Regensburg, Univ., Diss., 2008.

Frankfurt (Main), Universiẗat, Diss., 2008.

Gene and genome duplications are major mechanisms of eukaryotic genome evolution. Three rounds of genome duplication have occurred in the vertebrate lineage, two rounds (1R, 2R) during early vertebrate evolution and a third round, the fish-specific genome duplication (FSGD), in ray-finned fishes at the base of the teleost lineage. Whole genome duplications (WGDs) are considered to facilitate speciation processes and to provide the genetic raw material for major evolutionary transitions and increases in morphological complexity. In the present study, I have used comparative genomic approaches combining molecular phylogenetic reconstructions, synteny analyses as well as gene function studies (expression analyses and knockdown experiments) to investigate the evolutionary consequences and significance of the three vertebrate WGDs. First, the evolutionary history of the endothelin signaling system consisting of endothelin ligands and receptors was reconstructed. The endothelin system is a key component for the development of a major vertebrate innovation, the neural crest. This analysis shows that the endothelin system emerged in an ancestor of the vertebrate lineage and that its members in extant vertebrate genomes are derived from the vertebrate WGDs. Each round of WGD was followed by co-evolution of the expanding endothelin ligand and receptor repertoires. This supports the importance of genome duplications for the origin and diversification of the neural crest, but also underlines a major role for the co-option of new genes into the neural crest regulatory network. Next, I have studied the impact of the FSGD on the evolution of teleost pigment cell development and differentiation. The investigation of 128 genes showed that pigmentation genes have been preferentially retained in duplicate after the FSGD so that extant teleost genomes contain around 30% more putative pigmentation genes than tetrapods. Large parts of pigment cell regulatory pathways are present in duplicate being potentially involved in teleost pigmentary innovations. There are also important differences in the retention of duplicated pigmentation genes among divergent teleost lineages. Functional studies of pigment synthesis enzymes in zebrafish and medaka, particularly of the tyrosinase family, revealed lineage-specific functional evolution of duplicated pigmentation genes in teleosts, but also pointed to anciently conserved gene functions in vertebrates. These results suggest that the FSGD has facilitated the evolution of the teleost pigmentary system, which is the most complex and diverse among vertebrates. In conclusion, the present study supports a major role of WGDs for phenotypic evolution and biodiversity in vertebrates, particularly in fish. / Gen- und Genomverdopplungen sind wichtige Mechanismen der Genomevolution in Eukaryonten. Im Verlauf der Evolution der Wirbeltiere gab es drei wichtige Genomduplikationen. Zwei Genomverdopplungen (1R, 2R) fanden während der sehr frühen Vertebratenevolution statt. In der Linie der Fische kam es an der Basis der Teleostier zu einer weiteren, fischspezifischen Genomduplikation (FSGD). Man nimmt an, dass Genomduplizierungen Artbildungsprozesse begünstigen und dass sie zusätzliches genetisches Material für wichtige evolutionäre Übergänge und für die Steigerung morphologischer Komplexität erzeugen. In der vorliegenden Arbeit wurden Methoden der vergleichenden und funktionellen Genomik gewählt, um die Auswirkungen und die Bedeutung der drei Genomverdopplungen bei Vertebraten zu untersuchen. Dazu wurden molekularphylogenetische Stammbaumanalysen und Synteniedaten mit Genexpressionsstudien und Knockdown-Experimenten kombiniert. Zunächst wurde die Evolution des Endothelin-Signalsystems rekonstruiert. Dieses besteht aus Endothelin-Liganden und -Rezeptoren und hat eine Schlüsselrolle in die Entwicklung der Neuralleiste. Die Neuralleiste und die von ihr abgeleiteten Zelltypen sind wirbeltierspezifische Innovationen. Die Analyse zeigt, dass das Endothelin-System in einem gemeinsamen Vorfahren der Vertebraten entstanden ist. Die in den Genomen rezenter Vertebraten vorkommenden Komponenten des Endothelin-Systems sind durch die drei Genomverdoppelungen entstanden. Nach jeder der Duplizierungen kam es zur Ko-Evolution der Liganden- und Rezeptorenfamilien. Die Evolution des Endothelin-System unterstreicht daher die Bedeutung der Genomduplizierungen für den Ursprung und die Diversifizierung der Neuralleiste. Sie weist aber auch auf eine wichtige Rolle für die Integrierung neuer Gene in das regulatorische Netzwerk der Neuralleiste hin. Im Weiteren wurde der Einfluss der FSGD auf die Evolution der Pigmentzellentwicklung und differenzierung in Teleostiern untersucht. Die evolutionäre Analyse von 128 Genen zeigte, dass Pigmentierungsgene nach der FSGD bevorzugt in zwei Kopien erhalten geblieben sind. Daher besitzen rezente Teleostier im Vergleich zu Landwirbeltieren zusätzlich ca. 30% mehr Gene mit potentiellen Funktionen für die Pigmentierung. Große Teile der regulatorischen Signalwege in den Pigmentzellen liegen daher als zwei Kopien vor. Diese waren möglicherweise an der Evolution von Innovationen in der Körperfärbung von Teleostiern beteiligt. In der vorliegenden Arbeit wurden auch wichtige Unterschiede zwischen verschiedenen Fischgruppen im Erhalt duplizierter Pigmentierungsgene gefunden. Funktionelle Studien bei Zebrafish und bei Medaka an Enzymen der Pigmentsynthese, insbesondere der Tyrosinase-Familie, gaben Hinweise darauf, dass die funktionelle Evolution duplizierter Pigmentierungsgene in Fischen linienspezifisch verlaufen kann. Die Studien ergaben außerdem, dass bestimmte Funktionen der Pigmentsyntheseenzyme innerhalb der Vertebraten konserviert sind. Die Evolution des Pigmentierungssystems der Fische, welches das vielfältigste und komplexeste innerhalb der Wirbeltiere ist, wurde somit maßgeblich durch die FSGD beeinflusst. Zusammenfassend weisen die Ergebnisse der vorliegenden Arbeit darauf hin, dass die Verdopplung ganzer Genome ein wichtiger Mechanismus der phänotypische Evolution bei Vertebraten ist und damit in besonderem Maße zur ihrer Biodiversität beiträgt.

Regensburg, Univ., Diss., 2008.

Site-specific tyrosine-type recombinases are effective tools for genome engineering, with the first engineered variants having demonstrated therapeutic potential. So far, adaptation to new DNA target site selectivity of designerrecombinases has been achieved mostly through iterative cycles of directed molecular evolution. While effective, directed molecular evolution methods are laborious and time consuming. Here we present RecGen (Recombinase Generator), an algorithm for the intelligent generation of designerrecombinases. We gather the sequence information of over one million Crelike recombinase sequences evolved for 89 different target sites with whichwe train Conditional Variational Autoencoders for recombinase generation. Experimental validation demonstrates that the algorithm can predict recombinase sequences with activity on novel target-sites, indicating that RecGen is useful to accelerate the development of future designer-recombinases.

Für eine umfassende Untersuchung der Phylogenie der Decapoda wurden von mir die mitochondrialen Genome von 13 Dekapoden sequenziert. Zusammen mit den in der GenBank verfügbaren Sequenzen von 31 Dekapoden und dem von der Universität Bonn zur Verfügung gestellten mitochondrialen Genom von Dromia personata deckt dieser Datensatz alle großen Teilgruppen der Decapoda ab. Maximum likelihood (ML)-Analysen und Bayesian inference (BI)-Analysen der Nucleotidsequenzen und Aminosäuresequenzen ergaben bezüglich der Verwandtschaft der hochrangigen Taxa ähnliche Topologien: (((((((Anomala, Brachyura), Thalassinida: Gebiidea) Thalassinida: Axiidea), Astacidea), Achelata), Stenopodidea), Caridea), Dendrobranchiata). Gleichwohl wurde mit den Polychelida ein problematisches Taxon mit ungewissen Verwandtschaftsbeziehungen identifiziert. Auf der Eben der Unterordnungen sind die Thalassinida paraphyletisch, was mit einigen morphologischen und einigen jüngeren molekularen Studien konsistent ist, alle anderen gebräuchlichen Taxa sind monophyletisch. Es handelt sich um eine Inversion, die sich vom S-E-F tRNA cluster bis zum I-Q-M tRNA cluster erstreckt und in Procambarus fallax f. virginalis und Homarus gammarus auftritt. Im Vergleich mit dem Genarrangement des Limulus polyphemus zeigen beide Astaciden in dieser Region exakt dieselbe Inversion wie der Priapulide Priapulus caudatus, die daher innerhalb der Ecdysozoa als konvergent angenommen werden muss. Auch neben dieser Inversion innerhalb der Astacidea zeigen die Genarrangements aller verfügbaren Dekapoden mehrere interessante Eigenschaften. Um die beobachteten einzigartigen genomischen Eigenschaften zu erklären, schlage ich mit dem „inversion triggered duplication“ Model ein neues Modell für Gen-Rearrangements vor. / For a comprehensive study of decapod phylogeny at the mitochondrial genome level, I have sequenced the mitochondrial genome of 13 decapods. Together with available sequences of 31 decapods from GenBank, and the mitochondrial genome of Dromia personata provided by the Bonn University, the dataset now cover all major decapod taxa. Maximum likelihood (ML) and Bayesian inference (BI) of the nucleotide and amino acid datasets reveal similar topologies at the higher level relationships: (((((((Anomala, Brachyura), Thalassinida: Gebiidea) Thalassinida: Axiidea), Astacidea), Achelata), Stenopodidea), Caridea), Dendrobranchiata). Nevertheless, one problematic taxon, Polychelida, with ambiguous affinities is recognized. At the lower level, most taxa are monophyletic, whereas the Thalassinida is paraphyletic, which is consistent with some morphological and molecular results. An inversion spanning from S-E-F tRNA cluster to the I-Q-M tRNA cluster occurred in Procambarus fallax f. virginalis, Homarus gammarus, and one priapulid Priapulus caudatus. Compared with the gene arrangement of the horseshoe crab Limulus polyphemus, both astacids and the priapulid exhibit the same inversion, which is therefore supposed to be a convergent event of the clade Astacidea and Priapulida among Ecdysozoa. Other than this notable feature observed in astacids, the gene arrangements in all available decapods show some interesting characters. To explain these unique genomic features observed here, a new gene rearrangement model is proposed, which is called the “inversion triggered duplication” model.

Evolution of Piperales – matK gene and trnK intron sequence data reveal lineage specific resolution contrast. Piperales are one of the largest basal angiosperm orders with a nearly worldwide distribution. The order includes three species rich genera, Piper (ca. 1,000 species), Peperomia (ca. 1,500-1,700 species), and Aristolochia s. l. (ca. 500 species). Sequences of the matK gene and the non-coding trnK group II intron are analysed for a dense set of 105 taxa representing all families (except Hydnoraceae) and all generic segregates (except Euglypha within Aristolochiaceae) of Piperales. A large number of highly informative indels are found in the Piperales trnK/matK dataset. Within a narrow region approximately 500 nt downstream in the matK coding region (CDS), a length variable simple sequence repeat (SSR) expansion segment occurs, in which insertions and deletions have led to short frame-shifts. These are corrected shortly afterwards, resulting in a maximum of 6 amino acids being affected. Furthermore, additional non-functional matK copies were found in Zippelia begoniifolia, which can easily be discriminated from the functional open reading frame (ORF). The trnK/matK sequence data fully resolve relationships within Peperomia, whereas they are not effective within Piper. The resolution contrast is correlated with the rate heterogenity between those lineages. Parsimony, Bayesian and likelihood analyses result in virtually the same topology, and converge on the monophyly of Piperaceae and Saururaceae. Lactoris gains high support as sister to Aristolochiaceae subf. Aristolochioideae, but the different tree inference methods yield conflicting results with respect to the relationships of subfam. Asaroideae. In Piperaceae, a clade formed by the monotypic genus Zippelia and the small genus Manekia (=Sarcorhachis) is sister to the two large genera Piper and Peperomia. Systematics of pipevines – Combining morphological and fast-evolving molecular characters to investigate the relationships within subfamily Aristolochioideae (Aristolochiaceae) A combined phylogenetic analysis of the Aristolochioideae was conducted based on 72 morphological characters and molecular datasets (matK gene, trnK intron, trnL intron, trnL-trnF spacer). The analysis sampled 33 species as the ingroup, including two species of Thottea and 30 species of Aristolochia and the monotypic genus Euglypha, which represent all the infrageneric taxa formally described; Saruma henryi and Asarum caudatum were used as the outgroup. The results corroborate a sister-group relationship between Thottea and Aristolochia, and the paraphyly of Aristolochia with respect to Euglypha that consequently should be included into Aristolochia. Two of the three subgenera within Aristolochia (Isotrema and Pararistolochia) are shown to be monophyletic, whereas the signal obtained from the different datasets about the relationships within subg. Aristolochia is low and conflicting, resulting in collapsed or unsupported branches. The relationship between the New World and the Old World species of subgenus Aristolochia is conflictive because morphological data support these two groups as monophyletic, whereas molecular data show the monophyletic Old World species of Aristolochia nested within the New World species. A sister group relationship is proposed between A. lindneri and pentandrous species, which suggests that a group of five species from central and southern South America (including A. lindneri) could be monophyletic and sister to Aristolochia subsection Pentandrae, a monophyletic taxon consisting of about 35 species from southern USA, Mesoamerica, and the West Indies. Colonisation, phylogeography and evolution of endemism in Mediterranean Aristolochia (Aristolochiaceae). This study provides evidence for a multiple colonisation of the western Old World from Asian ancestors within Aristolochia section Diplolobus (subsection Aristolochia and Podanthemum). Within subsection Podanthemum it is assumed, that the colonisation of the African continent happened at least two times independently. In contrast, for subsection Aristolochia, a rapid morphological radiation in the Near East (or close to this area) with subsequent star like colonisation of the different current distribution areas, which is not paralleled on the molecular level, appears to be more likely. Phylogenetic tree reconstruction is unsupported for these clades, but most clades are highly supported as monophyletic. Interestingly the Mediterranean and temperate Eurasian species, which are morphologically distinct (A. pistolochia, A. clematitis) are not clustering within the main clades, but are independent lineages. Analogue, A. rigida a species from Somalia is well-supported sister to the subsection Aristolochia. Within subsection Podanthemum the colonisation event from an Asian ancestor is clearly traceable, whereas in subsection Aristolochia the path is not traceable, since the ancestors are extinct or not present in the connecting areas. Within the Mediterranean, Near East and Caucasian species of subsection Aristolochia two morphologically and biogeographically well supported groups can be identified: the Near East/Caucasian species and the West Mediterranean species. The previous groupings for the latter, based on morphological characters, could be substantiated only partly by our results. This study provides the first phylogeny of all West Mediterranean species. In addition an independent complex is established including some micro endemic species. The phylogenetic results are discussed with respect to biogeography, and morphology, to give a first insight into the radiation and colonisation of the genus Aristolochia in the Mediterranean region. Universal primers for a large cryptically simple cpDNA microsatellite region in Aristolochia. We provide a new and valuable marker to study species relationships and population genetics in order to trace evolutionary, ecological, and conservational aspects in the genus Aristolochia. Universal primers for amplification and subsequent sequencing of a chloroplast microsatellite locus inside the trnK intron are presented. Utility of the primers has been tested in 32 species representing all clades of Aristolochia, including population studies within the A. pallida complex, A. clusii and A. rotunda. The microsatellite region is characterized as a (AnTm)k repeat of 22–438 bp containing a combination of different repeats arranged as ‘cryptically simple’. Trapped! Pollination of Aristolochia pallida Willd. in the Mediterranean A first study of the pollination biology of a Mediterranean Aristolochia species in its natural habitat is presented. 183 flowers of Aristolochia pallida were investigated, which in total contained 73 arthropods, dominated by two groups of Diptera, Sciaridae (37%) and Phoridae (19%). However, only Phoridae are regarded as potential pollinators, since pollen has been found exclusively on the body surfaces of these insects. All Phoridae belong to the genus Megaselia and are recognised as four undescribed species. The measurements of flower and insect dimensions suggest that size is an important constrain for successful pollination: 1) the insects must have a definitive size for being able to enter the flower and 2) must be able to get in touch with the pollen. Only very few insect groups found in Aristolochia pallida fulfil these size requirements. However, size alone is not a sufficient constrain as too many fly species of the same size might be trapped but not function as pollinators. Instead, specific attraction is required as otherwise pollen is lost. Since all trapped Phoridae are males, a chemical attraction (pheromones) is proposed as an additional constrain. Since A. pallida flowers are protogynous, the record of Megaselia loaded with pollen found in a flower during its female stage proves that this insect must have been visited at least one different flower during its male stage before. Further on, this observation provides strong evidence that the flowers are cross-pollinated. All these factors indicate a highly specialised pollination of Aristolochia pallida by Megaselia species.

Major progress has been made during the last twenty years towards a better understanding of the evolution of angiosperms. Early molecular-phylogenetic analyses revealed three major groups, with eudicots as well as monocots being monophyletic, arisen from a paraphyletic group of dicotyledonous angiosperms (= basal angiosperms). Consistently, numerous phylogenetic studies based on sequence data have recovered the eudicot-clade and increased confidence in its existence. Furthermore this clade, which contains about 75% of angiosperm species diversity, is characterized by the possession of tricolpate and tricolpate-derived pollen and has thus also been called the tricolpate clade. Based on molecular-phylogenetic investigations several lineages, such as Ranunculales, Proteales (= Proteaceae, Nelumbonaceae, Platanaceae), Sabiaceae, Buxaceae plus Didymelaceae, and Trochodendraceae plus Tetracentraceae were shown as belonging to a early-diverging grade (early-diverging or “basal” eudicots), while larger groups like asterids, Caryophyllales, rosids, Santalales, and Saxifragales were identified as being members of a highly supported core clade, the so called “core eudicots”. Nevertheless, phylogenetic relationships among several lineages of the eudicots remained difficult to resolve. This thesis is mainly concentrated on fully resolving the branching order among the different clades of the early-diverging eudicots as well as on clarifying phylogenetic and systematic conditions within several lineages, based on phylogenetic reconstructions using sequence data of rapidly-evolving and non-coding molecular regions, such as spacers and introns. Commonly, fast-evolving and non-coding DNA was used to infer relationships among species and genera, as practised in chapter 3, due to the assumption of being inapplicable caused by putative high levels of homoplasy through multiple substitutions and frequent microstructural changes resulting in non-alignability. However, during the last few years numerous molecular-phylogenetic studies were able to present well resolved angiosperm trees on the basis of rapidly-evolving and non-coding regions from the large single copy region of the chloroplast genome comparable to multi-gene analyses concerning topology and statistical support. Mutational dynamics in spacers and introns was revealed to follow complex patterns related to structural constraints like the introns secondary structure. Therefore extreme sequence variability was always confirmed to mutational hotspots that could be excluded from calculations. Moreover it became clear that combining these non-coding regions with the fast-evolving matK gene can lead to further resolved and statistical supported trees. Chapter 1 deals with the placement of Sabiales inside the early-diverging eudicot grade, while investigating mutational dynamics as well as the utility of different kinds of non-coding and rapidly-evolving DNA within deep-level phylogenetics. It was done by analyzing a combination of nine regions from the large single copy region of the chloroplast genome, including spacers, the sole group I intron, three group II introns and the coding matK for a sampling of 56 taxa. The presented topology is in mainly congruence with the hypothesis on phylogenetic relationships among early-branching eudicots that was gained through the application of a reduced set of five non-coding and fast-evolving molecular markers, including the plastid petD (petB-petD spacer, petD group II intron) plus the trnL-F (trnL group I intron, trnL-F spacer) region and the matK gene. It showed a grade of Ranunculales, Sabiales, Proteales, Trochodendrales and Buxales. The current study differs in showing Sabiales as sister to Proteales in all phylogenetic analyses, in contrast to a second-branching inside early-diverging eudicots and a Bayesian tree displaying Sabiales branching after Proteales. All three hypotheses were tested concerning their likelihood. None of them was shown as being significantly declinable. Thus, albeit the number of characters and informative sites was doubled in comparision to the five-region investigation, the exact position of the Sabiales remained to be resolved with confidence. However, the advanced analyses of the phylogenetic structure of the three different non-coding partitions in comparison to coding genes resulted in the recognition of a significantly higher mean phylogenetic signal per informative character within spacers and introns than in the frequently applied slowly-evolving rbcL gene. The fast-evolving and well performing matK gene is shown to be nested within the non-coding partitions in this respect. Interestingly, the least constrained spacers displayed considerably less phylogenetic structure than both, the group I intron and the group II introns. Molecular evolution is again shown to follow certain patterns in angiosperms, as indicated by the occurrence of mutational hotspots and their connection to structural and functional constraints. This is especially shown for the group II introns studied where highly dynamic sequence parts were rather found in loops than stems. The aim of chapter 2 was to present a comprehensive reconstruction of the phylogenetic relationships inside the order of Ranunculales, the first-branching clade of the early-diverging eudicots, with an emphasis on the evolution of growth forms within the group. Currently, the order comprises seven families (Ranunculaceae, Berberidaceae, Menispermaceae, Lardizabalaceae, Circaeasteraceae – not included due to lacking plant material, Eupteleaceae, Papaveraceae) containing predominantly herbaceous groups as well as trees and lianescent/shrubby forms. A surprising result that emerged due to the increased use of molecular data within systematics during the last twenty years is the inclusion of the woody Eupteleaceae into Ranunculales. Because of its adaptation to wind pollination it was previously placed next to Hamamelididea. Although phylogenetic hypotheses agreed in the exclusion of Eupteleaceae and the predominantly herbaceous Papaveraceae from a core clade the branching order within early-diverging Ranunculales remained a question to be answered. Thus phylogenetic reconstructions based on molecular data of 50 taxa (including outgroup), applying the well-performing non-coding petD and trnL-F as well as the trnK/matK-psbA region including the coding matK, were carried out. The comprehensive sampling resulted in fully resolved and highly supported phylogenies in both, maximum parsimony and model based approaches, with family relations within the core clade being identical and Euptelea appearing as first branching lineage. However, the relationships among the early-diverging Ranunculales could not be resolved with confidence, a result in line with the finding made in chapter 1. The topology was further resolved as Lardizabalaceae being sister to the remaining members of the order, followed by Menispermaceae, Berberidaceae and Ranunculaceae, the latter sharing a sistergroup relationship. Inside the mainly lianescent Lardizabalaceae the shrubby Decaisnea was clearly depicted as first-branching. The systematic controversial Glaucidium and Hydrastis are shown to be early-diverging members of the Ranunculaceae. A central goal of chapter 3 was to test phylogenetic relationships among the members of the ranunculaceous tribe Anemoneae. Currently it consists of the subtribes Anemoninae including Anemone, Hepatica, Pulsatilla and Knowltonia, and Clematidinae, consisting of Archiclematis, Clematis and Naravelia. Furthermore the position and taxonomic rank of several lineages inside the subtribe Anemoninae were examined. Since recent comprehensive molecular-phylogenetic investigations have been carried out for the members of Clematidinae or Anemoninae, 63 species representing all major lineages of the two subtribes were included into analyses. Calculations were carried out on the basis of molecular data of the nuclear ribosomal ITS1&2 and the plastid atpB-rbcL intergenic spacer region. Phylogenetic reconstructions resulted in the recognition of two distinct clades within the tribe, thus corroborating the formation of the two subtribes. Within the subtribe Anemoninae the traditional genera Knowltonia, Pulsatilla and Hepatica are confidently shown to be nested within the genus Anemone. The preliminary classification of the genus, currently consisting of the two subgenera Anemone and Anemonidium, is complemented by the subgenus Hepatica.

Major progress has been made during the last twenty years towards a better understanding of the evolution of angiosperms. Early molecular-phylogenetic analyses revealed three major groups, with eudicots as well as monocots being monophyletic, arisen from a paraphyletic group of dicotyledonous angiosperms (= basal angiosperms). Consistently, numerous phylogenetic studies based on sequence data have recovered the eudicot-clade and increased confidence in its existence. Furthermore this clade, which contains about 75% of angiosperm species diversity, is characterized by the possession of tricolpate and tricolpate-derived pollen and has thus also been called the tricolpate clade. Based on molecular-phylogenetic investigations several lineages, such as Ranunculales, Proteales (= Proteaceae, Nelumbonaceae, Platanaceae), Sabiaceae, Buxaceae plus Didymelaceae, and Trochodendraceae plus Tetracentraceae were shown as belonging to a early-diverging grade (early-diverging or “basal” eudicots), while larger groups like asterids, Caryophyllales, rosids, Santalales, and Saxifragales were identified as being members of a highly supported core clade, the so called “core eudicots”. Nevertheless, phylogenetic relationships among several lineages of the eudicots remained difficult to resolve. This thesis is mainly concentrated on fully resolving the branching order among the different clades of the early-diverging eudicots as well as on clarifying phylogenetic and systematic conditions within several lineages, based on phylogenetic reconstructions using sequence data of rapidly-evolving and non-coding molecular regions, such as spacers and introns. Commonly, fast-evolving and non-coding DNA was used to infer relationships among species and genera, as practised in chapter 3, due to the assumption of being inapplicable caused by putative high levels of homoplasy through multiple substitutions and frequent microstructural changes resulting in non-alignability. However, during the last few years numerous molecular-phylogenetic studies were able to present well resolved angiosperm trees on the basis of rapidly-evolving and non-coding regions from the large single copy region of the chloroplast genome comparable to multi-gene analyses concerning topology and statistical support. Mutational dynamics in spacers and introns was revealed to follow complex patterns related to structural constraints like the introns secondary structure. Therefore extreme sequence variability was always confirmed to mutational hotspots that could be excluded from calculations. Moreover it became clear that combining these non-coding regions with the fast-evolving matK gene can lead to further resolved and statistical supported trees. Chapter 1 deals with the placement of Sabiales inside the early-diverging eudicot grade, while investigating mutational dynamics as well as the utility of different kinds of non-coding and rapidly-evolving DNA within deep-level phylogenetics. It was done by analyzing a combination of nine regions from the large single copy region of the chloroplast genome, including spacers, the sole group I intron, three group II introns and the coding matK for a sampling of 56 taxa. The presented topology is in mainly congruence with the hypothesis on phylogenetic relationships among early-branching eudicots that was gained through the application of a reduced set of five non-coding and fast-evolving molecular markers, including the plastid petD (petB-petD spacer, petD group II intron) plus the trnL-F (trnL group I intron, trnL-F spacer) region and the matK gene. It showed a grade of Ranunculales, Sabiales, Proteales, Trochodendrales and Buxales. The current study differs in showing Sabiales as sister to Proteales in all phylogenetic analyses, in contrast to a second-branching inside early-diverging eudicots and a Bayesian tree displaying Sabiales branching after Proteales. All three hypotheses were tested concerning their likelihood. None of them was shown as being significantly declinable. Thus, albeit the number of characters and informative sites was doubled in comparision to the five-region investigation, the exact position of the Sabiales remained to be resolved with confidence. However, the advanced analyses of the phylogenetic structure of the three different non-coding partitions in comparison to coding genes resulted in the recognition of a significantly higher mean phylogenetic signal per informative character within spacers and introns than in the frequently applied slowly-evolving rbcL gene. The fast-evolving and well performing matK gene is shown to be nested within the non-coding partitions in this respect. Interestingly, the least constrained spacers displayed considerably less phylogenetic structure than both, the group I intron and the group II introns. Molecular evolution is again shown to follow certain patterns in angiosperms, as indicated by the occurrence of mutational hotspots and their connection to structural and functional constraints. This is especially shown for the group II introns studied where highly dynamic sequence parts were rather found in loops than stems. The aim of chapter 2 was to present a comprehensive reconstruction of the phylogenetic relationships inside the order of Ranunculales, the first-branching clade of the early-diverging eudicots, with an emphasis on the evolution of growth forms within the group. Currently, the order comprises seven families (Ranunculaceae, Berberidaceae, Menispermaceae, Lardizabalaceae, Circaeasteraceae – not included due to lacking plant material, Eupteleaceae, Papaveraceae) containing predominantly herbaceous groups as well as trees and lianescent/shrubby forms. A surprising result that emerged due to the increased use of molecular data within systematics during the last twenty years is the inclusion of the woody Eupteleaceae into Ranunculales. Because of its adaptation to wind pollination it was previously placed next to Hamamelididea. Although phylogenetic hypotheses agreed in the exclusion of Eupteleaceae and the predominantly herbaceous Papaveraceae from a core clade the branching order within early-diverging Ranunculales remained a question to be answered. Thus phylogenetic reconstructions based on molecular data of 50 taxa (including outgroup), applying the well-performing non-coding petD and trnL-F as well as the trnK/matK-psbA region including the coding matK, were carried out. The comprehensive sampling resulted in fully resolved and highly supported phylogenies in both, maximum parsimony and model based approaches, with family relations within the core clade being identical and Euptelea appearing as first branching lineage. However, the relationships among the early-diverging Ranunculales could not be resolved with confidence, a result in line with the finding made in chapter 1. The topology was further resolved as Lardizabalaceae being sister to the remaining members of the order, followed by Menispermaceae, Berberidaceae and Ranunculaceae, the latter sharing a sistergroup relationship. Inside the mainly lianescent Lardizabalaceae the shrubby Decaisnea was clearly depicted as first-branching. The systematic controversial Glaucidium and Hydrastis are shown to be early-diverging members of the Ranunculaceae. A central goal of chapter 3 was to test phylogenetic relationships among the members of the ranunculaceous tribe Anemoneae. Currently it consists of the subtribes Anemoninae including Anemone, Hepatica, Pulsatilla and Knowltonia, and Clematidinae, consisting of Archiclematis, Clematis and Naravelia. Furthermore the position and taxonomic rank of several lineages inside the subtribe Anemoninae were examined. Since recent comprehensive molecular-phylogenetic investigations have been carried out for the members of Clematidinae or Anemoninae, 63 species representing all major lineages of the two subtribes were included into analyses. Calculations were carried out on the basis of molecular data of the nuclear ribosomal ITS1&2 and the plastid atpB-rbcL intergenic spacer region. Phylogenetic reconstructions resulted in the recognition of two distinct clades within the tribe, thus corroborating the formation of the two subtribes. Within the subtribe Anemoninae the traditional genera Knowltonia, Pulsatilla and Hepatica are confidently shown to be nested within the genus Anemone. The preliminary classification of the genus, currently consisting of the two subgenera Anemone and Anemonidium, is complemented by the subgenus Hepatica.

Despite advances in nuclease-based genome editing technologies, correcting human disease-causing genomic inversions remains a challenge. Here, we describe the potential use of a recombinase-based system to correct the 140 kb inversion of the F8 gene frequently found in patients diagnosed with severe Hemophilia A. Employing substrate-linked directed molecular evolution, we develop a coupled heterodimeric recombinase system (RecF8) achieving 30% inversion of the target sequence in human tissue culture cells. Transient RecF8 treatment of endothelial cells, differentiated from patient-derived induced pluripotent stem cells (iPSCs) of a hemophilic donor, results in 12% correction of the inversion and restores Factor VIII mRNA expression. In this work, we present designer-recombinases as an efficient and specific means towards treatment of monogenic diseases caused by large gene inversions.