40 Works

Data from: Demographic histories and genetic diversities of Fennoscandian marine and landlocked ringed seal subspecies

Tommi Nyman, Mia Valtonen, Jouni Aspi, Minna Ruokonen, Mervi Kunnasranta & Jukka U. Palo
Island populations are on average smaller, genetically less diverse, and at a higher risk to go extinct than mainland populations. Low genetic diversity may elevate extinction probability, but the genetic component of the risk can be affected by the mode of diversity loss, which, in turn, is connected to the demographic history of the population. Here, we examined the history of genetic erosion in three Fennoscandian ringed seal subspecies, of which one inhabits the Baltic...

Data from: The importance of microhabitat for biodiversity sampling

Zia Mehrabi, Eleanor M. Slade, Angel Solis & Darren J. Mann
Responses to microhabitat are often neglected when ecologists sample animal indicator groups. Microhabitats may be particularly influential in non-passive biodiversity sampling methods, such as baited traps or light traps, and for certain taxonomic groups which respond to fine scale environmental variation, such as insects. Here we test the effects of microhabitat on measures of species diversity, guild structure and biomass of dung beetles, a widely used ecological indicator taxon. We demonstrate that choice of trap...

Data from: Two-phase importance sampling for inference about transmission trees

Elina Numminen, Claire Chewapreecha, Jukka Sirén, Claudia Turner, Paul Turner, Stephen D. Bentley, Jukka Corander & J. Siren
There has been growing interest in the statistics community to develop methods for inferring transmission pathways of infectious pathogens from molecular sequence data. For many datasets, the computational challenge lies in the huge dimension of the missing data. Here, we introduce an importance sampling scheme in which the transmission trees and phylogenies of pathogens are both sampled from reasonable importance distributions, alleviating the inference. Using this approach, arbitrary models of transmission could be considered, contrary...

Data from: Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks

Ge Tan, Manuel Gil, Ari P. Löytynoja, Nick Goldman & Christophe Dessimoz
Multiple sequence aligners typically work by progressively aligning the most closely related sequences or group of sequences according to guide trees. In PNAS, Boyce et al. report that alignments reconstructed using simple chained trees (i.e., comb-like topologies) with random leaf assignment performed better in protein structure-based benchmarks than those reconstructed using phylogenies estimated from the data as guide trees. The authors state that this result could turn decades of research in the field on its...

Data from: Evidence for sex-specific selection in brain: a case study of the nine-spined stickleback

Gabor Herczeg, Kaisa Välimäki, Abigél Gonda & Juha Merilä
Theory predicts that the sex making greater investments into reproductive behaviours demands higher cognitive ability, and as a consequence, larger brains or brain parts. Further, the resulting sexual dimorphism can differ between populations adapted to different environments, or among individuals developing under different environmental conditions. In the nine-spine stickleback (Pungitius pungitius), males perform nest building, courtship, territory defence and parental care, whereas females perform mate choice and produce eggs. Also, predation-adapted marine and competition-adapted pond...

Data from: Phylum-wide comparative genomics unravel the diversity of secondary metabolism in Cyanobacteria

Alexandra Calteau, David P. Fewer, Amel Latifi, Thérèse Coursin, Thierry Laurent, Jouni Jokela, Cheryl A. Kerfeld, Kaarina Sivonen, Jörn Piel & Muriel Gugger
Background: Cyanobacteria are an ancient lineage of photosynthetic bacteria from which hundreds of natural products have been described, including many notorious toxins but also potent natural products of interest to the pharmaceutical and biotechnological industries. Many of these compounds are the products of non-ribosomal peptide synthetase (NRPS) or polyketide synthase (PKS) pathways. However, current understanding of the diversification of these pathways is largely based on the chemical structure of the bioactive compounds, while the evolutionary...

Data from: Combined effects of turbulence and different predation regimes on zooplankton in highly colored water – implications for environmental change in lakes

Laura Härkönen, Zeynep Pekcan-Hekim, Noora Hellén, Anne Ojala & Jukka Horppila
In aquatic ecosystems, predation is affected both by turbulence and visibility, but the combined effects are poorly known. Both factors are changing in lakes in the Northern Hemisphere; the average levels of turbulence are predicted to increase due to increasing wind activities, while water transparency is decreasing, e.g., due to variations in precipitation, and sediment resuspension. We explored experimentally how turbulence influenced the effects of planktivorous fish and invertebrate predators on zooplankton when it was...

Data from: Gut microbiota signatures predict host and microbiota responses to dietary interventions in obese individuals

Katri Korpela, Harry J. Flint, Alexandra M. Johnstone, Jenni Lappi, Kaisa Poutanen, Evelyne Dewulf, Nathalie Delzenne, Willem M. De Vos & Anne Salonen
Background: Interactions between the diet and intestinal microbiota play a role in health and disease, including obesity and related metabolic complications. There is great interest to use dietary means to manipulate the microbiota to promote health. Currently, the impact of dietary change on the microbiota and the host metabolism is poorly predictable and highly individual. We propose that the responsiveness of the gut microbiota may depend on its composition, and associate with metabolic changes in...

Data from: Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men

Anne Salonen, Leo Lahti, Jarkko Salojärvi, Grietje Holtrop, Katri Korpela, Sylvia H. Duncan, Priya Date, Freda Farquharson, Alexandra M. Johnstone, Gerald E. Lobley, Petra Louis, Harry J. Flint & Willem M. De Vos
There is growing interest in understanding how diet affects the intestinal microbiota, including its possible associations with systemic diseases such as metabolic syndrome. Here we report a comprehensive and deep microbiota analysis of fourteen obese males consuming fully controlled diets supplemented with resistant starch (RS) or non-starch polysaccharides (NSP), and a weight-loss diet (WL). We analyzed the composition, diversity and dynamics of the faecal microbiota on each dietary regime by phylogenetic microarray and quantitative PCR...

Data from: Human-facilitated metapopulation dynamics in an emerging pest species, Cimex lectularius

Toby Fountain, Gavin Horsburgh, Ludovic Duvaux, Klaus Reinhardt & Roger K. Butlin
The number and demographic history of colonists can have dramatic consequences for the way in which genetic diversity is distributed and maintained in a metapopulation. The bed bug (Cimex lectularius) is a re-emerging pest species whose close association with humans has led to frequent local extinction and colonisation, i.e. to metapopulation dynamics. Pest control limits the lifespan of sub-populations, causing frequent local extinctions, and human-facilitated dispersal allows the colonisation of empty patches. Founder events often...

Data from: Predator–vole interactions in northern Europe: the role of small mustelids revised

Katri Korpela, Pekka Helle, Heikki Henttonen, Erkki Korpimäki, Esa Koskela, Otso Ovaskainen, Hannu Pietiäinen, Janne Sundell, Jari Valkama, Otso Huitu, H. Pietiainen & E. Korpimaki
The cyclic population dynamics of vole and predator communities is a key phenomenon in northern ecosystems, and it appears to be influenced by climate change. Reports of collapsing rodent cycles have attributed the changes to warmer winters, which weaken the interaction between voles and their specialist subnivean predators. Using population data collected throughout Finland during 1986–2011, we analyse the spatio-temporal variation in the interactions between populations of voles and specialist, generalist and avian predators, and...

Data from: Causes and consequences of fine-scale population structure in a critically endangered freshwater seal

Mia Valtonen, Jukka U. Palo, Jouni Aspi, Minna Ruokonen, Mervi Kunnasranta & Tommi Nyman
Saimaa_ringed_seal_microsatSaimaa ringed seal genotypes based on 17 microsatellite loci. Individuals sampled between the years 1980-2008 from five regions of Lake Saimaa; Northern Saimaa (1st pop), Kolovesi (2nd pop), Main Haukivesi area (3rd pop), Pihlajavesi area (4th pop) and Southern Saimaa (5th pop). The data is in GenePop format.Saimaa_ringed_seal_sample_infoCollection information on the individual Saimaa ringed seals included in the study.

Data from: Disentangling plastic and genetic changes in body mass of Siberian jays

Phillip Gienapp & Juha Merilä
Spatial and temporal phenotypic differentiation in mean body size is of commonplace occurrence, but the underlying causes remain often unclear: both genetic differentiation in response to selection (or drift) and environmentally induced plasticity can create similar phenotypic patterns. Studying changes in body mass in Siberian jays (Perisoreus infaustus) over three decades, we discovered that mean body mass declined drastically (ca. 10%) over the first two decades, but increased markedly thereafter back to almost the initial...

Data from: Outbreeding effects in an inbreeding insect, Cimex lectularius

Toby Fountain, Roger K. Butlin, Klaus Reinhardt & Oliver Otti
In some species, populations with few founding individuals can be resilient to extreme inbreeding. Inbreeding seems to be the norm in the common bed bug, Cimex lectularius, a flightless insect that, nevertheless, can reach large deme sizes and persist successfully. However, bed bugs can also be dispersed passively by humans, exposing inbred populations to gene flow from genetically distant populations. The introduction of genetic variation through this outbreeding could lead to increased fitness (heterosis) or...

Data from: Cryptic ecology among host generalist Campylobacter jejuni in domestic animals

Samuel K. Sheppard, Lu Cheng, Guillaume Méric, Caroline P. A. De Haan, Ann-Katrin Llarena, Pekka Marttinen, Ana Vidal, Anne Ridley, Felicity Clifton-Hadley, Thomas R. Connor, Norval J. C. Strachan, Ken Forbes, Frances M. Colles, Keith A. Jolley, Stephen D. Bentley, Martin C. J. Maiden, Marja-Liisa Hänninen, Julian Parkhill, William P. Hanage & Jukka Corander
Homologous recombination between bacterial strains is theoretically capable of preventing the separation of daughter clusters, and producing cohesive clouds of genotypes in sequence space. However, numerous barriers to recombination are known. Barriers may be essential such as adaptive incompatibility, or ecological, which is associated with the opportunities for recombination in the natural habitat. Campylobacter jejuni is a gut colonizer of numerous animal species and a major human enteric pathogen. We demonstrate that the two major...

Data from: Secondary successional trajectories of structural and catabolic bacterial communities in oil polluted soil planted with hybrid poplar

Shinjini Mukherjee, Timo Sipilä, Pertti Pulkkinen & Kim Yrjälä
Poplars have widely been used for rhizoremediation of a broad range of organic contaminants for the past two decades. Still, there is a knowledge gap regarding the rhizosphere associated bacterial communities of poplars and their dynamics during the remediation process. It is envisaged that a detailed understanding of rhizosphere associated microbial populations will greatly contribute to a better design and implementation of rhizoremediation. In order to investigate the long-term succession of structural and catabolic bacterial...

Data from: Are ant supercolonies crucibles of a new major transition in evolution?

Patrick Kennedy, Tobias Uller & Heikki Helanterä
The biological hierarchy of genes, cells, organisms and societies is a fundamental reality in the living world. This hierarchy of entities did not arise ex nihilo at the origin of life, but rather has been serially generated by a succession of critical events known as ‘evolutionary transitions in individuality’ (ETIs). Given the sequential nature of ETIs, it is natural to look for candidates to form the next hierarchical tier. We analyse claims that these candidates...

Data from: Functional response of plant communities to clearcutting: management impacts differ between forest vegetation zones

Buntarou Kusumoto, Takayuki Shiono, Mai Miyoshi, Ryo Maeshiro, Shin-Jiro Fujii, Timo Kuuluvainen & Yasuhiro Kubota
1. Understanding of the ecological impacts of logging practices on biodiversity and associated ecosystem processes is essential for developing sustainable forest management approaches. We documented the impacts of clearcutting on the functional structure of tree and herbaceous communities in hemiboreal, cool-temperate, warm-temperate and subtropical forests in the Japanese archipelago and identified forest vegetation that is vulnerable to deterioration of important ecosystem functions. 2. We combined species data for leaf, stem, flower and fruit traits related...

Data from: Consensus RDA across dissimilarity coefficients for canonical ordination of community composition data

F. Guillaume Blanchet, Pierre Legendre, J. A. Colin Bergeron & Fangliang He
Understanding how habitat structures species assemblages in a community is one of the main goals of community ecology. To relate community patterns to particular factors defining habitat conditions, ecologists often use canonical ordinations such as canonical redundancy analysis (RDA). It is a common practice to use dissimilarity coefficients to perform canonical ordinations through distance-based RDA (db-RDA) or transformation-based RDA (tb-RDA). Dissimilarity coefficients are measures of resemblance where the information about species communities is condensed into...

Data from: The interplay between local ecology, divergent selection and genetic drift in population divergence of a sexually antagonistic female trait

Kristina Karlsson Green, Erik I. Svensson, Johannes Bergsten, Roger Härdling & Bengt Hansson
Genetically polymorphic species offer the possibility to study maintenance of genetic variation and the potential role for genetic drift in population divergence. Indirect inference of the selection regimes operating on polymorphic traits can be achieved by comparing population divergence in neutral genetic markers with population divergence in trait frequencies. Such an approach could further be combined with ecological data to better understand agents of selection. Here, we infer the selective regimes acting on a polymorphic...

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: Ecological and evolutionary effects of fragmentation on infectious disease

Jussi Jousimo, Ayco J. M. Tack, Otso Ovaskainen, Tommi Mononen, Hanna Susi, Charlotte Tollenaere & Anna-Liisa Laine
Ecological theory predicts that disease incidence increases with increasing density of host networks, yet evolutionary theory suggests that host resistance increases accordingly. To test the combined effects of ecological and evolutionary forces on host-pathogen systems, we analyzed the spatiotemporal dynamics of a plant (Plantago lanceolata)–fungal pathogen (Podosphaera plantaginis)relationship for 12 years in over 4000 host populations. Disease prevalence at the metapopulation level was low, with high annual pathogen extinction rates balanced by frequent (re-)colonizations. Highly...

Data from: Tipping elements in the human intestinal ecosystem

Leo Lahti, Jarkko Salojärvi, Anne Salonen, Marten Scheffer & Willem M. De Vos
The microbial communities living in the human intestine can have profound impact on our well-being and health. However, we have limited understanding of the mechanisms that control this complex ecosystem. Here, based on a deep phylogenetic analysis of the intestinal microbiota in a thousand western adults, we identify groups of bacteria that exhibit robust bistable abundance distributions. These bacteria are either abundant or nearly absent in most individuals, and exhibit decreased temporal stability at the...

Data from: Top-down effects of a lytic bacteriophage and protozoa on bacteria in aqueous and biofilm phases

Ji Zhang, Anni-Maria Örmälä-Odegrip, Johanna Mappes & Jouni Laakso
Lytic bacteriophages and protozoan predators are the major causes of bacterial mortality in natural microbial communities, which also makes them potential candidates for biological control of bacterial pathogens. However, little is known about the relative impact of bacteriophages and protozoa on the dynamics of bacterial biomass in aqueous and biofilm phases. Here, we studied the temporal and spatial dynamics of bacterial biomass in a microcosm experiment where opportunistic pathogenic bacteria Serratia marcescens was exposed to...

Data from: Heritability of flight and resting metabolic rates in the Glanville fritillary butterfly

Anniina L. K. Mattila & Ilkka Hanski
Dispersal capacity is a key life history trait especially in species inhabiting fragmented landscapes. Evolutionary models predict that, given sufficient heritable variation, dispersal rate responds to natural selection imposed by habitat loss and fragmentation. Here, we estimate phenotypic variance components and heritability of flight and resting metabolic rates in an ecological model species, the Glanville fritillary butterfly, in which flight metabolic rate is known to correlate strongly with dispersal rate. We modeled a two-generation pedigree...

Registration Year

  • 2014
    40

Resource Types

  • Dataset
    40

Affiliations

  • University of Helsinki
    40
  • University of Oulu
    4
  • Wageningen University & Research
    4
  • University of Eastern Finland
    3
  • University of Aberdeen
    3
  • University of Oxford
    3
  • Lund University
    2
  • Eötvös Loránd University
    2
  • Forest Research Institute
    2
  • Wellcome Trust
    2