Evaluation of Xylella fastidiosa genetic diversity by fAFPL markers

The first phytopathogenic bacterium with its DNA entirely sequenced is being detected and isolated from different host plants in several geographic regions. Although it causes diseases in cultures of economic importance, such as citrus, coffee, and grapevine little is known about the genetic relationships among different strains. Actually, all strains are grouped as a single species, Xylella fastidiosa, despite colonizing different hosts, developing symptoms, and different physiological and microbiological observed conditions. The existence of genetic diversity among X. fastidiosa strains was detected by different methodological techniques, since cultural to molecular methods. However, little is know about the phylogenetic relationships developed by Brazilian strains obtained from coffee and citrus plants. In order to evaluate it, fAFLP markers were used to verify genetic diversity and phylogenetic relationships developed by Brazilian and strange strains. fAFLP is an efficient technique, with high reproducibility that is currently used for bacterial typing and classification. The obtained results showed that Brazilian strains present genetic diversity and that the strains from this study were grouped distinctly according host and geographical origin like citrus-coffee, temecula-grapevine-mulberry and plum-elm.

The real estate markets : Players, institutions and territories

Revealing the parties, the processes and the institutions and, consequently, both the diversity and contingency of the real estate markets, the existing increasing literature emphasises the contemporary numerous links and interdependencies between real estate, land value, planning and town planning policy and even the financial system. This paper is an attempt to understand all the real estate markets, from the most peripheral ones, where the urban rent is the lowest, to the most dense city centres. To gain a better understanding of the real estate market, a process of firstly deconstruction and then reconstruction is used. The process of deconstruction involves identifying various market trends according to property type (principally residential buildings), players and institutions, territorial situations and temporalities based on research conducted in Switzerland. We then developed a meta-synthesis inspired by Fernand Braudel whose works put as much emphasis on day-to-day economic activity as on long-term activity, and on local as well as global issues.

Food traditions and landscape histories of the Indian Ocean World : theoretical and methodological reflections

Environmental histories of plant exchanges have largely centred on their eco- nomic importance in international trade and on their ecological and social impacts in the places where they were introduced. Yet few studies have at- tempted to examine how plants brought from elsewhere become incorporated over time into the regional cultures of material life and agricultural landscapes. This essay considers the theoretical and methodological problems in inves- tigating the environmental history, diversity and distribution of food plants transferred across the Indian Ocean over several millennia. It brings together concepts of creolisation, syncretism, and hybridity to outline a framework for understanding how biotic exchanges and diffusions have been translated into regional landscape histories through food traditions, ritual practices and articu- lation of cultural identity. We use the banana plant - which underwent early domestication across New Guinea, South-east Asia and peninsular India and reached East Africa roughly two thousand years ago - as an example for il- lustrating the diverse patterns of incorporation into the cultural symbolism, material life and regional landscapes of the Indian Ocean World. We show that this cultural evolutionary approach allows new historical insights to emerge and enriches ongoing debates regarding the antiquity of the plant's diffusion from South-east Asia to Africa.

Mites fluctuation population on peach tree (Prunus persica (L.) Batsch) and in associated plants

Despite the importance of peach (Prunus persica (L.) Batsch) in Rio Grande do Sul, little is known about mites fluctuation population considered important to this crop. The objective of this study was to know the population diversity and fluctuation of mite species associated with Premier and Eldorado varieties in Roca Sales and Venâncio Aires counties, Rio Grande do Sul. The study was conducted from July 2008 to June 2009 when 15 plants were randomly chosen in each area. The plants were divided in quadrants and from each one a branch was chosen from which three leaves were removed: one collected in the apical region, another in the medium and the other in the basal region, totalizing 180 leaves/area. Five of the most abundant associated plants were collected monthly in enough amounts for the screening under the stereoscopic microscope during an hour. A total of 1,124 mites were found belonging to 14 families and 28 species. Tetranychus ludeni Zacher, 1913, Panonychus ulmi (Koch, 1836) and Mononychellus planki (McGregor, 1950) were the most abundant phytophagous mites, whereas Typhlodromalus aripo Deleon, 1967 and Phytoseiulus macropilis (Banks, 1904) the most common predatory mites. The period of one hour under stereoscopic microscope was enough to get a representative sample. In both places evaluated the ecologic indices were low, but little higherin Premier (H' 0.56; EqJ: 0.43) when compared to Eldorado (H' 0.53; EqJ 0.40). In Premier constant species were not observed and accessory only Brevipalpus phoenicis (Geijskes, 1939), T. ludeni and T. aripo. Higher abundance was observed in December and January and bigger amount in April. Already in Eldorado, T. ludeni and P. ulmi were constants. Greater abundance was observed in November and December, whereas grater richness in December and January. In both orchards were not found mites in buds. Tetranychus ludeni is the most abundant phytophagous mites with outbreak population in November, December and January and high predator diversity was observed on associated plants and on peach plants, indicating the existence of species mobility in peach orchard.

Using species richness and functional traits predictions to constrain assemblage predictions from stacked species distribution models

Aim: Modelling species at the assemblage level is required to make effective forecast of global change impacts on diversity and ecosystem functioning. Community predictions may be achieved using macroecological properties of communities (MEM), or by stacking of individual species distribution models (S-SDMs). To obtain more realistic predictions of species assemblages, the SESAM framework suggests applying successive filters to the initial species source pool, by combining different modelling approaches and rules. Here we provide a first test of this framework in mountain grassland communities. Location: The western Swiss Alps. Methods: Two implementations of the SESAM framework were tested: a "Probability ranking" rule based on species richness predictions and rough probabilities from SDMs, and a "Trait range" rule that uses the predicted upper and lower bound of community-level distribution of three different functional traits (vegetative height, specific leaf area and seed mass) to constraint a pool of environmentally filtered species from binary SDMs predictions. Results: We showed that all independent constraints expectedly contributed to reduce species richness overprediction. Only the "Probability ranking" rule allowed slightly but significantly improving predictions of community composition. Main conclusion: We tested various ways to implement the SESAM framework by integrating macroecological constraints into S-SDM predictions, and report one that is able to improve compositional predictions. We discuss possible improvements, such as further improving the causality and precision of environmental predictors, using other assembly rules and testing other types of ecological or functional constraints.

Phylogeography and population genetics of north European Atlantic salmon (Salmo salar L.)

Although abundant in the number of individuals, the Atlantic salmon may be considered as a threatened species in many areas of its native distribution range. Human activities such as building of power plant dams, offshore overfishing, pollution, clearing of riverbeds for timber floating and badly designed stocking regimes have diminished the distribution of Atlantic salmon. As a result of this, many of the historical populations both in Europe and northern America have gone extinct or are severely depressed. In fact, only 1% of Atlantic salmon existing today are of natural origin, the rest being farmed salmon. All of this has lead to a vast amount of research and many restoration programmes aiming to bring Atlantic salmon back to rivers from where it has vanished. However, many of the restoration programmes conducted thus far have been unsuccessful due to inadequate scientific research or lack of its implementation, highlighting the fact that more research is needed to fully understand the biology of this complex species. The White and Barents Seas in northwest Russia are among the last regions in Europe where Atlantic salmon populations are still stable, thus forming an important source of biodiversity for the entire European region. Salmon stocks from this area are also of immense economic and social importance for the local people in the form of fishing tourism. The main aim of this thesis was to elucidate the post-glacial history and population genetic structure of north European and particularly northwest Russian Atlantic salmon, both of which are aspects of great importance for the management and conservation of the species. Throughout the whole thesis, these populations were studied by utilizing microsatellites as the main molecular tool. One of the most important discoveries of the thesis was the division of Atlantic salmon from the White and Barents Seas into four separate clusters, which has not been observed in previous studies employing nuclear markers although is supported by mtDNA studies. Populations from the western Barents Sea clustered together with the northeast Atlantic populations into a clearly distinguishable group while populations from the White Sea and eastern Barents Sea were separated into three additional groups. This has important conservation implications as this thesis clearly indicates that conservation of populations from all of the observed clusters is warranted in order to conserve as much of the genetic diversity as possible in this area. The thesis also demonstrates how differences in population life histories within a species, migratory behaviour in this case, and in their phylogeographic origin affect the genetic characteristics of populations, namely diversity and divergence levels. The anadromous populations from the Atlantic Ocean, White Sea and Barents Sea possessed higher levels of genetic diversity than the anadromous populations form the Baltic Sea basin. Among the non-anadromous populations the result was the opposite: the Baltic freshwater populations were more variable. This emphasises the importance of taking the life history of a population into consideration when developing conservation strategies: due to the limited possibilities for new genetic diversity to be generated via gene flow, it is expected that freshwater Atlantic salmon populations would be more vulnerable to extinction following a population crash and thus deserve a high conservation status. In the last chapter of this thesis immune relevant marker loci were developed and screened for signatures of natural selection along with loci linked to genes with other functions or no function at all. Also, a novel landscape genomics method, which combines environmental information with molecular data, was employed to investigate whether immune relevant markers displayed significant correlations to various environmental variables more frequently than other loci. Indications of stronger selection pressure among immune-relevant loci compared to non-immune relevant EST-linked loci was found but further studies are needed to evaluate whether it is a common phenomenon in Atlantic salmon.

Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome.

Long noncoding RNAs (lncRNAs) are one of the most intensively studied groups of noncoding elements. Debate continues over what proportion of lncRNAs are functional or merely represent transcriptional noise. Although characterization of individual lncRNAs has identified approximately 200 functional loci across the Eukarya, general surveys have found only modest or no evidence of long-term evolutionary conservation. Although this lack of conservation suggests that most lncRNAs are nonfunctional, the possibility remains that some represent recent evolutionary innovations. We examine recent selection pressures acting on lncRNAs in mouse populations. We compare patterns of within-species nucleotide variation at approximately 10,000 lncRNA loci in a cohort of the wild house mouse, Mus musculus castaneus, with between-species nucleotide divergence from the rat (Rattus norvegicus). Loci under selective constraint are expected to show reduced nucleotide diversity and divergence. We find limited evidence of sequence conservation compared with putatively neutrally evolving ancestral repeats (ARs). Comparisons of sequence diversity and divergence between ARs, protein-coding (PC) exons and lncRNAs, and the associated flanking regions, show weak, but significantly lower levels of sequence diversity and divergence at lncRNAs compared with ARs. lncRNAs conserved deep in the vertebrate phylogeny show lower within-species sequence diversity than lncRNAs in general. A set of 74 functionally characterized lncRNAs show levels of diversity and divergence comparable to PC exons, suggesting that these lncRNAs are under substantial selective constraints. Our results suggest that, in mouse populations, most lncRNA loci evolve at rates similar to ARs, whereas older lncRNAs tend to show signals of selection similar to PC genes.

How to introduce connectance in a frame of an expression for diversity

Systems made of parts that are totally connected do not work, neither ecosys- tems nor artifacts. Relative connectance is inversely related to diversity, and both magnitudes can find a common frame of expression, in which some constant expressing the constraints of any organization might be embodied. If S is Simp- son's index, the expression (1 - S)IS as a measure of diversity offers some advantages or, at least, helps further reasoning. Such expression is the ratio between total interspecific possible interactions and possible intraspecific inter- actions.

Differential regulation of horizontally acquired and core genome genes by the bacterial modulator H-NS

Horizontal acquisition of DNA by bacteria dramatically increases genetic diversity and hence successful bacterial colonization of several niches, including the human host. A relevant issue is how this newly acquired DNA interacts and integrates in the regulatory networks of the bacterial cell. The global modulator H-NS targets both core genome and HGT genes and silences gene expression in response to external stimuli such as osmolarity and temperature. Here we provide evidence that H-NS discriminates and differentially modulates core and HGT DNA. As an example of this, plasmid R27-encoded H-NS protein has evolved to selectively silence HGT genes and does not interfere with core genome regulation. In turn, differential regulation of both gene lineages by resident chromosomal H-NS requires a helper protein: the Hha protein. Tight silencing of HGT DNA is accomplished by H-NS-Hha complexes. In contrast, core genes are modulated by H-NS homoligomers. Remarkably, the presence of Hha-like proteins is restricted to the Enterobacteriaceae. In addition, conjugative plasmids encoding H-NS variants have hitherto been isolated only from members of the family. Thus, the H-NS system in enteric bacteria presents unique evolutionary features. The capacity to selectively discriminate between core and HGT DNA may help to maintain horizontally transmitted DNA in silent form and may give these bacteria a competitive advantage in adapting to new environments, including host colonization.

Differential regulation of horizontally acquired and core genome genes by the bacterial modulator H-NS

Horizontal acquisition of DNA by bacteria dramatically increases genetic diversity and hence successful bacterial colonization of several niches, including the human host. A relevant issue is how this newly acquired DNA interacts and integrates in the regulatory networks of the bacterial cell. The global modulator H-NS targets both core genome and HGT genes and silences gene expression in response to external stimuli such as osmolarity and temperature. Here we provide evidence that H-NS discriminates and differentially modulates core and HGT DNA. As an example of this, plasmid R27-encoded H-NS protein has evolved to selectively silence HGT genes and does not interfere with core genome regulation. In turn, differential regulation of both gene lineages by resident chromosomal H-NS requires a helper protein: the Hha protein. Tight silencing of HGT DNA is accomplished by H-NS-Hha complexes. In contrast, core genes are modulated by H-NS homoligomers. Remarkably, the presence of Hha-like proteins is restricted to the Enterobacteriaceae. In addition, conjugative plasmids encoding H-NS variants have hitherto been isolated only from members of the family. Thus, the H-NS system in enteric bacteria presents unique evolutionary features. The capacity to selectively discriminate between core and HGT DNA may help to maintain horizontally transmitted DNA in silent form and may give these bacteria a competitive advantage in adapting to new environments, including host colonization.

Predicting the future effectiveness of protected areas for bird conservation in Mediterranean ecosystems under climate change and novel fire regime scenarios

AimGlobal environmental changes challenge traditional conservation approaches based on the selection of static protected areas due to their limited ability to deal with the dynamic nature of driving forces relevant to biodiversity. The Natura 2000 network (N2000) constitutes a major milestone in biodiversity conservation in Europe, but the degree to which this static network will be able to reach its long-term conservation objectives raises concern. We assessed the changes in the effectiveness of N2000 in a Mediterranean ecosystem between 2000 and 2050 under different combinations of climate and land cover change scenarios. LocationCatalonia, Spain. MethodsPotential distribution changes of several terrestrial bird species of conservation interest included in the European Union's Birds Directive were predicted within an ensemble-forecasting framework that hierarchically integrated climate change and land cover change scenarios. Land cover changes were simulated using a spatially explicit fire-succession model that integrates fire management strategies and vegetation encroachment after the abandonment of cultivated areas as the main drivers of landscape dynamics in Mediterranean ecosystems. ResultsOur results suggest that the amount of suitable habitats for the target species will strongly decrease both inside and outside N2000. However, the effectiveness of N2000 is expected to increase in the next decades because the amount of suitable habitats is predicted to decrease less inside than outside this network. Main conclusionsSuch predictions shed light on the key role that the current N2000may play in the near future and emphasize the need for an integrative conservation perspective wherein agricultural, forest and fire management policies should be considered to effectively preserve key habitats for threatened birds in fire-prone, highly dynamic Mediterranean ecosystems. Results also show the importance of considering landscape dynamics and the synergies between different driving forces when assessing the long-term effectiveness of protected areas for biodiversity conservation.

Consequences of lineage-specific gene loss on functional evolution of surviving paralogs: ALDH1A and retinoic acid signaling in vertebrate genomes

Genome duplications increase genetic diversity and may facilitate the evolution of gene subfunctions. Little attention, however, has focused on the evolutionary impact of lineage-specific gene loss. Here, we show that identifying lineage-specific gene loss after genome duplication is important for understanding the evolution of gene subfunctions in surviving paralogs and for improving functional connectivity among human and model organism genomes. We examine the general principles of gene loss following duplication, coupled with expression analysis of the retinaldehyde dehydrogenase Aldh1a gene family during retinoic acid signaling in eye development as a case study. Humans have three ALDH1A genes, but teleosts have just one or two. We used comparative genomics and conserved syntenies to identify loss of ohnologs (paralogs derived from genome duplication) and to clarify uncertain phylogenies. Analysis showed that Aldh1a1 and Aldh1a2 form a clade that is sister to Aldh1a3-related genes. Genome comparisons showed secondarily loss of aldh1a1 in teleosts, revealing that Aldh1a1 is not a tetrapod innovation and that aldh1a3 was recently lost in medaka, making it the first known vertebrate with a single aldh1a gene. Interestingly, results revealed asymmetric distribution of surviving ohnologs between co-orthologous teleost chromosome segments, suggesting that local genome architecture can influence ohnolog survival. We propose a model that reconstructs the chromosomal history of the Aldh1a family in the ancestral vertebrate genome, coupled with the evolution of gene functions in surviving Aldh1a ohnologs after R1, R2, and R3 genome duplications. Results provide evidence for early subfunctionalization and late subfunction-partitioning and suggest a mechanistic model based on altered regulation leading to heterochronic gene expression to explain the acquisition or modification of subfunctions by surviving ohnologs that preserve unaltered ancestral developmental programs in the face of gene loss.

Distribution and population genetic variation of cryptic species of the Alpine mayfly Baetis alpinus (Ephemeroptera: Baetidae) in the Central Alps.

BACKGROUND: Many species contain evolutionarily distinct groups that are genetically highly differentiated but morphologically difficult to distinguish (i.e., cryptic species). The presence of cryptic species poses significant challenges for the accurate assessment of biodiversity and, if unrecognized, may lead to erroneous inferences in many fields of biological research and conservation. RESULTS: We tested for cryptic genetic variation within the broadly distributed alpine mayfly Baetis alpinus across several major European drainages in the central Alps. Bayesian clustering and multivariate analyses of nuclear microsatellite loci, combined with phylogenetic analyses of mitochondrial DNA, were used to assess population genetic structure and diversity. We identified two genetically highly differentiated lineages (A and B) that had no obvious differences in regional distribution patterns, and occurred in local sympatry. Furthermore, the two lineages differed in relative abundance, overall levels of genetic diversity as well as patterns of population structure: lineage A was abundant, widely distributed and had a higher level of genetic variation, whereas lineage B was less abundant, more prevalent in spring-fed tributaries than glacier-fed streams and restricted to high elevations. Subsequent morphological analyses revealed that traits previously acknowledged as intraspecific variation of B. alpinus in fact segregated these two lineages. CONCLUSIONS: Taken together, our findings indicate that even common and apparently ecologically well-studied species may consist of reproductively isolated units, with distinct evolutionary histories and likely different ecology and evolutionary potential. These findings emphasize the need to investigate hidden diversity even in well-known species to allow for appropriate assessment of biological diversity and conservation measures.

Machine Learning and Clinical Text. Supporting Health Information Flow

Fluent health information flow is critical for clinical decision-making. However, a considerable part of this information is free-form text and inabilities to utilize it create risks to patient safety and cost-­effective hospital administration. Methods for automated processing of clinical text are emerging. The aim in this doctoral dissertation is to study machine learning and clinical text in order to support health information flow.First, by analyzing the content of authentic patient records, the aim is to specify clinical needs in order to guide the development of machine learning applications.The contributions are a model of the ideal information flow,a model of the problems and challenges in reality, and a road map for the technology development. Second, by developing applications for practical cases,the aim is to concretize ways to support health information flow. Altogether five machine learning applications for three practical cases are described: The first two applications are binary classification and regression related to the practical case of topic labeling and relevance ranking.The third and fourth application are supervised and unsupervised multi-class classification for the practical case of topic segmentation and labeling.These four applications are tested with Finnish intensive care patient records.The fifth application is multi-label classification for the practical task of diagnosis coding. It is tested with English radiology reports.The performance of all these applications is promising. Third, the aim is to study how the quality of machine learning applications can be reliably evaluated.The associations between performance evaluation measures and methods are addressed,and a new hold-out method is introduced.This method contributes not only to processing time but also to the evaluation diversity and quality. The main conclusion is that developing machine learning applications for text requires interdisciplinary, international collaboration. Practical cases are very different, and hence the development must begin from genuine user needs and domain expertise. The technological expertise must cover linguistics,machine learning, and information systems. Finally, the methods must be evaluated both statistically and through authentic user-feedback.