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
This thesis describes the genetic and prokaryotic diversity of giant barrel sponges. Although it was originally believed that the giant barrel sponges in the AtlanticOcean and the Indo-Pacific... Show moreThis thesis describes the genetic and prokaryotic diversity of giant barrel sponges. Although it was originally believed that the giant barrel sponges in the AtlanticOcean and the Indo-Pacific Ocean were two different species, our analyses showed thatthere are several species in both ocean basins. Even more remarkable, is that each species is most closely related to a species in the other ocean basin. According to our analysis, there are threegiant barrel sponge species in the Atlantic Ocean, and, at least, six in the Indo-Pacific Ocean. Sponges house a large and diverse community of microorganisms. It is generally believed thatthese microorganisms play a central role in the physiological processes in the host. It appears that the region in which a giant barrel sponge occursmainly determines the composition of their microbial community. However, if you lookat a smaller scale within a region, for example within one reef or around an island suchas Curaçao, it appears that not only is the geographical location important, but the hostspecies to which an individual belongs also plays an important role. Show less
Streptomyces are multicellular, Gram-positive bacteria in the phylum of actinobacteria which produce a high amount of bioactive natural products of which the expression is tightly coordinated with... Show moreStreptomyces are multicellular, Gram-positive bacteria in the phylum of actinobacteria which produce a high amount of bioactive natural products of which the expression is tightly coordinated with the life cycle. This thesis shows the identification of S. roseifaciens, a novel species with an uncommon, verticillate spore morphology and a unique household of SsgA-like proteins. Analyses of the peptidoglycan composition show that S. coelicolor show a pattern of 3-3 cross-linking befitting a tip-growing organism and change in composition between vegetative mycelium and spores. Kitasatosporae carry meso-DAP in the peptidoglycan of vegetative mycelium and LL-DAP in the peptidoglycan of spores. In line with this difference, the peptidoglycan architecture of these two growth stages undergoes such radical changes that they would seem to be from different species. S. coelicolor is naturally vancomycin resistant, but the addition of D-alanine and disruption in a single gene increases vancomycin sensitivity by a thousandfold. A knockout mutant of the alanine racemase, alr, requires exogenous addition of D-alanine. The Alr crystal structure of S. coelicolor and the D-cycloserine producer S. lavendulae were compared as to look for possible mechanisms for D-cycloserine resistance. 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
This thesis describes the application of molecular typing methods to study the epidemiology and evolution of Clostridium difficile. C. difficile is a gut bacterium that is a major cause of... Show moreThis thesis describes the application of molecular typing methods to study the epidemiology and evolution of Clostridium difficile. C. difficile is a gut bacterium that is a major cause of antibiotic associated diahrrea in the developed world. The emergence of the __hypervirulent__ types causing C. difficile infections (CDI) with more severe complications has driven the demand for rapid molecular assays that can detect these types. We aimed to identify novel molecular markers for __hypervirulent__ C. difficile and use these markers to develop new rapid assays. This thesis describes the development and evaluation of a new (multiplex) real-time PCR assay to diagnose CDI. It also provides an overview of the currently applied methods to study CDI. We report on an internationally-standardized protocol for high resolution, capillary gel-based electrophoresis, PCR-ribotyping. Furthermore, we describe two novel genetic markers that are linked to two C. difficile phylogenetic lineages. We describe the application of multilocus sequence typing to study the population structure of C. difficile. We report on whole genome sequencing (WGS) and the related single nucleotide polymorphism (SNP) analysis, a recently emerged typing method that we used to study transmission of C. difficile type 078 between animals (pigs) and humans (farmers). Show less
Insights into the spatial distribution of genetic diversity is key for understanding the evolutionary history and for effective species conservation. For the lion, all African populations are... Show moreInsights into the spatial distribution of genetic diversity is key for understanding the evolutionary history and for effective species conservation. For the lion, all African populations are considered to belong to one subspecies, while the Asiatic subspecies is confined to a single population in India. However, it is suggested that the genetic diversity is greater than the taxonomy implies. Notably the West and Central African lion represents a unique clade, which is relevant because the populations in this region are generally small and isolated. Phylogenetic analyses of mtDNA data, microsatellites and autosomal SNPs from lion populations throughout their complete geographic range show congruent patterns in which the Asiatic subspecies has a nested position within the West/Central African lion. Recognizing a northern subspecies, including the Asiatic lion, and a southern subspecies, is more in line with the evolutionary history of the lion. A revision of the taxonomy is therefore warranted. Show less
Five research methods were used in Taxonomy, Systematics, and Biogeography of Ficus subsection Urostigma(Moraceae); Morphological characters, leaf anatomy, pollen morphology, molecular phylogeny,... Show moreFive research methods were used in Taxonomy, Systematics, and Biogeography of Ficus subsection Urostigma(Moraceae); Morphological characters, leaf anatomy, pollen morphology, molecular phylogeny, and historical biogeography. Seven topics are the result: 1) A revision was made based on morphology in which 27 species are recognized, but which also showed that morphology alone cannot solve all problems because of variation within the species. 2) Leaf anatomy displayed less variation in characters and anatomical characters proved to be useful for the classification of Ficus, especially in combination with morphology. 3) Pollen morphology appeared to be similar for all species and the characters can merely be used for generic recognition. 4) A new classification for subsection Urostigma is proposed in which the circumscription of the subsection and the species is the result of combining molecular phylogenetic information with morphology and leaf anatomy. 5) Ficus cornelisiana, a new species from Sino-Himalayan, was reported based on morphological and leaf anatomical evidence. 6) The historical biogeography was studied by using molecular dating and ancestral area reconstruction. 7) The use of some Thai species within subsect. Urostigma is reported, six of them are used as food, as ornamental, or the uses are related to religion or sacred purposes. 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
Derris Lour. (family Fabaceae/tribe Millettieae) is a quite well-known legume genus as many species are a source of Rotenone toxin, a commercial organic insecticide and fish poison used in many... Show moreDerris Lour. (family Fabaceae/tribe Millettieae) is a quite well-known legume genus as many species are a source of Rotenone toxin, a commercial organic insecticide and fish poison used in many countries. The genus is characterized mainly by its indehiscent, flat, thin but leathery pods with usually wing(s) along the suture(s). In the tribe Millettieae, however, there are several plants in the tropical areas of the old and new world which have similar pods and other morphological characters comparable to Derris. They all are called Derris-like taxa (or Derris-like plants) in this thesis. In the course of time, different generic circumscriptions of these plants were proposed by various taxonomists. The main objectives of this thesis are to clarify the relationships between species and genera within this complex group of Derris-like taxa [mainly focused on the old-world Asian genera: Aganope, Brachypterum and Derris (+Paraderris)] and to provide a new classification which reflects the evolutionary and biogeographic relationships of these plants. Show less
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
Hoverflies of the subfamily Microdontinae (Diptera: Syrphidae) have a reputation for causing confusion. Their diversity in shape and size is astonishing: from large, furry-haired species and... Show moreHoverflies of the subfamily Microdontinae (Diptera: Syrphidae) have a reputation for causing confusion. Their diversity in shape and size is astonishing: from large, furry-haired species and convincing wasp-mimics to tiny, unsightly creatures, easily mistaken for something uninteresting. The larvae resemble slugs so much that biologists have described them as molluscs on several occasions. Worldwide, hundreds of species of Microdontinae have been described, but so far there has been no comprehensive attempt to unravel this hotchpotch of names. This thesis examines the phylogenetic relationships of Microdontinae, based on morphological and molecular characters, in order to construct a new classification of the subfamily. A total number of 51 (sub)genera (11 new) are recognized, in which 472 valid species (49 new) are classified, resulting in many new combinations. The newly proposed classification facilitates species level taxonomy. In addition, it should provide a framework for further research on biogeography, (cryptic) speciation and evolution of host specialization. This thesis takes a first shot at some of these subjects by exploring the taxonomy of Neotropical Microdontinae that mimic stingless bees, reviewing and evaluating the associations of these flies with ants, and speculating on their historical biogeography. Show less
Forest damselflies (family Platystictidae) are widespread in southeast Asia from Sri Lanka to New Guinea, and are also known from Central America and the northern part of South America. The larvae... Show moreForest damselflies (family Platystictidae) are widespread in southeast Asia from Sri Lanka to New Guinea, and are also known from Central America and the northern part of South America. The larvae of most species live in small streams or seepages under forest canopy. Adults are found hanging from the tips of leaves or twigs along streams. The family is thought to have evolved more than 100 million years ago. Only 213 species are known worldwide, of which the author described 46 as new to science. Although most species are remarkably similar in general appearance, they show significant variation in structural details such as wing venation, pronotum, and secondary genitalia of the male. The group is ideal for biogeographical studies, since most species have small distributional ranges. A reconstruction of the phylogeny shows that several ancient lineages occur along the margin of the Indian Plate. Although Platystictidae are not known from Africa, it is hypothesized that the family evolved on that continent. The ancestors of the subfamilies Platystictinae and Sinostictinae drifted with India to Asia between 100 and 45 Ma. A scenario of the historical biogeography of the Platystictinae is described in relation to the palaeogeography of southeast Asia since the Eocene. The subfamily Palaemnematinae most likely dispersed from Africa to the New World via Europe and the ‘North Atlantic Land Bridge’. Show less
Through evolution the social amoebas have developed mechanisms to adapt to environmental changes and ensure survival. This thesis explores the evolutionary origins of cAMP signalling and regulation... Show moreThrough evolution the social amoebas have developed mechanisms to adapt to environmental changes and ensure survival. This thesis explores the evolutionary origins of cAMP signalling and regulation of developmental decisions in the model organism Dictyostelium discoideum. It also shows the first molecular-based phylogeny of the Dictyostelids. Development in Dictyostelium is characterized by the formation of a multicellular structure, the fruiting body, with a well-defined temporal and spatial pattern. cAMP, normally used as intracellular second messenger, in Dictyostelium is used also as an extracellular signal (chemoattractant) to mediate cell movement and cell differentiation. The study of the different components that control the formation of a multicellular fruiting body at a molecular level and from an evolutionary perspective shows that extracellular cAMP signalling was originally developed to control fruiting body morphogenesis. Furthermore it reinforces the idea that Dictyostelium is a simple but yet robust model to study the origins of multicellularity. Do to cAMP being so prevalent in Dictyostelium development I have studied the regulation of cAMP production during particular developmental stages showing in this thesis novel roles for the adenylyl cyclases that produce cAMP and their specific patters of expression during development. A thorough pharmacological analysis of these enzymes is also present in this work. Show less
The thesis focuses on the tropical plant genus Mallotus. This genus belongs to the Euphorbiaceae (spurge family), and comprises c. 110 species. These species are mainly found in (sub)tropical Asia... Show moreThe thesis focuses on the tropical plant genus Mallotus. This genus belongs to the Euphorbiaceae (spurge family), and comprises c. 110 species. These species are mainly found in (sub)tropical Asia and the West Pacific, with only two species in Africa and Madagascar. Mallotus and its sister genus Macaranga are important components of the forest vegetation of Southeast Asia and show a large variety of life-history strategies (both pioneer and climax). Most Mallotus species are shrubs or trees, seldom climbers. The variable morphology of these species has resulted in three main subgeneric classifications, of which the latest recognizes eight sections. The study presented here was part of a large project involving ecological, revisional and phylogenetic work on Mallotus. Five of the eight sections of the genus Mallotus were revised in the framework of the Flora Malesiana project, hereby provisionally accepting the sectional division of Airy Shaw (1968). The remaining three sections were already revised in a previous study. The monophyly of all eight sections and their evolutionary relationships were analyzed using morphological and molecular data (the chloropast gene matK and the nuclear gene gpd). Finally, the phylogenetic significance of the morphological characters used in the classification by Airy Shaw was evaluated. Show less
This thesis deals with the associations between parasitic snails and their mushroom coral hosts. Gittenberger has spent 800 hours under water and searched about 60,000 coral discs for these... Show moreThis thesis deals with the associations between parasitic snails and their mushroom coral hosts. Gittenberger has spent 800 hours under water and searched about 60,000 coral discs for these parasites. He dived in Egypt, the Maldives, Thailand, Malaysia, Japan, Palau, the Philippines, Indonesia and Australia. Places that are less popular with divers, like very deep or shallow sites, areas with strong currents, murky water, or sandy bottoms, received special attention. The greatest biodiversity was found off Sulawesi, a region that needs protection. Except for shell morphology, molecular, anatomical and ecological characters of the snails were studied. As a result it turned out that many more species exist than hitherto thought. Some dozens of unnamed cryptic ones were discovered. These can be distinguished most clearly by their DNA and their host specificity. The species of parasitic snails evolved most probably by bypassing the defence mechanism of one or a few coral species. Most of the data support a sympatric speciation model for these taxa. The molecular phylogenies of the parasites and their hosts were compared to investigate the amount of co-evolution. Show less
