ALBERT

Description: The aims of this study are: \n1) to reconstruct a skeleton phylogeny of the orchid genus Coelogyne and allied genera \nbased on molecular and morphological characters; \n2) to incorporate this phylogeny into a phylogenetic classification of the Coelogyninae; \n3) to provide taxonomic revisions of a selection of species groups of Coelogyne. \nCoelogyne comprises over 200 species distributed throughout southeast Asia with \nmain centers of diversity in Borneo, Sumatra and the Himalayas. Most species are \nepiphytes and occur in primary forests. They have a fairly large number of mediumsized to large flowers with delicate colours and a sweet scent, which are pollinated by \nbees, beetles or wasps. The genus is placed in subtribe Coelogyninae (subfamily Epidendroideae) together with 15 other genera with a total of approximately 550 species. \nThe subtribe is characterised by sympodial growth, pseudobulbs of one internode, \nterminal inflorescences, a winged column and massive caudicles. Separate maximum \nparsimony analyses of RFLPs, matK and nuclear rDNA ITS sequences, macromorphological and anatomical data collected for 27 Coelogyne species and 13 representatives \nof related genera produce largely congruent results. A total evidence analysis indicates \nthat Coelogyninae are monophyletic and diverged early into three major clades. \nClade I comprises species of Coelogyne sect. Coelogyne, subgenus Cyathogyne, \nsect. Rigidiformes, Tomentosae, Veitchiae and Verrucosae, from which Bracisepalum, \nChelonistele, Dendrochilum, Entomophobia, Geesinkorchis and Nabaluia split off. \nSynapomorphies for this group of species are the more than 15 flowers per inflorescence, presence of sterile bracts on the rachis and presence of hairs on the ovary. \nElongate trichomes with acute top on the leaf surface, synanthous inflorescences, \npresence of sterile bracts at the base of the rachis, simultaneously opening flowers, \npersistent floral bracts, ovate-oblong petals, and hairy sepals are present in the majority \nof taxa in this clade. Clade II subsequently diverged into species of Neogyna and \nPholidota nested within species of Coelogyne sect. Bicellae, Brachypterae, Elatae, \nFlaccidae, Fuliginosae, Hologyne, Lentiginosae, Longifoliae, Moniliformes, Ptychogyne and Speciosae. Synapomorphies for this group are the caducous floral bracts, \nglabrous ovaries, linear petals and a relatively low number of morphologically diverse \nkeels on the hypochile. Hysteranthous inflorescences, less than 15 flowers per inflorescence, intermediate-sized flowers and a relatively low number of keels on the epichile \nare present in the majority of taxa in this clade. Clade III consists of species of Pleione \nand is characterised by short-living pseudobulbs, a lack of stegmata in all sclerenchymatous tissues, a hypochile without lateral lobes and an epichile apex with fimbriate \nmargin. \nThe traditional circumscription of Coelogyne is not supported by the total evidence \nphylogeny presented here and should be abandoned. A redefinition of the genus is \nsuggested by including Neogyna and Pholidota and removing the species of Coelogyne \nsect. Coelogyne (in part), Cyathogyne, Tomentosae, Rigidiformes, Veitchiae and Verrucosae. A formal proposal for the creation of a new genus for these species is not made \nyet, as most internal nodes of the total evidence tree are only poorly supported and \nneed a larger taxon sampling and data from more variable genes. \n4 \nThe number of subgeneric groups recognised by various authors in Coelogyne \nvaries between 5 and 23, which is mainly due to the relative lack of morphological \ncharacters available to define groups of species. Of the 17 sections sampled in \nCoelogyne, just three (with only two sampled species each) form strongly supported \nmonophyletic groups in the total evidence analysis: sect. Longifoliae, Moniliformes \nand Verrucosae. This is consistent with the clear morphological synapomorphies that \ncharacterise those sections. Monophyly of Coelogyne sect. Flaccidae and Tomentosae \nis weakly supported, which is in accordance with the few and not unique synapomorphies that define these sections. Coelogyne sect. Coelogyne and sect. Elatae are \nclearly paraphyletic. This was already expected as the morphological diversity in both \nsections is high. A well-supported subset of species is formed by C. fimbriata (sect. \nFuliginosae) and C. stricta (sect. Elatae), which share the presence of sterile bracts \non the base of the scape. To investigate whether this clade warrants the status of a new \nsection, a much larger sampling within Coelogyne is needed. The species sampled of \nsubgenus Bicellae, Cyathogyne, Hologyne and Ptychogyne seem well nested within \nseveral sections of Coelogyne and do not warrant the status of subgenus. \nSeveral of the traditionally used floral traits for (sub)generic and sectional delimitation within Coelogyninae and Coelogyne (the \xe2\x80\x98key\xe2\x80\x99characters) were plotted on the \ntotal evidence tree. Inflorescence type, number of flowers per inflorescence, persistence \nof floral bracts, presence of sterile bracts on the rachis, ovary indumentum, petal \nshape, presence and shape of lateral lobes of hypochile, number of keels on the epichile \nand presence of a fimbriate margin on the epichile appear to be good synapomorphies \nfor major clades in Coelogyninae and Coelogyne. The number of leaves per pseudobulb, \nsize of the flowers, shape of the lip base and petals and presence of stelidia and calli \non the lip show many reversals and appear not to be phylogenetically informative. \nWith the phylogenetic boundaries of the total evidence analysis as a reference, a \nstart with a taxonomic treatment of the whole genus is made by revisions of three different groups of species in Coelogyne. An integrated phylogenetic analysis of morphological and molecular characters is performed for the 16 species of sect. Speciosae and \n8 species of sect. Verrucosae to check monophyly and study interspecific relationships, \nwhereas a complex of the closely related species of sect. Fuliginosae is resolved with \na phenetic analysis using morphological characters. The last three chapters of this \nthesis contain descriptions of all species (including three new ones), synonyms, \nphotographs, drawings, distribution maps and identification keys.

Description: Section Verrucosae Pfitzer & Kraenzl. of the genus Coelogyne Lindl. is revised using morphological and molecular data. Eight species are recognized, including two new ones ( C. marthae and C. verrucosa). One name is reduced to synonymy. Four species formerly included by several authors in sect. Verrucosae (C. brachyptera, C. papillosa, C. parishii and C. virescens) are excluded. A total evidence analysis of morphological characters and ITS and matK sequence data supports the monophyly of the section as here recognized. Coelogyne virescens (sect. Brachypterae) is identified as nearest neighbour to the species of sect. Verrucosae. The number of sterile bracts on the rhachis and the shape of the ornamentation on the epichile appear to be phylogenetically informative characters, in contrast with the inflorescence type, ovary indumentum and number of keels on the hypochile.

Description: Three new species of the Southeast Asian orchid genus Dendrochilum Blume are described. All three seem to belong to the phenetically defined subgenus Platyclinis (Benth.) Pfitzer. As indicated by the name, D. celebesense H.A. Pedersen & Gravend. originates from Sulawesi. The geographic origins of D. coccineum H.A. Pedersen & Gravend. and D. warrenii H.A. Pedersen & Gravend., on the other hand, are unknown, but parsimony analyses of sequences of the plastid accD-psaI intergenic spacer and nuclear ribosomal ITS1-5.8S-ITS2 region and morphological affinities suggest they should both be counted as members of the Philippine flora.

Description: An updated taxonomic description of the orchid genus Geesinkorchis and a new identification key are given in addition to a distribution map, photographs and analytical drawings. Two new species (G. quadricarinata and G. breviunguiculata) are described from Borneo and Sumatra, respectively.

Description: Section Fuliginosae Pfitzer & Kraenzl. of the genus Coelogyne Lindl. is revised. With the help of a pollen study, principal component and cluster analyses with morphological characters and a survey of some additional data, two species are recognized (C. fimbriata and C. triplicatula), including one dubious variety (C. fimbriata var. acuminata). Eleven names are reduced to synonymy. Three species formerly included in sect. Fuliginosae by several authors are excluded ( (C. micrantha, C. treutleri and C. schilleriana).

Description: Monitoring of airborne pollen concentrations provides an important source of information for the \nglobally increasing number of hay fever patients. Airborne pollen is traditionally counted under \nthe microscope, but with the latest developments in image recognition methods, automating this \nprocess has become feasible. A challenge that persists, however, is that many pollen grains cannot \nbe distinguished beyond the genus or family level using a microscope. Here, we assess the use of \nConvolutional Neural Networks (CNNs) to increase taxonomic accuracy for airborne pollen. As a case \nstudy we use the nettle family (Urticaceae), which contains two main genera ( \nUrtica \n and \nParietaria \n) \ncommon in European landscapes which pollen cannot be separated by trained specialists. While \npollen from \nUrtica \n species has very low allergenic relevance, pollen from several species of \nParietaria \nis severely allergenic. We collect pollen from both fresh as well as from herbarium specimens and \nuse these without the often used acetolysis step to train the CNN model. The models show that \nunacetolyzed Urticaceae pollen grains can be distinguished with 〉 \n98% accuracy. We then apply our \nmodel on before unseen Urticaceae pollen collected from aerobiological samples and show that the \ngenera can be confidently distinguished, despite the more challenging input images that are often \noverlain by debris. Our method can also be applied to other pollen families in the future and will thus \nhelp to make allergenic pollen monitoring more specific

Description: This practitioner\xe2\x80\x99s manual is the complement to the recently published volume \xe2\x80\x98Molecular Systematics and Evolution: Theory and Practice\xe2\x80\x99 and focuses on recently developed techniques for data acquisition and analysis in molecular systematics and evolutionary biology. The first section examines analytical methods in chapters dealing with DNA sequence alignment optimisations, techniques for analysing large data sets as implemented in the program TNT, measures of support and data partitions. Approaches that will develop further in the next few years are also covered and the reader is subsequently exposed to chapters on genome databases and comparative phylogenomics.\nThe second section is dedicated to obtaining and archiving specimens for molecular work and laboratory methods. Future developments are again included by chapters on high-throughput DNA sequencing and in situ hybridisation techniques. Due to the detailed protocols on DNA isolations of plants, algae, animals and bacteria from both fresh, silica-dried and ancient museum material, various PCR methods, microsatellite analysis and information on web-located sites, both systematists and evolutionary biologists can find a lot of information in this manual about modern molecular data collection techniques. In addition, molecular biologists might get ideas on how their data can be analysed in an evolutionary context.