Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens

We present the model and implementation of a workflow that blazes a trail in systematic biology for the re-usability of character data (data on any kind of characters of pheno- and genotypes of organisms) and their additivity from specimen to taxon level. We take into account that any taxon characterization is based on a limited set of sampled individuals and characters, and that consequently any new individual and any new character may affect the recognition of biological entities and/or the subsequent delimitation and characterization of a taxon. Taxon concepts thus frequently change during the knowledge generation process in systematic biology. Structured character data are therefore not only needed for the knowledge generation process but also for easily adapting characterizations of taxa. We aim to facilitate the construction and reproducibility of taxon characterizations from structured character data of changing sample sets by establishing a stable and unambiguous association between each sampled individual and the data processed from it. Our workflow implementation uses the European Distributed Institute of Taxonomy Platform, a comprehensive taxonomic data management and publication environment to: (i) establish a reproducible connection between sampled individuals and all samples derived from them; (ii) stably link sample-based character data with the metadata of the respective samples; (iii) record and store structured specimen-based character data in formats allowing data exchange; (iv) reversibly assign sample metadata and character datasets to taxa in an editable classification and display them and (v) organize data exchange via standard exchange formats and enable the link between the character datasets and samples in research collections, ensuring high visibility and instant re-usability of the data. The workflow implemented will contribute to organizing the interface between phylogenetic analysis and revisionary taxonomic or monographic work

Nested singletons in molecular trees: Utility of adding morphological and geographical data from digitized herbarium specimens to test taxon concepts at species level in the case of Casearia (Salicaceae)

Using the genus Casearia, we assessed the status of nested singletons: individual specimens corresponding to accepted species but in molecular trees appearing nested within clades of closely related species. Normally, such cases would be left undecided, while on the other hand, timely taxonomic decisions are required. We argue that morphological, chorological, and ecological data can be informative to illuminate patterns of speciation. Their use can provide a first step in testing taxon concepts at species level. We focused on five cases of nested singletons in trees of the genus Casearia. We employed PCA and cluster analysis to assess phenotypic differentiation. Using geocoordinates, we calculated niche space differentiation based on 19 bioclim variables, by means of PCA and niche equivalency and similarity tests and generated dot maps. We found that the singletons were morphologically distinctive in two of the five cases (Casearia selloana and C. manausensis), relatively distinctive in two other cases (C. zizyphoides and C. mariquitensis), and partially overlapping in the last case (C. grandiflora). For two cases (C. mariquitensis and C. selloana), ecological niche space was broadly overlapping, in two cases it was found broadly nested (C. grandiflora and C. zizyphoides), and in one case narrowly nested (C. manausensis), but in no case niche differentiation was observed. Niche overlap, similarity and equivalency showed corresponding patterns. Given these data, one would interpret C. selloana and C. manausensis as presumably well-distinguished taxa, their narrow distribution ranges suggesting recently emerging lineages. The other three cases are not clearcut. Morphological data would suggest particularly C. grandiflora conspecific with C. arborea, but differences in the distribution are intriguing. Our approach would reject the notion of potential synonymy based on nested phylogenetic placement for at least two of the five cases. The other case also shows no complete lack of differentiation which would support synonymy

Molecular Phylogeny, Evolution and Biogeography of the Andean Gynoxyoid Group (Compositae, Asteroideae-Senecioneae).

This study is focused on the Gynoxyoid group a species‐rich lineage with low genetic distances within the subtribe Tussilaginineae. The Andean clade within the Asteraceae family comprises four genera and ca. 160 species. The genus Paracalia represents the smallest genus within the Gynoxyoid comprising only two species, the genera Aequatorium and Paragynoxys include 12 and 13 species respectively, and the largest genus Gynoxys contains 131 species. This group includes shrubs to big trees and eventually scandent shrubs (meanly Paracalia) which are distributed from north to south Andes, representing important components of the Andean vegetation. Analyses on plastid and nuclear data have retrieved this group as monophyletic, nevertheless these studies include only some representatives of this clade as part of their investigations. In that sense, the phylogenetic relationships at inter- and infrageneric level remained largely unresolved. Likewise, the morphological studies within this group is limited to close-distributed group of species. The aim of this study is to elucidate the phylogenetic relationships of the Gynoxyoid clade and define genera and (for a reduced group) species limits within it. In that sense, 21 complete annotated chloroplast genomes from a representative subgroup of the Gynoxyoids and four related members of the Tussilaginineae were generated. Thereafter, phylogenetic analyses were performed under maximum likelihood and Bayesian approaches. In order to estimate the strength of the phylogenetic signal in each genome partition trees topologies supported by gene, intron, and intergenic spacer partitions were compared. In a second instance, the impact of indel coding as well as manual adjustments of multiple automatic DNA sequence on the reconstruction of phylogenetic tree was evaluated. Given the phylogenetic backbone retrieved in the first phase of this study, genera delimitation was evaluated. Morphological variation among genera was evaluated by selecting a representative group of members of the Gynoxyoids and searching for discontinuities. The set of characters contributing to the discontinuities and already stated diagnostic characters in prologues were evaluated with a character reconstruction analysis. A second evaluation of the potential set of morphological characters retrieved in the previous analysis was further extended to all remaining members of the Gynoxyoids. Consequently, a revision of the current genera and species circumscription is made and a checklist including all members of the clade is provided. When necessary, new circumscriptions were proposed. Finally, species delimitation was evaluated for a reduced number of species distributed exclusively in Bolivia. The Asteraceae checklist for Bolivia was the basis for the species selection. A morphological revision as described for the genera evaluation was carried out at species level. Based on the discontinuities, morpho-species were defined. Additionally, phylogenetic inferences were reconstructed on the nuclear markers ETS and ITS. The set of putative characters suitable for morpho-species was tested with a principal component analysis in order to test the clustering of morpho-species and phylogenetic clades. The results of all analyses resulted in the elaboration of a taxonomic treatment for all supported Bolivian species. The phylogenetic results resolve the Gynoxyoid group as monophyletic. Phylogenetic trees on all three plastid genomic partitions retrieved well-supported clades. Nevertheless, incongruences in tree topologies were found among all three partitions. Moreover, significant differences were found among tree inferences before and after the manual curation of the alignments, meaning that the automatic multiple sequence alignment failed at the assessment of homology. Furthermore, the results show that a manual alignment correction is essential for phylogeny reconstruction, specially for closely related taxa. The phylogeny retrieved in this study is partially incongruent with the current generic classification, which was purely based on morphological data. The genus Aequatorium was represented by only one representative and its monophyly could not be tested, nevertheless, this unique specimen was retrieved as an independent clade. The genus Paragynoxys was retrieved as monophyletic. All members of the genus Nordenstamia were retrieved as being part of the Gynoxys clade, as well as one of the two members of the genus Paracalia. The second member of the genus Paracalia was retrieved as basal clade of the tree inference. In the second part of the study, the ancestral character reconstruction suggested a set of potential characters for genera delimitation. After testing the validity of this characters set in all members of the Gynoxyoids the delimitation and characterization of four genera was achieved. In that sense, the genus Aequatorium comprises all species with radiate white capitula, Paragynoxys includes trees with discoid white capitula distributed in Colombia and Venezuela, Paracalia characterizes by the absence of outer phyllaries and a central (Bolivia and Peru) distribution, and finally all members with yellow capitula are included in Gynoxys. The checklist resulted in a total of 158 species belonging to the four previously mentioned genera. The genus Nordenstamia was synonymized under Gynoxys and so all its members were newly synonymized in this study. Finally, although the phylogeny on the ETS and ITS markers of the Bolivian species retrieved incongruent topologies, it supported the circumscription of some species. The results of the principal component analysis supported most of the morpho-species, but vaguely the clades retrieved in the phylogenetic inference. Interestingly, both molecular and morphological analysis suggested the presence of at least one putative hybrid species. Based on these results, the taxonomic treatment for the Bolivian species of the Gynoxyoid clade resulted in 14 species belonging to Paracalia (1 sp) and Gynoxys (13 sp). This represented a reduction on the species number stated in the Asteraceae checklist for Bolivia as seven names were synonymized, and three names were excluded because of misidentifications. This investigation represents the first comprehensive study on the Gynoxyoid clade. It includes a phylogenetic backbone, character states reconstruction and a morphological analysis. The molecular datasets reveled closely relationships among species, suggesting rapid-radiating evolution, which was supported by morphological data. Furthermore, based on this analysis we were able to delimit genera and in a more reduced geographic scale, at species level. This study aims to contribute to the Flora de Bolivia which is part of the cooperation agreement between the Botanic Garden and Botanical Museum Berlin (Germany), the “Herbario Nacional de Bolivia” and the “Instituto de Ecología” de La Paz-Bolivia. That aims of this association are to collaborate in the formation of professionals in the area of botany for the subsequent application of knowledge

Biogeography, evolution and systematics of Casearia Jacq. (Salicaceae) in the Neotropics

Casearia is a pantropical genus of circa 240 species of the Salicaceae family, and the most species rich genus of the tribe Samydeae. The Neotropics harbours half of all Casearia species, which are present in every biome of the New World. Despite its abundance in tropical biomes, Casearia has been poorly studied, mostly because of the complexity of identification at the species level. This thesis presents the first well-resolved phylogenetic study of the genus Casearia. The objectives were to test its monophyly and to elucidate its relationships to other taxa of the Samydeae tribe, as well as to study the biogeography of the genus. Furthermore, species boundaries of some Neotropical taxa were investigated, using an integrative taxonomy approach. Finally, the last objective was to elaborate a reliable World checklist of every currently accepted Casearia species, a tool most needed for taxonomy, conservation and biodiversity management. A molecular dataset of 103 accessions from four plastid regions (petD, rpl16, rps4/trnLF and trnK/matK) and on nuclear region (ITS) was generated, corresponding to 54 species, of which 42 belong to Casearia. The study focuses on Neotropical species and the dataset included five Samydeae genera: Euceraea, Lunania, Neoptychocarpus, Ryania and Tetrathylacium, to understand the relationship between Casearia and the Samydeae tribe. Phylogenetic relationships were inferred using Bayesian inference, maximum likelihood and parsimony analysis. The origin of Casearia in the Caribbean and its biogeographical relationships to species from the South American mainland was investigated. Therefore, divergence time and ancestral area were estimated. Seven key morphological characters were studied, in order to retrieve synapomorphies for the genus, using BayesTraits. The results of the phylogenetic reconstruction showed a well-supported Samydeae clade and a well-supported Casearia clade, as sister to the other Samydeae. The genus Casearia was identified as not monophyletic, because the included species of the two Neotropical genera Euceraea and Neoptychocarpus were found nested with good support within the Casearia clade. Several major clades were retrieved, mostly constituted of entirely Neotropical species, one of which being consisted of only species from the Caribbean. A clade of all Paleotropical species was found nested in the clade with the New World Casearia taxa. Two morphological characters that work well to delimitate a monophyletic genus concept were identified. First, a branched inflorescence (fasciculate, glomerulous or cymous) and second a single row of stamen. In addition, some traits previously used as diagnostic for the genus, have been identified as homoplastic.For example, the presence of pellucid dots or lines on the leaves, that appeared earlier within Samydeae and were lost in Ryania and Tetrathylacium, a dioeceous reproduction system, used to diagnose Neoptychocarpius, or a higher number of stamen, used to diagnose Laetia and Zuelania. The time estimation analysis of the present study showed that the Samydeae clade originated in South America during the Cretaceous, 102 Ma, which corresponds to the rapid radiation of the Malpighiales. The Casearia clade is of South American origin and begins to diversify in the Eocene, 90 Ma. The Paleotropical clade of Casearia was found to have originated later than the Neotropical one, therefore from New World ancestors, in the Oligocene/Miocene boundary, 40 Ma and that it was divided into two clades, an African and an Asian one. More sampling from Old World taxa would be needed, in order to identify the origin of this Paleotropical clade. The results show that Casearia migrated multiple times to the Caribbean, and gave rise to a clade of Caribbean endemics in the late Miocene, 9 Ma, most likely of South American origin. In addition, the species limits of five Neotropical taxa were investigated. Those taxa were retrieved as nested singletons, which are taxa with a single or few accessions of an accepted species, nested within a clade of another accepted species. Here, an integrative taxonomy approach was applied as a successful way to study the taxonomical status of those taxa, to evaluate whether the singletons may be considered as a synonym, or if they constitute an emerging species, using both morphological and ecological analysis. To that aim, morphological and ecological differentiations were calculated, or on the contrary the absence of differentiation, between those nested singleton and the taxa in which it it nested. Phenotypic differentiation was analysed using morphometry based on the characters that are used as diagnostic characters of the taxa. For the ecological analysis, the niche space differentiation was evaluated and ecological niche equivalency and similarity tests were performed. Furthermore, the distribution range of those species was mapped. One species, C. grandiflora, is recovered nested within a C. arborea clade. However, the analyses showed that it presents some degree of differentiation, both morphological and ecological. Therefore, the results suggest that they are indeed two species and C. grandiflora is most likely a recent emerging lineage. Two other cases of nested singleton were found, C. selloana and C. zizyphoides, retrieved within the C. sylvestris clade. The results show that they present little to no morphological and ecological differentiation and a narrower distribution range as the widely distributed C. sylvestris. Therefore, it suggests that they most likely represent a subspecies of C. sylvestris. Another nested singleton of C. mariquitensis is retrieved within a C. mollis clade and they are most likely synonyms, given the absence of morphological or ecological differentiation. Finally, an up-to-date checklist of all currently accepted Casearia species is presented, which includes both Neotropical and Paleotropical taxa. The database was created using information from floristic treatments, monographs, regional checklists and taxonomic treatments at species level. For each taxon, the complete information on protologue, types and synonyms has been provided. Our aim was to give the genus a taxonomic backbone that can serve as a basis for further research in taxonomy, ecology and species conservation. The EDIT platform for Cybertaxonomy was used; it is an open-source platform that presents all the tools necessary to establish a taxonomic checklist. It provides the user with a taxonomic editor where every relevant taxonomic information can be entered and an online data portal Here, the most complete checklist of Casearia species to date at a global scale is presented. 708 names, 222 accepted species, 464 synonyms and 22 unresolved names were included, combining information from taxonomical revision, floristic treatments and regional checklists

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

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