107 research outputs found

    An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network

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    Background: Alternative representations of biochemical networks emphasise different aspects of the data and contribute to the understanding of complex biological systems. In this study we present a variety of automated methods for visualisation of a protein-protein interaction network, using the basic helix-loop-helix ( bHLH) family of transcription factors as an example. Results: Network representations that arrange nodes ( proteins) according to either continuous or discrete information are investigated, revealing the existence of protein sub-families and the retention of interactions following gene duplication events. Methods of network visualisation in conjunction with a phylogenetic tree are presented, highlighting the evolutionary relationships between proteins, and clarifying the context of network hubs and interaction clusters. Finally, an optimisation technique is used to create a three-dimensional layout of the phylogenetic tree upon which the protein-protein interactions may be projected. Conclusion: We show that by incorporating secondary genomic, functional or phylogenetic information into network visualisation, it is possible to move beyond simple layout algorithms based on network topology towards more biologically meaningful representations. These new visualisations can give structure to complex networks and will greatly help in interpreting their evolutionary origins and functional implications. Three open source software packages (InterView, TVi and OptiMage) implementing our methods are available

    Untying Gordian knots: The evolution and biogeography of the large European apomictic polyploid Ranunculus auricomus plant complex

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    Polyploidie, das Vorhandensein von zwei oder mehr vollständigen Chromosomensätzen, tritt wiederholt über den gesamten Baum des Lebens auf. Bei Pflanzen ist die wirtschaftliche, aber vor allem auch die evolutionäre Bedeutung überwältigend. Polyploidisierungen, wahrscheinlich verbunden mit Schlüsselinnovationen (z.B. die Entwicklung der Gefäßelemente oder des Fruchtblattes), traten in der Evolution der Blütenpflanzen häufig auf. Blütenpflanzen sind die artenreichste Gruppe im Pflanzenreich mit ca. 370,000 Arten und umfassen 30–70% Neopolyploide. Es wird angenommen, dass Polyploidie und Hybridisierung (Allopolyploidie) besonders zur Entstehung von Biotypen mit neuartiger genomischer Zusammensetzung beitragen und damit Schlüsselfaktoren für nachfolgende Artbildungen und Makroevolution sind. Bei Pflanzen sind beide Prozesse häufig mit Apomixis, der Reproduktion über asexuell gebildete Samen, verbunden. Das rätselhafte Phänomen der von Polyploidie und Apomixis begleiteten Artbildung ist jedoch trotz enormer Fortschritte auf dem Gebiet der Genomik noch immer kaum verstanden. Die Frage „Was ist eine Art?“ hat für Evolutionsbiologen höchste Priorität: Arten sind die Grundlage der Biodiversitätsforschung, und die evolutionäre und ökologische Forschung stützt sich auf gut definierte Einheiten. Evolutionär junge Artkomplexe bieten eine einzigartige Möglichkeit die Artbildung bei Pflanzen und deren begleitende Prozesse zu erforschen und zu verstehen. Sie umfassen meist wenige sexuelle Stammarten und zahlreiche polyploide, teilweise apomiktische, hybridogene Derivate. Das Fehlen von Rekombination und Kreuzbestäubung in apomiktischen Linien kann zu einer Vielzahl klonaler Hybridlinien mit fixierten morphologischen und ökologischen Merkmalen führen (Agamospezies). Selbst das Erkennen und Abgrenzen der sexuellen Stammarten ist aufgrund geringer genetischer Divergenz, eventuellen hybridogenen Ursprüngen, stetigem Genfluss und/oder unvollständiger genetischer Auftrennung der Abstammungslinien (ILS) methodisch herausfordernd. Integrative Ansätze, die sowohl genomische als auch morphometrische Daten verwenden, um die jungen Stammarten aufzutrennen, fehlen bisher. Die Biogeographie und Evolution der Artkomplexe ist weitaus komplexer. Apomikten besetzen im Vergleich zu ihren sexuellen Verwandten häufig größere Areale oder sind in nördlicheren Regionen verbreitet, ein Phänomen, das als Geographische Parthenogenese (GP) bezeichnet wird. GP-Muster haben meist einen pleistozänen Kontext. Klimatische Schwankungen in den gemäßigten und borealen Zonen boten häufig Möglichkeiten zur interspezifischen Hybridisierung, was wahrscheinlich auch zur Entstehung von Apomixis auf der Nordhalbkugel geführt hat. Faktoren, die diese Muster erzeugen, werden immer noch kontrovers diskutiert. GP-Muster wurden bisher oft den Vorteilen apomiktischer Populationen aufgrund von (Allo)polyploidie und uniparentaler Fortpflanzung zugeschrieben: Fixierte, hohe Heterozygotie führt zu einer erhöhten Stresstoleranz, und Selbstfertilität bedingt eine bessere Kolonisierungsfähigkeit. Einerseits sind die komplexen Wechselwirkungen von genomweiter Heterozygotie, Ploidie, Reproduktionssmodi (sexuell versus asexuell) und klimatischer Umweltfaktoren auf GP-Muster nicht ausreichend untersucht worden, andererseits wurden potentielle Nachteile sexueller Stammarten aufgrund ihres Fortpflanzungssystems auf Fitness und genetische Vielfalt bisher kaum betrachtet. Schließlich sind neben der Biogeographie die retikulate Evolution und die genomische Zusammensetzung und Evolution junger, großer polyploider Pflanzenartenkomplexe noch nicht detailliert entschlüsselt worden. Neben Herausforderungen, die auf eine hohe Anzahl an Polyploidisierungs- und Hybridisierungsereignissen zurückzuführen sind, werden bioinformatische Analysen oft durch fehlende Informationen zu sexuellen Stammarten, Ploidiegraden und Reproduktionsmodi erschwert. Der europäische, polyploid-apomiktische Ranunculus auricomus (Gold-Hahnenfuß) Pflanzenkomplex ist gut geeignet, um alle aufgeworfenen Fragestellungen zu untersuchen. Der Komplex entstand wahrscheinlich durch unzählige Hybridisierungen weniger sexueller Stammarten. Bisher wurden mehr als 800 morphologisch sehr diverse Agamospezies (Derivate) beschriebenen. Die sexuellen Stammarten werden weniger als 1.0 Millionen Jahren alt geschätzt, und die Agamospezies sind wahrscheinlich noch viel jünger. In meiner Dissertation habe ich unter Verwendung des R. auricomus Komplexes als Modellsystem die bisher wenig verstandenen phylogenetischen, genomischen und biogeographischen Beziehungen junger, polyploider Pflanzengruppen untersucht. Ich habe einen umfassenden theoretischen und bioinformatischen Workflow entwicklelt, beginnend mit der Untersuchung der Evolution der sexuellen Stammarten, über die Entschlüsselung der Reproduktionsmodi und Biogeographie polyploid-apomiktischer Derivate bis hin zur Aufdeckung der retikulaten Ursprünge und Genomzusammensetzung und -evolution des Polyploidkomplexes. Diese Arbeit umfasst 251 Populationen und 87 R. auricomus Taxa europaweit. Die Analysen basieren auf 97,312 genomischen Loci (RADseq), 663 Kerngenen (target enrichment) und 71 Plastidenregionen, und 1,474 Blattploidie-, 4,669 Reproduktions- Samen-, 284 Kreuzungs- (Samenansatz), und 1,593 Morphometrie-Messungen. Phylogenomische Daten basierend auf RADseq, Kerngenen und geometrischer Morphometrie unterstützten die Zusammenlegung der zwölf sexuellen Morphospezies in fünf neu klassifizierte Stammarten. Diese Arten stellen klar unterscheidbare genetische Hauptlinien oder Cluster dar, die sowohl geographisch gut isoliert als auch morphologisch klar differenziert sind: R. cassubicifolius s.l., R. envalirensis s.l., R. flabellifolius, R. marsicus und R. notabilis s.l. Enorme retikulate Beziehungen innerhalb der Kladen, die nicht-vorhandene geographische Isolation und das Fehlen markanter morphologischer Merkmale haben zu diesem taxonomischen Konzept geführt. Allopatrische Artbildungsereignisse fanden interessanterweise vor ca. 0.83–0.58 Millionen Jahren während enormer klimatischer Schwankungen statt und wurden wahrscheinlich durch Vikarianzprozesse aus einer weit verbreiteten europäischen Stammart ausgelöst. Darüber hinaus wurde die neue Umschreibung der sexuellen Stammarten durch Populationskreuzungsexperimente unterstützt. Kreuzungen zeigten neben Inzuchtdepression, Auszuchtvorteilen und plötzlicher Selbstkompatibilität auch völlig fehlende Reproduktionsbarrieren zwischen einigen Morphospezies. Darüber hinaus wurden durchflusszytometrische Ploidy- und Reproduktions-, genomweite RADseq- und klimatische Umweltdaten in einer genetisch-informierten Pfadanalyse basierend auf Generalisierten Linearen Gemischten Modellen (GLMMs) kombiniert. Die Analyse hat ein komplexes europäisches GP-Szenario aufgedeckt, in der Diploide im Vergleich zu Polyploiden eine signifikant höhere Sexualität (Prozent sexueller Samen), mehr Blütenblätter (petaloide Nektarblätter) und bis zu dreimal weniger genomweite Heterozygotie zeigten. Die Sexualität war überaschenderweise positiv mit Sonneneinstrahlung und Isothermalität verbunden, und die Heterozygotie zeigte einen positiven Zusammenhang mit der Temperatursaisonalität. Die Ergebnisse stimmen mit der südlichen Verbreitung diploid-sexueller Populationen überein und deuten auf eine höhere Resistenz polyploid-apomiktischer Populationen gegenüber extremeren klimatischen Bedingungen hin. Ein neu entwickelter, multidisziplinärer Workflow, der alle bisherigen Daten einbezieht, deckte zum ersten Mal den weitestgehend allopolyploiden Ursprung und die Genomzusammensetzung und -evolution des R. auricomus Komplexes auf. Die Taxa waren in nur drei bis fünf unterstützten, nord-süd verbreiteten Kladen oder Clustern organisiert, die jeweils meistens diploid-sexuelle Stammarten enthielten. Allopolyploidisierungsereignisse bezogen jeweils zwei bis drei verschiedene, diploid-sexuelle Subgenome ein. Es wurde nur ein autotetraploides Ereignis nachgewiesen. Allotetraploide Genome sind gekennzeichnet durch Subgenomdominanz und einer enormen Evolution nach ihrer Entstehung (z.B. Mendelsche Segregation der Hybridgenerationen, Rückkreuzungen zu Elternarten und Genfluss aufgrund fakultativer Sexualität der Apomikten). Die über 800 Taxa des europäischen R. auricomus-Komplexes sind vermutlich aus vier diploiden Stammarten und eine bisher unbekannte, aktuell wahrscheinlich ausgestorbene Stammart, entstanden. Analysen zeigten auch, dass die Mehrzahl der beschriebenen polyploiden Agamospezies nicht monophyletisch ist und ähnliche Morphotypen wahrscheinlich mehrfach entstanden sind. Eine umfassende taxonomische Überarbeitung des gesamten Komplexes ist daher angebracht. In der Allgemeinen Diskussion kombiniere ich die Ergebnisse meiner Dissertation mit bereits existierenden Pflanzenstudien zur diploid-sexuellen und polyploid-apomiktischen Phylogenetik, Biogeographie und Genomzusammensetzung und -evolution junger Artkomplexe. Ich gebe zudem taxonomische Schlussfolgerungen und erkläre wie Artkomplexe mikro- und makroevolutionäre Prozesse miteinander verbinden. Abschließend gebe ich ein Fazit über die Ergebnisse meiner Dissertation und einen Ausblick für das laufende Forschungsprojekt und der Forschungsdisziplin der polyploiden Phylogenetik.Polyploidy, the presence of two or more full genomic complements, repeatedly occurs across the tree of life. In plants, not only the economic but particularly the evolutionary importance is overwhelming. Polyploidization events, probably connected to key innovations (e.g., vessel elements or the carpel), occurred frequently in the evolutionary history of flowering plants, which are the most species-rich group in the plant kingdom (ca. 370,000 species) and contain 30–70% neopolyploids. Polyploidy and hybridization (i.e., allopolyploidy) are particularly considered to create biotypes with novel genomic compositions and to be key factors for subsequent speciation and macroevolution. In plants, both processes are frequently connected to apomixis, i.e., the reproduction via asexually-formed seeds. However, the enigmatic phenomenon of plant speciation accompanied by polyploidy and apomixis is still poorly understood despite tremendous progress in the field of genomics. The question of “What is a species?” is of highest priority for evolutionary biologists: Species are the fundamental units for biodiversity, and further evolutionary and ecological research relies on well-defined entities. Evolutionarily young plant species complexes offer a unique opportunity to study plant speciation and accompanying processes. They usually comprise a few sexual progenitor species, and numerous polyploid, partly apomictic, hybrid derivatives. In apomictic lineages, the lack of recombination and cross-fertilization can result in numerous clonal lineages with fixed morphological and ecological traits (agamospecies). Nevertheless, even recognizing and delimiting the sexual progenitors of species complexes is methodically challenging due to low genetic divergence, possible hybrid origins, ongoing gene flow, and/or incomplete lineage sorting (ILS). Integrative approaches using both genomic and morphometric data for disentangling the young progenitors are still lacking so far. The biogeography and evolution of those plant complexes is even more challenging. Apomicts frequently occupy larger areas or more northern regions compared to their sexual relatives, a phenomenon called geographical parthenogenesis (GP). GP patterns usually have a Pleistocene context because climatic range shifts in temperate to boreal zones offered frequent opportunities for interspecific hybridization, probably giving rise to apomixis in the Northern Hemisphere. Factors shaping GP patterns are still controversially discussed. GP has been widely attributed to advantages of apomicts caused by polyploidy and uniparental reproduction, i.e., fixed levels of high heterozygosity leading to increased stress tolerance, and self-fertility leading to better colonizing capabilities. On the one hand, complex interactions of genome-wide heterozygosity, ploidy, reproduction mode (sexual versus asexual), and climatic environmental factors shaping GP have not been studied enough. On the other hand, potential disadvantages of sexual progenitors due to their breeding system on fitness and genetic diversity have received even less attention. Finally, alongside biogeography, the reticulate relationships and genome composition and evolution of young, large polyploid plant species complexes have not yet been deciphered comprehensively. Besides challenges attributed to numerous numbers of polyploidization and hybridization events, bioinformatic analyses are also often hampered by missing information on progenitors, ploidy levels, and reproduction modes. The European apomictic polyploid Ranunculus auricomus (goldilock buttercup) plant complex is well-suited to study all the aforementioned issues. The majority of goldilock buttercups probably arose from hybridization of a few sexual progenitors, leading to more than 800 described, morphologically highly diverse agamospecies. Sexuals are estimated to have speciated less than 1.0 million years ago, and agamospecies are probably much younger. In this thesis, using R. auricomus as a model system, I examined the recalcitrant and hitherto poorly understood phylogenetic, genomic, and biogeographical relationships of young polyploid apomictic plant complexes. I developed a comprehensive theoretical and bioinformatic workflow, starting with analyzing the evolution of the sexual progenitor species, continuing with unraveling reproduction modes and biogeography of apomictic polyploids, and ending up with revealing the reticulate origins and genome composition and evolution of the polyploid complex. Spanning up to 251 populations and 87 R. auricomus taxa Europe-wide, this work gathered data of 97,312 genomic loci (RADseq), 663 nuclear genes (target enrichment), and 71 plastid regions, and 1,474 leaf ploidy, 4,669 reproductive seed, 284 reproductive crossing (seed sets), as well as 1,593 geometric morphometric measurements. First of all, phylogenomics based on RADseq, nuclear gene, and geometric morphometric data supported the lumping of the twelve described sexual morphospecies into five newly circumscribed progenitor species. These species represent clearly distinguishable genetic main lineages or clusters, which are both well geographically isolated and morphologically differentiated: R. cassubicifolius s.l., R. envalirensis s.l., R. flabellifolius, R. marsicus, and R. notabilis s.l. Mainly within-clade reticulate relationships, missing geographical isolation, and a lack of distinctive morphological characters led to this taxonomic treatment. Interestingly, allopatric speciation events took place ca. 0.83–0.58 million years ago during a period of severe climatic oscillations, and were probably triggered by vicariance processes of a widespread European forest-understory ancestor. Sexual species re-circumscriptions were additionally supported by population crossing experiments. Besides inbreeding depression, outbreeding benefits, and sudden self-compatibility, crossings also revealed a lack of reproductive barriers among some of the formerly described morphospecies. Moreover, flow cytometric ploidy and reproductive, RADseq, and environmental data were combined into a genetically informed path analysis based on Generalized Linear Mixed Models (GLMMs). The analysis unveiled a complex European GP scenario, whereby diploids compared to polyploids showed significantly higher sexuality (percent of sexual seeds), more petals (petaloid nectary leaves), and up to three times less genome-wide heterozygosity. Surprisingly, sexuality was positively associated with solar radiation and isothermality, and heterozygosity was positively related to temperature seasonality. Results fit the southern distribution of diploid sexuals and suggest a higher resistance of polyploid apomicts to more extreme climatic conditions. Finally, a self-developed, multidisciplinary workflow incorporating all previously gathered data demonstrated, for the first time, the predominantly allopolyploid origin, genome composition, and post-origin genome evolution of the R. auricomus complex. Taxa were organized in only three to five supported, north-south distributed clades or cluster, each usually containing diploid sexual progenitor species. Allopolyploidizations involved two to three different diploid sexual subgenomes per event. Only one autotetraploid event was detected. Allotetraploids were characterized by subgenome dominance and enormous post-origin evolution, i.e., Mendelian segregation of hybrid generations, back-crossing to parents, and/or gene flow due to facultative sexuality of apomicts. Four diploid sexual progenitors and a previously unknown, nowadays extinct progenitor, probably gave rise to the more than 800 taxa of the European R. auricomus complex. Analyses also showed that the majority of analyzed polyploid agamospecies are non-monophyletic and similar morphotypes probably originated multiple times. The lack of monophyly suggests a comprehensive taxonomic revision of the entire complex. In the General Discussion, I combine my thesis results with existing plant studies on diploid sexual and polyploid apomictic phylogenetics, biogeography, and composition and genome evolution of young species complexes. I explain the taxonomic conclusions and how species complexes link micro- and macroevolutionary processes. Finally, I give conclusions of my thesis and an outlook of the project and the field of polyploid phylogenetics.2021-10-2

    Modelling early modern human dispersal patterns through the Wallacean Archipelago

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    Archaeological records from Australia provide the earliest, indirect evidence for maritime crossings by early modern humans anywhere in the world. As the island archipelago of Wallacea has never been connected to the continental landmasses of Sunda in the west (mainland Southeast Asia) or Sahul in the east (Australia and New Guinea), water crossings through this region were essential for the human colonisation of Australia. The archaeological record for human movement in Wallacea is still a work in progress, however, and none of the evidence pre-dates the archaeological record from Sahul. In 1977 the American anthropologist Joseph B. Birdsell suggested two main initial routes from Sunda to Sahul, a northern route with a landing in New Guinea, and a southern route landing in northern Australia. Models of this significant colonisation event have since been suggested, however, there has been little consensus about which model describes the most parsimonious pathway for first landfall in Sahul. Likewise, later movements between islands is still in question. The dearth of sampled islands and sites in Wallacea has made testing movement models against archaeological evidence difficult, if not impossible. This PhD attempted to examine inter-island movements using a three-pronged approach: 1) archaeological survey and excavation of Wallacean sites, combined with review and revision of the archaeological literature, to identify the timings of early human occupation in the region and enlarge the number of archaeological sample points; 2) reconstructing the palaeogeography of the Wallacean archipelago for the likely periods of initial human colonisation, and through this, model island connectivity and develop a model for human movement through the region; and 3) identify proxy records of human movement between islands to provide information on networks of connection between prehistoric island communities, and in doing so test the reliability of the model outcomes. This study provides a much needed up date to Birdsell's model from over 40 years ago, with an innovative use of geographic information systems to digitise and expand upon the reconstructions of palaeo-Wallacea and the differing variables which would have impacted early modern human movements through the region. The resulting reconstructions and models identified a multitude of now-submerged islands throughout Wallacea which would have significantly increased the connectivity between islands in the prehistoric archipelago, produced the first reconstructions of palaeo-hydrology for the region, developed two measures of intervisibility between islands and in applying these calculations to the Wallacean archipelago, identified ca. 65 ka and ca. 45 ka as the periods of likely human arrival with the greatest intervisibility. This study is also the first to apply least-cost modelling techniques to sea travel, enabling the model to be expanded across the Wallacean archipelago for the first time. Models and palaeogeographic reconstructions constructed herein provide overwhelming support for an initial northern route through Wallacea, with a landing on the modern island of Misool, near the Papuan Bird's Head. Extensive archaeological research on islands of the southern route has so far failed to recover any dates which pre-date those for Sahul, and thus support this inference. Human translocations of cuscus (Phalangeridae) throughout Wallacea found good support for a humanly-assisted introduction from Papua to Timor ca. 3ka, supporting movement between these islands by at least the mid-Holocene

    Algorytmy i modele do analizy struktur białkowych

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    In this work we present several algorithmic approaches designed to help researchers in the study of various orders of protein structure. To facilitate the study of molecular sequence evolution we present an algorithm for multiple alignment of sequence profiles, describe a tool that can be used to study the relationship between residue co-evolution and structure, and a database of structures modeled based co-evolutionary approach. On the structure side, a new algorithm for knot type assignment in biological molecules is introduced, a database of linked protein structures is described, and a method of fixing structure models in a topologically-conscious way is presented. Additionally, folding pathways of several newly discovered knotted proteins are proposed, and the influence of coevolution-based interactions of folding simulations discussed.Niniejsza rozprawa doktorska omawia szereg metod mających zastosowanie w badaniu białek na wielu płaszczyznach. Pierwszy rozdział wprowadza nowy algorytm pozwalający na określenie typu węzła w biocząsteczkach. Drugi rozdział poświęcony jest ewolucji sekwencji molekularnych. Na początku opisany jest nowy algorytm do multiuliniawiania profili sekwencyjnych oraz jego zastosowanie w badaniu ewolucji białek membranowych zawierających zduplikowane domeny. Następnie przedstawione jest narzędzie pozwalające na badanie związków między koewolucją sekwencji (znalezioną poprzez metodę Direct Coupling Analysis), a strukturą cząsteczki, oraz baza danych struktur wymodelowanych na podstawie koewolucji sekwencji. Wreszcie przedstawione jest zastosowanie oddziaływań wskazanych przez koewolucję w symulacjach zwijania białek. Ostatni rozdział poświęcony jest badaniom nietrywialnych topologicznie struktur białek, poprzez bazę danych struktur zawierających linki oraz metodę naprawy modeli struktur z zachowaniem właściwej topologii. Na koniec przedstawione są propozycje ścieżek zwijania dla nowopoznanych struktur białek z węzłami

    Population genetic processes of a Populus nigra/P. x canadensis hybrid complex-spatially explicit studies on gene flow as abasis for conservation measures

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    English summary Limitations of gene flow in populations lead to spatial aggregation of related individuals, which implicates inbreeding and a loss of genetic diversity. The theoretical consequences of these processes are generally understood. However, consequences for real populations, distributed across man made landscapes are not immediately apparent. The anthropogenic introduction of exotic species or domesticated cultivars into landscapes has increased the possibility of introgressive gene flow to their wild relatives. The two taxa Populus nigra and P. x canadensis were used as a model system to obtain knowledge on the quantitative patterns of dispersal within and between the mosaic of remnant native individuals of P. nigra and plantations of P. x canadensis. For this purpose, key features of nSSR markers (nuclear simple sequence repeats), namely high polymorphism, codominant inheritance and availability of species-specific alleles were utilised to create an easy-to-handle tool for obtaining multilocus genetic fingerprints. As publicly available allelic ladders of each locus have been created, the presented marker system enables the generation of transferable genetic data on poplar in different laboratory settings. By this means, the marker assay can help to enlarge present clonal molecular data bases. It is also essential for certification purposes in commercial forestry. Using the marker assay, a natural population of P. nigra was analysed for genetic diversity and spatial genetic structure. Parentage analyses of seedlings as well as juveniles from a restricted area of natural regeneration enabled the quantification of pollen and seed-mediated gene flow, respectively. Consequences for genetic diversity could be concluded and consequences for the management of natural recruitment could be deduced. Spatial genetic patterns of the P. nigra adult tree population suggest prevailing short-distance gene flow, the major part of which (i. e.70 %) takes place within distances of less than 1 km. This helps to explain the reduced diversity in investigated juveniles. In the context of surrounding plantations, introgressive gene flow between P. nigra and the bred taxon P. x canadensis was studied. For this purpose, progeny of both taxa was analysed. Introgressive gene flow was found in both directions. Particular rates varied greatly and were probably due to stochastic environmental conditions and the spatial distribution of trees. However, preferential hybridisation was found between female P. x canadensis and male P. nigra. Moreover, introgressed individuals could be found in natural recruitment. Practical consequences for both upcoming studies and the conservation of natural P. nigra populations are implicated. Results of this research are discussed with respect to hybridisation processes and concerning the risk assessment of transgene flow from genetically modified taxa. Findings may also be transferred to management plans of plant species exhibiting similar dispersal mechanisms as poplar

    Coarse-grained modelling of protein structure and internal dynamics: comparative methods and applications

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    The first chapter is devoted to a brief summary of the basic techniques commonly used to characterise protein's internal dynamics, and to perform those primary analyses which are the basis for our further developments. To this purpose we recall the basics of Principal Component Analysis of the covariance matrix of molecular dynamics (MD) trajectories. The overview is aimed at motivating and justifying a posteriori the introduction of coarse-grained models of proteins. In the second chapter we shall discuss dynamical features shared by different conformers of a protein. We'll review previously obtained results, concerning the universality of the vibrational spectrum of globular proteins and the self-similar free energy landscape of specific molecules, namely the G-protein and Adk. Finally, a novel technique will be discussed, based on the theory of Random Matrices, to extract the robust collective coordinates in a set of protein conformers by comparison with a stochastic reference model. The third chapter reports on an extensive investigation of protein internal dynamics modelled in terms of the relative displacement of quasi-rigid groups of amino acids. Making use of the results obtained in the previous chapters, we shall discuss the development of a strategy to optimally partition a protein in units, or domains, whose internal strain is negligible compared to their relative uctuation. These partitions will be used in turn to characterise the dynamical properties of proteins in the framework of a simplified, coarse-grained, description of their motion. In the fourth chapter we shall report on the possibility to use the collective uctuations of proteins as a guide to recognise relationships between them that may not be captured as significant when sequence or structural alignment methods are used. We shall review a method to perform the superposition of two proteins optimising the similarity of the structures as well as the dynamical consistency of the aligned regions; then, we shall next discuss a generalisation of this scheme to accelerate the dynamics-based alignment, in the perspective of dataset-wide applications. Finally, the fifth chapter focuses on a different topic, namely the occurrence of topologically-entangled states (knots) in proteins. Specifically, we shall investigate the sequence and structural properties of knotted proteins, reporting on an exhaustive dataset-wide comparison with unknotted ones. The correspondence, or the lack thereof, between knotted and unknotted proteins allowed us to identify, in knotted chains, small segments of the backbone whose `virtual' excision results in an unknotted structure. These `knot-promoting' loops are thus hypothesised to be involved in the formation of the protein knot, which in turn is likely to cover some role in the biological function of the knotted proteins

    Phylogenetic inference using Hamiltonian Monte Carlo

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    Ph. D. Thesis.Phylogenetics is the study of evolutionary structure, aiming to reconstruct the branching structure of speciation from a common ancestor. There are many methods of infering the tree-like structure from the most basic, physical traits (morphology) to analysing the distances between genetic code based on a prede ned metric. For viruses such a method is the best way to access their hereditity. Bayesian inference enables us to learn a region of possible trees and alter the distribution of trees according to prior beliefs. The most common method of conducting Bayesian inference over evolutionary trees, called Tree space (Billera et al., 2001), is by Markov Chain Monte Carlo (MCMC). Tree space is big and exploration is slow; a modern technique for speeding up MCMC is Hamiltonian Monte Carlo (HMC), developed by Duane et al. (1987). We incorporate HMC into Tree space by creating our own algorithm: Cross-Orthant HMC (COrtHMC). Many methods of increasing HMC convergence speed have been developed, such as Riemannian Manifold HMC (RM-HMC) (Girolami et al., 2011). Where applicable, we adapted such methods to COrtHMC and then compared COrtHMC to pre-existing methods of phylogenetic inference and probabilistic path HMC (Dinh et al., 2017). We found that all forms of COrtHMC perform similarly, including ppHMC, but that the increased computational cost in using such HMC methods outweighs any bene t.EPSR

    Phylogeography of Austral soil invertebrates

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    Soil invertebrates are terrestrial animals belonging to ancient phyla that emerged almost half a billion years ago. They have since spread throughout all known landmasses, with contemporary distributions governed by geological and environmental change across spatial and temporal gradients across the globe. However, limited knowledge of southern hemisphere (Austral) species hampers our ability to discern the general patterns of distribution and speciation. The lack of robust taxonomic information has also constrained our understanding of the evolutionary relationships and functional roles of the diverse soil fauna. This thesis capitalises on the development in molecular tools and improved sequence libraries to explore the factors that define the distribution and diversity of common soil invertebrates, specifically oribatid mites (Acari), springtails (Collembola) and nematodes (Nematoda). I investigated communities at continental-scales from maritime Antarctica and Australia to enable greater resolution of the drivers of distribution that might be applicable to southern hemisphere taxa more broadly. In a literature review I introduce the bioinformatic approaches using phylogeography to resolve evolutionary theories concerning soil fauna indigenous to Antarctica. Phylogenetic evidence supports most soil faunal groups as having ancient origins, refugial survival and repeated colonisation, whilst also highlighting the benefits of comparative analyses over larger scales. In addition, I show in a perspectives paper that morphological and functional traits are phylogenetically constrained in nematodes and springtails, allowing function to be partially conferred for ‘unknown’ species using sequencing approaches. Baseline biodiversity across a transect through maritime Antarctica found contrasting distributions of mites and springtails and the influences of climatic factors at broad scales and soil microhabitat conditions at local scales. Detailed population genetic analysis of genotypes of the oribatid mites Podacarus auberti and Membranoppia loxolineata alongside the springtail Cryptopygus antarcticus revealed the importance of multiple dispersal events in their ancestral past, supporting theories of refugial survival. Comparative analysis of phylogeographic reconstructions with an analogous Australian transect highlighted that the importance of dispersal differs among mites and springtails and supported the influences of climate and edaphic factors on assemblage structure. These different influences of biogeography and climatic variability related to inherent morphological and physiological traits of the study organisms demonstrate potentially contrasting responses to future episodes of environmental change. With such knowledge, conservation strategies of Austral soil fauna can be re-focussed to ensure their continued persistence in terrestrial ecosystems

    IENE 2020 International Conference LIFE LINES – Linear Infrastructure Networks with Ecological Solutions. Abstract Book

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    In the past 12 to 14 of January 2021, the University of Évora, in the framework of the LIFE LINES project, and the Infrastructure and Ecology Network Europe held the online event IENE International Conference, under the theme “LIFE LINES – Linear Infrastructure Networks with Ecological Solutions”. We had 293 attendees from 40 different countries representing the five continents. During three days, participants were able to assist to 115 full oral presentations, 36 lightning talks, 13 workshops and chat with 40 posters authors, representing studies and projects worldwide. The event counted with 50 thematic sessions, running in five parallel sessions mixing live and pre-recorded interventions
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