53 Works

Data from: A linkage map and QTL analysis for pyrethroid resistance in the bed bug Cimex lectularius

Toby Fountain, Mark Ravinet, Richard Naylor, Klaus Reinhardt & Roger K. Butlin
The rapid evolution of insecticide resistance remains one of the biggest challenges in the control of medically and economically important pests. Insects have evolved a diverse range of mechanisms to reduce the efficacy of the commonly used classes of insecticides and finding the genetic basis of resistance is a major aid to management. In a previously unstudied population, we performed an F2 resistance mapping cross for the common bed bug, Cimex lectularius, for which insecticide...

Data from: Altered trait variability in response to size-selective mortality

Silva Uusi-Heikkilä, Kai Lindström, Noora Parre, Robert Arlinghaus, Josep Alós & Anna Kuparinen
Changes in trait variability owing to size-selective harvesting have received little attention in comparison with changes in mean trait values, perhaps because of the expectation that phenotypic variability should generally be eroded by directional selection typical for fishing and hunting. We show, however, that directional selection, in particular for large body size, leads to increased body-size variation in experimentally harvested zebrafish (Danio rerio) populations exposed to two alternative feeding environments: ad libitum and temporarily restricted...

Data from: Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis

Marcin J. Skwark, Nicholas J. Croucher, Santeri Puranen, Claire Chewapreecha, Maiju Pesonen, Ying Ying Xu, Paul Turner, Simon R. Harris, Stephen B. Beres, James M. Musser, Julian Parkhill, Stephen D. Bentley, Erik Aurell & Jukka Corander
Recent advances in the scale and diversity of population genomic datasets for bacteria now provide the potential for genome-wide patterns of co-evolution to be studied at the resolution of individual bases. Here we describe a new statistical method, genomeDCA, which uses recent advances in computational structural biology to identify the polymorphic loci under the strongest co-evolutionary pressures. We apply genomeDCA to two large population data sets representing the major human pathogens Streptococcus pneumoniae (pneumococcus) and...

Data from: Quantifying uncertainty of taxonomic placement in DNA barcoding and metabarcoding

Panu Somervuo, Douglas W. Yu, Charles C.Y. Xu, YinQiu Ji, Jenni Hultman, Helena Wirta & Otso Ovaskainen
A crucial step in the use of DNA markers for biodiversity surveys is the assignment of Linnaean taxonomies (species, genus, etc.) to sequence reads. This allows the use of all the information known based on the taxonomic names. Taxonomic placement of DNA barcoding sequences is inherently probabilistic because DNA sequences contain errors, because there is natural variation among sequences within a species, and because reference data bases are incomplete and can have false annotations. However,...

Data from: Deciphering the genomic architecture of the stickleback brain with a novel multi-locus gene-mapping approach

Zitong Li, Baocheng Guo, Jing Yang, Gábor Herczeg, Abigél Gonda, Gergely Balázs, Takahito Shikano, Federico C.F. Calboli, Juha Merilä & Federico C. F. Calboli
Quantitative traits important to organismal function and fitness, such as brain size, are presumably controlled by many small-effect loci. Deciphering the genetic architecture of such traits with traditional quantitative trait locus (QTL) mapping methods is challenging. Here, we investigated the genetic architecture of brain size (and the size of five different brain parts) in nine-spined sticklebacks (Pungitius pungitius) with the aid of novel multi-locus QTL mapping approaches based on a de-biased LASSO method. Apart from...

Data from: Population genomic evidence for adaptive differentiation in the Baltic Sea herring

Baocheng Guo, Zitong Li & Juha Merilä
Detecting and estimating the degree of genetic differentiation among populations of highly mobile marine fish having pelagic larval stages is challenging because their effective population sizes can be large, and thus, little genetic drift and differentiation is expected in neutral genomic sites. However, genomic sites subject to directional selection stemming from variation in local environmental conditions can still show substantial genetic differentiation, yet these signatures can be hard to detect with low-throughput approaches. Using a...

Data from: Treating cattle with antibiotics affects greenhouse gas emissions, and microbiota in dung and dung beetles

Tobin J. Hammer, Noah Fierer, Bess Hardwick, Asko Simojoki, Eleanor Slade, Juhani Taponen, Heidi Viljanen & Tomas Roslin
Antibiotics are routinely used to improve livestock health and growth. However, this practice may have unintended environmental impacts mediated by interactions among the wide range of micro- and macroorganisms found in agroecosystems. For example, antibiotics may alter microbial emissions of greenhouse gases by affecting livestock gut microbiota. Furthermore, antibiotics may affect the microbiota of non-target animals that rely on dung, such as dung beetles, and the ecosystem services they provide. To examine these interactions, we...

Data from: Wolbachia increases the susceptibility of a parasitoid wasp to hyperparasitism

Saskya Van Nouhuys, Minna Kohonen & Anne Duplouy
The success of maternally transmitted endosymbiotic bacteria, such as Wolbachia, is directly linked to their host reproduction but in direct conflict with other parasites that kill the host before it reaches reproductive maturity. Therefore, symbionts that have evolved strategies to increase their host’s ability to evade lethal parasites may have high penetrance, while detrimental symbionts would be selected against, leading to lower penetrance or extinction from the host population. In a natural population of the...

Data from: Dung beetle species interactions and multifunctionality are affected by an experimentally warmed climate

Eleanor M. Slade & Tomas Roslin
While substantial effort has been invested in modelling changes in species distribution with climate change, less attention has been given to how climate warming will affect interactions among co-occurring species, and the cascading functional consequences. In this study, realistic dung beetle communities were subjected to an experimental warming treatment and the net effect on the functions of dung decomposition (in terms of dung mass) and plant productivity (in terms of biomass production of ryegrass grown...

Data from: Genomewide scan for adaptive differentiation along altitudinal gradient in the Andrew's toad Bufo andrewsi

Baocheng Guo, Di Lu, Wen Bo Liao & Juha Merilä
Recent studies of humans, dogs and rodents have started to discover the genetic underpinnings of high altitude adaptations, yet amphibians have received little attention in this respect. To identify possible signatures of adaptation to altitude, we performed a genome scan of 15 557 single nucleotide polymorphisms (SNPs) obtained with restriction site-associated DNA sequencing of pooled samples from 11 populations of Andrew's toad (Bufo andrewsi) from the edge of the Tibetan Plateau, spanning an altitudinal gradient...

Data from: Impact of male condition on his spermatophore and consequences for female reproductive performance in the Glanville fritillary butterfly

Anne Duplouy, Luisa Woestmann, Juan Gallego-Zamorano, Marjo Saastamoinen & Juan Gallego Zamorano
In butterflies, male reproductive success is highly related to the quality and the size of the spermatophore transferred to the female. The spermatophore is a capsule produced by the male during copulation, which in many species contains sperm in addition to a nuptial gift, and which is digested by the female after copulation. The nuptial gift may contribute to egg production and offspring quality, and in some cases also to female body maintenance. The production...

Data from: Genetic heterogeneity underlying variation in a locally adaptive clinal trait in Pinus sylvestris revealed by a Bayesian multipopulation analysis

Sonja T. Kujala, Timo Knürr, Katri Kärkkäinen, David B. Neale, Mikko J. Sillanpää & Outi Savolainen
Local adaptation is a common feature of plant and animal populations. Adaptive phenotypic traits are genetically differentiated along environmental gradients, but the genetic basis of such adaptation is still poorly known. Genetic association studies of local adaptation combine data over populations. Correcting for population structure in these studies can be problematic since both selection and neutral demographic events can create similar allele frequency differences between populations. Correcting for demography with traditional methods may lead to...

Data from: Sublethal streptomycin concentrations and lytic bacteriophage together promote resistance evolution

Johannes Cairns, Lutz Becks, Matti Jalasvuori & Teppo Hiltunen
Sub-minimum inhibiting concentrations (sub-MICs) of antibiotics frequently occur in natural environments owing to wide-spread antibiotic leakage by human action. Even though the concentrations are very low, these sub-MICs have recently been shown to alter bacterial populations by selecting for antibiotic resistance and increasing the rate of adaptive evolution. However, studies are lacking on how these effects reverberate into key ecological interactions, such as bacteria–phage interactions. Previously, co-selection of bacteria by phages and antibiotic concentrations exceeding...

Data from: Spatial and temporal genetic structure at the fourth trophic level in a fragmented landscape

Abhilash Nair, Toby Fountain, Suvi Ikonen, Sami P. Ojanen & Saskya Van Nouhuys
A fragmented habitat becomes increasingly fragmented for species at higher trophic levels, such as parasitoids. To persist, these species are expected to possess life-history traits, such as high dispersal, that facilitate their ability to use resources that become scarce in fragmented landscapes. If a specialized parasitoid disperses widely to take advantage of a sparse host, then the parasitoid population should have lower genetic structure than the host. We investigated the temporal and spatial genetic structure...

Data from: Primary production calculations for sea ice from bio-optical observations in the Baltic Sea

Susann Müller, Anssi V. Vähätalo, Jari Uusikivi, Markus Majaneva, Sanna Majaneva, Riitta Autio & Janne-Markus Rintala
Bio-optics is a powerful approach for estimating photosynthesis rates, but has seldom been applied to sea ice, where measuring photosynthesis is a challenge. We measured absorption coefficients of chromophoric dissolved organic matter (CDOM), algae, and non-algal particles along with solar radiation, albedo and transmittance at four sea-ice stations in the Gulf of Finland, Baltic Sea. This unique compilation of optical and biological data for Baltic Sea ice was used to build a radiative transfer model...

Data from: Grazed wet meadows are sink habitats for the southern dunlin (Calidris alpina schinzii) due to nest trampling by cattle

Veli-Matti Pakanen, Sami Aikio, Aappo Luukkonen & Kari Koivula
The effect of habitat management is commonly evaluated by measuring population growth, which does not distinguish changes in reproductive success from changes in survival or the effects of immigration or emigration. Management has rarely been evaluated considering complete life cycle of the target organisms, including also possible negative impacts from management. We evaluated the effectiveness of cattle grazing in the restoration of coastal meadows as a breeding habitat for small and medium-sized ground-nesting birds by...

Data from: Strong dispersal in a parasitoid wasp overwhelms habitat fragmentation and host population dynamics

Christelle Couchoux, Perttu Seppä & Saskya Van Nouhuys
The population dynamics of a parasite depend on species traits, host dynamics, and the environment. Those dynamics are reflected in the genetic structure of the population. Habitat fragmentation has a greater impact on parasites than on their hosts because resource distribution is increasingly fragmented for species at higher trophic levels. This could lead to either more or less genetic structure than the host, depending on the relative dispersal rates of species. We examined the spatial...

Data from: Sex allocation conflict between queens and workers in Formica pratensis wood ants predicts seasonal sex ratio variation

Heikki Helanterä, Jonna Kulmuni & Pekka Pamilo
Sex allocation theory predicts parents should adjust their investment in male and female offspring in a way that increases parental fitness. This has been shown in several species and selective contexts. Yet, seasonal sex ratio variation within species and its underlying causes are poorly understood. Here we study sex allocation variation in the wood ant Formica pratensis. This species displays conflict over colony sex ratio as workers and queens prefer different investment in male and...

Data from: Cross-frequency synchronization connects networks of fast and slow oscillations during visual working memory maintenance

Felix Siebenhühner, Sheng H. Wang, J. Matias Palva & Satu Palva
Neuronal activity in sensory and fronto-parietal (FP) areas underlies the representation and attentional control, respectively, of sensory information maintained in visual working memory (VWM). Within these regions, beta/gamma phase-synchronization supports the integration of sensory functions, while synchronization in theta/alpha bands supports the regulation of attentional functions. A key challenge is to understand which mechanisms integrate neuronal processing across these distinct frequencies and thereby the sensory and attentional functions. We investigated whether such integration could be...

Data from: What you need is what you eat? Prey selection by the bat Myotis daubentonii

Eero J. Vesterinen, Lasse Ruokolainen, Niklas Wahlberg, Carlos Peña, Tomas Roslin, Veronika N. Laine, Ville Vasko, Ilari E. Sääksjärvi, Kai Norrdahl & Thomas M. Lilley
Optimal foraging theory predicts that predators are selective when faced with abundant prey, but become less picky when prey gets sparse. Insectivorous bats in temperate regions are faced with the challenge of building up fat reserves vital for hibernation during a period of decreasing arthropod abundances. According to optimal foraging theory, prehibernating bats should adopt a less selective feeding behaviour – yet empirical studies have revealed many apparently generalized species to be composed of specialist...

Data from: Diagnosing depression in chronic pain patients: DSM-IV Major Depressive Disorder vs. Beck Depression Inventory (BDI)

Peter Knaster, Ann-Mari Estlander, Jaakko Kaprio, Hasse Karlsson & Eija Kalso
Background: Diagnosing depression in chronic pain is challenging due to overlapping somatic symptoms. In questionnaires, such as the Beck Depression Inventory (BDI), responses may be influenced more by pain than by the severity of depression. In addition, previous studies have suggested that symptoms of negative self-image, a key element in depression, are uncommon in chronic pain-related depression. The object of this study is to assess the relationship of the somatic and cognitive-emotional items of BDI...

Data from: The genetic contribution to sex determination and number of sex chromosomes vary among populations of common frogs (Rana temporaria)

Nicolas Rodrigues, Yvan Vuille, Alan Brelsford, Juha Merilä & Nicolas Perrin
The patterns of sex determination and sex differentiation have been shown to differ among geographic populations of common frogs. Notably, the association between phenotypic sex and linkage group 2 (LG2) has been found to be perfect in a northern Swedish population, but weak and variable among families in a southern one. By analyzing these populations with markers from other linkage groups, we bring two new insights: (1) the variance in phenotypic sex not accounted for...

Data from: Controlling for p-value inflation in allele frequency change in experimental evolution and artificial selection experiments

Petri Kemppainen, Bernt Rønning, Thomas Kvalnes, Ingerid J. Hagen, Thor Harald Ringsby, Anna M. Billing, Henrik Pärn, Sigbjorn Lien, Arild Husby, Bernt-Erik Sæther, Henrik Jensen & Bernt-Erik Saether
Experimental evolution studies can be used to explore genomic response to artificial and natural selection. In such studies, loci that display larger allele frequency change than expected by genetic drift alone are assumed to be directly or indirectly associated with traits under selection. However, such studies report surprisingly many loci under selection, suggesting that current tests for allele frequency change may be subject to p-value inflation and hence be anti-conservative. One factor known from genome...

Data from: Bridge under troubled water: turbulence and niche partitioning in fish foraging

Zeynep Pekcan-Hekim, Noora Hellén, Laura Härkönen, Per Anders Nilsson, Leena Nurminen & Jukka Horppila
The coexistence of competing species relies on niche partitioning. Competitive exclusion is likely inevitable at high niche overlap, but such divide between competitors may be bridged if environmental circumstances displace competitor niches to enhance partitioning. Foraging-niche dimension can be influenced by environmental characteristics, and if competitors react differently to such conditions, coexistence can be facilitated. We here experimentally approach the partitioning effects of environmental conditions by evaluating the influence of water turbulence on foraging-niche responses...

Data from: Towards a common methodology for developing logistic tree mortality models based on ring-width data

Maxime Cailleret, Christof Bigler, Harald Bugmann, J. Julio Camarero, Katarina Cufar, Hendrik Davi, Ilona Mészáros, Francesco Minunno, Mikko Peltoniemi, Elisabeth Robert, María-Laura Suarez, Roberto Tognetti & Jordi Martinez-Vilalta
Tree mortality is a key process shaping forest dynamics. Thus, there is a growing need for indicators of the likelihood of tree death. During the last decades, an increasing number of tree-ring based studies have aimed to derive growth–mortality functions, mostly using logistic models. The results of these studies, however, are difficult to compare and synthesize due to the diversity of approaches used for the sampling strategy (number and characteristics of alive and death observations),...

Registration Year

  • 2016
    53

Resource Types

  • Dataset
    53

Affiliations

  • University of Helsinki
    53
  • University of Jyväskylä
    10
  • University of Turku
    4
  • University of Oslo
    3
  • Natural Resources Institute Finland
    3
  • University of Oxford
    3
  • Lund University
    2
  • University of Groningen
    2
  • University of Lausanne
    2
  • Aarhus University
    2