58 Works

Data from: Frequency of virus-resistant hosts determines experimental community dynamics

Sebastian Coloma, Ursula Gaedke, Kaarina Sivonen & Teppo Hiltunen
Parasites, such as bacterial viruses (phages), can have large effects on host populations both at the ecological and evolutionary levels. In the case of cyanobacteria, phages can reduce primary production and infected hosts release intracellular nutrients influencing planktonic food web structure, community dynamics and biogeochemical cycles. Cyanophages may be of great importance in aquatic food webs during large cyanobacterial blooms unless the host population becomes resistant to phage infection. The consequences on plankton community dynamics...

Data from: Stream diatoms exhibit weak niche conservation along global environmental and climatic gradients

Janne Soininen, Aurelien Jamoneau, Juliette Tison-Rosebery, Thibault Leboucher, Jianjun Wang, Mikolaj Kokocinski & Sophia I. Passy
Niche conservatism (NC) describes the scenario in which species retain similar characteristics or traits over time and space, and thus has potentially important implications for understanding their biogeographic distributions. Evidence consistent with NC includes similar niche properties across geographically distant regions. We investigated whether NC was evident in stream diatom morphospecies by modeling species responses to environmental and climatic variables in a set of calibration sites (from the US) and then evaluated the models with...

Data from: Return to work after ischemic stroke in young adults: a registry-based follow-up study

Karoliina Aarnio, Jorge Rodriguez-Pardo, Bob Siegerink, Juliane Hardt, Jenna Broman, Lauri Tulkki, Elena Haapaniemi, Markku Kaste, Turgut Tatlisumak & Jukka Putaala
Objective: We aimed to investigate the proportion of young patients not returning to work (NRTW) at one year after ischemic stroke (IS) and during follow-up, and clinical factors associated with NRTW. Methods: Patients from Helsinki Young Stroke Registry with an IS occurring in the years 1994-2007, who were at paid employment within one year before IS, and with National Institutes of Health Stroke Scale (NIHSS) score ≤15 points at hospital discharge, were included. Data on...

Data from: Frequency and distribution of 152 genetic disease variants in over 100,000 mixed breed and purebred dogs

Jonas Donner, Heidi Anderson, Stephen Davison, Angela M. Hughes, Julia Bouirmane, Johan Lindqvist, Katherine M. Lytle, Balasubramanian Ganesan, Claudia Ottka, Päivi Ruotanen, Maria Kaukonen, Oliver P. Forman, Neale Fretwell, Cynthia A. Cole & Hannes Lohi
Knowledge on the genetic epidemiology of disorders in the dog population has implications for both veterinary medicine and sustainable breeding. Limited data on frequencies of genetic disease variants across breeds exists, and the disease heritage of mixed breed dogs remains poorly explored to date. Advances in genetic screening technologies now enable comprehensive investigations of the canine disease heritage, and generate health-related big data that can be turned into action. We pursued population screening of genetic...

Data from: Environmental and genetic control of cold tolerance in the Glanville fritillary butterfly

Maaike A. De Jong & Marjo Saastamoinen
Thermal tolerance has a major effect on individual fitness and species distributions, and can be determined by genetic variation as well as phenotypic plasticity. We investigate the effects of developmental and adult thermal conditions on cold tolerance, measured as chill coma recovery (CCR) time, during the early and late adult stage in the Glanville fritillary butterfly. We also investigate the genetic basis of cold tolerance by associating CCR variation with polymorphisms in candidate genes that...

Data from: Positive cytoplasmic UCHL5 tumor expression in gastric cancer is linked to improved prognosis

Leena Arpalahti, Alli Laitinen, Jaana Hagström, Harri Mustonen, Arto Kokkola, Camilla Böckelman, Caj Haglund & Carina I. Holmberg
Gastric cancer is the second most common cause of cancer-related mortality worldwide. Accurate prediction of disease progression is difficult, and new biomarkers for clinical use are essential. Recently, we reported that the proteasome-associated deubiquitinating enzyme UCHL5/Uch37 is a new prognostic marker in both rectal cancer and pancreatic ductal adenocarcinoma. Here, we have assessed by immunohistochemistry UCHL5 tumor expression in gastric cancer. The study cohort comprised 650 patients, who underwent surgery in Helsinki University Hospital, Finland,...

Data from: Hierarchical Bayesian model reveals the distributional shifts of Arctic marine mammals

Jussi Mäkinen & Jarno Vanhatalo
Aim: Our aim involved developing a method to analyze spatiotemporal distributions of Arctic marine mammals (AMMs) using heterogeneous open source data, such as scientific papers and open repositories. Another aim was to quantitatively estimate the effects of environmental covariates on AMMs’ distributions and to analyze whether their distributions have shifted along with environmental changes. Location: Arctic shelf area. The Kara Sea. Methods: Our literature search focused on survey data regarding polar bears (Ursus maritimus), Atlantic...

Data from: Inference of genetic architecture from chromosome partitioning analyses is sensitive to genome variation, sample size, heritability and effect size distribution

Petri Kemppainen & Arild Husby
Genomewide association studies have contributed immensely to our understanding of the genetic basis of complex traits. One major conclusion arising from these studies is that most traits are controlled by many loci of small effect, confirming the infinitesimal model of quantitative genetics. A popular approach to test for polygenic architecture involves so‐called “chromosome partitioning” where phenotypic variance explained by each chromosome is regressed on the size of the chromosome. First developed for humans, this has...

Data from: Counting with DNA in metabarcoding studies: how should we convert sequence reads to dietary data?

Bruce E. Deagle, Austen C. Thomas, Julie C. McInnes, Laurence J. Clarke, Eero J. Vesterinen, Elizabeth L. Clare, Tyler R. Kartzinel & J. Paige Eveson
Advances in DNA sequencing technology have revolutionised the field of molecular analysis of trophic interactions and it is now possible to recover counts of food DNA sequences from a wide range of dietary samples. But what do these counts mean? To obtain an accurate estimate of a consumer’s diet should we work strictly with datasets summarising frequency of occurrence of different food taxa, or is it possible to use relative number of sequences? Both approaches...

Data from: Environmental disturbance alters the ecological impact of an invading shrimp

Ulrika Candolin, Elina Bertell & Jarkko Kallio
1. Alien species are altering ecosystems around the globe. To predict and manage their impacts, the underlying mechanisms need to be understood. This is challenging in ecosystems undergoing multiple disturbances as unexpected interactions can alter the impact of individual disturbances. Such interactions are likely to be common in disturbed ecosystems, but have so far received little attention. 2. We investigated whether interactions between an invading shrimp Palaemon elegans and another human-induced disturbance, the population growth...

Data from: Linkage disequilibrium clustering-based approach for association mapping with tightly linked genome-wide data

Zitong Li, Petri Kemppainen, Pasi Rastas & Juha Merilä
Genome-wide association studies (GWAS) aim to identify genetic markers strongly associated with quantitative traits by utilizing linkage disequilibrium (LD) between candidate genes and markers. However, because of LD between nearby genetic markers, the standard GWAS approaches typically detect a number of correlated SNPs covering long genomic regions, making corrections for multiple testing overly conservative. Additionally, the high dimensionality of modern GWAS data poses considerable challenges for GWAS procedures such as permutation tests, which are computationally...

Data from: Ecological conditions alter cooperative behaviour and its costs in a chemically defended sawfly

Carita Lindstedt, Antti Miettinen, Dalial Freitak, Tarmo Ketola, Andrés López-Sepulcre, Elina Mäntylä & Hannu Pakkanen
The evolution of cooperation and social behaviour is often studied in isolation from the ecology of organisms. Yet, the selective environment under which individuals evolve is much more complex in nature, consisting of ecological and abiotic interactions in addition to social ones. Here we measured the life-history costs of cooperative chemical defence in a gregarious social herbivore, Diprion pini pine sawfly larvae, and how these costs vary under different ecological conditions. We ran a rearing...

Data from: Impacts of urbanization on insect herbivory and plant defences in oak trees

Xoaquín Moreira, Luis Abdala-Roberts, Jorge Berny Mier C. Y Terán, Felisa Covelo, Raúl De La Mata, Marta Francisco, Bess Hardwick, Ricardo M. Pires, Tomas Roslin, Dmitry S. Schigel, Jan P.J.G. Ten Hoopen, Bart G.H. Timmermans, Laura J.A. Van Dijk, Bastien Castagneyrol, Ayco J.M. Tack, Jorge C. Berny Mier Y Teran, Laura J. A. Van Dijk & Ayco J. M. Tack
Systematic comparisons of species interactions in urban vs. rural environments can improve our understanding of shifts in ecological processes due to urbanization. However, such studies are relatively uncommon and the mechanisms driving urbanization effects on species interactions (e.g., between plants and insect herbivores) remain elusive. Here we investigated the effects of urbanization on leaf herbivory by insect chewers and miners associated with the English oak (Quercus robur) by sampling trees in rural and urban areas...

Data from: Rapid sex-specific evolution of age at maturity is shaped by genetic architecture in Atlantic salmon

Yann Czorlich, Tutku Aykanat, Jaakko Erkinaro, Panu Orell & Craig R. Primmer
Understanding the mechanisms by which populations adapt to their environments is a fundamental aim in biology. However, it remains challenging to identify the genetic basis of traits, provide evidence of genetic changes and quantify phenotypic responses. Age at maturity in Atlantic salmon represents an ideal trait to study contemporary adaptive evolution as it has been associated with a single locus in the vgll3 region, and has also strongly changed in recent decades. Here, we provide...

Data from: Table for five, please: dietary partitioning in boreal bats

Eero J. Vesterinen, Anna I. E. Puisto, Anna S. Blomberg & Thomas M. Lilley
Differences in diet can explain resource partitioning in apparently similar, sympatric species. Here, we analyzed 1,252 fecal droppings from five species (Eptesicus nilssonii, Myotis brandtii, M. daubentonii, M. mystacinus, and Plecotus auritus) to reveal their dietary niches using fecal DNA metabarcoding. We identified nearly 550 prey species in 13 arthropod orders. Two main orders (Diptera and Lepidoptera) formed the majority of the diet for all species, constituting roughly 80%–90% of the diet. All five species...

Data from: Inferences of genetic architecture of bill morphology in house sparrow using a high‐density SNP array point to a polygenic basis

Sarah L. Lundregan, Ingerid J. Hagen, Jostein Gohli, Alina K. Niskanen, Petri Kemppainen, Thor Harald Ringsby, Thomas Kvalnes, Henrik Pärn, Bernt Rønning, Håkon Holand, Peter S. Ranke, Anna S. Båtnes, Linn-Karina Selvik, Sigbjorn Lien, Bernt-Erik Sæther, Arild Husby, Henrik Jensen & Bernt-Erik Saether
Understanding the genetic architecture of quantitative traits can provide insights into the mechanisms driving phenotypic evolution. Bill morphology is an ecologically important and phenotypically variable trait, which is highly heritable and closely linked to individual fitness. Thus, bill morphology traits are suitable candidates for gene mapping analyses. Previous studies have revealed several genes that may influence bill morphology, but the similarity of gene and allele effects between species and populations is unknown. Here, we develop...

Data from: Quantifying in situ phenotypic variability in the hydraulic properties of four tree species across their distribution range in Europe

Sylvain Delzon, N. González-Muñoz, J. M. Torres-Ruiz, G. Capdeville, F. Sterck, P. Copini, G. Petit, G. Von Arx, A. Lintunen, L. Grönlund, T. Hölttä, M. C. Caldeira, R. Lobo-Do-Vale & M. Peltoniemi
Many studies have reported that hydraulic properties vary considerably between tree species, but little is known about their intraspecific variation and, therefore, their capacity to adapt to a warmer and drier climate. Here, we quantify phenotypic divergence and clinal variation for embolism resistance, hydraulic conductivity and branch growth, in four tree species, two angiosperms (Betula pendula, Populus tremula) and two conifers (Picea abies, Pinus sylvestris), across their latitudinal distribution in Europe. Growth and hydraulic efficiency...

Data from: Give me a sample of air and I will tell which species are found from your region – molecular identification of fungi from airborne spore samples

Nerea Abrego, Veera Norros, Panu Halme, Panu Somervuo, Heini Ali-Kovero & Otso Ovaskainen
Fungi are a megadiverse group of organisms, they play major roles in ecosystem functioning, and are important for human health, food production, and nature conservation. Our knowledge on fungal diversity and fungal ecology is however still very limited, in part because surveying and identifying fungi is time demanding and requires expert knowledge. We present a method that allows anyone to generate a list of fungal species likely to occur in a region of interest, with...

Data from: Association mapping reveals candidate loci for resistance and anemic response to an emerging temperature-driven parasitic disease in a wild salmonid fish

Freed Ahmad, Paul Debes, Gemma Palomar & Anti Vasemägi
Even though parasitic infections are often costly or deadly for the host, we know very little which genes influence parasite susceptibility and disease severity. Proliferative kidney disease (PKD) is an emerging and, at elevated water temperatures, potentially deadly disease of salmonid fishes that is caused by the myxozoan parasite Tetracapsuloides bryosalmonae. By screening > 7.6 K SNPs in 255 wild brown trout (Salmo trutta) and combining association mapping and random forest approaches, we identified several...

Data from: Ecology determines how low antibiotic concentration impacts community composition and horizontal transfer of resistance genes

Johannes Cairns, Lasse Ruokolainen, Jenni Hultman, Manu Tamminen, Marko Virta & Teppo Hiltunen
Low concentrations of antibiotics have numerous effects on bacteria. However, it is unknown whether ecological factors such as trophic interactions and spatial structuring influence the effects of low concentrations of antibiotics on multispecies microbial communities. Here, we address this question by investigating the effects of low antibiotic concentration on community composition and horizontal transfer of an antibiotic resistance plasmid in a 62-strain bacterial community in response to manipulation of the spatial environment and presence of...

Data from: A plant pathogen modulates the effects of secondary metabolites on the performance and immune function of an insect herbivore

Elena Rosa, Luisa Woestmann, Arjen Biere & Marjo Saastamoinen
Host plant chemical composition critically shapes the performance of insect herbivores feeding on them. Some insects have become specialized on plant secondary metabolites, and even use them to their own advantage such as defense against predators. However, infection by plant pathogens can seriously alter the interaction between herbivores and their host plants. We tested whether the effects of the plant secondary metabolites, iridoid glycosides (IGs), on the performance and immune response of an insect herbivore...

Data from: Platichthys solemdali sp. nov. (Actinopterygii, Pleuronectiformes): a new flounder species from the Baltic Sea

Paolo Momigliano, Gaël P.J. Denys, Henri Jokinen & Juha Merilä
The European flounders Platichthys flesus (Linnaeus, 1758) displays two contrasting reproductive behaviors in the Baltic Sea: offshore spawning of pelagic eggs and coastal spawning of demersal eggs, a behavior observed exclusively in the Baltic Sea. Previous studies showed marked differences in behavioral, physiological, and life-history traits of flounders with pelagic and demersal eggs. Furthermore, a recent study demonstrated that flounders with pelagic and demersal eggs represent two reproductively isolated, parapatric species arising from two distinct...

Data from: High resistance towards herbivore-induced habitat change in a high arctic arthropod community

Niels M. Schmidt, Jesper B. Mosbacher, Bernhard Eitzinger, Eero J. Vesterinen & Tomas Roslin
Mammal herbivores may exert strong impacts on plant communities, and are often key drivers of vegetation composition and diversity. We tested whether such mammal-induced changes to a high Arctic plant community are reflected in the structure of other trophic levels. Specifically, we tested whether substantial vegetation changes following the experimental exclusion of muskoxen (Ovibos moschatus) altered the composition of the arthropod community and the predator-prey interactions therein. Overall, we found no impact of muskox-exclusion on...

Data from: Black Queen evolution and trophic interactions determine plasmid survival after the disruption of conjugation network

Johannes Cairns, Katariina Koskinen, Reetta Penttinen, Tommi Patinen, Anna Hartikainen, Roosa Jokela, Liisa Ruusulehto, Sirja Viitamäki, Sari Mattila, Teppo Hiltunen & Matti Jalasvuori
Mobile genetic elements such as conjugative plasmids are responsible for antibiotic resistant phenotypes in many bacterial pathogens. The ability to conjugate, the presence of antibiotics and ecological interactions all have a notable role in the persistence of plasmids in bacterial populations. Here, we set out to investigate the contribution of these factors when the conjugation network was disturbed by a plasmid-dependent bacteriophage. Phage alone effectively caused the population to lose plasmids, thus rendering them susceptible...

Data from: Silk properties and overwinter survival in gregarious butterfly larvae

Anne Duplouy, Guillaume Minard, Meri Lähteenaro, Susu Rytteri & Marjo Saastamoinen
All organisms are challenged by encounters with parasites, which strongly select for efficient escape strategies in the host. The threat is especially high for gregarious species entering immobile periods, such as diapause. Larvae of the Glanville fritillary butterfly, Melitaea cinxia, spend the winter in diapause in groups of conspecifics each sheltered in a silk-nest. Despite intensive monitoring of the population, we have little understanding of the ecological factors influencing larval survival over the winter in...

Registration Year

  • 2018
    58

Resource Types

  • Dataset
    58

Affiliations

  • University of Helsinki
    58
  • University of Turku
    10
  • Natural Resources Institute Finland
    5
  • Swedish University of Agricultural Sciences
    5
  • University of Oulu
    4
  • Uppsala University
    4
  • Aarhus University
    3
  • University of Cambridge
    2
  • Helsinki University Central Hospital
    2
  • Chinese Academy of Sciences
    2