60 Works

Genomics of humic adaptation in Eurasian perch (Perca fluviatilis): SNP genotypes of 32 perch individuals, supplementary figures and tables

Mikhail Ozerov, Kristina Noreikiene, Siim Kahar, Magnus Huss, Ari Huusko, Toomas Kõiv, Margot Sepp, María López, Anna Gårdmark, Riho Gross & Anti Vasemägi
Extreme environments are inhospitable to the majority of species, but some organisms are able to survive in such hostile conditions due to evolutionary adaptations. For example, modern bony fishes have colonized various aquatic environments, including perpetually dark, hypoxic, hypersaline and toxic habitats. Eurasian perch (Perca fluviatilis) is among the few fish species of northern latitudes that is able to live in very acidic humic lakes. Such lakes represent almost “nocturnal” environments; they contain high levels...

The strength and form of natural selection on transcript abundance in the wild

Freed Ahmad, Paul Debes, Ilkka Nousiainen, Siim Kahar, Lilian Pukk, Riho Gross, Mikhail Ozerov & Anti Vasemägi
Gene transcription variation is known to contribute to disease susceptibility and adaptation, but we currently know very little about how contemporary natural selection shapes transcript abundance. Here, we propose a novel analytical framework to quantify the strength and form of ongoing natural selection at the transcriptome level in a wild vertebrate. We estimated selection on transcript abundance in a cohort of a wild salmonid fish (Salmo trutta) affected by an extracellular myxozoan parasite (Tetracapsuloides bryosalmonae)...

Data recorded for leaf size, and leaf vein and areole measurements taken from nine Magnoliaceae species

Peijian Shi, Qinyue Miao, Ülo Niinemets, Mengdi Liu, Yirong Li, Kexin Yu & Karl Niklas
Across species, the density of major veins in leaves scales inversely with leaf area. Yet, minor vein density manifests no clear relationship with respect to leaf are, despite having the potential to provide important insights into the trade-off between investments in leaf mechanical support, hydraulics, and light interception. To examine this phenomenon, between 120−380 mature leaves from each of nine Magnoliaceae species were sampled from Nanjing Forestry University campus and Nanjing Botanical Garden, Chinese Academy...

Emerging stability of forest productivity by mixing two species buffers temperature destabilizing effect

Miren Del Rio, Ricardo Ruiz‐Peinado, Stig‐Olof Holm, Aris Jansons, Thomas Nord‐Larsen, Kris Verheyen, Andrés Bravo‐Oviedo, Hans Pretzsch, Ricardo Ruiz-Peinado, Hervé Jactel, Lluís Coll, Magnus Löf, Jorge Aldea, Christian Ammer, Admir Avdagić, Ignacio Barbeito, Kamil Bielak, Felipe Bravo, Gediminas Brazaitis, Jakub Cerný, Catherine Collet, Sonia Condés, Lars Drössler, Marek Fabrika, Michael Heym … & Andrés Bravo-Oviedo
The increasing disturbances in monocultures around the world are testimony to their instability under global change. Many studies have claimed that temporal stability of productivity increase with species richness, although the ecological fundaments have mainly been investigated through diversity experiments. To adequately manage forest ecosystems, it is necessary to have a comprehensive understanding of the effect of mixing species on the temporal stability of productivity and the way in which this it is influenced by...

International Scientific Conference „Sustainable fruit and berry cultivation“ : the book of abstracts

Reelika Rätsep, Hedi Kaldmäe & Karmen Pääso
Dear conference participants and guests, As director of the Institute of Agricultural and Environmental Sciences of Estonian University of Life Sciences, I have a great honour to greet you at the scientific conference dedicated to the 100th anniversary of Polli Horticultural Research Centre. Research on fruits and berries in Estonia and at our University is carried out in two locations – at horticultural research centre at Polli village in Southern Estonia and on our university...

Data from: Genes that affect Atlantic salmon growth in hatchery do not have the same effect in the wild

Anti Vasemägi, Siim Kahar & Mikhail Y. Ozerov
Dissecting the genetic mechanisms of phenotypic traits that influence fitness in diverse environments provides the important first step towards understanding the robustness of the observed genotype–phenotype associations, the role of genotype-by-environment interaction (GEI) shaping fitness trade-offs and maintaining genetic variation of quantitative traits. However, the molecular basis of complex traits in vertebrates has rarely, if ever, been studied simultaneously in natural and controlled laboratory environments. To evaluate whether the same genomic regions affect the growth...

Data from: Are leaf functional traits “invariant” with plant size, and what is “invariance” anyway?

Charles A. Price, Ian J. Wright, David D. Ackerly, Ülo Niinemets, Peter B. Reich & Erik J. Veneklaas
Studies of size-related plant traits have established a suite of mathematical functions describing whole plant investment and allocation. In parallel, studies of plant “economic spectra” have measured the scaling and variance composition of traits related to the major dimensions of both structure and function. Here we explore the intersection of these two broad areas by exploring the notion that many leaf economic traits are invariant with species differences in adult plant size. Invariant traits are...

Data from: Drivers of vegetative dormancy across herbaceous perennial plant species

Richard P. Shefferson, Tiiu Kull, Michael J. Hutchings, Marc-André Selosse, Hans Jacquemyn, Kimberly M. Kellett, Eric S. Menges, Richard B. Primack, Juha Tuomi, Kirsi Alahuhta, Sonja Hurskainen, Helen M. Alexander, Derek S. Anderson, Rein Brys, Emilia Brzosko, Slavomir Dostálik, Katharine Gregg, Zdeněk Ipser, Anne Jäkäläniemi, Jana Jersáková, W. Dean Kettle, Melissa K. McCormick, Ana Mendoza, Michael T. Miller, Asbjørn Moen … & Dennis F. Whigham
Vegetative dormancy, that is the temporary absence of aboveground growth for ≥ 1 year, is paradoxical, because plants cannot photosynthesise or flower during dormant periods. We test ecological and evolutionary hypotheses for its widespread persistence. We show that dormancy has evolved numerous times. Most species displaying dormancy exhibit life‐history costs of sprouting, and of dormancy. Short‐lived and mycoheterotrophic species have higher proportions of dormant plants than long‐lived species and species with other nutritional modes. Foliage...

Data from: High genotypic diversity and strong spatial structure in populations of Trifolium alpestre with low seed production

Karin Kaljund, Malle Leht & Vello Jaaska
The studies on clonal plant populations indicate that the proportion between clonal and sexual reproduction may be highly variable, depending on the biological characteristics of species and the ecological conditions of habitats. We focused on the genotypic diversity of Trifolium alpestre populations in Estonia. We assayed the genetic diversity, spatial genotypic structure and diversity with the use of allozyme markers. Populations revealed high levels of genotypic diversity and showed strong spatial structure of MLGs. The...

Data from: How much would it cost to monitor farmland biodiversity in Europe?

Ilse R. Geijzendorffer, Stefano Targetti, Manuel K. Schneider, Dick J. Brus, Philippe Jeanneret, Robert H. G. Jongman, Martin Knotters, Davide Viaggi, Siyka Angelova, Michaela Arndorfer, Debra Bailey, Katalin Balzacs, András Báldim, Marion M. B. Bogers, Robert G.H. Bunce, Jean-Philippe Choisis, Peter Dennis, Sebastian Eiter, Wendy Fjellstad, Jürgen F. Friedel, Tiziano Gomiero, Arjan Griffioen, Max Kainz, Anikó Kovács-Hostyánszki, Gisela Lüscher … & András Báldi
To evaluate progress on political biodiversity objectives, biodiversity monitoring provides information on whether intended results are being achieved. Despite scientific proof that monitoring and evaluation increase the (cost) efficiency of policy measures, cost estimates for monitoring schemes are seldom available, hampering their inclusion in policy programme budgets. Empirical data collected from 12 case studies across Europe were used in a power analysis to estimate the number of farms that would need to be sampled per...

Data from: Canopy leaf area index at its higher end: dissection of structural controls from leaf to canopy scales in bryophytes

Ülo Niinemets & Mari Tobias
There is evidence that mosses with miniature foliage elements have extremely large leaf area indices (LAI), but it is unclear what canopy traits are responsible for these high LAI values in architecturally divergent mosses, and how the inherent tradeoffs limiting maximum LAI in vascular plants can be overcome in mosses. To determine the quantitative significance of different traits in determining LAI, we developed a method to dissect LAI into underlying functionally dependent constituent traits at...

Data from: Different functional characteristics can explain different dimensions of plant invasion success

Huixuan Liao, Robert Pal, Ülo Niinemets, Michael Bahn, Bruno Cerabolini & Shao-Lin Peng
The success of invasive plant species can be evaluated using different dimensions, such as, range size, abundance, and impact. These different dimensions do not always covary but are rarely separated, suggesting an urgency to disentangle the functional mechanisms behind them. A dataset of leaf traits and four dimensions of invasion success (i.e., range size, local abundance, impact on native plant abundance, and impact on native plant diversity) were compiled for 395 non-native plant species in...

Data from: Less is more: extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology

Lilian Pukk, Freed Ahmad, Shihab Hasan, Veljo Kisand, Riho Gross & Anti Vasemägi
Massively parallel sequencing a small proportion of the whole genome at high coverage enables answering a wide range of questions from molecular evolution and evolutionary biology to animal and plant breeding and forensics. In this study, we describe the development of restriction-site associated DNA (RAD) sequencing approach for Ion Torrent PGM platform. Our protocol results in extreme genome complexity reduction using two rare-cutting restriction enzymes and strict size selection of the library allowing sequencing of...

Opposing community assembly patterns for dominant and non-dominant plant species in herbaceous ecosystems globally

Carlos Alberto Arnillas, Elizabeth Borer, Eric Seabloom, Juan Alberti, Selene Baez, Jonathon Bakker, Elizabeth Boughton, Yvonne Buckley, Miguel Bugalho, Ian Donohue, John Dwyer, Jennifer Firn, Riley Gridzak, Nicole Hagenah, Yann Hautier, Aveliina Helm, Anke Jentsch, , Kimberly Komatsu, Lauri Laanisto, Ramesh Laungani, Rebecca McCulley, Joslin Moore, John Morgan, Pablo Peri … & Marc Cadotte
Biotic and abiotic factors interact with dominant plants —the locally most frequent or with the largest coverage— and non-dominant plants differently, partially because dominant plants modify the environment where non-dominant plants grow. For instance, if dominant plants compete strongly, they will deplete most resources, forcing non-dominant plants into a narrower niche space. Conversely, if dominant plants are constrained by the environment, they might not exhaust available resources but instead may ameliorate environmental stressors that usually...

Impact of Gastrointestinal Protozoan Infections on the Acute Phase Response in Neonatal Ruminants

Tarmo Niine
After birth, neonatal ruminants go through crucial and sensitive period of rapid development and growth. During this period, they may interact with variety of microorganisms found in the surrounding environment. It would be beneficial for both the farmer and the veterinarian to have general biomarkers, useful in managing of this adaptation process. Such a tool could help in improving the prediction of the animals’ performance in the herd. The interactions between the ruminant and infectious...

Marketing și dezvoltarea produsului

Tiiu Ohvril & Birgit Maasing
Dragi cititori, Această lucrare este publicată ca urmare a unui proiect implementat în Republica Moldova de către Universitatea Estoniană de Științe ale Vieții. Rezultatul primului proiect a fost o carte care a oferit o imagine de ansamblu asupra diversificării economiei rurale estoniene. Ulterior, partenerii proiectului au dorit să afle mai multe despre experiențele specifice de dezvoltare a produselor și despre problemele micilor producători estonieni. De fapt, două tipuri de agricultură se pot încadra într-o țară...

Species lists of 14 Estonian coastal meadow sites with different management history

Marika Kose, Karin Kaljund & Kaili Kattai
The data were collected during July-August 2015 in locations with coordinates in dataset. The sites have unique names and their management has been evaluated as permanently managed, restored before 2005 and restored after 2005. Their condition is estimated on expert level as good or poor, regarding vegetation composition and height. The data were collected from 20 plots of the size 0,5 x 0,5 m. In the dataset the number marks in how many plots out...

Catchment properties and the photosynthetic trait composition of freshwater plant communities

Lars Lønsmann Iversen, A. Winkel, L. Baastrup-Spohr, A. B. Hinke, J. Alahuhta, A. Baattrup-Pedersen, S. Birk, P. Brodersen, P. A. Chambers, F. Ecke, T. Feldmann, D. Gebler, J. Heino, T. S. Jespersen, S. J. Moe, T. Riis, L. Sass, O. Vestergaard, S. C. Maberly, K. Sand-Jensen & O. Pedersen
Unlike in land plants, photosynthesis in many aquatic plants relies on bicarbonate in addition to carbon dioxide (CO2) to compensate for the low diffusivity and potential depletion of CO2 in water. Concentrations of bicarbonate and CO2 vary greatly with catchment geology. In this study, we investigate whether there is a link between these concentrations and the frequency of freshwater plants possessing the bicarbonate use trait. We show, globally, that the frequency of plant species with...

Data from: Salmon behavioural response to robots in an aquaculture sea cage

Maarja Kruusmaa, Roza Gkliva, Jeffrey Tuhtan, Arvo Tuvikene & Jo Alfredsen
Animal-robot studies can inform us about animal behaviour and inspire advances in agriculture, environmental monitoring and animal health and welfare. Currently, experimental results on how fish are affected by the presence of underwater robots are largely limited to laboratory environments with few individuals and a focus on model species. Laboratory studies provide valuable insight, but their results are not necessarily generalizable to larger scales such as marine aquaculture. This paper examines the effects of underwater...

Global gradients in intraspecific variation in vegetative and floral traits are partially associated with climate and species richness

Jonas Kuppler, Cécile H. Albert, Gregory M. Ames, W. Scott Armbruster, Gerhard Boenisch, Florian C. Boucher, Diane R. Campbell, Liedson T. Carneiro, Eduardo Chacón-Madrigal, Brian J. Enquist, Carlos R. Fonseca, José M. Gómez, Antoine Guisan, Pedro Higuchi, Dirk N. Karger, Jens Kattge, Michael Kleyer, Nathan J. B. Kraft, Anne-Amélie C. Larue-Kontić, Amparo Lázaro, Martin Lechleitner, Deirdre Loughnan, Vanessa Minden, Ülo Niinemets, Gerhard E. Overbeck … & Robert R. Junker
Aim Intraspecific trait variation (ITV) within natural plant communities can be large, influencing local ecological processes and dynamics. Here, we shed light on how ITV in vegetative and floral traits responds to large-scale abiotic and biotic gradients (i.e. climate and species richness). Specifically, we tested if associations of ITV with temperature, precipitation and species richness were consistent with any of from four hypotheses relating to stress-tolerance and competition. Furthermore, we estimated the degree of correlation...

Plankton samples of inland waters : [catalog]

Reet Laugaste, Henn Timm & Evi Lill
The number of sampled waterbodies was 1017. Most of the samples (22,900) have been collected from Estonia. There are also more than 800 samples from Russia (mainly from the eastern and southern part of Lake Peipsi) and ca 100 from other countries. In addition, there are also some samples of the Baltic Sea. Register code: according to the Estonian environmental register: https://keskkonnaagentuur.ee/en Of the total material, more than 13,000 specimens are phytoplankton, the rest is...

Tree water uptake enhances nitrogen acquisition in a fertilized boreal forest – but not under nitrogen poor conditions

Nils Henriksson, Hyungwoo Lim, John Marchall, Oskar Franklin, Ross McMurtrie, Reimo Lutter, Ruth Magh, Tomas Lundmark & Torgny Näsholm
Understanding how plant water uptake interacts with acquisition of soil nitrogen (N) and other nutrients is fundamental for predicting plant responses to a changing environment, but it is an area where models disagree. We present a novel isotopic labelling approach which reveals spatial patterns of water and N uptake, and their interaction, by trees. The stable isotopes 15N and 2H were applied to a small area of the forest floor in stands with high and...

eDNA metabarcoding in lakes to quantify influences of landscape features and human activity on aquatic invasive species prevalence and fish community diversity

Lilian Pukk, Jeannette Kanefsky, Amanda Heathman, Ellen Weise, Lucas Nathan, Seth Herbst, Nicholas Sard, Kim Scribner & John Robinson
Aim: Our goal was to use eDNA metabarcoding to characterize fish community diversity, detect aquatic invasive species (AIS), and assess how measures of community (or AIS) diversity are influenced by lake physical and environmental covariates, measures of hydrological connectivity, and human accessibility. Location: Michigan, USA. Methods: eDNA samples collected from 22 lakes were sequenced using two mitochondrial gene regions (12S and 16S rRNA). Metabarcoding data were compared to traditional fisheries survey data for a subset...

Data from: Age-specific patterns of maternal investment in common gull egg yolk

Janek Urvik, Kalev Rattiste, Mathieu Giraudeau, Monika Okuliarova, Peeter Horak & Tuul Sepp
While the general patterns of age-specific changes in reproductive success are quite well established in long-lived animals, we still do not know if allocation patterns of maternally-transmitted compounds are related to maternal age. We measured yolk testosterone, carotenoids and vitamins A and E levels in a population of known-aged common gulls (Larus canus) and found an age-specific pattern in yolk lutein and vitamin A concentrations. Middle-aged mothers allocated more of these substances to yolk compared...

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...

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  • Estonian University of Life Sciences
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