Laboratory of Plant Ecology Master thesis subjects 2012-2013

1. Laboratory of Plant EcologyMaster thesis subjects 2012-2013

2. 1. Genetic diversity and survival chances of the last remaining populations of Broad-Leaved Thyme (Thymus pulegioides) in Flanders Hageland Supervisor: Olivier Honnay & Joachim Mergeay

3. Aims:- Quantify population genetic diversity in remnant populations using SNPs- Quantify population fitness based on seed viability- Quantify Soil chemical composition (N, P, C, pH)- Statistically relate genetic diversity with degree of habitat fragmentation, fitness and local habitat chracateristicsInfer gene flow (pollen and seeds) among populations- Provide guidelines for conservation

4. 2. Genomic diversity and local adaptation in Frangulaalnus(Sporkehout) Supervisor: Hanne De Kort

5. General objective Examine both adaptive and neutral genetic variation between Belgian and foreign (Italian, Swedish and French) populations. • Basically, our most important research questions are: • Is Frangula alnus adapted to its local growing conditions? • How genetically diverged are Frangula populations, and are the observed patterns different in Flanders than abroad?

6. Methodology • Measurement of seedling characteristics in a common garden • Measurement of seedling characteristics in transplant sites • Apply single nucleotide polymorphism (SNP) analysis, and calculategeneticdiversity parameters. • Comparemorphologicalvariationamongseedling characteristics (Qst) withgeneticmarker (SNP) variation(Fst) to detectnatural selection (Qst-Fst)

7. 3. The impact of sex ratio on genetic diversity and differentiation in the gynodioeciousSaxifragagranulata • Gynodioecy is a special sexual system in which populations consist of female and hermaphroditic plants. • Gynodioecy can only exist if female plants have a reproductive advantage relative to hermaphroditic plants. • Females need pollen from hermaphrodites for seed production

8. Aims • In this study you will investigate the relationship between sex ratio and: • genetic diversity • population size • population differentiation • gene flow in Saxifragagranulata (Knolsteenbreek)

9. Practical • Fieldwork Leaf sampling of females and hermaphrodites (Dijle Valley) • Labwork Genetic analysis of polymorphic loci (SSRs) • Statistics Analysis of results

10. 4. The taste of nectar: Effects of nectar amino acids on pollinator behavior To increase reproductive success, many plants produce nectar to attract insect pollinators. Very little is known about the role of amino acids in nectar. Amino acid concentration is expected to be an important source of nitrogen for pollinators but also composition could be of importance since aa can influences the taste of nectar. The aim of the project is to test the effect of changes in amino acid concentration and composition on the behavior of butterflies pollinating the orchid Gymnadeniaconopsea. Supervisor: Pieter Gijbels

11. Practical: • Select pairs of individuals and enrich the nectar of one individual of each pair • Determine nectar aa composition of both enriched and control individuals using HPLC • Monitor pollinator behavior on individuals with control and enriched nectar. • Collect and dissect flowers of all individuals and determine the number of pollinaria removed and deposited. • Statistically compare the different elements of pollinator behavior, pollen removal and pollen deposition between treatments

12. 5. Impact of coffee forest management on AMF diversity of coffee in Southwest Ethiopia • Coffee is the most important economic export product of Ethiopia. More than 15 millionEthiopiansdependonitfortheirmainincome. Arbuscular mycorrhiza are important forsustainable and organic cofee cultivation. A high diversity of AMF oncoffeerootscanbeexpected to have a broadfunctionality. supervisor: Matthias De Beenhouwer

13. What is the effect of forestmanagement intensityof coffeeforestson the diversity of AMF in coffeeroots? Does the age of the coffeeshrub affect AMFdiversity?

14. practical • Sampling campaign in Ethiopia (Jimma region) summer 2012 • DNA extraction soil samples • 454 sequencing • Bioinformatics • Statistical analysis of AMF diversity vs. forest stand characteristics

15. 6. Effects of plant trait diversity on the stability of functioning of Dutch dune grasslands Functionerenecosysteem Niveau van biodiversiteit Supervisor: Nils Van Rooijen

16. With Joop Schaminee (Nijmegen University)

17. Kwantificeren van plantendiversiteit Funcionelediversiteit • Trait diversity • Trait richness • Functional species groups • Species richness • Species diversity • Species evenness Taxonomischediversiteit 2 1 • Continous trait measures • Hypervolumes • Dendrograms 3 Vegetatie-opname Homogenevegetatie = RS MODIS pixel

18. 7. Adaptive evolution in floral traits in response to changes in pollinator composition across the distribution range of a distylous forest herb Geographic ranges of plants and their pollinators do not always entirely overlap. A shift in pollinator composition from specialized pollinators in the centre of the plant species’ range to more generalist insect species in the periphery and introduced populations may lead to adaptation of the floral morphology and mating system. Specialists Generalists Supervisor: Sofie Meeus

19. Practical: • Floral measurements of 12 traits on flowers collected in spring 2012 from populations within the range (Germany) and outside the range (Flanders) of P. officinalis • Statisticsof floralvariationwithdifferences in pollinatorcomposition in the threeregions

20. 8. Factors affecting natural regeneration of pedunculate oak, implications for sustainable forestry? Forest policy increasingly promotes a sustainable forest management in which natural regeneration plays an important role (FAO 2011). Besides the economical and ecological benefits, natural regeneration allows permanent natural selection on the regeneration, favoring well adapted progeny. However, in many forest stands successful establishment of seedlings is limited or completely absent, jeopardizing a sustainable forestry . Supervisor: Guy Vranckx

21. General objective • The general objective is to examine which environmental factors (vegetation, light, soil) affect natural regeneration of pedunculate oak (Quercusrobur) in forest stands across Flanders. Methodology • Vegetation surveys in ca. 20 pedunculate oak stands across Flanders (Summer 2012) • Measurements of stand characteristics in 10 x10m plots: • Number and diameter adults and seedlings • Health status trees (defoliation index), tree mortality • Analysis of light conditions (Leaf area index (LAI) using a hemispherical lens) • Measurements of soil water and thickness of the Ah horizon • Analysis of soil samples (pH, nitrogen, organic matter content…)

22. 9. Hybridization between Dactylorhizamaculata and the rare D. sphagnicola: implications for conservation Hybridization between species may be an important threat to the long-term viability of rare taxa. We will investigate the extent of hybridization between D. maculata and D. sphagnicola using both molecular and morphological analyses. Pre- and post-zygotic mating barriers will estimated using controlled pollinations. This study involves both field work and laboratory analysis. All field work will be conducted in the HogeVenen Nature Reserve. Supervisor: Rein Brys & Hans Jacquemyn

23. Methodology • Assessment of prezygotic and postzygoticreproductive barriers using controlled pollinations between the two study species. • Measurement of morphological traits in hybrid populations and pure populations of both D. maculata and D. sphagnicola. • Collection of leaf samples and genetic AFLP analysis of pure and hybrid populations. • Assessing the extent of hybridization and introgression using multivariate techniques and assignment analyses.

24. 10. Changes in the soil seed bank during community assembly on the calcareous grasslands of the Viroin valley. Due to the LIFE-project “restoration of calcareous grasslands”, more than 100 ha calcareous grassland have been restored since 2002. This allows us to create establish a chronosequence of grasslands fragments of different age (and thus of different succession stage), making it possible to compare the seedbank composition of the restored fragments between different successional stages. Supervisor: Kenny Helsen

25. Aim: • Look at the evolution of seed abundances and species composition of the seed bank under calcareous grasslands of different restoration age using germination experiments. This allows us to reconstruct the succession within the seedbank.

26. Practical: • Sampling in the summer: taking soil samples in the Viroin valley. • Doing vegetation surveys • Lab work: germination protocol and identification of seedlings. • Statistical analysis (multivariate, mixed models).

27. Habitat fragmentation has been shown to affect the genetic constitution of populations in a large number of plant species, but the ecological consequences on plant and population viability are, however, often poorly understood. You will study the consequences of habitat fragmentation and the resulting genetic consequences on the process of reproduction, dispersal capacity and offspring fitness in the rare calcareous grassland plant, Cirsiumacaule. This study involves both field work (in the Viroin valley) and experiments in the laboratory. 11. Impact of habitat fragmentation on reproductive success, dispersal capacity and offspring fitness in the rare Cirsiumacaule Laboratory of Plant Ecology Supervisor: Rein Brys & Hans Jacquemyn

28. Methodology • Investigation of successful pollination and pollen limitation in the field, via comparisons of seeds set resulting from open vs. supplemental hand-pollinations in a large number of natural populations. • Measurement of seed quality, seed mass and dispersal traits (pappus size and width) in the laboratory. • Measurement of seed dispersal capacity under experimental conditions. • Common garden experiment to examine offspring fitness of each of the studied populations at the level of: germination rates, seedling survival, offspring fitness etc. • Statistical analysis (multivariate, mixed models)

29. 12. Mycorrhizal diversity in tropical epiphytic orchids: the case of orchid communities in Cameroon and Gabon The ecology of many epiphytic orchid species is still poorly known, mainly due to their high diversity in tropical regions coupled to sampling difficulties due to their unusual lifestyle. In particular, little is known about the diversity and specificity of mycorrhizal associations in tropical epiphytic orchids, even though those symbiosis are crucial in determining their distribution and abundance. The aim of this study is to investigate the diversity and specificity of orchid mycorrhizal associations in a number of orchid species found in Cameroon and Gabon through field and laboratory work. Laboratory of Plant Ecology Supervisor: Bruno Cachapa Bailarote

30. Methodology • Sampling of orchid roots and leaves on the field in tropical rainforests in Atlantic Central Africa (Cameroon and Gabon). This include tree climbing with appropriate gears in order to get access to most of the local species. • DNA extraction of mycorrhizal fungi from orchid roots and identification using the 454 technology (next generation sequencing). • Determination of mycorrhizal specificity and spatial variation in mycorrhizal associations across different species and populations.