462 Works

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: 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: Differential responses to related hosts by nesting and non-nesting parasites in a brood-parasitic duck

Kim Jaatinen, Markus Öst, Philip Gienapp & Juha Merilä
Host-parasite relatedness may facilitate the evolution of conspecific brood parasitism (CBP), but empirical support for this contention remains inconclusive. One reason for this disparity may relate to the diversity of parasitic tactics, a key distinguishing feature being whether the parasite has a nest of her own. Previous work suggests that parasites without nests of their own may be of inferior phenotypic quality, but due to difficulties in identifying these parasitic individuals, little is known about...

Data from: Galega orientalis is more diverse than Galega officinalis in Caucasus – whole-genome AFLP analysis and phylogenetics of symbiosis-related genes

Janina Österman, Elena P. Chizhevskaja, Evgeny E. Andronov, David P. Fewer, Zewdu Terefework, Marina L. Roumiantseva, Olga P. Onichtchouk, Aneta Dresler-Nurmi, Boris V. Simarov, Nikolay I. Dzyubenko & Kristina Lindstrom
Legume plants can obtain combined nitrogen for their growth in an efficient way through symbiosis with specific bacteria. The symbiosis between Rhizobium galegae and its host plant Galega is an interesting case where the plant species G. orientalis and G. officinalis form effective, nitrogen fixing, symbioses only with the appropriate rhizobial counterpart, R. galegae bv. orientalis and R. galegae bv. officinalis respectively. There is plenty of information available on the symbiotic properties of nitrogen fixing...

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: 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: 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: Local adaptation to salinity in the three-spined stickleback?

Jacquelin DeFaveri & Juha Merilä
Different lines of evidence suggest that the occurrence and extent of local adaptation in high gene flow marine environments – even in mobile and long-lived vertebrates with complex life cycles – may be more widespread than earlier thought. We conducted a common garden experiment to test for local adaptation to salinity in Baltic Sea sticklebacks (Gasterosteus aculeatus). Fish from three different native salinity regimes (high, mid and low) were subjected to three salinity treatments (high,...

Data from: Evidence for adaptive phenotypic differentiation in Baltic Sea sticklebacks

Jacquelin DeFaveri & Juha Merilä
The evidence for adaptive phenotypic differentiation in mobile marine species remains scarce, partly due to the difficulty of obtaining quantitative genetic data to demonstrate the genetic basis of the observed phenotypic differentiation. Using a combination of phenotypic and molecular genetic approaches, we elucidated the relative roles of natural selection and genetic drift in explaining lateral plate number differentiation in threespine sticklebacks (Gasterosteus aculeatus) across the entire Baltic Sea basin (ca. 392 000 km2). We found...

Data from: Distribution and bioinformatic analysis of the cerato-platanin protein family in Dikarya

Hongxin Chen, Andriy Kovalchuk, Susanna Keriö & Fred O. Asiegbu
The cerato-platanin family is a group of small cysteine-rich fungal proteins new to science. They usually are abundantly secreted extracellularly and are involved in fungus-host interactions. With the advance of available fungal genome sequences, we performed a genomewide study of the distribution of this family in fungi and analyzed the common characteristics of the protein sequences. A total of 55 fungal genomes, including 27 from Ascomycota and 28 from Basidiomycota, were used. A total of...

Data from: Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

Jenni Harmoinen, Alina Von Thaden, Jouni Aspi, Laura Kvist, Berardino Cocchiararo, Anne Jarausch, Andrea Gazzola, Teodora Sin, Hannes Lohi, Marjo Hytönen, Ilpo Kojola, Astrid Vik Stronen, Romolo Caniglia, Federica Mattucci, Marco Galaverni, Raquel Godinho, Aritz Ruiz-González, Ettore Randi, Violeta Muñoz-Fuentes & Carsten Nowak
Background: Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due to the low number of markers showing distinctive allele frequencies between wolves and dogs. Moreover, calibration across laboratories is time-consuming and costly. In this study, we selected...

Intraspecific genetic variation matters when predicting seagrass distribution under climate change

Zi-Min Hu, Quan-Sheng Zhang, Jie Zhang, Kass Jamie, Mammola Stefano, Fresia Pablo, Draisma Stefano, Assis Jorge, Jueterbock Alexander, Yokota Masashi & Zhixin Zhang
Seagrasses play a vital role in structuring coastal marine ecosystems, but their distributional range and genetic diversity have declined rapidly over the past decades. In order to improve conservation of seagrass species, it is important to predict how climate change may impact their ranges. Such predictions are typically made with correlative species distribution models (SDMs), which can estimate a species’ potential distribution under present and future climatic scenarios given species’ presence data and climatic predictor...

Data from: Pellets of proof: first glimpse of the dietary composition of adult odonates as revealed by metabarcoding of feces

Kari M. Kaunisto, Tomas Roslin, Ilari E. Sääksjärvi & Eero J. Vesterinen
Recent advances in molecular techniques allow us to resolve the diet of unstudied taxa. Odonates are potentially important top-down regulators of many insects. Yet, to date, our knowledge of odonate prey use is based mainly on limited observations of odonates catching or eating their prey. In this study, we examine the potential use of metabarcoding in establishing the diet of three adult odonate species (Lestes sponsa, Enallagma cyathigerum, and Sympetrum danae) at a site in...

Data from: Related herbivore species show similar temporal dynamics

F. Guillaume Blanchet, Tomas Roslin, Masahito T. Kimura, Tea Huotari, Riikka Kaartinen, Sofia Gripenberg & Ayco J. M. Tack
1.Within natural communities, different taxa display different dynamics in time. Why this is the case we do not fully know. This thwarts our ability to predict changes in community structure, which is important for both the conservation of rare species in natural communities and for the prediction of pest outbreaks in agriculture. 2.Species sharing phylogeny, natural enemies and/or life history traits have been hypothesized to share similar temporal dynamics. We operationalized these concepts into testing...

Data from: Seasonality determines patterns of growth and age structure over a geographic gradient in an ectothermic vertebrate

Juha Merilä, Mårten B. Hjernquist, Fredrik Söderman, K. Ingemar Jönsson, Gábor Herczeg & Anssi Laurila
Environmental variation connected with sea- sonality is likely to affect the evolution of life-history strategies in ectotherms, but there is no consensus as to how important life-history traits like body size are influ- enced by environmental variation along seasonal gradients. We compared adult body size, skeletal growth, mean age, age at first reproduction and longevity among 11 common frog (Rana temporaria) populations sampled along a 1,600-km-long latitudinal gradient across Scandinavia. Mean age, age at first...

Data from: Epigenome-wide association study of lung function level and its change

Medea Imboden, Matthias Wielscher, Faisal I Rezwan, Andre F S Amaral, Emmanuel Schaffner, Ayoung Jeong, Anna Beckmeyer-Borowko, Sarah E Harris, John M Starr, Ian J Deary, Claudia Flexeder, Melanie Waldenberger, Annette Peters, Holger Schulz, Su Chen, Shadia KHan Sunny, Wilfried J J Karmaus, Yu Jiang, Gertraud Erhart, Florian Kronenberg, Ryan Arathimos, Gemma C Sharp, Alexander John Henderson, Yu Fu, Paivi Piirila … & Nicole M Probst-Hensch
Previous reports link differential DNA methylation (DNAme) to environmental exposures which are associated with lung function. Direct evidence on lung function DNAme is however limited. We undertook an agnostic epigenome-wide association study (EWAS) on pre-bronchodilation lung function and its change in adults. In a discovery-replication EWAS design, DNAme in blood and spirometry were measured twice, six-to-15 years apart, in the same participants of three adult population-based discovery cohorts (n=2,043). Associated DNAme markers (P<5x10-7) were tested...

Threats from the air: damselfly predation on diverse prey taxa

Eero J. Vesterinen, Kari Kaunisto, , Mark Forbes, Andre Morrill, Anna Puisto, Ilari Sääksjärvi & Thomas Lilley
1. To understand the diversity and strength of predation in natural communities, researchers must quantify the total amount of prey species in the diet of predators. Metabarcoding approaches have allowed widespread characterization of predator diets with high taxonomic resolution. To determine the wider impacts of predators, researchers should combine DNA techniques with estimates of population size of predators using mark-release-recapture (MRR) methods, and with accurate metrics of food consumption by individuals. 2. Herein, we estimate...

Data from: Growth mode and carbon source impact the surfaceome dynamics of Lactobacillus rhamnosus GG

Kirsi Savijoki, Tuula A. Nyman, Veera Kainulainen, Ilkka Miettinen, Pia Siljamäki, Adyary Fallarero, Jouko Sandholm, Reetta Satokari & Pekka Varmanen
Bacterial biofilms have clear implications in disease and in food applications involving probiotics. Here, we show that switching the carbohydrate source from glucose to fructose increased the biofilm formation and the total surface-antigenicity of a well-known probiotic, Lactobacillus rhamnosus GG. Surfaceomes (all cell surface-associated proteins) of GG cells grown with glucose and fructose in planktonic and biofilm cultures were identified and compared, which indicated carbohydrate source-dependent variations, especially during biofilm growth. The most distinctive differences...

Genomic signatures of domestication in Old World camels

Robert Fitak, Elmira Mohandesan, Jukka Corander, Adiya Yadamsuren, Battsetseg Chuluunbat, Omer Abdelhadi, Abdul Raziq, Peter Nagy, Chris Walzer, Bernard Faye & Pamela Burger
Domestication begins with the selection of animals showing less fear of humans. In most domesticates, selection signals for tameness have been superimposed by intensive breeding for economical or other desirable traits. Old World camels, conversely, have maintained high genetic variation and lack these secondary bottlenecks associated with breed development. By re-sequencing multiple genomes from dromedaries, Bactrian camels, and their endangered wild relatives, we show that positive selection for candidate genes underlying traits collectively referred to...

Data from: Exposing the structure of an Arctic food web

Eero J. Vesterinen, Helena K. Wirta, Peter A. Hambäck, Elisabeth Weingartner, Claus Rasmussen, Jeroen Reneerkens, Niels M. Schmidt, Olivier Gilg & Tomas Roslin
How food webs are structured has major implications for their stability and dynamics. While poorly studied to date, arctic food webs are commonly assumed to be simple in structure, with few links per species. If this is the case, then different parts of the web may be weakly connected to each other, with populations and species united by only a low number of links. We provide the first highly resolved description of trophic link structure...

Data from: Comparison of dogs and humans in visual scanning of social interaction

Heini Törnqvist, Sanni Somppi, Aija Koskela, Christina M. Krause, Outi Vainio & Miiamaaria V. Kujala
Previous studies have demonstrated similarities in gazing behaviour of dogs and humans, but comparisons under similar conditions are rare, and little is known about dogs' visual attention to social scenes. Here, we recorded the eye gaze of dogs while they viewed images containing two humans or dogs either interacting socially or facing away: the results were compared with equivalent data measured from humans. Furthermore, we compared the gazing behaviour of two dog and two human...

Data from: Environmental fluctuations restrict eco-evolutionary dynamics in predator-prey system

Teppo Hiltunen, Gökçe B. Ayan & Lutz Becks
Environmental fluctuations, species interactions and rapid evolution are all predicted to affect community structure and their temporal dynamics. Although the effects of the abiotic environment and prey evolution on ecological community dynamics have been studied separately, these factors can also have interactive effects. Here we used bacteria–ciliate microcosm experiments to test for eco-evolutionary dynamics in fluctuating environments. Specifically, we followed population dynamics and a prey defence trait over time when populations were exposed to regular...

Data from: Migration and isolation during the turbulent Ponto-Caspian Pleistocene create high diversity in the crustacean Paramysis lacustris

Asta Audzijonyte, Laima Baltrūnaitė, Risto Väinölä & Kęstutis Arbačiauskas
The Ponto-Caspian brackish-water fauna inhabits estuaries and rivers of the Black, Azov and Caspian seas and is fragmented by higher salinity waters and a major interbasin watershed. The fauna is known for the high levels of endemism, complex zoogeographic histories, and as a recent source of successful invasive species. It remains debated whether the Black and Azov Sea brackish-water populations survived unfavourable Pleistocene conditions in multiple separate refugia or whether the two seas were (repeatedly)...

Data from: Patterns of modern pollen and plant richness across northern Europe

Triin Reitalu, Anne E. Bjune, Ansis Blaus, Thomas Giesecke, Aveliina Helm, Isabelle Matthias, Sylvia H. Peglar, J. Sakari Salonen, Heikki Seppa, Vivika Väli & H. John B. Birks
1. Sedimentary pollen offers excellent opportunities to reconstruct vegetation changes over past millennia. Number of different pollen taxa or pollen richness is used to characterise past plant richness. To improve the interpretation of sedimentary pollen richness, it is essential to understand the relationship between pollen and plant richness in contemporary landscapes. This study presents a regional-scale comparison of pollen and plant richness from northern Europe and evaluates the importance of environmental variables on pollen and...

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...

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