59 Works

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: 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: Auxotrophy and intra-population complementary in the 'interactome' of a cultivated freshwater model community

Sarahi L. Garcia, Moritz Buck, Katherine D. McMahon, Hans-Peter Grossart, Alexander Eiler & Falk Warnecke
Microorganisms are usually studied either in highly complex natural communities or in isolation as monoclonal model populations that we manage to grow in the laboratory. Here, we uncover the biology of some of the most common and yet-uncultured bacteria in freshwater environments using a mixed culture from Lake Grosse Fuchskuhle. From a single shotgun metagenome of a freshwater mixed culture of low complexity, we recovered four high-quality metagenome-assembled genomes (MAGs) for metabolic reconstruction. This analysis...

Data from: A multi-breed genome-wide association analysis for canine hypothyroidism identifies a shared major risk locus on CFA12

Matteo Bianchi, Stina Dahlgren, Jonathan Massey, Elisabeth Dietschi, Marcin Kierczak, Martine Lund-Ziener, Katarina Sundberg, Stein Istre Thoresen, Olle Kämpe, Göran Andersson, William E. R. Ollier, Åke Hedhammar, Tosso Leeb, Kerstin Lindblad-Toh, Lorna J. Kennedy, Frode Lingaas, Gerli Rosengren Pielberg & Stein Istre Thoresen
Bianchi, Dahlgren et al., Canine Hypothyroidism data

Data from: A prezygotic transmission distorter acting equally in female and male zebra finches Taeniopygia guttata

Ulrich Knief, Holger Schielzeth, Hans Ellegren, Bart Kempenaers & Wolfgang Forstmeier
The two parental alleles at a specific locus are usually inherited with equal probability to the offspring. However, at least three processes can lead to an apparent departure from fair segregation: early viability selection, biased gene conversion and various kinds of segregation distortion. Here, we conduct a genome-wide scan for transmission distortion in a captive population of zebra finches (Taeniopygia guttata) using 1302 single-nucleotide polymorphisms (SNPs) followed by confirmatory analyses on independent samples from the...

Data from: Geographic and temporal dynamics of a global radiation and diversification in the killer whale

Phillip A. Morin, Kim M. Parsons, Frederick I. Archer, María C. Ávila-Arcos, Lance G. Barrett-Lennard, Luciano Dalla Rosa, Sebastián Duchêne, John W. Durban, Graeme M. Ellis, Steven H. Ferguson, John K. Ford, Michael J. Ford, Cristina Gabrilao, M. Thomas P. Gilbert, Kristin Kaschner, Craig O. Matkin, Stephen D. Petersen, Kelly M. Robertson, Ingrid N. Visser, Paul R. Wade, Simon Y. W. Ho & Andrew D. Foote
Global climate change during the Late Pleistocene periodically encroached and then released habitat during the glacial cycles, causing range expansions and contractions in some species. These dynamics have played a major role in geographic radiations, diversification and speciation. We investigate these dynamics in the most widely distributed of marine mammals, the killer whale (Orcinus orca), using a global data set of over 450 samples. This marine top predator inhabits coastal and pelagic ecosystems ranging from...

Data from: Initiation and spread of escape waves within animal groups

James E. Herbert-Read, Jerome Buhl, Feng Hu, Ashley J. W. Ward, David J. T. Sumpter, J. E. Herbert-Read, D. J. T. Sumpter, J. Buhl, A. J. W. Ward & F. Hu
The exceptional reactivity of animal collectives to predatory attacks is thought to be owing to rapid, but local, transfer of information between group members. These groups turn together in unison and produce escape waves. However, it is not clear how escape waves are created from local interactions, nor is it understood how these patterns are shaped by natural selection. By startling schools of fish with a simulated attack in an experimental arena, we demonstrate that...

Data from: Disruption of memory reconsolidation erases a fear memory trace in the human amygdala: An 18-month follow-up

Johannes Björkstrand, Thomas Agren, Andreas Frick, Jonas Engman, Elna-Marie Larsson, Tomas Furmark & Mats Fredrikson
Fear memories can be attenuated by reactivation followed by disrupted reconsolidation. Using functional magnetic resonance imaging we recently showed that reactivation and reconsolidation of a conditioned fear memory trace in the basolateral amygdala predicts subsequent fear expression over two days, while reactivation followed by disrupted reconsolidation abolishes the memory trace and suppresses fear. In this follow-up study we demonstrate that the behavioral effect persists over 18 months reflected in superior reacquisition after undisrupted, as compared...

Data from: The evolution of sex chromosomes in organisms with separate haploid sexes

Simone Immler & Sarah Perin Otto
The evolution of dimorphic sex chromosomes is driven largely by the evolution of reduced recombination and the subsequent accumulation of deleterious mutations. While these processes are increasingly well understood in diploid organisms, the evolution of dimorphic sex chromosomes in haploid organisms (U/V) has been virtually unstudied theoretically. We analyze a model to investigate the evolution of linkage between fitness loci and the sex-determining region in U/V species. In a second step, we test how prone...

Data from: Into and out of the tropics: global diversification patterns in a hyper-diverse clade of ectomycorrhizal fungi

Brian P. Looney, Martin Ryberg, Felix Hampe, Marisol Sánchez-García & P. Brandon Matheny
Ectomycorrhizal (ECM) fungi, symbiotic mutualists of many dominant tree and shrub species, exhibit a biogeographic pattern counter to the established latitudinal diversity gradient of most macroflora and fauna. However, an evolutionary basis for this pattern has not been explicitly tested in a diverse lineage. In this study, we reconstructed a mega-phylogeny of a cosmopolitan and hyper-diverse genus of ECM fungi, Russula, sampling from annotated collections and utilizing publically available sequences deposited in GenBank. Metadata from...

Data from: Transcriptomics of colour patterning and colouration shifts in crows

Jelmer W. Poelstra, Nagarjun Vijay, Marc P. Höppner, Jochen B. W. Wolf, M. P. Hoeppner, J. B. W. Wolf, J. W. Poelstra & N. Vijay
Animal coloration is one of the most conspicuous phenotypic traits in natural populations and has important implications for adaptation and speciation. Changes in coloration can occur over surprisingly short evolutionary timescales, while recurrence of similar colour patterns across large phylogenetic distances is also common. Even though the genetic basis of pigment production is well understood, little is known about the mechanisms regulating colour patterning. In this study, we shed light on the molecular elements regulating...

Data from: Looking into the past – the reaction of three grouse species to climate change over the last million years using whole genome sequences

Radoslav Kozma, Páll Melsted, Kristinn P. Magnússon & Jacob Höglund
Tracking past population fluctuations can give insight into current levels of genetic variation present within species. Analysing population dynamics over larger time scales can be aligned to known climatic changes to determine the response of species to varying environments. Here, we applied the Pairwise Sequentially Markovian Coalescent (PSMC) model to infer past population dynamics of three widespread grouse species; black grouse, willow grouse and rock ptarmigan. This allowed the tracking of the effective population size...

Data from: Phenotypic variability in unicellular organisms: from calcium signaling to social behavior

David Vogel, Stamatios C. Nicolis, Alfonso Perez-Escudero, Vidyanand Nanjundiah, David J. T. Sumpter & Audrey Dussutour
Historically, research has focused on the mean and often neglected the variance. However, variability in nature is observable at all scales: among cells within an individual, among individuals within a population and among populations within a species. A fundamental quest in biology now is to find the mechanisms that underlie variability. Here, we investigated behavioural variability in a unique unicellular organism, Physarum polycephalum. We combined experiments and models to show that variability in cell signalling...

Data from: The nature of nurture in a wild mammal’s fitness

S. Eryn McFarlane, Jamieson C. Gorrell, David W. Coltman, Murray M. Humphries, Stan Boutin, Andrew G. McAdam, M. M. Humphries, A. G. McAdam, S. Boutin, D. W. Coltman, J. C. Gorrell & S. E. McFarlane
Genetic variation in fitness is required for the adaptive evolution of any trait but natural selection is thought to erode genetic variance in fitness. This paradox has motivated the search for mechanisms that might maintain a population's adaptive potential. Mothers make many contributions to the attributes of their developing offspring and these maternal effects can influence responses to natural selection if maternal effects are themselves heritable. Maternal genetic effects (MGEs) on fitness might, therefore, represent...

Data from: Effects of mating order and male size on embryo survival in a pipefish

Ines Braga Goncalves, Kenyon B. Mobley, Ingrid Ahnesjö, Gry Sagebakken, Adam G. Jones, Charlotta Kvarnemo & Ines Braga Goncalves
In species that provide parental care, individuals should invest adaptively in their offspring in relation to the pre- and post-zygotic care provided by their partners. In the broad-nosed pipefish, Syngnathus typhle L., females transfer large, nutrient-rich eggs into the male brood pouch during mating. The male broods and nourishes the embryos for several weeks before independent juveniles emerge at parturition. Given a choice, females clearly prefer large partners. Yet, females provide protein-richer eggs when the...

Data from: Within species support for the expensive tissue hypothesis: a negative association between brain size and visceral fat storage in females of the Pacific seaweed pipefish

Masahito Tsuboi, Jun Shoji, Atsushi Sogabe, Ingrid Ahnesjö & Niclas Kolm
The brain is one of the most energetically expensive organs in the vertebrate body. Consequently, the high cost of brain development and maintenance is predicted to constrain adaptive brain size evolution (the expensive tissue hypothesis, ETH). Here, we test the ETH in a teleost fish with predominant female mating competition (reversed sex roles) and male pregnancy, the pacific seaweed pipefish Syngnathus schlegeli. The relative size of the brain and other energetically expensive organs (kidney, liver,...

Data from: The evolutionary puzzle of egg size, oxygenation and parental care in aquatic environments

Ines Braga Goncalves, Ingrid Ahnesjö & Charlotta Kvarnemo
Offspring fitness generally improves with increasing egg size. Yet, eggs of most aquatic organisms are small. A common but largely untested assumption is that larger embryos require more oxygen than they can acquire through diffusion via the egg surface, constraining egg size evolution. However, we found no detrimental effects of large egg size on embryo growth and survival under hypoxic conditions. We tested this in the broad-nosed pipefish, Syngnathus typhle, whose males provide extensive care...

Data from: Female Salix viminalis are more severely infected by Melampsora spp. but neither sex experiences associational effects

Kim K. Moritz, Christer Björkman, Amy L. Parachnowitsch & Johan A. Stenberg
Associational effects of plant genotype or species on plant biotic interactions are common, not least for disease spread, but associational effects of plant sex on interactions have largely been ignored. Sex in dioecious plants can affect biotic interactions with herbivores and pollinators; however, its effects on plant–pathogen interactions are understudied and associational effects are unknown. In a replicated field experiment, we assessed Melampsora spp. leaf rust infection in monosexual and mixed sex plots of dioecious...

Data from: Non-linear costs of reproduction in a long-lived plant

Nina Sletvold & Jon Ågren
A trade-off between current reproduction and future performance is a key component of life-history theory, but the shape of this trade-off for any specific fitness component remains elusive. We induced 3-5 levels of reproductive effort (RE) by manipulating fruit set of a long-lived orchid in two populations that differed in the length of the growing season and local climate, and examined survival, size and fecundity the following year. Natural fruit set was 72% higher in...

Data from: The alignment between phenotypic plasticity, the major axis of genetic variation and the response to selection

Martin I. Lind, Kylie Yarlett, Julia Reger, Mauricio J. Carter & Andrew P. Beckerman
Phenotypic plasticity is the ability of a genotype to produce more than one phenotype in order to match the environment. Recent theory proposes that the major axis of genetic variation in a phenotypically plastic population can align with the direction of selection. Therefore, theory predicts that plasticity directly aids adaptation by increasing genetic variation in the direction favoured by selection and reflected in plasticity. We evaluated this theory in the freshwater crustacean Daphnia pulex, facing...

Data from: Emotion reactivity is increased 4-6 weeks postpartum in healthy women: a longitudinal fMRI study

Malin Gingnell, Elin Bannbers, Harmen Moes, Jonas Engman, Sara Sylvén, Alkistis Skalkidou, Kristiina Kask, Johan Wikström & Inger Sundström-Poromaa
Marked endocrine alterations occur after delivery. Most women cope well with these changes, but the postpartum period is associated with an increased risk of depressive episodes. Previous studies of emotion processing have focused on maternal–infant bonding or postpartum depression (PPD), and longitudinal studies of the neural correlates of emotion processing throughout the postpartum period in healthy women are lacking. In this study, 13 women, without signs of post partum depression, underwent fMRI with an emotional...

Data from: Himalayan Cambrian brachiopods

Leonid E. Popov, Lars E. Holmer, Nigel C. Hughes, Mansoureh Ghabadi Pour, Paul M. Myrow & Mansoureh Ghobadi Pour
A synoptic analysis of previously published material and new finds reveals that Himalayan Cambrian brachiopods can be referred to 18 genera, of which 17 are considered herein. These contain 20 taxa assigned to species, of which five are new: Eohadrotreta haydeni, Aphelotreta khemangarensis, Hadrotreta timchristiorum, Prototreta? sumnaensis and Amictocracens? brocki. Well-preserved topotype material from the classic Parahio Valley section is described for three species that have not previously been illustrated photographically. A biostratigraphical scheme based...

Data from: Genetic differentiation of western capercaillie in the Carpathian Mountains reveal the importance of post glacial expansions and habitat connectivity in understanding the present day European distribution

Peter Klinga, Martin Mikoláš, Petar Zhelev, Jacob Höglund & Ladislav Paule
Population structure and barriers to gene flow are important components for understanding the evolutionary history of a species. Here we study population structure and differentiation in the western capercaillie (Aves: Phasianidae) along the Carpathian Mountains. Further, we compared the levels of population differentiation among capercaillie from the Carpathian Mountains, Balkans (Bulgaria) and the boreal forest (Russia and Sweden) in order to reveal past and current processes which may influence population structure. Tissue samples, non-invasive faeces...

Registration Year

  • 2015
    59

Resource Types

  • Dataset
    59

Affiliations

  • Uppsala University
    59
  • Swedish University of Agricultural Sciences
    6
  • French National Centre for Scientific Research
    4
  • University of Tennessee at Knoxville
    3
  • University of Zurich
    3
  • Bielefeld University
    3
  • University of Bern
    3
  • University of Copenhagen
    3
  • University of Sheffield
    3
  • Ghent University
    2
  • University of Alberta
    2
  • University of Lausanne
    2
  • University of Gothenburg
    2
  • University of Oslo
    2
  • University of Manchester
    2