding gne predictions for the C. moneduloides de novo genome assembly (available at the National Center for Biotechnology Information (NCBI); assembly accession number: VRTO00000000), generated using the MAKER2 pipeline.

Quantifying the structure and dynamics of fish shoals under predation threat in three-dimensions

Maksym Romenskyy, James Herbert-Read, Christol Ioannou, Alex Szorkovszky, Ashley Ward & David Sumpter
Detailed quantifications of how predators and their grouping prey interact in three dimensions (3D) remain rare. Here we record the structure and dynamics of fish shoals (Pseudomugil signifer) in 3D both with and without live predators (Philypnodon grandiceps) under controlled laboratory conditions. Shoals adopted two distinct types of shoal structure; ‘sphere-like’ geometries at depth, and flat ‘carpet-like’ structures at the water’s surface, with shoals becoming more compact in both horizontal and vertical planes in the...

Data from: Antibiotic uptake across gram-negative outer membranes: better predictions towards better antibiotics

Peter Kasson & Ricardo Ferreira
Crossing the gram-negative bacterial membrane poses a major barrier to antibiotic development, as many small molecules that can biochemically inhibit key bacterial processes are rendered microbiologically ineffective by their poor cellular uptake. The outer membrane is the major permeability barrier for many drug-like molecules, and the chemical properties that enable efficient uptake into mammalian cells fail to predict bacterial uptake. We have developed a computational method for accurate prospective prediction of outer-membrane uptake of drug-like...

Distribution patterns of fungal taxa and inferred functional traits reflect the non-uniform vertical stratification of soil microhabitats in a coastal pine forest

Kerri Kluting, Karina Clemmensen, Stanislovas Jonaitis, Rimvydas Vasaitis, Sara Holmström, Roger Finlay & Anna Rosling
In boreal systems, soil profiles typically consist of distinct stratified horizons, with organic layers at the surface overlying deeper mineral horizons providing microhabitat variation along a depth gradient, and vertical stratification of fungal communities along such soil profiles is commonly observed. We studied fungal community structure in a coastal pine forest along a gradient of decreasing influence from the coast. In this system, the vertical stratification pattern of soil microhabitats (defined here as organic, mineral...

Data from: Sex-biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome

Ludovic Dutoit, Carina Mugal, Paulina Bolivar, Mi Wang, Krystyna Nadachowska-Brzyska, Linnea Smeds, Homa Papoli, Lars Gustavsson & Hans Ellegren
Theoretical work suggests that sexual conflict should promote the maintenance of genetic diversity by the opposing directions of selection on males and females. If such conflict is pervasive, it could potentially lead to genomic heterogeneity in levels of genetic diversity an idea that so far has not been empirically tested on a genome-wide scale. We used large-scale population genomic and transcriptomic data from the collared flycatcher (Ficedula albicollis) to analyse how sexual conflict, for which...

Gene flow limits adaptation along steep environmental gradients

Judith Bachmann, Alexandra Jansen Van Rensburg, Maria Cortazar-Chinarro, Anssi Laurila & Josh Van Buskirk
When environmental variation is spatially continuous, dispersing individuals move among nearby sites with similar habitat conditions. But as an environmental gradient becomes steeper, gene flow may connect more divergent habitats, and this is predicted to reduce the slope of the adaptive cline that evolves. We compared quantitative genetic divergence of Rana temporaria frog populations along a 2000-m elevational gradient in eastern Switzerland (new experimental results) with divergence along a 1550-km latitudinal gradient in Fennoscandia (previously...

How does joint evolution of consumer traits affect resource specialization?

Paula Vasconcelos & Claus Rueffler
Consumers regularly experience trade-offs in their ability to find, handle and digest different resources. Evolutionary ecologists recognized the significance of this observation for the evolution and maintenance of biological diversity long ago and continue to elaborate on the conditions under which to expect one or several specialists, generalists or combinations thereof. Existing theory based on a single evolving trait predicts that specialization requires strong trade-offs such that generalists perform relatively poorly, while weak trade-offs favor...

Data from: Structural classification and scaffold diversity of sesquiterpene lactones in the angiosperms

Astrid Henz Ryen, Rosa Buonfiglio, Anders Backlund & Thierry Kogej
Sesquiterpene lactones (STLs) present one of the largest groups of plant specialized metabolites with a wide range of biological activities. They are a valuable source for new plant derived drugs and drug leads since they contain several important chemical properties responsible for their versatile therapeutic potential. The aim of this study was to analyze and compare the chemical diversity of all types of STLs in different plant groups, both qualitatively and quantitatively. For this purpose,...

Data from: Comparative support for the expensive tissue hypothesis: big brains are correlated with smaller gut and greater parental investment in Lake Tanganyika cichlids

Masahito Tsuboi, Arild Husby, Alexander Kotrschal, Alexander Hayward, Séverine Denise Büchel, Josefina Zidar, Hanne Løvlie & Niclas Kolm
The brain is one of the most energetically expensive organs in the vertebrate body. Consequently, the energetic requirements of encephalization are suggested to impose considerable constraints on brain size evolution. Three main hypotheses concerning how energetic constraints might affect brain evolution predict covariation between brain investment and i) investment into other costly tissues, ii) overall metabolic rate, and iii) reproductive investment. To date, these hypotheses have mainly been tested in homeothermic animals and the existing...

Data from: Biochemical determinants of litter quality in 15 species of Sphagnum

Fia Bengtsson, Håkan Rydin & Tomáš Hájek
Background and aims: Sphagnum mosses are ecosystem engineers that create and maintain boreal peatlands. With unique biochemistry, waterlogging and acidifying capacities, they build up meters-thick layers of peat, reducing competition and impeding decomposition. We quantify within-genus differences in biochemical composition to make inferences about decay rates, related to hummock–hollow and fen–bog gradients and to phylogeny.Methods: We sampled litter from 15 Sphagnum species, abundant over the whole northern hemisphere. We used regression and Principal Components Analysis...

Data from: A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them

E. Humble, A. Martinez-Barrio, J. Forcada, P.N. Trathan, M.A.S. Thorne, M. Hoffmann, J. B W. Wolf, J.I. Hoffman, J. I. Hoffman, P. N. Trathan, M. A. S. Thorne & J. B. W. Wolf
Custom genotyping arrays provide a flexible and accurate means of genotyping single nucleotide polymorphisms (SNPs) in a large number of individuals of essentially any organism. However, validation rates, defined as the proportion of putative SNPs that are verified to be polymorphic in a population, are often very low. A number of potential causes of assay failure have been identified, but none have been explored systematically. In particular, as SNPs are often developed from transcriptomes, parameters...

Data from: Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments.

Nagarjun Vijay, Jelmer W. Poelstra, Axel Künstner & Jochen B. W. Wolf
Transcriptome Shotgun Sequencing (RNA-seq) has been readily embraced by geneticists and molecular ecologists alike. As with all high-throughput technologies, it is critical to understand which analytic strategies are best suited and which parameters may bias the interpretation of the data. Here we use a comprehensive simulation approach to explore how various features of the transcriptome (complexity, degree of polymorphism π, alternative splicing), technological processing (sequencing error ε, library normalization) and bioinformatic workflow (de novo vs....

Data from: Fine-scale kin recognition in the absence of social familiarity in the Siberian jay, a monogamous bird species

Michael Griesser, Peter Halvarsson, Szymon M. Drobniak & Carles Vilà
Kin recognition is a critical element to kin cooperation, and in vertebrates, it is primarily based on associative learning. Recognition of socially unfamiliar kin occurs rarely, and it is reported only in vertebrate species where promiscuity prevents recognition of first-order relatives. However, it is unknown whether the recognition of socially unfamiliar kin can evolve in monogamous species. Here, we investigate whether genetic relatedness modulates aggression among group members in Siberian jays (Perisoreus infaustus). This bird...

Data from: Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd’s purse (Capsella bursa-pastoris)

Amandine Cornille, Adriana Salcedo, Dmytro Kryvokhyzha, Sylvain Glémin, Kalle Holm, Stephen Wright & Martin Lascoux
Polyploidization is a dominant feature of flowering plant evolution. However, detailed genomic analyses of the inter-population diversification of polyploids following genome duplication are still in their infancy, mainly because of methodological limits, both in terms of sequencing and computational analyses. The shepherd’s purse (Capsella bursa-pastoris) is one of the most common weed species in the world. It is highly self-fertilizing, and recent genomic data indicate that it is an allopolyploid, resulting from hybridization between the...

Data from: Brain – endocast relationship in the Australian lungfish, Neoceratodus forsteri, elucidated from tomographic data (Sarcopterygii: Dipnoi)

Alice M. Clement, Johan Nysjö, Robin Strand & Per E. Ahlberg
Although the brains of the three extant lungfish genera have been previously described, the spatial relationship between the brain and the neurocranium has never before been fully described nor quantified. Through the application of virtual microtomography (μCT) and 3D rendering software, we describe aspects of the gross anatomy of the brain and labyrinth region in the Australian lungfish, Neoceratodus forsteri and compare this to previous accounts. Unexpected characters in this specimen include short olfactory peduncles...

Data from: Genomic and phenotypic differentiation of Arabidopsis thaliana along altitudinal gradients in the North Italian Alps

Torsten Günther, Christian Lampei, Ivan Barilar & Karl J. Schmid
Altitudinal gradients in mountain regions are short-range clines of different environmental parameters such as temperature or radiation. We investigated genomic and phenotypic signatures of adaptation to such gradients in five Arabidopsis thaliana populations from the North Italian Alps that originated from 580 to 2350 m altitude by resequencing pools of 19–29 individuals from each population. The sample includes two pairs of low- and high-altitude populations from two different valleys. High-altitude populations showed a lower nucleotide...

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