Education

MSc Projects:

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1. Conservation of Magnolias from the Dominican Republic

​The Dominican Republic, located on the eastern part of the Caribbean island of Hispaniola, boasts an astounding 6,000 species of plants. Over a third of them, 2,050 species, are endemic – only found in the Dominican Republic. The endemic plant species include three Magnolia species: Magnolia pallescens, M. hamorii and M. domingensis. All three species are threatened according to the IUCN (International Union for Conservation of Nature) Red List. Information on the genetic makeup of populations, and on the reproductive biology is currently lacking. This data shortage hampers effective conservation work by our local partner organization, Fundacion Progressio. In 2015, we conducted an expedition and collected plant samples and GPS data of 30+ trees from two populations per species. We extracted DNA from the samples and we developed and tested microsatellite (SSR) markers on these species.

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The aim is to investigate and compare the genetic diversity of the six populations. This will allow us to assess the genetic makeup and viability of these populations. The student will need to optimize the SSR multiplexes and genotype the different collected populations. The resulting data will provide interesting information to analyse using conservation genetic software (e.g. Arlequin, FSTAT, GenAlEx, STRUCTURE). Even more so, using predictive species distribution modelling we can model where to search for more Magnolia populations. Though not compulsory, we highly encourage the student to join in on a field expedition that we plan to undertake in the course of 2020-2021. During this expedition more population genetic and ecological data on the species will be collected, directed by the results of the species distribution modeling. The newly collected samples their DNA will be extracted in the lab at Ghent University. Once genotyped, the results can be added to the those based on the samples collected in 2015. We highly encourage students at the Systematic and Evolutionary Botany Lab to publish their MSc thesis as an A1 paper. This thesis will give opportunity for the student to:

1. Execute lab work: DNA extractions & SSR PCRs.

2. Genotype the SSR data using Geneious.

3. Conduct conservation genetic analyses.

4. Analyse location and climatic data to model where to go to on our next expedition with the R packages ‘sdm’ and ‘humboldt’.

5. If interested: join an expedition to the Dominican Republic to

• Search and sample more populations.

• Collect ecological data.

• Comparative study between the species their seed dispersers (birds).

• Floral scent collection & comparison.

• Study of self- and cross-pollination within the tree species by supplementary pollination, emasculation and bagging experiments.

• Phenology observations and comparisons between the three species.

• Placing pollinator sticky traps around the flowers to catch the pollinators, identify them and compare within and between the species.

6. Compile the comparative genetic and ecological data of the Dominican Magnolias in an A1 publication.

 

 

2. Deep time conflicts: tracing ancient hybridisation in tropical trees using phylogenomics

​The application of phylogenetic trees has revolutionized the field of botany in the past 30 years or so. For a long time, chloroplast markers have been the most widely used type of data to infer phylogenies. With phylogenies, based on chloroplast DNA sequence data, all kinds of fascinating questions have been addressed, for example related to ecology, biogeography, molecular evolution, or the evolution of life history features. The application of next generation sequencing techniques is particularly exciting for plant phylogenetics. Using a relatively cheap sequencing approach called genome skimming, it is possible to routinely generate genomic data from all three plant genomes, so not just from the chloroplasts only. An ongoing project on a genus of South and Central American tropical trees has demonstrated the value of a genome skimming approach, even when sequencing from herbarium material. So far, this project has revealed something remarkable: the phylogeny based on chloroplast data is in strong conflict with the phylogenies based on nuclear and mitochondrial data. The most probable explanation so far is an old hybridization event that facilitated chloroplast capture. This is how far we have got, and you can take this project further.

 

What tree species are we talking about? The name of the genus is Oxandra, which belongs to the soursop family, with the scientific name Annonaceae. The Annonaceae consist of roughly 2500 species of trees and lianas, almost exclusively confined to wet tropical rain forests on all continents. You may know the delicious fruit of Annona muricata, ‘zuurzak’ in Dutch, or the enticing smell of Cananga odorata, better known as ylang-ylang, both of which are species of this family. The genus Oxandra comprises 27 species of small to large (50 m!) trees. They occur from Mexico down to the Atlantic rain forests of Brazil, with many species having their home in the Amazon. Now, here is the reason why we wanted to know more about the evolution of this genus: based on leaf, flower and fruit characters, and reproductive systems it is difficult to paint a coherent picture of the genus. This could be an indication that these species did not evolve from a single common ancestor. This hunch turned out to be true… but only if you look at phylogenetic trees based on chloroplast data. Nuclear and mitochondrial data, on the other hand, indicate that most species of Oxandra are monophyletic, that is, did evolve from a single common ancestor. The analyses up to now are based on 18 species of Oxandra. In order to advance our understanding of the processes that produced the conflicting phylogenetic patterns, you will expand the sampling of species of Oxandra and some closely related genera. Questions that you will focus on in your project are:

• is the phylogenetic conflict of chloroplast phylogenies vs. nuclear and mitochondrial phylogenies maintained after increasing species sampling?

• does the monophyly of in nuclear and mitochondrial phylogenies involve all species, or are there aberrant species falling outside this clade?

• can the phylogenetic patterns be related to morphological or life history features of the tree species?

• is it possible to describe the scenario that led to the ancient hybridization (species involved, geographical area)?

Techniques that you will use are:

• laboratory techniques: high throughput sequencing, involving DNA isolation, DNA library preparation, and sequencing

• bioinformatics: data assembly and annotation

• phylogenetics: aligning, likelihood and Bayesian phylogenetics, character optimization.

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Do come knocking on our door when you are a motivated student with a broad interest in different biological disciplines like evolutionary biology, botany, genomics, biogeography.

 

 

3. Dipping below the Equator: disentangling a difficult Magnolia species complex

​This project will be done in cooperation with EcoMinga, and Ecuadorian foundation dedicated to the conservation of Andean ecosystems. EcoMinga has seven reserves in the centre of Ecuador with unique environmental conditions. All of these reserves are home to a remarkably high number of plant and animla species. Two species of Magnolia occurs in these reserves: M. vargasiana and M. llangtanensis. Some trees have been found in the reserve, however, the identification of which is uncertain. These tree either are either hybrids of the two species known to occur in the area, or represent a new species.

The main aim of this project is to clarify the status of the Magnolia species in the reserve using morphological, ecological and genetic data. Some morphological and location data is already available due to sampling efforts in 2018. Moreover, HybSeq sequence data is also available of eight reference samples from this reserve, including trees that belong to the two known Magnolia species as well as the putative hybrids / new species. The existing data can provide a quick start for the extraction of discriminating genetic sites or “barcodes”. The student will mine the HybSeq data to design primers for Sanger sequencing. During fieldwork, the student will screen more trees, and collect morphological data and samples for further genetic analysis when back in Ghent. We highly encourage students at the Systematic and Evolutionary Botany Lab to publish their MSc thesis as a scientific paper. This thesis will give opportunity for the student to:

• Mine HybSeq data of the species under question and search for DNA barcodes to discriminate the species.

• Join an expedition to the Ecuador to collect genetic, morphological and ecological data.

• Execute lab work: DNA extractions & Sanger sequencing.

• Test the DNA barcodes on newly collected individuals.

• Work on a report for the EcoMinga website whereby you bring the results to a broader audience.

• Compile the genetic and ecological data in scientific paper.

 

 

4. Patterns and rates of species evolution in tropical rain forests

​Tropical rain forests are the most species-rich terrestrial ecosystems, containing astonishing numbers of species in almost any group of organisms. This master thesis dives into the evolutionary build-up of this diversity. There is a long-standing debate on the pattern of species accumulation in tropical rain forests over evolutionary time, known as the museum vs. cradle debate. The museum hypothesis goes back to Alfred Russell Wallace, who proposed that tropical forests accumulated species over long periods of time due to their age and climatic stability. Ledyard Stebbins coined Wallace’s idea the ‘museum hypothesis’, and suggested that the climatic stability is connected to low extinction rates and the survival over evolutionary time of archaic forms. Contrasting with the museum model, is the model of rapid speciation in clades, so-called radiations. This model, coined the ‘cradle hypothesis’ would necessarily involve extinction rates that are elevated compared to those associated with the museum model.

An excellent plant group for testing these hypotheses is the family Annonaceae, containing ca 2500 species of trees and lianas that almost exclusively are found in tropical rain forests on all continents. In recent years we have learned a lot about the phylogenetic relationships within this plant family. Also, we know that the common ancestor of the family was around some 100 million years ago. However, we only have a limited understanding of patterns of diversification (speciation minus extinction) that gave rise to the present-day diversity.

The reasons for this are twofold: first, our efforts to estimate the age of Annonaceae are seriously hampered by lineage-specific heterogeneity of molecular substitution rates. Indeed, processes at the level of DNA have a huge impact on our understanding of large-scale processes covering millions of years. The second cause is the incompleteness of species sampling in most family-wide analyses so far. Tree shape of the two main clades of the Annonaceae, the subfamilies Annonoideae (1400 species) and Malmeoideae (900 species), is very different. Our preliminary results suggest that the species in the Malmeoideae have accumulated at an even pace, which would be consistent with the museum model. Phylogenetic patterns in the Annonoideae, on the other hand, appear more radiation-like with periods without traceable speciation being followed by abrupt and fast bursts of speciation.

 

Your task will be to further explore evolutionary ages and diversification patterns in the light of these observations. You will bring together data from several data sets and from online data repositories, and gathered a data set containing all species of Annonaceae, for which sequence data of multiple plastid markers are available. Using mainly Bayesian statistical approaches you will infer phylogenies and clade ages, and infer diversification patterns. Questions that you will focus on in your project are:

• do pattern and rates of species evolution in Annonaceae conform to the museum model or the cradle model?

• does the accumulation of species over evolutionary time follow a pattern that is universal for the entire family, or do clades within the family have different diversification patterns?

• do diversification patterns differ among the major continents containing tropical rain forests (South America, Africa, Asia)?

• are differences in patterns and rates of species evolution, if present, attributable to species characteristics, for example of flowers or fruit?

• how large are the uncertainties of the results, and what is the effect of using different assumptions in the analyses?

You will use bioinformatics and phylogenetics techniques: data gathering, aligning, likelihood and Bayesian phylogenetics, including inference of ages and diversification patterns. The ability to use R would be helpful, but isn’t required and can be learned during the project. Also, no preliminary knowledge of Bayesian phylogenetics is required but will help. By far the most important is enthusiasm for, and an interest in, biological disciplines like evolutionary biology, botany, biogeography, and a feel for data analyses.

 

 

5. Plants as a medicine for sexual, reproductive and urogenital problems and improvement – a Congolese experience in Belgium

Migrant communities often hold on to their cultural preferences of herbal medicines. Also, after migration, they often maintain traditional concepts on health and illness. The use of medicinal plants is widespread in the Democratic Republic of Congo (hereafter referred to as DR Congo), largely due to an insufficient primary healthcare system. It is known that this use of medicinal plants is at least partly continued among people from Congolese descent in Belgium. As sex, fertility and reproduction are seen as very important in Sub-Sahara Africa, the use of a significant part of the available medicinal plants is related to these concepts. However, data on the use of medicinal plants for these purposes in DR Congo and among the Congolese migrant communities is lacking. In this master dissertation, an ethnobotanical study will be conducted on the use of medicinal plants among the Congolese migrant communities for sexual, reproductive and urogenital problems and improvement.

 

The goal of this master thesis is to make an overview of the medicinal plants used for reproductive health care. Through interviews with people from Congolese descent in Belgium, you will investigate which plants are used, what these plants are used for and how they are used. Besides this, the underlying reasons why the Congolese community use these plants in Belgium will be investigated. A voucher collection of dried plant specimen and possibly a living plant collection will be made up. The collected plants will be identified up to the species level, applying a variety of techniques. For some plants the study of morphology and comparison with herbarium specimens (Plantentuin, Meise) may suffice, other will need to be identified by sequencing selected genetic markers and BLAST search in databases with publicly available nucleotide sequences.

 

 

6. Pollen evolution in response to drought in wild relatives of the sweet potato (Convolvulaceae)

Sweet potato ranks among one of the sixth most important crops for human diet. Recently, in the face of climatic emergency, it has been targeted as a potential famine crop, for its resilience to harsh environmental conditions, and high nutritional value. However, the evolution and biogeography of sweet potato and its wild relatives is still poorly understood, in particular the impact of climatic change on the morphology and ecological niche of the species. Highly aperturate pollen has been suggested to be an adaptation to xeric environmental conditions. Apertures are areas on the walls of a pollen grain, where the wall is thinner and/or softer and the pollen tube is able to break through the (elsewhere very tough) pollen wall. It is hypothesized that a high number of apertures in the pollen grains allow a faster germination of the pollen tube, and therefore benefit a quicker reproductive cycle when the environmental conditions are unfavourable (e.g. drier and hotter). Yet, this has not been formally tested in a large scale evolutionary framework in any group of plants. This project will focus on a group of wild relatives of the sweet potato which cover a wide range of habitats, from tropical forests to savannah and desert-like environments, and with an exceptional variation in the number and disposition of the apertures on their pollen grains, from 3 to well over 90 apertures. This makes it a perfect model group of plants to formally investigate in an evolutionary context, if the adaptation to drier and hotter environments could be at the heart of the development of high number of apertures in pollen grains. In addition, it will, in a broad sense, contribute to a better understanding of the impact of changing environmental conditions in the morphology and reproductive biology of the sweet potato wild relatives.

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The goal of this project is to investigate the evolution of high number of apertures in the tropical family Convolvulaceae, particularly subfamily Convolvuloideae, in a phylogenomic framework. The methodology will involve genome skimming of c. 200 species, phylogenetic analyses and character reconstruction of pollen and ecological characters - these will be extracted from available taxonomic literature and an extensive pollen dataset already compiled by Dr. Ana Rita Simões who is collaborating in the project, and with expertise in the plant group. Pollen acetolysis and SEM imaging may be conducted to fill in certain species gaps in the dataset. Techniques and analyses methods that you will use include:

• Scanning electron microscopy

• DNA sequencing (genome skimming)

• Bioinformatics tools for genome assembly

• Phylogenetic methods for tree inference and character evolution

 

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7. Sansevieria @ the pub

Sansevieria (mother-in-law's tongue, devil's tongue) is a well-known plant found in many homes and brown pubs (bruin café). They are often used as window decoration due to their low maintenance requirements. Sansevieria trifasciata is the most widely cultivated species. In Africa, Madagascar and southern Asia, there are about 70 wild species of Sansevieria, however. Species of Sansevieria were recently placed in synonymy with Dracaena, belonging to the asparagus family (Asparagaceae), and phylogenetic studies have been conducted in the past based on both chloroplast and nuclear markers. The boundaries between species still remain vague and difficult to establish. Based on Illumina sequence reads, produced by the research group Systematic and Evolutionary Botany, a more in-depth phylogenetic analysis can be performed. Genomic data, derived from 50 species, is available to perform Chloroplast (Cp) genome assembly and in addition, the same data can be used for skimming the nuclear genome to locate and characterize single nucleotide polymorphism (SNP). These SNP’s can consequently be used as potential barcodes to help identify species of Sansevieria, a tool that would be very helpful for plant breeders.

 

The goal is to engage in comparative genomics and phylogenetics of Sansevieria. You will familiarize yourself with the species of Sansevieria and assemble and annotate the available genomic data. In addition, potential barcodes can be extracted from the generated data, and tested for their use in phylogenetic analyses of the genus. Objectives

• Learn bioinformatic tools in command line

• Assemble and annotate chloroplast genomes of species of Sansevieria

• SNP mining to select for potential barcodes for species

• Perform comparative genomic and phylogenetic analyses

• Become comfortable in using bioinformatic tools in command line, as well as phylogenetic tools

 

 

8. The complete botanist: integrating herbarium taxonomy, high-throughput sequencing and phylogenetics of tropical trees

Tropical rainforests are home to an astonishing species diversity in almost any group of organisms. Unlike in Europe, a significant part of the tropical diversity is still to be discovered and described. A robust knowledge framework of the systematics of tropical plants is important. Firstly, up-to-date species descriptions and identification keys provide baseline data for the assignment of biodiversity hotspots, an important concept in conservation. Furthermore, groups of organisms for which the taxonomy and the phylogenetic relationships are well-known, provide model groups for downstream studies in, for example, ecology, evolutionary biology and genomics. This project revolves around the genus Klarobelia, belonging to the plant family Annonaceae. Klarobelia contains 13 species of tropical rain forest trees in Central and South America. Klarobelia is a recently described genus (1998), but the taxonomic revision has not been published in a peer-reviewed journal. Also, phylogenetic relationships of the species are unknown. You will bring together existing data, as well as produce new data, that will lead to a publication in a peer-reviewed scientific journal. The project offers you the possibility to become a complete botanist who has become acquainted with a variety of techniques to study patterns of plant diversity in the tropics, as well as the evolutionary history behind those patterns.

 

The goal is to learn several techniques for describing plant diversity in the tropics and testing hypotheses about their phylogenetic relationships. These techniques involve:

• Morphological studies of herbarium specimens

• Preparation of identification keys

• GIS techniques to study geographic distributions

• DNA sequencing techniques (genome skimming by Illumina sequencing)

• Bioinformatic tools for sequence assembly

• Phylogenetic methods

 

The techniques mentioned equip you with a set of tools that would enable the testing of further hypotheses, e.g. related to the evolution of characters, on biogeography, or the evolution of climatic preferences. During the preparation of this thesis, it is up to you to decide what kind of hypothesis you would like to test.

 

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9. The evolution of floral scent in tropical rain forest trees

Flowering plants dominate tropical ecosystems, and in many cases these plants require their pollen to be moved via a pollinator such as a bee, beetle, or butterfly, to the flowers of another individual plant of the same species in order to successfully reproduce. This is no small feat in a tropical rain forest. Plants are densely packed together, yet due to the incredible biodiversity and heterogeneity of plant communities of tropical forests, individuals of the same species may be separated by many meters and other plant species. Flowers use combinations of visual and olfactory cues to attract and manipulate insects as pollinators. In the low and variable light within and below the canopy of the rain forest, olfactory chemical cues (floral odour) play a particularly important role in attracting appropriate pollinators. Very little is known about the chemical composition of floral odours for species of Annonaceae, a family of tropical rain forest trees and lianas. The majority of the species which have had their floral scent described by human perception in the literature are described as sweetly fruity or as ripe, rotten, or fermented fruit. The fruity odour of a number of species has been linked to attraction of beetle pollinators, with the general assumption being that these fruity, fermented odours mimic actual rotting fruits, duping the beetle pollinators into visiting the flowers while in search of brood sites. A line of research has started recently in the Systematic and Evolutionary Botany lab, and you can be part of that. This project offers the possibility to do fieldwork in Bangladesh, and sample the floral scent of several species Annonaceae. At Ghent University, these scent samples will be analysed and interpreted.

 

The goal is to learn several techniques for sampling and analysing the volatile organic compounds that make up the scent

of flowers. Also, you will acquire experience with analytical tools to analyses the data in a phylogenetic context. These

techniques involve:

• Headspace sampling of floral scent

• Gas chromatography–mass spectrometry (GC-MS)

• Transformation of volatile organic compounds into characters for evolutionary analysis.

• Phylogenetic methods

 

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