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
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: Some of the spore-forming strains of Bacillus probiotics are marketed commercially as they survive harsh gastrointestinal conditions and bestow health benefits to the host.Results: We... Show moreBackground: Some of the spore-forming strains of Bacillus probiotics are marketed commercially as they survive harsh gastrointestinal conditions and bestow health benefits to the host.Results: We report the composite genome of Bacillus clausii ENTPro from a commercially available probiotic Enterogermina (R) and compare it with the genomes of other Bacillus probiotics. We find that the members of B. clausii species harbor high heterogeneity at the species as well as genus level. The genes conferring resistance to chloramphenicol, streptomycin, rifampicin, and tetracycline in the B. clausii ENTPro strain could be identified. The genes coding for the bacteriocin gallidermin, which prevents biofilm formation in the pathogens Staphylococcus aureus and S. epidermidis, were also identified. KEGG Pathway analysis suggested that the folate biosynthesis pathway, which depicts one of the important roles of probiotics in the host, is conserved completely in B. subtilis and minimally in B. clausii and other probiotics.Conclusions: We identified various antibiotic resistance, bacteriocins, stress-related, and adhesion-related domains, and industrially-relevant pathways, in the genomes of these probiotic bacteria that are likely to help them survive in the harsh gastrointestinal tract, facilitating adhesion to host epithelial cells, persistence during antibiotic treatment and combating bacterial infections. 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
Snake envenomation globally is attributed to an ever-increasing human population encroaching into snake territories. Responsible for many bites in Asia is the widespread genus Trimeresurus. While... Show moreSnake envenomation globally is attributed to an ever-increasing human population encroaching into snake territories. Responsible for many bites in Asia is the widespread genus Trimeresurus. While bites lead to haemorrhage, only a few species have had their venoms examined in detail. We found that Trimeresurus venom causes haemorrhaging by cleaving fibrinogen in a pseudo-procoagulation manner to produce weak, unstable, short-lived fibrin clots ultimately resulting in an overall anticoagulant effect due to fibrinogen depletion. The monovalent antivenom `Thai Red Cross Green Pit Viper antivenin', varied in efficacy ranging from excellent neutralisation of T. albolabris venom through to T. gumprechti and T. mcgregori being poorly neutralised and T. hageni being unrecognised by the antivenom. While the results showing excellent neutralisation of some non-T. albolabris venoms (such as T. flavomaculaturs, T. fucatus, and T. macrops) needs to be confirmed with in vivo tests, conversely the antivenom failure T. hageni, and the very poor results against T. gumprechti and T. mcgregori, despite being conducted in the ideal scenario of preincubation of antivenom:venom, indicates that the likelihood of clinically relevant cross-reactivity for these species is low (T. gumprechti and T. mcgregori) to non-existent (T. hageni). These same latter three species were also not inhibited by the serine protease inhibitor AEBSF, suggesting that the toxins leading to a coagulotoxic effect in these species are non-serine proteases while in contrast T. albolabris coagulotoxicity was completely impeded by AEBSF, and thus driven by kallikrein-type serine proteases. There was a conspicuous lack of phylogenetic pattern in venom variation, with the most potent venoms (T. albolabris and T. hageni) being distant to each other on the organismal tree, and with the three most divergent and poorly neutralised venoms (T. gumprechti, T. hageni, and T. mcgregori) were also not each others closest relatives. This reinforces the paradigm that the fundamental dynamic evolution of venom results in organismal phylogeny being a poor predictor of venom potency or antivenom efficacy. This study provides a robust investigation on the differential venom effects from a wide range of Trimeresurus species on coagulation, highlighting differential fibrinogenolytic effects, while also investigating the relative antivenom neutralisation capabilities of the widely available Thai Red Cross Green Pit Viper antivenom. These results therefore have immediate, real-world implications for patients envenomed by Trimeresurus species. Show less
Insight into the inter- and intra-family relationship of protein families is important, since it can aid understanding of substrate specificity evolution and assign putative functions to proteins... Show moreInsight into the inter- and intra-family relationship of protein families is important, since it can aid understanding of substrate specificity evolution and assign putative functions to proteins with unknown function. To study both these inter- and intra-family relationships, the ability to build phylogenetic trees using the most sensitive sequence similarity search methods (e.g. profile hidden Markov model (pHMM)–pHMM alignments) is required. However, existing solutions require a very long calculation time to obtain the phylogenetic tree. Therefore, a faster protocol is required to make this approach efficient for research. To contribute to this goal, we extended the original Profile Comparer program (PRC) for the construction of large pHMM phylogenetic trees at speeds several orders of magnitude faster compared to pHMM-tree. As an example, PRC Extended (PRCx) was used to study the phylogeny of over 10,000 sequences of lytic polysaccharide monooxygenase (LPMO) from over seven families. Using the newly developed program we were able to reveal previously unknown homologs of LPMOs, namely the PFAM Egh16-like family. Moreover, we show that the substrate specificities have evolved independently several times within the LPMO superfamily. Furthermore, the LPMO phylogenetic tree, does not seem to follow taxonomy-based classification. 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
Kazem, S.; Lauber, C.; Meijden, E. van der; Kooijman, S.; Kravchenko, A.A.; Feltkamp, M.C.W.; ... ; TrichSpin Network 2016
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
