42 Works

The Enterprise, a massive transposon carrying Spok meiotic drive genes

Sandra Lorena Ament-Velásquez, Aaron A. Vogan, Eric Bastiaans, Ola Wallerman, Sven J. Saupe, Alexander Suh & Hanna Johannesson
The genomes of eukaryotes are full of parasitic sequences known as transposable elements (TEs). Most TEs studied to date are relatively small (50 – 12000 bp), but can contribute to very large proportions of genomes. Here we report the discovery of a putative giant tyrosine-recombinase-mobilized DNA transposon, Enterprise, from the model fungus Podospora anserina. Previously, we described a large genomic feature called the Spok block which is notable due to the presence of meiotic drive...

Integrating stakeholders’ perspectives and spatial modelling to develop scenarios of future land use and land cover change in northern Tanzania

Rebecca Kariuki, Linus Munishi, Colin Courtney-Mustaphi, Claudia Capitani, Anna Shoemaker, Paul Lane & Rob Marchant
Rapid rates of land use and land cover change (LULCC) in eastern Africa and limited instances of genuinely equal partnerships involving scientists, communities and decision makers challenge the development of robust pathways toward future environmental and socioeconomic sustainability. We use a participatory modelling tool, Kesho, to assess the biophysical, socioeconomic, cultural and governance factors that influenced past (1959-1999) and present (2000-2018) LULCC in northern Tanzania and to simulate four scenarios of land cover change to...

Data from: Dispersal in a house sparrow metapopulation: an integrative case study of genetic assignment calibrated with ecological data and pedigree information

Dilan Saatoglu, Alina K. Niskanen, Markku Kuismin, Peter S. Ranke, Ingerid J. Hagen, Yimen G. Araya-Ajoy, Thomas Kvalnes, Henrik Pärn, Bernt Rønning, Thor Harald Ringsby, Bernt-Erik Sæther, Arild Husby, Mikko J. Sillanpää & Henrik Jensen
Dispersal has a crucial role determining eco-evolutionary dynamics through both gene flow and population size regulation. However, to study dispersal and its consequences, one must distinguish immigrants from residents. Dispersers can be identified using telemetry, capture-mark-recapture (CMR) methods, or genetic assignment methods. All of these methods have disadvantages, such as, high costs and substantial field efforts needed for telemetry and CMR surveys, and adequate genetic distance required in genetic assignment. In this study, we used...

Data from: Host-parasite dynamics shaped by temperature and genotype: quantifying the role of underlying vital rates

Marjolein Bruijning, Erlend Fossen, Eelke Jongejans, Héléne Vanvelk, Joost Raeymaekers, Lynn Govaert, Kristien Brans, Sigurd Einum & Luc De Meester
1. Global warming challenges the persistence of local populations, not only through heat-induced stress, but also through indirect biotic changes. We study the interactive effects of temperature, competition and parasitism in the water flea Daphnia magna. 2. We carried out a common garden experiment monitoring the dynamics of Daphnia populations along a temperature gradient. Halfway through the experiment, all populations became infected with the ectoparasite Amoebidium parasiticum, enabling us to study interactive effects of temperature...

Beneficial cumulative effects of old parental age on offspring fitness

Laura Travers, Hanne Carlsson, Martin Lind & Alexei Maklakov
Old parental age is commonly associated with negative effects on offspring life-history traits. Such parental senescence effects are predicted to have a cumulative detrimental effect over successive generations. However, old parents may benefit from producing higher quality offspring when these compete for seasonal resources. Thus, old parents may choose to increase investment in their offspring, thereby producing fewer but larger and more competitive progeny. We show that Caenorhabditis elegans hermaphrodites increase parental investment with advancing...

Using BART to Perform Pareto Optimization and Quantify its Uncertainties

Akira Horiguchi, Thomas J. Santner, Ying Sun & Matthew T. Pratola
Techniques to reduce the energy burden of an industrial ecosystem often require solving a multiobjective optimization problem. However, collecting experimental data can often be either expensive or time-consuming. In such cases, statistical methods can be helpful. This article proposes Pareto Front (PF) and Pareto Set (PS) estimation methods using Bayesian Additive Regression Trees (BART), which is a nonparametric model whose assumptions are typically less restrictive than popular alternatives, such as Gaussian Processes (GPs). These less...

Data for: Sexual conflict drives micro- and macroevolution of sexual dimorphism in immunity

David Berger, Basabi Bagchi, Quentin Corbel, Imroze Khan, Ellen Payne, Devshuvam Banerji, Johanna Liljestrand-Rönn, Ivain Martinossi-Allibert, Julian Baur, Ahmed Sayadi, Elina Immonen, Göran Arnqvist & Irene Söderhäll
Background: Sexual dimorphism in immunity is believed to reflect sex-differences in reproductive strategies and trade-offs between competing life history demands. Sexual selection can have major effects on mating rates and sex-specific costs of mating and may thereby influence sex-differences in immunity as well as associated host-pathogen dynamics. Yet, experimental evidence linking the mating system to evolved sexual dimorphism in immunity are scarce and the direct effects of mating rate on immunity are not well established....

Do genetic differences in growth thermal reaction norms maintain genetic variation in timing of diapause induction?

Erlend Fossen, Joost Raeymaekers & Sigurd Einum
An optimal timing for diapause induction through the sexual production of dormant propagules is expected in organisms with temporary populations. Yet, empirical studies often find high within-population genetic variation in the sexual production of such propagules, suggesting that this is a common feature of such organisms. Here, we hypothesize that genetic variation in the propensity to produce dormant propagules, Pd, is maintained by a genotype-by-environment interaction in clonal reproductive rates, where fast-growing genotypes within an...

How model assumptions affect our understanding of the evolution of ectomycorrhizal symbiosis in fungi

Sanea Sheikh, Faheema Khan, Mohammad Bahram & Martin Ryberg
The kingdom of Fungi comprises one of the most diverse set of functions and species. Fungi are heterotrophic and can obtain their nutrients from living organisms (biotrophic) or dead matter (saprotrophic). One of the most common biotrophic lifestyles is mycorrhizal association, including ectomycorrhiza (ECM) that involves the largest number of mycorrhizal fungi and is essential for nutrient uptake and health of many stand forming trees. Despite our growing understanding of the diversity of ECM fungi,...

Comprehensive analysis of PPPCs family reveals the clinical significance of PPP1CA and PPP4C in breast cancer

Wenjun Xie, Ying Sun, Yu Zeng, Linfei Hu, Jingtai Zhi, Hang Ling, Xiangqian Zheng, Xianhui Ruan & Ming Gao
The phosphoprotein phosphatase catalytic subunit (PPPCs) family has been shown to play an important role in the development and progression of various malignancies, but its expression patterns and biological functions in breast cancer (BC) remain unclear. Therefore, we aimed to investigate the clinical significance and biological functions of the PPPCs family to understand its possible significance in the diagnosis, prognosis and treatment of breast cancer. We comprehensively investigated the expression levels, diagnostic accuracy, prognostic outcomes,...

Using BART to Perform Pareto Optimization and Quantify its Uncertainties

Akira Horiguchi, Thomas J. Santner, Ying Sun & Matthew T. Pratola
Techniques to reduce the energy burden of an industrial ecosystem often require solving a multiobjective optimization problem. However, collecting experimental data can often be either expensive or time-consuming. In such cases, statistical methods can be helpful. This article proposes Pareto Front (PF) and Pareto Set (PS) estimation methods using Bayesian Additive Regression Trees (BART), which is a nonparametric model whose assumptions are typically less restrictive than popular alternatives, such as Gaussian Processes (GPs). These less...

OPT data from: A novel cis-regulatory element drives early expression of Nkx3.2 in the gnathostome primary jaw joint

Jake Leyhr, Laura Waldmann, Beata Filipek-Górniok, Hanqing Zhang, Amin Allalou & Tatjana Haitina
The acquisition of movable jaws was a major event during vertebrate evolution. The role of NK3 homeobox 2 (Nkx3.2) transcription factor in patterning the primary jaw joint of gnathostomes (jawed vertebrates) is well known, however, knowledge about its regulatory mechanism is lacking. In this study, we report a proximal enhancer element of Nkx3.2 that is deeply conserved in most gnathostomes but undetectable in the jawless hagfish and lamprey. This enhancer is active in the developing...

Data from: Compensatory growth in C. elegans is regulated by a thermosensitive TRP channel and increases reproductive fitness

Zuzana Sekajova, Elena Rosa, Foteini Spagopoulou, PanagiotisIoannis Zervakis & Martin Lind
Animals are often not growing at the maximum rate, but can compensate for a bad start of life by further increasing growth rate. While this compensatory growth is widespread, its direct fitness consequences are seldom investigated and its genetic basis is unknown. We investigated the genetic regulation, as well as fitness and lifespan consequences of compensatory growth in response to temperature, using C. elegans knockout of the thermo-sensitive TRP ion channel TRPA-1, involved in temperature...

VCF-file for: The effects of GC-biased gene conversion on patterns of genetic diversity among and across butterfly genomes

Niclas Backström
Recombination reshuffles the alleles of a population through crossover and gene conversion. These mechanisms have considerable consequences on the evolution and maintenance of genetic diversity. Crossover, for example, can increase genetic diversity by breaking the linkage between selected and nearby neutral variants. Bias in favor of G or C alleles during gene conversion may instead promote the fixation of one allele over the other, thus decreasing diversity. Mutation bias from G or C to A...

Rapid evolution of sexual size dimorphism facilitated by Y-linked genetic variance data set

Philipp Kaufmann & Elina Immonen
The three datasets were collected to study the genetic architecture of sexual size dimorphism in the seed beetle Callosobruchus maculatus (Quantitative_genetics_data_set), the response of sexual dimorphism to artificial selection (artificial_selection_data_set) and to isolate and quantify the effect of Y haplotypes on male body size (Y_introgression_data_set). Quantitative genetics: A four generation breeding design with pedigree information for 8022 individuals and body size measurements for 7356 individuals. The breeding design and sample size of the study allows...

Mullerian mimicry and the colouration patterns of sympatric coral snakes

Renan Bosque, Chaz Hyseni, Maria Luiza Gonçalves Santos, Eduardo Rangel, Camila Juliana Da Silva Dias, Jacob Hearin, , Fabricius Maia, Guarino Colli & Brice Noonan
This dataset cointains data used for the study of Müllerian mimicry in coral snakes. Coral snakes in the genus Micrurus are venomous, aposematic organisms that signal danger to predators through vivid colouration. Previous studies found that they serve as models to several harmless species of Batesian mimics. However, the extent to which Micrurus species engage in Müllerian mimicry remains poorly understood. We integrate detailed morphological and geographical distribution data to investigate if coral snakes are...

ITS and nrLSU DNA sequence data from four species of Coreomyces (Laboulbeniomycetes)

Henrik Sundberg, Åsa Kruys, Johannes Bergsten & Stefan Ekman
The genus Coreomyces (Laboulbeniaceae, Laboulbeniomycetes, Ascomycota) includes minute parasites on water boatmen (Corixidae, Hemiptera, Insecta). This taxonomic study is primarily based on freshly sampled corixids infected by Coreomyces from Sweden, although a few samples from Denmark and Turkey were also included. All records were verified using DNA sequence data from the internal transcribed spacer region and large subunit of the nuclear ribosomal DNA repeat region. We recognise four species, two of which are new to...

Size-mediated priority effects are trait-dependent and consistent across latitudes in a damselfly

Mateusz Raczyński, Robby Stoks, Frank Johansson & Szymon Sniegula
Variation in hatching time (phenology) might cause size differences within populations resulting in size-mediated priority effects (SMPEs) shaping intraspecific interactions. These phenology-driven effects potentially can be strengthened by seasonal time constraints caused by a short growth season, and depend on latitude. Here the single and combined effects of phenology and latitude-associated time constraints on SMPEs in larvae of an aquatic insect, the damselfly Lestes sponsa, are studied. We did so by rearing larvae in groups...

Unexpected cryptic species among streptophyte algae most distant to land plants

Iker Irisarri, Tatyana Darienko, Thomas Pröschold, Janine M. R. Fürst-Jansen, Mahwash Jamy & Jan De Vries
Streptophytes are one of the major groups of the green lineage (Chloroplastida or Viridiplantae). During one-billion-years of evolution, streptophytes have radiated into an astounding diversity of uni- and multicellular green algae as well as land plants. Most divergent from land plants is a clade formed by Mesostigmatophyceae, Spirotaenia spp., and Chlorokybophyceae. All three lineages are species-poor and the Chlorokybophyceae consist of a single described species, Chlorokybus atmophyticus. In this study, we used phylogenomic analyses to...

Data from: Spring and autumn phenology in an understorey herb are uncorrelated and driven by different factors

Elsa Fogelström, Giulia Zacchello, Daniela Guasconi, Johan Petter Dahlgren & Johan Ehrlén
Premise: Climate warming has altered the start and end of growing seasons in temperate regions. Ultimately, these changes occur at the individual level, but little is known about how previous seasonal life history events, temperature, and plant resource state simultaneously influence the spring and autumn phenology of plant individuals. Methods: We studied the relationships between the timing of leaf-out and shoot senescence over three years in a natural population of the long-lived understory herb Lathyrus...

Links between boreal forest management, soil fungal communities and belowground carbon sequestration

Karolina Jörgensen, Gustaf Granath, Joachim Strengbom & Björn Lindahl
Forest management has a potential to alter belowground carbon storage. However, the underlying mechanisms, and the relative importance of carbon input and decomposition in regulation of soil carbon dynamics are poorly understood. We examined whether interactive effects of forest fertilization and thinning on carbon stocks in the topsoil of boreal forests were linked to changes in fungal community composition, biomass, and enzyme activities, in a long-term fertilization and thinning experiment distributed across 29 Pinus sylvestris...

Selection in males purges the mutation load on female fitness

Karl Grieshop, Paul Maurizio, Göran Arnqvist & David Berger
Theory predicts that the ability of selection and recombination to purge mutation load is enhanced if selection against deleterious genetic variants operates more strongly in males than females. However, direct empirical support for this tenet is limited, in part because traditional quantitative genetic approaches allow dominance and intermediate-frequency polymorphisms to obscure the effects of the many rare and partially recessive deleterious alleles that make up the main part of a population’s mutation load. Here, we...

Phylogenomic insights into the origin of primary plastids

Iker Irisarri, Jürgen FH Strassert & Fabien Burki
The origin of plastids was a major evolutionary event that paved the way for an astonishing diversification of photosynthetic eukaryotes. Plastids originated by endosymbiosis between a heterotrophic eukaryotic host and cyanobacteria, presumably in a common ancestor of the primary photosynthetic eukaryotes (Archaeplastida). A single origin of primary plastids is well supported by plastid evidence but not by nuclear phylogenomic analyses, which have consistently failed to recover the monophyly of Archaeplastida hosts. Importantly, plastid monophyly and...

Marasmius oreades genome assembly v2: Linkage map & repeat library

Markus Hiltunen, Sandra Lorena Ament-Velásquez, Martin Ryberg & Hanna Johannesson
The fairy-ring mushroom Marasmius oreades can be used as a natural model system for mutation accumulation studies. During this project we constructed a genetic linkage map and used it for re-assembly of the M. oreades genome sequence. Genes and repeats were predicted in the genome, and a custom library of repetitive sequences was manually compiled and curated. In this repository we provide the linkage map and repeat library of the species.

The mating system affects the temperature sensitivity of male and female fertility

Julian Baur, Dorian Jagusch, Piotr Michalak, Mareike Koppik & David Berger
1. To mitigate effects of climate change it is important to understand species’ responses to increasing temperatures. This has often been done by studying survival or activity at temperature extremes. Before such extremes are reached, however, effects on fertility may already be apparent. 2. Sex differences in the thermal sensitivity of fertility (TSF) could impact species persistence under climate warming because female fertility is typically more limiting to population growth than male fertility. However, little...

Registration Year

  • 2021

Resource Types

  • Dataset


  • Uppsala University
  • Sun Yat-sen University
  • Capital Medical University
  • Shandong University
  • Shandong University of Technology
  • Northeast Normal University
  • Northeast Forestry University
  • Anhui Agricultural University
  • Zhongshan Hospital
  • Jining Medical University