Phalaenopsis is an important ornamental pot plant for the global horticultural market. The inflorescences of Phalaenopsis horticultural hybrids require support from a stick during plant... Show morePhalaenopsis is an important ornamental pot plant for the global horticultural market. The inflorescences of Phalaenopsis horticultural hybrids require support from a stick during plant cultivation because of the weight of multiple large flowers. Developing a horticultural hybrid with a sufficiently lignified inflorescence stem that does not require additional support could be a way to reduce the costs of production. This study aimed to (i) determine the orientation and degree of lignification in the inflorescence stem of different species and horticultural hybrids of Phalaenopsis and investigate whether these lignification patterns follow any (ii) topological or (iii) phylogenetic pattern of interest to further explore in genetic precision breeding. Inflorescences of comparable devel- opmental stages of six species and 17 horticultural hybrids of flowering Phalaenopsis orchids were sampled. The orientation of the inflorescence varied from erect, sub-erect, arching, to pendant. The degree of lignification was measured with ImageJ using stained microscopic tissue sections and statistically analyzed. A molecular phylogeny of the species of Phalaenopsis was reconstructed based on plastid and nuclear ribosomal DNA sequences to analyze phylogenetic patterns. Our results show a significant difference in the degree of lignification between the different Phalaenopsis species and hybrids, between peduncle and rachis, and among the six different inflorescence positions analyzed. We found a positive correlation between inflorescence orientation and the proportion of lignified area per total stem area and the proportional thickness of the lignified fiber walls in the peduncle. We conclude that the degree of lignification is heritable, as we observed among our sample size a higher positive correlation between stem lignification variables among closely related taxa compared to more distantly related ones. However, a larger species sampling is needed to further validate our results. 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
Phylogenetic relationships in species complexes and lineages derived from rapid diversifications are often challenging to resolve using morphology or standard DNA barcoding markers. The hyper... Show morePhylogenetic relationships in species complexes and lineages derived from rapid diversifications are often challenging to resolve using morphology or standard DNA barcoding markers. The hyper-diverse genus Lepanthes from Neotropical cloud forest includes over 1200 species and many recent, explosive diversifications that have resulted in poorly supported nodes and morphological convergence across clades. Here, we assess the performance of 446 nuclear-plastid-mitochondrial markers derived from an anchored hybrid enrichment approach (AHE) coupled with coalescence- and species network-based inferences to resolve phylogenetic relationships and improve species recognition in the Lepanthes horrida species group. In addition to using orchid-specific probes to increase enrichment efficiency, we improved gene tree resolution by extending standard angiosperm targets into adjacent exons. We found high topological discordance among individual gene trees, suggesting that hybridization/polyploidy may have promoted speciation in the lineage via formation of new hybrid taxa. In addition, we identified ten loci with the highest phylogenetic informativeness values from these genomes. Most previous phylogenetic sampling in the Pleurothallidinae relies on two regions (ITS and matK), therefore, the evaluation of other markers such as those shown here may be useful in future phylogenetic studies in the orchid family. Coalescent-based species tree estimation methods resolved the phylogenetic relationships of the L. horrida species group. The resolution of the phylogenetic estimations was improved with the inclusion of extended anchor targets. This approach produced longer loci with higher discriminative power. These analyses also disclosed two undescribed species, L. amicitiae and L. genetoapophantica, formally described here, which are also supported by morphology. Our study demonstrates the utility of combined genomic evidence to disentangle phylogenetic relationships at very shallow levels of the tree of life, and in clades showing convergent trait evolution. With a fully resolved phylogeny, is it possible to disentangle traits evolving in parallel or convergently across these orchid lineages such as flower color and size from diagnostic traits such as the shape and orientation of the lobes of the petals and lip. Show less
Bogarin Chaves, D.G.; Fernandez, M.; Borkent, A.; Heemskerk, A.; Pupulin, F.; Ramirez, S.; ... ; Gravendeel, B. 2018
Pleurothallidinae (Epidendreae) are a megadiverse Neotropical orchid subtribe comprising > 5100 species, most of which are probably pollinated by Diptera. The role of pollinators as drivers of... Show morePleurothallidinae (Epidendreae) are a megadiverse Neotropical orchid subtribe comprising > 5100 species, most of which are probably pollinated by Diptera. The role of pollinators as drivers of species diversity is largely unknown because knowledge of pollination systems in Pleurothallidinae is still scarce. Here, we addressed the pollination of Trichosalpinx s.s. through study of floral anatomy, pollinator behaviour and floral traits shared with other angiosperms to elucidate its pollination mechanisms. We identified midge specimens with DNA bar-coding and morphology, documented pollination with video recordings, studied the anatomy of flowers by combining microscopy (light microscopy, scanning electron microscopy and transmission electron microscopy) and histochemistry and analysed floral scents with gas chromatography-mass spectrometry. We found that two Trichosalpinx spp. are pollinated exclusively by female biting midges of a Forcipomyia (Euprojoannisia) sp. (Ceratopogonidae). The midges land on the motile lip and appear to suck substances from its papillose surface. We detected secretion of carbohydrates and proteins on the lip and sepals, and thus, Trichosalpinx might stimulate a protein collection instinct in female biting midges. The well-developed mandibles and poorly developed laciniae of the pollinators indicate that they mainly feed on invertebrate hosts from which they draw haemolymph. Thus, Trichosalpinx flowers offer small quantities of proteins and carbohydrates that may act as flavour teases and together with the colour, fragrances, trichomes and movement of the lip, they probably form part of a complex deceptive system. Some other angiosperms that are also pollinated by biting midges possess similar dark purple flowers with ciliate ornamentation and use myophily, sapromyophily or kleptomyiophily as strategies to exploit different families of Diptera as pollinators. One Forcipomyia sp. (Euprojoannisia) is kleptoparasitic, suggesting that kleptomyiophily may have evolved in Trichosalpinx. The similar floral morphology among members of Trichosalpinx and some species of the closely related genera Anathallis and Lankesteriana suggests that they are also pollinated by biting midges. Show less
Karremans, A.P.; Bogarin Chaves, D.G.; Gravendeel, B. 2015
Specklinia lugduno-batavae from the Caribbean lowlands of Nicaragua and Costa Rica is formally described and illustrated. The new species belongs to the Specklinia digitalis group and can be... Show moreSpecklinia lugduno-batavae from the Caribbean lowlands of Nicaragua and Costa Rica is formally described and illustrated. The new species belongs to the Specklinia digitalis group and can be recognised by the creeping habit, purple spotted abaxial surface of the leaf and the almost immaculate whitish cream flowers, which are produced in succession on a very short, flexuous inflorescence. The name honours Leiden University and the Hortus botanicus Leiden. The novelty is compared with its closest relatives, Specklinia digitalis, S. pisinna and S. succulenta. Show less
DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To... Show moreDNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF–atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK–psbI spacer, and trnH–psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants. Show less
