The liver-X-receptors (LXRs) act as cholesterol sensors and participate in the regulation of lipid and cholesterol metabolism. The objective of this study was to determine the role of LXR during development using the zebrafish model. By in situ hybridization we showed distinct expression of lxr in the brain and the retina in the developing and adult zebrafish. Lxr ligand activation affected the expression of genes involved in lipid metabolism in zebrafish adult brain and eye as well as in zebrafish embryos. Morpholino knock down of lxr resulted in an overall impaired lipid deposition as determined by oil red O staining particularly in the head and around the eyes, and to significantly elevated levels of both total and free cholesterol in the yolk of lxr morphant embryos. The expression of genes involved in lipid and cholesterol metabolism was also changed in the lxr morphants. Furthermore, alcian blue staining revealed malformation of the pharyngeal skeleton in the lxr morphant. Our data show that Lxr is an important component of the regulatory network governing the lipid homeostasis during zebrafish development, which in turn may support a role of Lxr for normal development of the central nervous sytem, including the retina.

The circular distribution of the willow warbler Phylloscopus trochilus around the Baltic Sea shares many features with the classic examples of ring species; however, the system is much younger. It has previously been shown that a secondary contact zone is located in central Scandinavia, where there are narrow clines for several morphological traits coincident with a migratory divide. Here we analyse multiple traits and genes from > 1700 males captured on breeding territories at 77 sites spread around the Baltic Sea to test the following hypothesis. If the secondary contact zone in Scandinavia is a result of divergence in two allopatric refuge populations during the last glaciation, we expect to find a similar secondary contact zone somewhere else around the circular distribution. Our results show that the trait clines were wider and displaced from each other along the eastern side of the Baltic Sea. Analyses of 12 microsatellite loci confirmed that the genome is very similar between the terminal forms (F(ST) = 0). Two AFLP-derived markers filtered out from a genomic scan instead appear to be maintained by selection. These markers exhibited steep clines at the secondary contact zone in Scandinavia, but as for the phenotypic traits, had vastly different cline centres east of the Baltic Sea. The trait clines along the ring distribution outside the Scandinavian secondary contact zone thus seem to have been shaped by independent action of selection or drift during the process of postglacial colonization.

We tested whether differences in ploidy level and previous exposure to herbivory can affect plant tolerance to herbivory. We conducted a common garden experiment with 12 populations of two ploidy levels of the perennial herb Cardamine pratensis (five populations of tetraploid ssp. pratensis and seven populations of octoploid ssp. paludosa). Earlier studies have shown that attack rates by the main herbivore, the orange tip butterfly Anthocharis cardamines, are lower in populations of octoploids than in populations of tetraploids, and vary among populations. In the common garden experiment, a combination of natural and artificial damage significantly reduced seed and flower production. We measured tolerance based on four plant-performance metrics: survival, growth, seed production and clonal reproduction. For three of these measurements, tolerance of damage did not differ between ploidy levels. For clonal reproduction, the octoploids had a higher tolerance than the tetraploids, although they experience lower herbivore attack rates in natural populations. Populations from sites with high levels of herbivory had higher tolerance, measured by seed production, than populations with low levels of herbivory. We did not detect any significant costs of tolerance. We conclude that high intensity of herbivory has selected for high tolerance measured by seed production in C. pratensis.

Rapid evolutionary change is increasingly being recognized as commonplace, but the evolutionary consequences for species and ecosystems under human-induced selection regimes have not been explored in detail, although many species occur in such environments. In a common garden experiment and with amplified fragment length polymorphism markers, we examined whether genetic differentiation has taken place between spatially intermixed populations of creeping thistles Cirsium arvense (Asteraceae) collected from a natural habitat (maritime shores), a semi-natural habitat (road verges) and arable fields under two management regimes: conventional and organic farming. Populations of C. arvense have altered genetically and locally adapted their growth patterns with changed land use. Although plants from different habitats showed similar total biomass production, shoot and root production was higher for maritime populations, suggesting selection for increased competitive ability. Competitive ability then declined in the order semi-natural, conventional farms and organic farms. Thistles in arable fields may be more selected for tolerance against disturbances from herbicides and mechanical weed control. In addition, early shoot sprouting and genetic analysis showed differentiation between plants originating from conventional farms and farms that were converted to organic 9–30 years ago, suggesting some adaptation to altered crop cultivation practices

Parmelioid lichens are a diverse and ubiquitous group of foliose lichens. Generic delimitation in parmelioid lichens has been in a state of flux since the late 1960s with the segregation of the large, heterogeneous genus Parmelia into numerous smaller genera. Recent molecular phylogenetic studies have demonstrated that some of these new genera were monophyletic, some were not, and others, previously believed to be unrelated, fell within single monophyletic groups, indicating the need for a revision of the generic delimitations. This study aims to give an overview of current knowledge of the major clades of all parmelioid lichens. For this, we assembled a dataset of 762 specimens, including 31 of 33 currently accepted parmelioid genera (and 63 of 84 accepted genera of Parmeliaceae). We performed maximum likelihood and Bayesian analyses of combined datasets including two, three and four loci. Based on these phylogenies and the correlation of morphological and chemical characters that characterize monophyletic groups, we accept 27 genera within nine main clades. We re-circumscribe several genera and reduce Parmelaria to synonymy with Parmotrema. Emodomelanelia Divakar & A. Crespo is described as a new genus (type: E. masonii). Nipponoparmelia (Kurok.) K.H. Moon, Y. Ohmura & Kashiw. ex A. Crespo & al. is elevated to generic rank and 15 new combinations are proposed (in the genera Flavoparmelia, Parmotrema, Myelochroa, Melanelixia and Nipponoparmelia). A short discussion of the accepted genera is provided and remaining challenges and areas requiring additional taxon sampling are identified.

The bird cherry-oat aphid (Rhopalosiphum padi L.) is an important pest on cereals causing plant growth reduction without specific leaf symptoms. Breeding of barley (Hordeum vulgare L.) for R. padi resistance shows that there are several resistance genes, reducing aphid growth. To identify candidate sequences for resistance-related genes, we performed microarray analysis of gene expression after aphid infestation in two susceptible and two partially resistant barley genotypes. One of the four lines is a descendant of two of the other genotypes. There were large differences in gene induction between the four lines, indicating substantial variation in response even between closely related genotypes. Genes induced in aphid-infested tissue were mainly related to defence, primary metabolism and signalling. Only 24 genes were induced in all lines, none of them related to oxidative stress or secondary metabolism. Few genes were down-regulated, with none being common to all four lines. There were differences in aphid-induced gene regulation between resistant and susceptible lines. Results from control plants without aphids also revealed differences in constitutive gene expression between the two types of lines. Candidate sequences for induced and constitutive resistance factors have been identified, among them a proteinase inhibitor, a serine/threonine kinase and several thionins.

A multiple regression model was used to analyse if the structure of vegetation and soil patches in grazed units (pastures) can be used as explanatory variables to predict the prevalence of Dicrocoelium dendriticum, a common parasite of cattle and sheep, in grazing cattle stocks on the Baltic island of land in southern Sweden. The scale dependency was evaluated by comparing three levels of spatial resolution of patches. Prevalence data were obtained from slaughtered animals. Our models predict that the prevalence of D. dendriticum increases in grazed areas with woody vegetation, whereas moist and wet areas decrease parasite prevalence. The predictive power of the statistical models increased with increasing level of patch resolution. Approximately 42% of the variation in parasite prevalence (angular transformation) was explained by the areal proportion of vegetation types (4th-root-transformed). Based on the results obtained, we believe that our model strategy provides a rational and systematic tool to identify habitats that carry risk for D. dendriticum infection of ruminants, and that it can be applied to other parasites with similar life cycles such as Fasciola hepatica.

Tick-borne encephalitis virus (TBEV) is a flavivirus with major impact on global health. The geographical TBEV distribution is expanding, thus making it pivotal to further characterize the natural virus populations. In this study, we completed the earlier partial sequencing of a TBEV pulled out of a pool of RNA extracted from 115 ticks collected on Torö in the Stockholm archipelago. The total RNA was sufficient for all sequencing of a TBEV genome (Torö-2003), without conventional enrichment procedures such as cell culturing or suckling mice amplification. To our knowledge, this is the first time that the genome of TBEV has been sequenced directly from an arthropod reservoir. The Torö-2003 sequence has been characterized and compared with other TBE viruses. In silico analyses of secondary RNA structures formed by the two untranslated regions revealed a temperature-sensitive structural shift between a closed replicative form and an open AUG accessible form, analogous to a recently described bacterial thermoswitch. Additionally, novel phylogenetic conserved structures were identified in the variable part of the 3'-untranslated region, and their sequence and structure similarity when compared with earlier identified structures suggests an enhancing function on virus replication and translation. We propose that the thermo-switch mechanism may explain the low TBEV prevalence often observed in environmentally sampled ticks. Finally, we were able to detect variations that help in the understanding of virus adaptations to varied environmental temperatures and mammalian hosts through a comparative approach that compares RNA folding dynamics between strains with different mammalian cell passage histories.

Habitats of Swedish conservation interests are in general small and fragmented following the extensive and intensive forest management history. This study covering 71 000 ha of boreal Sweden investigates how history influences present-day distribution and composition of forests identified as high conservation value habitats and how they are protected. We also investigated if the habitat criteria used to describe reservations differed between reservation types and if habitat criteria were associated with the size of Woodland Key Habitats. The results show strong effects from historical ownership and historical forest type on the probability of an area being set aside as formally protected or as voluntary protected Woodland Key Habitats. We also found that both formal reservations and Woodland Key Habitats primarily cover coniferous forest in the age interval 70-110 years but not the presumably most valuable oldest coniferous category >110 or deciduous forests, which are as common in reservations as in other areas. Old deciduous forests (>110 years) are significantly more rare in formal reservations compared to the forest matrix. When viewed in a context of fragmentation and edge effects the results underline the importance of evaluating reserved areas and Woodland Key Habitats in a wider temporal and larger spatial perspective to optimize conservation management efforts. Maximal representation and biodiversity can be better achieved if new reservations are chosen to represent different ownership and forest history, and if they are selected in a landscape context related to present reservations and the present surrounding production forest.

In this study we reconstruct forest composition during the 1860s for a 71000 ha area in southern boreal Sweden. The aim is to show how historical ownership and associated anthropogenic disturbances act as a source of heterogeneity in the present-day distribution and composition of coniferous and deciduous forest within the commercial production forest. We use older (>110 years) and mature (70-110 years) forest as response variables in generalized linear models with a binominal error distribution. The explanatory variables include size of zone, historical type of ownership zone (village, company, and farm), amount of forest, and forest type. We focus in particular on investigating effects from interacting explanatory variables. The significant statistical associations in the study indicate that patterns of deciduous and coniferous older patches differ, and that deciduous patches differ in relation to age interval. The oldest deciduous patches, for example, are today more likely on areas that had deciduous cover also in the past and stood on forestland managed by farmers, but less likely on the same habitat managed by companies. We show that there are strong effects on present forest composition from historical ownership and forest composition. We argue that by including local data on past ownership combined with knowledge on use patterns management could be better adapted to local landscape dynamics compared to the application of overly generalized patterns or models of boreal dynamics that excludes interactions with management.

We combine historical maps and satellite derived data to reconstruct the development of a Swedish boreal landscape over the past 300 years. The aim is to understand legacies from past use patterns in present-day forest composition and consequences for conservation objectives from a landscape perspective. We analyze landscape development in cross-tabulation matrixes, building change trajectories. These trajectories are tested in linear models to explain the distribution of present-day landscape composition of coniferous, mixed, and deciduous forests >110 years. Of 49 tested change trajectories, 11 showed a significant association. Associations for mixed and coniferous forests were similar and linked to characteristics such as forest continuity, which characterized the studied landscape. Deciduous older forests did not show any association to forest continuity but were more likely to occur on areas that specifically shifted from forests with grazing in the 1720s to open impediment (likely indicating low tree coverage) in the 1850s. There were large shifts and spatial redistribution in ownerships over time. Use patterns and legacies varied between small- and large-scale ownership categories as well as within small-scale categories. The legacies found in the study indicate a complex origin of heterogeneous landscape elements such as older deciduous forests. Additionally, the origin of the legacies indicates a potential need to diversify conservation management based on the influence of past use patterns. Despite large inconsistencies in historical and contemporary data we argue that this type of analysis could be used to further understand the distribution of landscape elements important for conservation objectives.

Membrane traffic is tightly regulated and the Rab protein family of small GTPases plays a central role in this regulation. One member of this family is the Saccharomyces cerevisae protein Ypt6. To search for new genes interacting with Ypt6-related pathways, we performed a genetic screen for high copy suppressors of ypt6 Delta temperature sensitivity at 35 degrees C. Among the suppressors, MYR1 was also able to suppress the temperature sensitive mutant lacking Ric1, a subunit of the Ypt6 guanine exchanging factor complex Ric1/Rgp1. Myr1 is characterized by a coiled coil region and a GYF domain, a protein module binding proline-rich sequences. Myr1 is able to bind membranes but is also associated with larger structures insoluble in Triton X-100. By immunofluorescence, Myr1 shows a network-like pattern as well as small foci. Overexpression of Myr1 influences nuclear envelope morphology and high levels are lethal. This lethality is rescued when the N-terminal region, containing the GYF domain, is deleted. The transcription profile of a myr1 Delta strain shows effects on genes involved in nuclear migration, Ras signalling and transcription. Taken together, these results suggest that Myr1 is a novel factor linked to the secretory pathway and important cellular regulatory mechanisms.

In this book Artur Granstedt - Ph.D. in Agronomics and Associate Professor at Södertörn University, and Coordinator of the BERAS project (Baltic Ecological Recycling Agriculture and Society) - describes how ecologically adapted farming based on local recycling and renewable energy sources can reduce the eutrophication of the Baltic Sea and even help to reduce global warming. Widespread conversion to organic farming methods would furthermore stop the spread of toxic chemicals on farmland, benefit biodiversity and stimulate social and economic development in rural areas in the Baltic Sea region.

The book starts with a description of the ecosystems that support the health of the biosphere - terrestrial and marine, the climate, and global food production. Granstedt also gives a historical overview of agricultural practices, noting the various ways in which human activity alters the natural order of things and, if we are not mindful, can deplete the resources that support our existence. But he also gives examples of how we can turn negative trends to the better, how we can restore fertility to the soil and bring depleted land to bloom once again and produce nourishing food that can feed the world.

Artur Granstedt writes on the basis of decades of experience as an organic farmer, researcher, adviser and teacher of ecologically sustainable agriculture. The book reports the results of field trials and evaluation on farms in eight countries around the Baltic Sea that were conducted in the BERAS project. This comprehensive project, which was supported in part by funding from the European Union, is now continuing in an implementation phase, focusing on how agriculture throughout the region can be converted to profitable and ecologically sustainable methods of production.

The publication of this book has been made possible through a grant from the European Regional Development Fund (ERDF) to the BERAS project at Södertörn University and the Biodynamic Research Institute in Järna, and funding from the Swedish Government and the Swedish Research Council, Formas.

Artur Granstedt, agronomie doktor, docent vid Södertörns högskola och koordinator för Östersjöprojektet BERAS beskriver här hur ett ekologiskt jordbruk, baserat på lokala kretslopp och förnyelsebar energi, kan minska övergödningen av Östersjön och även bidra till att minska den globala uppvärmningen. Det kan dessutom förhindra spridningen av kemiska bekämpningsmedel, gynna den biologiska mångfalden och stimulera social och ekonomisk landsbygdsutveckling i Östersjöområdet.

Boken inleds med en beskrivning av de livsuppehållande ekosystemen och deras betydelse för jorden, havet, klimatet och vår mat. Författaren ger också en överblick över odlandets historia: hur vi människor griper in och förändrar det naturgivna och hur vi på kort tid kan förbruka det som naturen byggt upp. Han visar också på hur vi kan odla jord, skapa ökad bördighet, få jorden att blomstra och ge närande mat åt alla.

Till grund för boken ligger Artur Granstedts mångåriga arbete med odling, forskning, rådgivning och undervisning i ekologiskt jordbruk. Här redovisas också resultat från studier av det rent praktiska arbetet på ett antal gårdar, dokumenterade och utvärderade i åtta länder i det av EU delfinansierade Östersjöprojektet BERAS (Baltic Ecological Recycling Agriculture and Society). Detta arbete drivs nu vidare med fokus på hur en omläggning av jordbruket kan ske i hela Östersjöregionen i fortsättningsprojektet BERAS Implementation.

Bokens utgivning har finansierats av Europeiska regionala utvecklingsfonden (ERUF) inom ramen för Östersjöprojektet BERAS vid Södertörns högskola samt Biodynamiska Forskningsinstitutet i Järna med bidrag från den svenska regeringen via det statiliga forskningsrådet Formas.

The effects of the strobilurin fungicide azoxystrobin were studied in rackish water microcosms, with natural plankton communities and ediment. Two experiments were conducted: Experiment 1 (nominal conc. 0, 5 and 60 mu g/L, 24-L outdoor microcosms for 21 days) and a second, ollow-up, Experiment 2 (nominal conc. 0, 3, 7.5, 15 mu g/L, 4-L indoor icrocosms for 12 days). The microcosms represent a simplified brackish ater community found in shallow semi-enclosed coastal areas in gricultural districts in the Baltic Sea region. Measured water oncentrations of the fungicide (Experiment 1) were, on average, 83 and 2% of nominal concentrations directly after application, and 25 and 30% fter 21 days, for the low and high dose treatments, respectively, orresponding to mean DT50-values of 15.1 and 25.8 days, for low and igh dose treatments, respectively. In Experiment 1, direct toxic ffects on calanoid copepods at both test concentrations were observed. imilarly, in Experiment 2, the copepod abundance was significantly educed at all tested concentrations. There were also significant econdary effects on zooplankton and phytoplankton community structure, tanding stocks and primary production. Very few ecotoxicological tudies have investigated effects of plant protection products on Baltic rganisms in general and effects on community structure and function pecifically. Our results show that azoxystrobin is toxic to brackish ater copepods at considerably lower concentrations than previously eported from single species tests on freshwater crustaceans, and that irect toxic effects on this ecologically important group may lead to ascade effects altering lower food webs and ecosystem functioning.

Brain estrogen production, performed by the enzyme aromatase, can be disrupted/affected in teleost fish exposed to endocrine disruptors found in polluted aquatic environments. The guppy (Poecilia reticulata) was previously studied and confirmed to suffer negative effects on reproductive behaviors following inhibition of the brain aromatase reaction. Here adult guppies (Poecilia reticulata) of both genders were subjected to known endocrine disruptors: the androgen androstenedione (A), the synthetic estrogen 17 alpha-ethinylestradiol (EE2), and the estrogenic surfactant 4-nonylphenol (NP), at high (50 mu g/L) and at environmentally relevant concentrations (10 ng/L EE2, 5 mu g/L NP, and 0.7 mu g/L A) for 2 weeks followed by measurements of brain aromatase activity (bAA). In the adult males, bAA was stimulated by A and EE2 at 50 mu g/L. Female activity was also stimulated by the higher estrogenic treatment. At environmentally relevant concentrations only the EE2 treatment affected bAA, and only in males. The alkylphenolic substance NP produced no effect in either of the experiments, not on males nor females. The results indicate that short-term steroid treatments have stimulatory effects on guppy brain aromatase even at concentrations that can be found in the environment. We thus suggest bAA of adult guppies to be a suitable bioindicator of endocrine disruptors.

Behaviour studies are used in toxicology research as they are excellent tools to measure physiological end-points caused by exogenous chemicals. In mammals both reproductive and non-reproductive behaviours have been used for a long period of time, whereas in teleost fishes non-reproductive behaviours have received little attention compared to reproductive behaviours. Recent advances in measuring stress related behaviours in zebrafish have provided additional tools to understand behaviour toxicology in fish. One species with well documented reproductive behaviour disturbed by different toxicants is the guppy, which is better suited than zebrafish for reproductive behaviour studies and therefore might be a better model organism for comparative behaviour studies in fish toxicology. Here we report new applications for non-reproductive behaviours in guppy and test these behaviours on males treated with the endocrine disruptor 17α-ethynylestradiol at environmentally relevant concentrations. 17α-ethynylestradiol increased freezing and bottom-dwelling when fish were placed in a non-familiar aquarium, but did not significantly affect shoaling behaviour. These results are similar to the anxiogenic behaviours seen in rats treated perinatally with 17α-ethynylestradiol and add more concern to the impacts of endocrine disruptors on aquatic wildlife.

There is a growing demand for wild caught juvenile fish to supply the market for aquaculture. However, little is known about the genetic effects of juvenile collection from wild populations. There are a number of imminent threats to both aquaculture systems and wild fish populations. Juvenile collection from a single population can for example reduce population’s evolutionary potential as well as the disease resistance within an aquaculture pond. In this study, we investigated the local genetic structure of juvenile mullets collected from five sites around Bagamoyo (Tanzanian mainland) and Zanzibar Island, East Africa. Fish were caught in low tide using a seine net. The fish were morphologically identified, and then genetically identified using direct sequencing of the CO1 gene with cross referencing with the Barcode of Life Database (BOLD) systems.  Molecular variance analyses were used to infer genetic subdivision based on geographic sampling site as well as inferring population structure through the Bayesian assignment test implemented in STRUCTURE 2.3. Our results showed that samples morphologically identified as Mugil cephalus where in fact Valamugil buchanani and we also found evidence of an introgression genome event, where the gene flow from one species may have affected the general gene pool. The Bayesian analysis revealed a clear genetic population structure among the sampled fish; the main difference was the presence of a unique mainland cluster. Our findings may have important implications for management and conservation of mullet fishes in the region and elsewhere.

The effects of cypermethrin, copper and glyphosate on the endocrine system and subsequent response to female pheromones were investigated in mature male brown trout (Salmo trutta) parr.  Responses measured were the amount of strippable milt, blood plasma levels of both an androgen (11-ketotestosterone (11-KT)) and a progestin (17α,20β-dihydroxy-4-pregnen-3-one (17,20b-P)), and behavioural changes. This was done in a two phased investigation where parr were exposed to one of the following via ambient water: 1) 0.1 or 1.0 μg L^-1 cypermethrin, 2) 10 or 100 μg L^-1 copper (Cu²⁺), or 3) 150 μg L^-1 glyphosate for a 96 hour period.  Phase one was a priming experiment exposing parr to a treatment followed by priming with PGF_2α or ovarian fluid (OVF). Atlantic salmon (Salmo salar) parr were, also exposed to glyphosate during phase I. The second phase was centered on behavioural observations.  Exposed parr were placed in a 35,000 L stream aquarium together with two ovulated females and four anadromous males. After the experiments a blood sample was taken, milt volumes measured and testes weighed.  The plasma was analyzed for 11-KT and 17,20b-P concentrations using radioimmunoassay (RIA).

Results from phase I-priming: 1.0 μg L^-1 cypermethrin exposure lowered 17,20b-P and 11-KT; Copper exposure lowered milt volumes; glyphosate exposure lowered 11-KT in salmon and raised 17,20b-P in trout.  Results from phase II-behaviour: 1.0 μg L^-1 cypermethrin exposure lowered 11-KT, milt and spawning behaviour; copper exposure lowered spawning behaviour and raised 11-KT; Glyphosate exposure lowered 11KT; continuous cypermethrin exposure raised 17,20b-P, 11-KT and gave a tendency towards increased aggression. It is concluded that low concentration exposure to the compounds examined can induce negative effects on male salmonid endocrine systems, either through a disruption in the olfactory system or through a direct effect.

In the present study, the effects of copper (CuSO4) on the ability of mature male brown trout Salmo trutta parr to detect and react both physiologically and behaviourally to female pheromones were studied. The study was composed of two parts. In the first experiment, priming effects of the female pheromone prostaglandin F-2 alpha (PGF(2 alpha)) were evaluated by determining the amount of milt produced and the blood plasma levels of 11-ketotestosterone (11-KT) and 17 alpha,20 beta-dihydroxy-4-pregnen-3-one (17,20 beta-P) after the PGF(2 alpha) exposure. In the second experiment, male parr were placed in a large stream tank together with a group of adult males and ovulated females and their individual behaviours were recorded. In the priming experiment, the amount of expressible milt was significantly lower, less than half, in groups exposed during 4 days to 10 or 100 mu g l-1 copper compared with control parr only exposed to water. No significant differences were observed in plasma levels of 11-KT and 17, 20 beta-P. During the behavioural experiment, exposed parr spent less time with the female and had a lower number of courting events. Blood plasma levels of 11-KT were, however, significantly higher in the group exposed to 100 mu g l-1 copper compared with the control group. Furthermore, the exposed group spent significantly less time swimming upstream than did the control group. The present study demonstrates that exposure to copper affects reproductive behaviours and endocrinology of S. trutta male parr.

Environmental change challenges local and global survival of populations and species. In a species-poor environment like the Baltic Sea this is particularly critical as major ecosystem functions may be upheld by single species. A complex interplay between demographic and genetic characteristics of species and populations determines risks of local extinction, chances of re-establishment of lost populations, and tolerance to environmental changes by evolution of new adaptations. Recent studies show that Baltic populations of dominant marine species are locally adapted, have lost genetic variation and are relatively isolated. In addition, some have evolved unusually high degrees of clonality and others are representatives of endemic (unique) evolutionary lineages. We here suggest that a consequence of local adaptation, isolation and genetic endemism is an increased risk of failure in restoring extinct Baltic populations. Additionally, restricted availability of genetic variation owing to lost variation and isolation may negatively impact the potential for evolutionary rescue following environmental change.

Oaks (Quercus robur) can reach a considerable age, which makes them an important substrate for many epiphytic lichens, including several red-listed species. We studied the importance of tree size and other environmental factors for the occurrence of six epiphytic lichens at two sites, in southeastern Sweden, differing in quality as judged by tree size distribution and number of old trees. The effects of tree circumference, light availability, trunk inclination and site were analysed. Results showed that different lichen species responded differently to these factors, but, overall, tree size was most important for lichen occurrence. Five species showed a positive relation to tree size, but the 50% probability of occurrence was reached at different tree sizes among these species and there were also site differences. This study shows that the maintenance of old trees is crucial for several lichen species, which highlights the importance of long-term management plans.

This doctoral thesis examines the challenges to co-management in the Tanzania part of Lake Victoria. The study mainly addresses the Nile perch fishery and uses the fishing communities of Bukoba Rural district, Tanzania as a case study. Co-management in Lake Victoria is defined as the sharing of the management responsibilities between the state and the fishing communities. Co-management was adopted in the Lake Victoria fisheries on the understanding that it has the capacity to provide space in which the poor resource users could be empowered to sustainably manage their resource base. The assumption was that the sharing of the management responsibilities between the state and the community of users would have led to equity in resource access, poverty reduction and resource sustainability. Thus, reducing the role of the state and enhancing that of the communities was seen as a solution to the problems of poverty and illegal fishing that are threatening the sustainability of the fishery and the fishers dependent on it. However, in spite of these proclaimed efforts, illegal fishing and poverty in Lake Victoria remain major threats to the long-term sustainability of the fishery, a fact that is raising questions on the efficacy of co-management in Lake Victoria. These questions have particularly focused on the co-management model and the neo-liberal ideals that underlie it, namely decentralization, participation and accountability. The central argument in this thesis, however, is that co-management performance in Lake Victoria is to a large extent shaped by the complex international, national, and local context in which it is implemented and which in turn shapes the problems of poverty and illegal fishing that co-management is supposed to address. The study concludes that the international and national politics behind the Nile perch fishery intersect with the cultural and social context in which the fishery is embedded to shape co-management performance at the local level.

For analysis, the study applies a multi-level approach and draws insights from the common pool resources theory, the actor-oriented approach, the entitlement framework, and the theory of the state. Detailed interviews across scale, secondary data, policy documents, and laws, supported by quantitative data are the methods applied.

Abstract—Uncontrolled growth of sea urchin populations may have a negative effect on coral reefs, making them barren. To avoid this, different methods of sea urchin reduction have been developed but, without knowledge of their genetic structure and connectivity, these methods may be ineffective. The aim of this study was to examine the fine-scale genetic structure and connectivity in the sea urchin, Diadema setosum, population around Unguja, Zanzibar, using AFLP. We found evidence of different genetic clusters, high migration between the sites and high genetic diversity within the sites. These findings indicate that a manual reduction of sea urchins with similar genetic connectivity, implemented on the same geographic scale as our study, would be ineffective since sites are probably repopulated from many sources.

The expression of NMT (3-aminomethylindole/N-methyl-3-aminomethylindole N-methyltransferase; EC 2.1.1.), involved in the biosynthesis of the indole alkaloid gramine, was investigated in aphid-infested barley (Hordeum vulgare L). NMT is induced by methyl jasmonate and it was hypothesized that the gene would be more strongly upregulated in aphid-resistant barley. We examined the effects of feeding by three aphid species; Russian wheat aphid (Diuraphis noxia Mordvilko), rose-grain aphid (Metopolophium dirhodum Walker) and bird cherry-oat aphid (Rhopalosiphum padi L.) on barley genotypes with varying resistance characteristics. The barley genotypes selected included the cultivar Libra, known to upregulate gramine after feeding by Schizaphis graminum. Infestation by R. padi and M. dirhodum resulted in higher NMT expression in the doubled haploid line 5172-28:4 (DH28:4), which has moderate resistance against R. padi, but not in other aphid barley combinations. None of the aphid plant combinations had however increased gramine, suggesting that aphid-induction of gramine is specific to S. graminum. The increased abundance of NMT transcript in aphid-infested DH28:4 did not lead to higher amounts of NMT protein or NMT enzyme activity, neither did 200 times upregulation of NMT transcript in cotyledons incubated with methyl jasmonate, illustrating that even large differences measured at transcript level may have no metabolic consequences. Drought stress or treatments with abscisic acid did lead to higher gramine concentrations in several barley cultivars, but without any concomitant increase of NMT transcripts. Thus, the regulation of the biosynthetic pathway to gramine at transcript and metabolite level diverges during two different stress conditions.

Contamination can cause a rapid environmental change which may require populations to respond with evolutionary changes. To evaluate the effects of pulp mill effluents on population genetics, we sampled three-spined sticklebacks (Gasterosteus aculeatus) near four pulp mills and four adjacent reference sites and analyzed Amplified Fragment Length Polymorphism (AFLP) to compare genetic variability. A fine scale genetic structure was detected and samples from polluted sites separated from reference sites in multidimensional scaling plots (P < 0.005, 1000 permutations) and locus-by-locus Analysis of Molecular Variance (AMOVA) further confirmed that habitats are significantly separated (F(ST) = 0.021, P < 0.01, 1023 permutations). The amount of genetic variation between populations did not differ between habitats, and populations from both habitats had similar levels of heterozygosity (polluted sites Nei's Hs = 0.11, reference sites Nei's Hs = 0.11). Still, pairwise F(ST): s between three, out of four, pairs of polluted-reference sites were significant. A F(ST)-outlier analysis showed that 21 (8.4%) loci were statistically different from a neutral distribution at the P < 0.05 level and therefore indicated to be under divergent selection. When removing 13 F(ST)-outlier loci, significant at the P < 0.01 level, differentiation between habitats disappeared in a multidimensional scaling plot. In conclusion, pulp mill effluence has acted as a selective agent on natural populations of G. aculeatus, causing a convergence in genotype composition change at multiple sites in an open environment.

Lichens are an important group of organisms in terms of environmental issues, conservation biology and biodiversity, since lichens are sensitive to changes in their environment. Therefore it is important that we develop our understanding of the factors that affect lichen distribution. In this thesis both spatial and temporal distributions of epiphytic lichens at different scales have been studied in southern Sweden.

Brokind was chosen as the study site to investigate the succession of epiphytic lichens on Quercus robur using a chronosequencial approach. Fourteen of the investigated taxa out of 50 proved to be significant. The taxa were divided into three groups according to whether they occurred on young, middle-aged or old trees.

Generation length of the red-listed lichen Cliostomum corrugatum was examined using Bjärka-Säby as the study site. The results showed that the average age of an individual of C. corrugatum is 25–30 years at the onset of spore production.

Generation length of the red-listed lichen Cliostomum corrugatum was examined using Bjärka-Säby as the study site. The results showed that the average age of an individual of C. corrugatum is 25–30 years at the onset of spore production.

The rarity of C. corrugatum was also examined. DNA of an intron from 85 samples, collected at five sites in Östergötland, yielded 11 haplotypes. Results from the coalescent analysis, mantel test and AMOVA indicated that C. corrugatum have a high ability to disperse. The study concluded that its rarity is most likely connected with the low amount of available habitat, old Q. robur.

The changes in the distribution of epiphytic lichens in southern Sweden between 1986 and 2003 were compared. For each year a centroid was calculated on all combinations of tree and lichen species. The three significant cases showed that the centroid movement pointed toward a north-east or north-north-east direction.

Regional gradients of abundance and size of Hypogymnia physodes at 66 sites in southern Sweden were examined. The coordinate system rotating the reference system of investigated sites around the origin was used to search for the best explanatory power for the angle of the explanatory variables. The results showed a gradient of increase in the probability of occurrence in a north-north-east direction and an increase in diameter on thallus size in a west-north-west direction.

Lichens are an important group of organisms in terms of environmental issues, conservation biology and biodiversity, principally due to their sensitivity to changes in their environment. Therefore it is important that we develop our understanding of the factors that affect lichen distribution. In this thesis, both spatial and temporal distributions of epiphytic lichens at different scales have been studied in southern Sweden.

Generation time of the red-listed lichen Cliostomum corrugatum was examined using Bjärka-Säby as the study site. The results showed that the average age of an individual of C. corrugatum is 25–30 years at the onset of spore production.

The rarity of C. corrugatum was also examined. DNA analysis of an intron from 85 samples, collected at five sites in Östergötland, yielded 11 haplotypes. Results from coalescent analysis, mantel test and AMOVA indicated that C. corrugatum have a high ability to disperse. The study concluded that its rarity is most likely connected with the low amount of available habitat, old Quercus robur.

The changes in the distribution of epiphytic lichens in southern Sweden, between 1986 and 2003, were also compared. For each year a centroid was calculated on all combinations of tree and lichen species. The three significant cases showed that the centroid movement pointed toward a north-east or north-north-east direction.

Finally differences in species richness and cover of lichens on large Q. robur were examined between urban and rural environment. The results demonstrated that species number and percent cover was significantly higher on oaks standing rural compared to oaks standing urban. Effects of urban sprawl showed a decline in species richness and cover with increasing age of the surrounding buildings.

Biodiversity often suffers from urbanisation. In the present study, we focused on how the age of urbanisation affects the richness of 17 epiphytic lichens species and their cover on large oaks, with a minimum spacing of 250 m, in urban environments in the city of Linköping (100,000 inhabitants), SE Sweden. We also surveyed trees in adjacent rural areas, selected to have similar distributions of tree trunk circumference and oak density within 300 m. Lichen richness and cover were significantly lower on urban trees compared to rural trees. Furthermore, richness and cover decreased with the length of time that urban trees had been surrounded by houses. Roughly one species is lost every 30 years. Most of the species that were analysed demonstrated a drop in occurrence with respect to the duration of housing development. The reduction in the probability of occurrence varied from 60% (Calicium viride, Evernia prunastri), 80% (Chrysotrix candelaris) to 90% (Ramalina spp.) during the 160-year period of urbanisation considered. Therefore, even if valuable trees survive over the course of development, their lichen flora are likely to become depleted over time.

The objective was to investigate at what the age specimen of Cliostomum corrugatum become fertile in order to estimate the time span between the meiosis events. The species has its main distribution in Europe but has also been found on the west coast of British Columbia and is red listed, e.g., in Sweden (nearly threatened), Denmark, Germany and England. In the province of Östergötland, southern Sweden it is most frequent on old Quercus robur trees in open oak forest or meadows. I may also be found on other deciduous trees as Ulmus and Fraxinus species. It is mainly groving on the flat terminal parts of the rough bark of the tree trunks and not on the sides of the cracks. Cliostomum corrugatum does not grow on young oak trees. The smallest tree trunk diameter with Cliostomum corrugatum was is 0.65 m, a tree of at least 100 years of age. On two localities in Östergötland all oaks were studied and the size of the trees and the size of the largest thallus of Cliostomum corrugatum were recorded. Out of this data the size of how small a tree can possibly be for hosting Cliostomum corrugatum. This estimate was compared with the size of the smallest thalli with apothecia and the size of trees on which these appeared. With knowledge of the peripheral secondary growth of oaks it was possible to estimate the age of the youngest fertile Cliostomum corrugatum to about 30 years. Thus, equal to the time span between two meiosis events.

The objective of this study was to estimate the dispersal rate in an organism assumed to be confined to tree stands with unbroken continuity. We used the lichen-forming ascomycete Cliostomum corrugatum, which is largely confined to old oak stands. Five populations, with pairwise distances ranging from 6.5 to 83 km, were sampled in Ostergotland, south-eastern Sweden. DNA sequence data from an intron in the small subunit nuclear ribosomal RNA gene was obtained from 85 samples. Nearly all molecular variance (99.6%) was found within populations and there were no signs of isolation-by-distance. The absolute number of immigrants per population per generation (estimated to 30 years), inferred by Bayesian MCMC, was found to be between 1 and 5. Altogether, evidence suggests abundant gene flow in the history of our sample. A simulation procedure demonstrated that we cannot know whether effective dispersal is ongoing or if it ceased at the time when oaks started to decrease dramatically around 400 years BP. However, a scenario where effective dispersal ceased already at the time when the postglacial reinvasion of oak had reached the region around 6000 years BP is unlikely. Vegetation history suggests that the habitat of C. corrugatum was patchily distributed in the landscape since the early Holocene. Combined with the high dispersal rate estimate, this suggests that the species has been successful at frequently crossing distances of at least several kilometres and possibly that it has primarily been limited by the availability of habitat rather than by dispersal.

The aim with this study is to determine genetic variation, dispersal potential and the migration history to Sweden since the last glaciation of the rare lichen Cliostomum corrugatum, a crustose epiphytic lichen with a grey greenish thallus,conspicuous light yellow to light brown apothecia and black pycnidia. Collections were made in January and February in 2005 at five sites in Östergötland, Sweden. The most frequent common habitat for Cliostomum corrugatumis on Quercus and sometimes also on other deciduous trees for example Ulmus and Fraxinus. On the tree trunk it is the rough bark it prefers and the flat terminal parts of the bark structure and not on the sides of the cracks. The main distribution of Cliostomum corrugatum is in Europe but a satellite population has been found on the west coast of North American in British Columbia. It is red listed in Sweden, with the status near threatened. Three sequences SSUintron, IGS and ITS were studied and the two latter appear to lack genetic variation. A total of 85 sequences with a length of 614 base pairs were studied of a rRNA SSU intron. Eleven haplotypes were detected, two was common 46 and 30 in numbers respectively and was present on all five localities the other nine were detected only once each. The two common haplotypes are in the centre of a rooted net work and the rare in the periphery. Cliostomum corrugatum does not seem to have problem with its dispersal. The limiting factor seems to be the occurrence big oaks. In the studied area the smallest tree trunk diameter that Cliostomum corrugatum was found on is 0,65 metre. The tree with the largest diameter in the research area is 1,65 metre. A tree that is 0,65 metre in diameter is at least 100 years old. Oaks of this age are scarce and this is one of the reasons for the rareness of Cliostomum corrugatum. When Cliostomum corrugatum colonized Sweden after the last ice age, all eleven haplotypes may already have existed. However, it is possible, that some haplotypes evolved after the migration to Östergötland.

Past studies on changes in species distribution have mainly been based on analysis of range boundaries. In contrast, the method used here evaluates shifts in species' geographic centroids within a predefined area. We used presence/absence data on epiphytic lichens collected 1986 and 2003 from 64 sites in southern Sweden. A centroid was calculated each year, for each lichen species and substrate. The distance of centroid movement was evaluated in a permutation procedure. In total, 56 lichen species on 22 tree species were involved in the analyses, yielding 30 cases that had sufficient sample sizes both years to be evaluated. Out of these, three exhibited a significant movement of their centroid. The shift of lichen centroids of Hypogymnia physodes (L.) Nyl. and Vulpicida pinastri (Scop.) J.-E. Mattsson & M. J. Lai on the tree species Juniperus communis L. was 50 and 151 km with the direction 27 degrees and 48 degrees, respectively. For Hypogymnia physodes on Pinus sylvestris L., corresponding values were 41 km and 30 degrees. The northnortheast shifts of these species in Sweden could be a response to a warming climate.

Genetic variation in lichens has mainly been examined in rare or threatened species or species with an otherwise fragmented geographical distribution. The main objectives have often been to compare the diversity between populations in relation to nature conservation issues. In addition, most studied species are sexual reproductive and, hence, produce small spores which may disperse over long distances. More common species have usually been neglected, although they are more easily collected, both because collecting results in a comparatively small disturbance of the populations and because they occur in a larger selection of habitats. Here we present a study on the genetic variation in the lichenized ascomycete Hypogymnia physodes in Northern Europe based on nrDNA data. The species was selected as it probably is the most common lichen in the area, it is corticolous, found on almost all woody plants in most habitats, and has a predominantly asexual dispersal mode. The material was collected in Estonia, Finland, and Sweden as a part of a larger project aiming at identifying localities with high biodiversity of interest for nature conservation projects. We examined the correlations between genetic diversity and substrate ecology as well as spatial distances. An important result is the large genetic variation within a mainly asexual lichen species. The results also show genetic similarity between specimens from similar substrates.

Genetic variability and its relationship to substratum preferences within and among populations of the sorediate foliose lichen Hypogymnia physodes was investigated using sequence variation in the complete nrDNA internal transcribed spacer (ITS) region. A few samples of the putatively closely related, sorediate, H. tubulosa were also included. Samples were collected from each tree species in study sites in Estonia, Finland, and Sweden. In total, DNA sequences from 104 individuals of H. physodes and 16 of H. tubulosa were obtained. A group I intron situated at the end of the small subunit (SSU) of the nrDNA was detected in both species. Within-species variability was observed in both species: fifteen haplotypes were found for H. physodes and seven for H. tubulosa for the combined alignment of the intron and the ITS. Possible recombination within the total gene fragment was detected and hence the different regions (intron, ITS1, 5.8S, ITS2) were analysed separately. They show a different degree of variability both between each other and between the species. The number of haplotypes of H. physodes in the four regions are 5, 5, 1, and 5 and for H. tubulosa 5, 2, 1 and 2, respectively. A statistical parsimony estimation resulted in two unconnected networks; one containing all the samples of H. physodes and one containing all H. tubulosa samples. It was not possible to show different potentials of the different haplotypes for establishment on different substrata as the network of H. physodes indicates recombination within the ITS region which may be frequent enough to make this primarily clonally reproducing species to behave like a sexual species.

Bedömningstillfällen i naturvetenskap vid lärarutbildning som kan användas i skolan

Inom lärarutbildningen vid Södertörns högskola har vi inom de naturvetenskapliga ämnena sedan flera år arbetat med olika typer av bedömningstillfällen vid examinationen av studenter. Oftast är dessa bedömningstillfällen konstruerade för att vara examinerande av olika lärandemål som representerar önskade didaktiska förmågor hos den blivande läraren. De kan därför samtidigt fungera som modeller för hur man som lärare kan arbeta inom grund- och gymnasieskolan för bedömning av elevers förmågor. Förutom muntliga och skriftliga redovisningar kan dessa t.ex. bestå av redovisande exkursioner i natur- eller kulturmiljöer, laborationer, självreflektioner, traditionella eller estetiska loggböcker, självdiagnoser med kamratbedömning, museivisningar och webbaserade laborationer. För att studenterna skall få motsvarande träning har undervisningen på högskolan i allt högre utsträckning utvecklats från föreläsningar och demonstrativa laborationer och exkursioner mot många olika typer av interaktiva aktiviteter. Motsvarande utveckling återspeglas internationellt där sedan tio år den traditionella läroboken med beskrivande texter som skall läsas och läras ersatts av läromedel, fortfarande ofta i bokform, som ger anvisningar om hur studenter tillsammans kan arbeta med sin kunskapsutveckling, genom exempel, arbetsuppgifter, diskussionsfrågor, problematiseringar, lärande diagnoser etc.

Bedömning av naturvetenskap enligt Lgr 11 och Lgy 11

I de nya läroplanerna Lgr 11 och Lgy 11 skall elevers förmåga, att använda sina kunskaper, användas som grund för betygsättningen. Detta innebär stora förändringar jämfört med tidigare betygsystem där fokus oftast låg på bedömning utifrån elevers redovisning av kunskaper inhämtade från olika typer av läromedel. Enkelt uttryckt kan man säga att tidigare bedömningar försökte värdera elevens förmögenhet i form av samlad (minnes)kunskap medan dagens läroplaner fokuserar på bedömning av elevers förmåga att använda sina kunskaper inom olika områden. Det har följaktligen skett en stor förändring i synsättet på det som skall bedömas och hur detta kan genomföras vilket även får konsekvenser för undervisningen.

Av reportage, diskussioner och andra inslag i massmedia framkommer att många, även rutinerade lärare, har svårt att förstå hur de skall arbeta med lärande bedömning och vill ha klarare anvisningar och exempel.

Lärande bedömning

Jönsson (Lärande bedömning, 2012) beskriver hur undervisning bör planeras utifrån den bedömning av förmågor baserade på betygskriterier som läraren skall utföra. Till skillnad från tidigare där undervisningen först planerades och genomfördes och där resultatet slutligen bedömdes genom skrivningar eller förhör utgår Jönsson från bedömningen och utformar undervisningen utifrån denna. I korthet ser modellen ut så här:

Läraren konstruerar utifrån betygskriterierna ett bedömningstillfälle (performance assessment) och skapar en bedömningsmatris inför observationen av nivån på de förmågor hos eleven som skall bedömas. Det är inte nödvändigt att betrakta en viss handling, bedömningen kan göras genom av produkter som eleven producerar. Därefter planeras undervisningen dvs. de tillfällen där eleverna skall få möjlighet att träna de förmågor som skall bedömas.

Workshop med olika bedömningstillfällen i naturvetenskap

Vi kommer att i mindre grupper genomföra olika bedömningstillfällen anpassade till de nya betygskriterierna och med användande av olika metoder som samtidigt kan utgöra exempel på hur man t.ex. kan arbeta med estetiska lärprocesser (ELP), IKT, laborationer, kamratbedömning utifrån de nya läroplanernas betygskriterier för naturvetenskapliga ämnen inkl. naturgeografi. De modellerar bedömningstillfällen men blir samtidigt exempel på hur man kan arbeta med undervisning enligt de nya läroplanerna. Alla kan inte få pröva allt men genom att erbjuda ett antal olika moment kan deltagarna snabbt få en inblick i olika sätt att bedöma elevers utvecklingsnivå utifrån betygskriterierna. Den tid som krävs vid bedömning, enligt den nu i läroplanerna introducerade betygsskalan, där flera färdigheter förekommer i olika former i flera ämnen, medför ett behov av bedömning av kvaliteten hos flera färdigheter under samma bedömningstillfälle. Därför kommer exemplen i hög utsträckning vara ämnesintegrerade och med vissa modifieringar kunna användas i olika årskurser.

In studies concerning nature conservation issues common lichen species have usually been neglected although collecting of these results gives comparatively small disturbance of the populations and is easily done. Instead rare or threatened species or species usually have been used as indicators of sites with high biodiversity. Here, the macrolichen diversity is compared with the diversity of woody plants and other characteristics of different sites in Estonia, Finland and Sweden as a part of a larger project including comparative studies on habitats with presumably high species diversity The site selection was based on the occurrence of Daphne mezereum which usually occurs in semi-open habitats in transitions zones containing species from the surrounding biotopes. One of the main objectives with the study was to develop a fairly rapid method of evaluation of biodiversity using easily identified species. As total inventories are time consuming and reflects snapshots of a certain occasion it is beneficial to use other methods which may give a little less but sufficient information for many purposes, e.g., estimations on biodiversity. The ecological and evolutionary processes that shape diversity and distributions are general and results are assumed to be translatable from the target species to other species. The combination of data from a small number of species may constitute a useful monitoring protocol for lichens and higher plants. In total about 50 lichen species and 25 substrates are included and analyzed in the study. Most of the most common lichens are sorediate or isidiate and asexually reproducing and occur on several substrates. The relation between the diversity of lichen and woody plants is presented.

Plants are simultaneously exposed to abiotic and biotic hazards. Here, we show that local and systemic acclimation in Arabidopsis thaliana leaves in response to excess excitation energy (EEE) is associated with cell death and is regulated by specific redox changes of the plastoquinone (PQ) pool. These redox changes cause a rapid decrease of stomatal conductance, global induction of ASCORBATE PEROXIDASE2 and PATHOGEN RESISTANCE1, and increased production of reactive oxygen species (ROS) and ethylene that signals through ETHYLENE INSENSITIVE2 (EIN2). We provide evidence that multiple hormonal/ROS signaling pathways regulate the plant's response to EEE and that EEE stimulates systemic acquired resistance and basal defenses to virulent biotrophic bacteria. In the Arabidopsis LESION SIMULATING DISEASE1 (lsd1) null mutant that is deregulated for EEE acclimation responses, propagation of EEE-induced programmed cell death depends on the plant defense regulators ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1) and PHYTOALEXIN DEFICIENT4 (PAD4). We find that EDS1 and PAD4 operate upstream of ethylene and ROS production in the EEE response. The data suggest that the balanced activities of LSD1, EDS1, PAD4, and EIN2 regulate signaling of programmed cell death, light acclimation, and holistic defense responses that are initiated, at least in part, by redox changes of the PQ pool.

ABSTRACT: BACKGROUND: Understanding the adaptive changes that alter the function of proteins during evolution is an important question for biology and medicine. The increasing number of completely sequenced genomes from closely related organisms, as well as individuals within species, facilitates systematic detection of recent selection events by means of comparative genomics. RESULTS: We have used genome-wide strain-specific single nucleotide polymorphism data from 64 strains of budding yeast (Saccharomyces cerevisiae or Saccharomyces paradoxus) to determine whether adaptive positive selection is correlated with protein regions showing propensity for different classes of structure conformation. Data from phylogenetic and population genetic analysis of 3746 gene alignments consistently shows a significantly higher degree of positive Darwinian selection in intrinsically disordered regions of proteins compared to regions of alpha helix, beta sheet or tertiary structure. Evidence of positive selection is significantly enriched in classes of proteins whose functions and molecular mechanisms can be coupled to adaptive processes and these classes tend to have a higher average content of intrinsically unstructured protein regions. CONCLUSIONS: We suggest that intrinsically disordered protein regions may be important for the production and maintenance of genetic variation with adaptive potential and that they may thus be of central significance for the evolvability of the organism or cell in which they occur.