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
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
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
