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Research Assessment Exercise 2007 University of Oulu

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2. Publications

2a. Description of the research profile and research training

1. Research profile

Research in the Department of Biology is organized into five main areas: Animal ecology, animal physiology, genetics, plant ecology, and plant physiology. A unifying theme in the research is biodiversity and the evolution of adaptations at various levels of biological organization. Biodiversity studies have included components from the genetic diversity through ecosystem analysis and economical evaluation of biodiversity. The study of adaptation involves population and ecosystem ecology, physio­logi­cal and ecophysiological approaches, studies in pop­ulat­ion genetics, genomics and gene expression studies. The research projects in each research area are, however, extensively inter­connect­ed, as shown in the diagram (figures indicate the numer of professors). The research also has good connections to the national relevant applied research institutes.

Animal Ecology
Main research themes in terrestrial ecology include A) Population biology of species in fragmented and ephemeral landscapes, B) Local adaptations of resident and immigrant species/individuals, C) Impact of climate and environment change on populations and implications of these changes on biodiversity, D) Conservation biology and genetics and E) Evolutionary history and phylogeography. These issues are studied focusing on several bird and mammal species.
A long term data is used first, to develop population projections for populations inhabiting fragmented landscapes (e.g. coniferous forests and seashore meadows) and, second, to analyze the relationship between stochastic influences on the demography and population dynamics for species with different conservation status. These aspects are studied with population genetic and molecular tools also. The research has important management contributions because anthropogenic causes (habitat fragmentation, climate change) impose a multitude of threats to a number of species adapted to the unique habitats in the area. Long-term data can also be applied to resolve the impact of global change. Evolutionary histories and phylogeographic structures of species and populations are studied in palearctic scale, related to post-glacial and antropogenic effects on genetic population structures.
Research in the freshwater ecology is focused on freshwater biodiversity and conservation. Most of the research deals with large-scale ecological patterns at the level of landscapes (drainage systems), ecoregions, or even larger spatial entities (landscape ecology, macroecology). The applied aspects of the research relates to stream restoration and management, with the aim of testing whether restorations conducted for fishery purposes also enhance the recovery of stream biodiversity and ecosystem processes. Research combines broad-scale observational studies with well-targeted field and laboratory experiments. This research is not focused on any particular group of organisms, but instead multiple taxonomic groups are used (fish, benthic invertebrates, benthic algae, zooplankton, macrophytes, bryophytes).
Evolutionary and behavioural ecology research is concentrating on three topics:

A) What maintains variation in insect life histories, especially in reproductice tactics? In most insects, the number of generations decrease along with the latitude from south to north. Different selection pressures shape the optimal phenotype in different directions in each generation. This research explores, how female reproductive tactics change when the number of generations decrease or densities become lower. The focus is also on the variation in social interactions among individuals under different environmental conditions, especially on the conflict of interest between individuals of the same and opposite sex. Secondly, research is focused on the consequences of low population density on reproductive tactics when females are dependent on other individual’s aid. Most of the questions are explored experimentally, but theoretical work will be carried out as well.

B) Evolution of Lepidoptera. Lepidopteran phylogeny is currently poorly resolved. Therefore the group studies Lepidopteran evolutionary history using molecular markers. Also utility of “DNA barcodes” and geometric morphometrics in clarifying evolutionary and systematic relationships between lepidopteran taxa is studied.

C) Dispersal capacity and rapid invasion of the deer ked (Lipoptena cervi)

The species is a very common and abundant ectoparasite on deer animals, especially on moose. The principal aims are to explore why the species has been so successful in Finland, and has it potential to establish itself to a novel host (reindeer) in Lapland. The focus of the research programme is on the two life-history stages that are of crucial importance for successful invasion, but most sensitive to northern climate and the change of climate. Using controlled experiments, the hatching success of pupae, female host choice and the dispersal capacity of adults is explored.
Research is funded mainly by the Academy of Finland, Finnish Ministry of Environment, Finnish Ministry of Agriculture and Forestry and several private funding organizations (e.g. Koneen säätiö, Emil Aaltosen säätiö, Kulttuurirahasto). All the research is performed in co-operation with many Finnish (e. g. Finnish Environment Institute (FEI), Finnish Game and Fisheries Research Institute, Metsähallitus) and international institutes in several scientific network regimes.
Animal Physiology
In animal physiology there are two main research themes: (1) Energetic and metabolic adaptations of endotherms and (2) Role of calcium receptors/channels in the adaptation of skeletal and cardiac muscle to exercise and other challenges.

In theme (1) we focus on basic physiological mechanisms of thermoregulation, thermogenesis, seasonal adaptation including various hypometabolic states, hormonal regulation of body fat stores and energy balance, and evolutionary aspects of endothermic physiology. The approach is comparative and evolutionary, and a variety of endothermic model species are used (birds, mammals). These include both wild species and laboratory species. The methodology includes biochemical and endocrinological techniques, electrophysiology, whole animal calorimetry and telemetry. The main focus is in basic research, but a number of applied studies have arisen as spin-offs, e.g. muscle function of humans in during work in the cold.

Theme (2) combines the cellular physiology of calcium receptors/channels to muscle performance and training effects. These effects are studied in relation to changes in muscle fibre composition and oxidative metabolism. The approach here also is comparative, and a variety of model species (fish, laboratory rodents) are used. Methods include immunostaining with confo­cal microscopy, gene expression analysis, histochemistry, and functional muscle studies. In addi­tion to basic research, studies on the role of these molecules in the muscular performance of cultivated vs. wild fish have obvious applied underpinnings.

The research in animal physiology is based on active national and international collaboration. Within our own university, an active collaboration with animal ecologists in Oulu has recently been established in theme (1). In this project, the metabolic and hypometabolic adaptations of Northern passerine birds are studied in relation to their life histories. A collaborative study with the Faculty of Medicine in theme (2) examines the role of calcium channels in the functional changes in ischemic heart muscle. Other national collaborators are Universities of Kuopio and Joensuu, research Institutes (e.g. Game and Fisheries Research Institute, Institute of Occupational Health).

Additionally, an active research project on photobiology and vision research in invertebrates is carried out in a project where the scientist (Meyer-Rochow) is based elsewhere, but conducts many of his studies in affiliation with the University of Oulu.
Genetics in Oulu aims at a broad undergraduate education, but research is centered on population genetics and evolution. The Center for Population Genetics Analyses, a center of excellence designated by the Academy of Finland for 2002-2007, is driving this research, and the focus is in applying molecular genetics and bioinformatics to analyze the genetic structure, history and adaptation of plant and animal populations. One hallmark is the development of a Bayesian approach for analysing population structures (BAPS), an approach that has been widely applied and further developed for different types of data Access to genomic data has dramatically changed the research projects, and the emphasis has shifted from marker-based population genetics to population genomics.

The availability of the honeybee genome sequence has redirected the social insect research and our results show that social insects have the highest known recombination rates in higher eukaryotes and the nuclear genome of the honeybee has the highest density of mitochondrially derived sequences (NUMTs) known in any animal. Genomic resources are currently used to compare the evolutionary rates of genes involved in the insect innate immunity.

The plant genetics group has used both quantitative genetic and molecular population genetics tools in searching for the genetic basis of the extensive genetic differentiation of adaptive both pine trees and outcrossing relative species of Arabidopsis, the plant molecular biology model organism. The group first showed characteristic patterns of nucleotide diversity in forest tree populations, and compared outcrossing and selfing species of Arabidopsis in terms of nucleotide diversity. With comparative mapping, measured the rate of chromosomal evolution between A. thaliana and its close relative A. lyrata.

Other genetic projects focus on speciation, phylogeography and population structures, particularly in the context of conservation. The importance of host switch for speciation has been shown both in parthenogenetic fish parasite Gyrodactylus and in gall-forming sawflies. The phylogeographic projects have clarified the colonization history of northern areas, including both terrestrial (birds, trees, ants) and aquatic (salmonids, marine algae) organisms. The conservation genetic projects have produced relevant data for practical conservation of endangered species and also important information on genetic aspects of rarity in declining populations of Drosophila and in fragmented plant populations.

The research groups have enough common in their approaches and questions, such that they form a shared population genetics research community, with interaction with ecologists and physiologists within the department. The Centre for Population Genetics Analyses also coordinates a national graduate school in population genetics, and the relevant research groups in the department are involved. The graduate school finances some doctoral students, organizes workshops and short courses, and provides a platform for contacts between the graduate students in different Finnish universities and research institutes.

The research groups are involved in many international collaborations, e.g. through EU projects (such as TREESNIPS 2002-2007, a collaboration of European tree geneticists, coordinated by Oulu), in EU-training networks (INSECTS), or more informal collaborations. There are also good contacts to the national research agencies, such as the Game and Fisheries Research Institute or the Finnish Forest Research Institute.

Plant ecology
Research profile of plant ecology in Oulu can be characterized with the words “Plant survival in the north”. The below mentioned subtitles indicate our three focus areas:
Plant population and evolutionary ecology

In plant population dynamics, the emphasis is in metapopulation dynamics and conservation of endangered plant species. Long-term population surveys are combined with theoretical modelling and molecular biological studies of dispersal and population structure. Evolutionary ecological studies have especially investigated plant adaptations related to resource acquisition, reproduction (clonality, sex allocation, and breeding systems) and species interactions and coevolution (herbivory, parasitism, and symbiosis). Empirical and theoretical work has been carried out on plant tolerance to herbivory and the evolution of defence responses as well as various symbiotic interactions from lichens and mycorrhizas to endophyte-grass symbiosis.

Support from graduate school in evolutionary ecology.
Functional plant ecology, ecophysiology and environmental ecology

In ecophysiology, research is focused to plant ecophysiology in northern areas, air pollution and climate change responses: programmes e.g COST Action E 6 “EUROSILVA” Forest tree physiology research (chaired in Oulu). Our studies concerning sulphur in the environment have participated in COST Action 829 on Fundamental, Agronomical and Enviornmental Aspects of Sulphur Nutrition and Assimilation in Plants. Traditionally, we have worked within IUFRO project groups, 7 Division on Forest Health Project 7.04.00. We have been active in Arctic Climate Impact Assessment and Arctic Monitoring and Assessment Programme (AMAP).

Our current interests are protective functions in evergreens under changing climate: using mosses as model plants”, and an integrated approach of cuticular functions in subarctic and arctic evergreens (e.g., FUVIRC Finnish ultraviolet research center, TARANTELLA Polar Year network) and some EU-projects; Plant – atmosphere interaction studies are connected to cuticular functions research( e.g.UNECE Ozone level II cooperation, nitrogen critical loads and elevated temperatures ). More plant physiology oriented questions are undet the title “ Seasonality and frost hardiness of northern plants under global change and environmental stress”;
Population, community and ecosystem ecology

We concentrate on plant community and vegetation ecology. We focus on the factors controlling species diversity and species interactions, mainly in northern environment. We have strong methodological skills on multivariate analysis, and research of species-environment relationship, where we also study practical aspects of using communities in environmental assessment.

Plant Physiology
In Plant Physiology we are studying how the plants are functioning both at cellular, molecular and whole plant level. The research topics are in sensu lato related to plant developmental biology. We are particularly interested in lignin biosynthesis, polyamine metabolism during Scots pine embryo development, structural maturation of conifer seed, molecular events and regulation during berry ripening, plant-microbe interactions in development of pine seedlings. Methodologically that is done by taking the advantage of the methods of traditional plant physiology and anatomy, plant biochemistry, molecular biology and biotechnology. We are focusing on the Northern plants, especially on forest trees (Populus tremula x tremuloides, Betula pendula, Pinus sylvestris, Picea abies) but also on small berry fruits (Vaccinium myrtillus), the crop plant potato (Solanum tuberosum) and some medicinal northern plants (Rhodiola, Hypericum, and Drosera). The inter-disciplinary research targets include forest studies, investigations on environmental effects of genetically modified trees and bioactive products of plant secondary metabolism.

The research in the field of plant physiology is based on active national and international collaboration. With the national collaborators MTT (Agrifood Research Finland), Metla (Forest Research Institute) and other universities (University of Helsinki, University of Joensuu and University of Kuopio) we are in active co-operation which has led to joint publications. At international level we have actively participated in COST actions (COST 834) and we have several co-operating partners abroad (ARS, Austria; ETH, Switzerland; Univ. Barcelona, Spain; Ukrainian Academy of Sciences / IMBG; Russian Academy of Sciences / IBPM; NCSU, NC, USA; USDA-ARS / Albany, CA, USA).

2. Research training
Research training is a major goal of all research in The Department of Biology. Each year about 10 new doctoral students are recruited, and the number of active doctoral students is close to 100. Many students have full-time funding for several years of doctoral studies, either their own or from the supervisor. Others are teaching at the department. Some of the doctoral students are conducting their doctoral research while being employed full-time outside the department in other jobs. Most students participate at least in a minor way to the teaching of the department in practical courses.

  • Active supervision. At the beginning of their studies, each doctoral students presents a plan that shows the formal studies at home university and in other doctoral courses. Each doctoral student has two supervisors. In addition, each doctoral student also has a follow-up group that meets annually to evaluate the progress and to discuss potential problems.

  • Graduate schools. Many doctoral students are members of national graduate schools in biology. They are thus entitled to participate in the education, seminars and special courses organised by these graduate schools.

  • Doctoral training organised by the department. The department organises training for all students, representing the various research fields. This involves participation in a graduate seminar, where the students present a seminar on their research plans. The seminar also deals with general issues related to a research career (funding, project management, employment aspects). Special courses, some of interest to all, such as scientific communication are organised. Methodological courses are also organised, e.g. on statistical methods. There is an annual two-day sympo­sium, a congress-style meeting organized and chaired by doctoral students. This training is available to all students, including those that are affiliated to a national graduate school or who are conducting their research outside the university, e.g in a research institute.
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