The haplolepideous mosses (Dicranidae) comprise about 4000 species distributed over a wide range of habitats, with great gametophytic and sporophytic morphological variation. Their monophyly is... Show moreThe haplolepideous mosses (Dicranidae) comprise about 4000 species distributed over a wide range of habitats, with great gametophytic and sporophytic morphological variation. Their monophyly is well supported by the results of several molecular phylogenetic studies, which shed light on their relationships and circumscriptions, and thus also contributed to identify many remaining problems. Dicranidae ordinal classification is not congruent with current relationship hypotheses and is not supported by morphology. Morphological circumscriptions of some families do not correspond to monophyletic groups. Furthermore, the monophyly of many families and genera with weak morphological circumscriptions remains to be tested. In this thesis, systematics and relationships of the leucobryoid mosses and some families and genera segregated from the former Dicranaceae s.l. were studied using molecular phylogenetic methods. 37 out of the 38 haplolepideous moss families were represented by markers from the three genomes (nrITS, nad5, trnS-trnF, atpB-rbcL). Phylogenetic reconstructions were based on maximum parsimony, maximum likelihood, and Bayesian inference. Ancestral state reconstructions, phylogenetic network analysis (NeighborNet), and relationship hypothesis testing (Shimodaira-Hasegawa test) were performed to contribute to the interpretation of the results of the phylogenetic reconstructions. Morphological circumscriptions were evaluated and improved whenever possible, in line with the results of all analyses performed. Show less
Based on recent achievements in phylogenetic studies of the Brassicaceae, a novel infrafamilial classification is proposed that includes major improvements at the subfamilial and supertribal levels... Show moreBased on recent achievements in phylogenetic studies of the Brassicaceae, a novel infrafamilial classification is proposed that includes major improvements at the subfamilial and supertribal levels. Herein, the family is subdivided into two subfamilies, Aethionemoideae (subfam. nov.) and Brassicoideae. The Brassicoideae, with 57 of the 58 tribes of Brassicaceae, are further partitioned into five supertribes, including the previously recognized Brassicodae and the newly established Arabodae, Camelinodae, Heliophilodae, and Hesperodae. Additional tribus-level contributions include descriptions of the newly recognized Arabidopsideae, Asperuginoideae, Hemilophieae, Schrenkielleae, and resurrection of the Chamireae and Subularieae. Further detailed comments on 17 tribes in need of clarifications are provided. Show less
The largest genus within the Phyllanthaceae family is a group called Phyllanthus L. Recent studies have shown, that Phyllanthus is paraphyletic with the genera Glochidion, Breynia and Synostemon... Show moreThe largest genus within the Phyllanthaceae family is a group called Phyllanthus L. Recent studies have shown, that Phyllanthus is paraphyletic with the genera Glochidion, Breynia and Synostemon nested within it. In this thesis, I study the evolution and systematics of Phyllanthus and how to solve the apparent paraphyly. First we explore past morphological subgroups to come to a subdivision, which was tested using molecular phylogenetics. Several species of Phyllanthus are also used in traditional medicine and by utilizing the living collections of the Hortus botanicus Leiden, we tested for antibacterial and antifungal bioactivity. The phylogeny resulting from this study is used to study the historical biogeography and diversification of the tribe and to propose a new classification where Phyllanthus is separated into several smaller genera. Show less
The majority of tribe Phyllantheae (Phyllanthaceae) is currently placed in the paraphyletic genus Phyllanthus and discussions have persisted on how to resolve this issue. Here, we split Phyllanthus... Show moreThe majority of tribe Phyllantheae (Phyllanthaceae) is currently placed in the paraphyletic genus Phyllanthus and discussions have persisted on how to resolve this issue. Here, we split Phyllanthus into ten monophyletic genera, which are all reinstatements of former genera, but with changes made to the circumscription and constituent species of each group. The genera Breynia, Glochidion and Synostemon were recently found to be nested within Phyllanthus and discussions ensued whether or not to subsume everything into Phyllanthus s.l. Instead of combining all these genera, we here implement the solution of splitting Phyllanthus into strictly monophyletic genera to ensure that the classification is consistent with the latest phylogenetic results. The new classification is based on a phylogenetic framework combined with differences in habit, branching type, floral, fruit and pollen morphology. With this new division of the genus Phyllanthus, tribe Phyllantheae will consist of the following 18 genera: Breynia, Cathetus, Cicca, Dendrophyllanthus, Emblica, Flueggea, Glochidion, Heterosavia, Kirganelia, Lingelsheimia, Lysiandra, Margaritaria, Moeroris, Nellica, Nymphanthus, Phyllanthus, Plagiocladus and Synostemon. As a result of the reinstated genera, five new names for illegitimate combinations or previous overlooked nomenclatural anomalies and 645 new combinations are proposed. Several keys are provided to distinguish the reinstated genera. Full species lists are given for the reinstated genera treated here except for Breynia, Synostemon and Glochidion. Show less
Dissochaeta Blume (Melastomataceae, tribe Dissochaeteae) is well-known as a scrambling plant genus found in Southeast Asia, where it is an inhabitant of the tropical rainforests or evergreen... Show moreDissochaeta Blume (Melastomataceae, tribe Dissochaeteae) is well-known as a scrambling plant genus found in Southeast Asia, where it is an inhabitant of the tropical rainforests or evergreen forests.The main objectives of this thesis are to clarify the relationships among species and genera within the Dissochaeta alliance and to provide a new classification, which reflects the evolutionary and biogeographic traits of this plant group. The study focuses on three aspects of the Dissochaetaalliance: the taxonomy, molecular phylogeny and historical biogeography. Show less
Taxonomy as a science has accumulated data and knowledge for more than 250 years. The quality and usefulness of the facts recorded in taxonomic literature has greatly improved from the early... Show moreTaxonomy as a science has accumulated data and knowledge for more than 250 years. The quality and usefulness of the facts recorded in taxonomic literature has greatly improved from the early descriptive texts to the modern data-rich, hypothesis-driven works. Our work illustrates the application of some of the “e-taxonomic” tools and the “New Taxonomy” thinking explored in the introduction. Here, we analyzed specimen data contained in legacy taxonomic literature in Chapters 2 and 3—to observe species distribution of one spider group and genital evolution, respectively—and also explored an integrative perspective that involves describing new taxa and testing phylogenetic hypotheses using molecular and morphological data, as done in Chapter 4 and 5. Show less
Background: Bone tissue represents a large systemic compartment of the human body, with an active metabolism, that controls mineral deposition and removal, and where several factors may play a role... Show moreBackground: Bone tissue represents a large systemic compartment of the human body, with an active metabolism, that controls mineral deposition and removal, and where several factors may play a role. For these reasons, several non-skeletal diseases may influence bone metabolism. It is of a crucial importance to classify these disorders in order to facilitate diagnosis and clinical management. This article reports a taxonomic classification of non-skeletal rare congenital disorders, which have an impact on bone metabolismMethods: The International Osteoporosis Foundation (IOF) Skeletal Rare Diseases Working Group (SRD-WG), comprised of basic and clinical scientists, has decided to review the taxonomy of non-skeletal rare disorders that may alter bone physiology.Results: The taxonomy of non-skeletal rare congenital disorders which impact bone comprises a total of 6 groups of disorders that may influence the activity of bone cells or the characteristics of bone matrix.Conclusions: This paper provides the first comprehensive taxonomy of non-skeletal rare congenital disorders with impact on bone physiology. Show less
The genus Phyllanthus is paraphyletic as currently circumscribed, with the genera Breynia, Glochidion and Synostemon nested within it. A phylogeny based on nuclear (ITS, PHYC) and chloroplast (matK, .Show moreThe genus Phyllanthus is paraphyletic as currently circumscribed, with the genera Breynia, Glochidion and Synostemon nested within it. A phylogeny based on nuclear (ITS, PHYC) and chloroplast (matK, accD-psaI, trnS-trnG) markers is presented, including 18/18 subgenera and 53/70 sections. Differences in habit, branching type, floral and fruit characters are discussed, and we find indications for shifts in pollination and dispersal strategies possibly underlying the convergent evolution of these characters in multiple clades. Several taxonomic issues were found in the subgeneric classification of Phyllanthus that will require new transfers and rank changes. Phyllanthus subg. Anesonemoides, subg. Conami, subg. Emblica, subg. Gomphidium, subg. Kirganelia and subg. Phyllanthus are polyphyletic, and several sections appear to be paraphyletic (e.g., P. sect. Anisonema, sect. Emblicastrum, sect. Pseudoactephila, sect. Swartziani, and sect. Xylophylla); P. subg. Phyllanthodendron is furthermore paraphyletic with the genus Glochidion nested within. To create a classification of tribe Phyllantheae that comprises exclusively monophyletic taxa, it is necessary to treat several clades at the same taxonomic rank as the genera Breynia, Glochidion and Synostemon. Since combining all genera would lead to one giant heterogeneous genus that is difficult to define, we recommend dividing Phyllanthus into several monophyletic genera, which have previously been recognized and often possess diagnostic (combinations of) morphological characters. This new classification is forthcoming. Show less
In this thesis, I targeted the orchid genus Lepanthes, one of the six genera of angiosperms that surpasses 1,000 species in the Neotropics, as a study model to investigate the evolutionary... Show moreIn this thesis, I targeted the orchid genus Lepanthes, one of the six genera of angiosperms that surpasses 1,000 species in the Neotropics, as a study model to investigate the evolutionary processes that promoted species diversifications. To investigate this, we improved the taxonomy of the group integrating a solid phylogenetic framework with morphological evolution, assessing inter-specific relationships in species complexes with hundreds of DNA markers using anchored hybrid enrichment approach, and describing new species. In addition, we addressed the pollination of Trichosalpinx through the study of floral anatomy, pollinator behavior, and floral traits. Trichosalpinx flowers are pollinated exclusively by female biting midges that are attracted by the small quantities of proteins secreted on the flowers. Finally, we inferred the biogeographical history and diversification dynamics of the two largest Neotropical orchid groups (Cymbidieae and Pleurothallidinae), using densely sampled phylogenies coupled with geological datasets and discussed the impact of biogeographical events and orogeny on the species richness of Lepanthes. Species diversification is correlated with Andean orogeny, and multiple migrations and recolonizations across the Andes indicate that mountains do not constrain orchid dispersal over long timescales. This thesis provides new insights into the complex evolution of one of the most species-rich angiosperm. Show less
Octocorallia (primarily soft corals and gorgonians) occur in cold-water environments as well as in tropical seas and can form a major component of reef communities. Because of their... Show more Octocorallia (primarily soft corals and gorgonians) occur in cold-water environments as well as in tropical seas and can form a major component of reef communities. Because of their abundance and three-dimensional structure octocorals are an important habitat for symbiotic species such as crustaceans, worms, fishes and molluscs. Among the latter group are snails of the family Ovulidae, obligate associates of octocorals. Ovulid snails have adapted their morphological appearance to avoid predation. They can either be perfectly camouflaged or ambiguously coloured to advertise their toxic properties. It was therefore expected that these morphological adaptations would have an evolutionary background, which would corresponds with that of their octocoral hosts. In this thesis the evolutionary history of the Ovulidae and Octocorallia are examined within and between both taxa by using a multifaceted approach, consisting of (calibrated) phylogenetic and co-evolutionary analyses, taxonomic revisions and coral bioactivity research. The results show that snails and octocorals did not coevolve, but that the evolutionary history between both groups is best described as sequential evolution in which the host affects the symbiont but not vice versa. Show less
Gall crabs (Crustacea : Cryptochiridae) are small, coral-dwelling crabs that live in obligate association with their host corals (Scleractinia), on which they rely for food and shelter. They have... Show moreGall crabs (Crustacea : Cryptochiridae) are small, coral-dwelling crabs that live in obligate association with their host corals (Scleractinia), on which they rely for food and shelter. They have been recorded from shallow and deeper waters (over 500 m), but the majority of the species live in reef corals in the photic zone. The highest number of species is recorded from the Indo-West Pacific, where coral diversity is highest. This PhD thesis deals with various aspects of their evolution and diversification; four species are described as new to science, and the host specificity, biogeography, distribution and reproductive morphology of gall crabs are studied. In addition, the close association between gall crabs and corals allowed for studies on (cryptic) speciation and possible coevolution. Results show that the observed coevolutionary events should most probably be ascribed to sequential evolution, which indicates that the phylogeny of the gall crabs has been directed by the evolution of the corals. Show less
Mollusca form an important animal phylum that first appeared in the Cambrian, and today is,after Arthropoda, the second largest animal phylum, with more than 100,000 extant species(Bieler, 1992,... Show moreMollusca form an important animal phylum that first appeared in the Cambrian, and today is,after Arthropoda, the second largest animal phylum, with more than 100,000 extant species(Bieler, 1992, Brusca and Brusca, 2003), with the class Gastropoda accounting for 80% of the extant species in the Mollusca. Despite its species-richness, a generalised gastropod shell architecture is maintained because of conserved developmental processes. All of the shelled gastropods grow by adding, in a unidirectional accretionary way, shell material with the mantle edge organ, usually at different deposition rates around the existing aperture. This shell ontogeny, or to be more specific aperture ontogeny, gives the general spiral form for the shells. However, spiral forms can vary when there are changes in any one of the aspects in the aperture ontogeny profiles, namely, the rate and direction of shell deposition around the aperture, size and shape of the aperture (i.e. mantle edge), and the total length of the shell ontogeny processes. The interplays between these developmental parameters have generated a great diversity in shell form, for which taxonomists and evolutionary biologist are now trying to accurately characterise and to understand with regard to its evolution.This thesis reveals several hitherto unknown aspects of Plectostoma shell forms,in terms of the developmental homology, the aperture ontogeny profile, anti-predation functionality, and evolutionary pattern in shell characters and ontogenetic morphospace evolution. In fact, these are the issues that have been targeted by biologists for centuries in order to improve the way shell shape is characterised and to improve understanding of shell form evolution. Show less
This thesis presented eight studies in the field of systematic botany, with a focus on the molecular phylogenetics, taxonomy, and pollen morphology of the tribe Miliuseae (formerly known as the... Show moreThis thesis presented eight studies in the field of systematic botany, with a focus on the molecular phylogenetics, taxonomy, and pollen morphology of the tribe Miliuseae (formerly known as the miliusoid clade) of the pantropical flowering plant family Annonaceae. The general aims were: (1) to investigate intertribal relationships of the tribe Miliuseae, (2) to clarify generic delimitations by investigating the intergeneric relationships within the tribe Miliuseae, and (3) to understand patterns of character evolution within the tribe Miliuseae. To achieve these aims, a molecular phylogeny of a subclade of the subfamily Malmeoideae consisting of the tribes Maasieae, Malmeeae, Fenerivieae, Dendroking- stonieae (sampled for the first time), Monocarpieae, and Miliuseae was reconstructed using a much expanded taxon and chloroplast DNA marker sampling in comparison to previous studies. In addition, detailed taxonomic and/or palynological studies of the monogeneric tribes Dendrokingstonieae and Monocarpieae, and several genera in Miliuseae have been presented. The evolution of selected macromorphological and palynological characters was investigated using ancestral character-state reconstructions. Generic delimitations within Miliuseae, in light of the results of the molecular phylogenetic studies, were discussed, and two new genera, Hubera and Winitia, have been characterized based on macromorphology and pollen morphology. Show less
he papers in which are part of this theses describe the global diversity and conservation status of damselflies and dragonflies, contain a moleculair revision of the damselflies and discuss the... Show morehe papers in which are part of this theses describe the global diversity and conservation status of damselflies and dragonflies, contain a moleculair revision of the damselflies and discuss the biogeography of damselflies and dragonflies in the Australasian region. Show less
Dirksen, C.D.; Utens, C.M.A.; Joore, M.A.; Barneveld, T.A. van; Boer, B.; Dreesens, D.H.H.; ... ; Weijden, T. van der 2013
The northwest corner of South America harbours a region of spectacular and mysterious landscapes called Pantepui. Due to its ancient age and fragmented topography Pantepui has been assumed to be an... Show moreThe northwest corner of South America harbours a region of spectacular and mysterious landscapes called Pantepui. Due to its ancient age and fragmented topography Pantepui has been assumed to be an ideal nursery of speciation, and tepuis (table mountains) have been seen as potential inland counterparts to oceanic islands. Tepuis are often called __islands in the sky__ and their summits seem indeed ideal candidates to harbour relict species, isolated from the rest of the world for millions of years. However our knowledge about the origin and diversification of the Pantepui biota is at least as fragmentary as the tepui physiography itself. This led some authors to consider the origin of local biodiversity and endemism a still-unresolved evolutionary enigma. This work aims to (1) better understand the species diversity, the evolutionary history, the dynamics of biotic interchanges between tepui summits, and the patterns of endemism of the fauna in the Pantepui region, using morphological analyses and molecular phylogenies of six amphibian and reptile taxa; (2) provide new insights in the timing of the geomorphological evolution of the tepuis in the light of amphibian and reptile species diversification inferred from molecular phylogeny reconstructions and estimates of divergence time. Show less
The objective of this thesis was to obtain insight into the processes that play a role in biodiversity patterns of tropical marine species by using marine lakes as a model. Marine lakes are... Show moreThe objective of this thesis was to obtain insight into the processes that play a role in biodiversity patterns of tropical marine species by using marine lakes as a model. Marine lakes are landlocked water bodies that maintain a marine character through narrow submarine connections to the sea. Two regions in Indonesia were studied: Berau (East Kalimantan) and Raja Ampat (West Papua). The following questions were addressed: 1. What are the different types of marine lakes in Indonesia? 2. Are the species assemblages in marine lakes distinct from those in the adjacent coastal environments? 3. To what extent are the populations in the lakes isolated? 4. Can marine lakes in Indonesia be considered natural laboratories of evolution? There is a large diversity in types of marine lakes and many more remain to be documented in Indonesia. The spatial variation in sponge species composition in marine lakes, coastal mangroves and coral reefs show that marine lakes contain three groups of sponge species: (a) widespread species known from various locations in Indo-Pacific reefs, (b) lake species that only occur in lake systems, (c) endemic species restricted to a single lake. The patterns of genetic variation found in the marine lake populations are generally consistent with populations in isolated environments. The lakes appear to be both cradles and refuges of diversity Show less
We described a total of 4 species and 4 subspecies of Coelogyne and one species of Panisea from the Himalayan region as new species to science based on analysis of morphological characters and DNA... Show moreWe described a total of 4 species and 4 subspecies of Coelogyne and one species of Panisea from the Himalayan region as new species to science based on analysis of morphological characters and DNA sequences. Extrafloral nectar produced by Nepalese Coelogyninae was found to play a key role in attracting aggressive ants protecting flowers and leaves against herbivorous beetles. This nectar was found to be exudated by nectary-modified stomata positioned just below the pedicels on the inflorescence. Our ethnobotanical survey showed that a total of 60 species of wild orchids were found to be used as energizers, aphrodisiacs and treatments of burnt skin, fractured or dislocated bones, headaches, fever and wounds. The antibacterial screening carried out by us indicated that the majority of the medicinal orchid species used by local people in Nepal showed biological activity. A total of 10% of confiscated orchids remained sterile but could be identified to species level by applying DNA barcoding and chemical profiling. Our market surveys in central Nepal showed that many wild orchid species are involved in illegal trade and exported to China and India for preparation of herbal products and traditional Chinese medicines. Wild orchids were found to be immensely important to sustain local livelihoods in Nepal. Due to large scale ille_gal trade, many species are rapidly becoming endangered in the wild. Establishing sustainable orchid breeding enterprises could be a valuable alternative for the production of medicinal orchids for local communities. Critically endangered species should be placed on CITES Appendix I to prevent their extinc_tion from the wild. DNA barcoding and chemical profiling seem promising tools for a better control of cross-border illegal trade. Show less
