Master theses topics Department of Biology. Laboratory of Biodiversity and Evolutionary Genomics Prof. Flip Volckaert

Transcription

1 Master theses topics Department of Biology Laboratory of Biodiversity and Evolutionary Genomics Prof. Flip Volckaert

2 The VOLCKAERT Team Ecology Evolution Fundamental research at the interface of ecology & evolution with applications in fisheries, aquaculture, human biology and conservation biology

3 Topics for master theses Human Parasites Marine ecology Adaptation in Fish Ocean Connectivity

4 Topics Master in Biology The following seven topics can be selected by students following the English taught Master in Biology or Dutch taught Master Biologie.

5 Evolutionary ecology Genetic structure of polar cod (Boreogadus saida): connectivity in a changing ecosystem Promoter Prof. Dr. Filip Volckaert (filip.volckaert@bio.kuleuven.be, ) Supervisor Aim Sarah Maes (sarah.maes@student.kuleuven.be) Climate-induced changes put an increasing pressure on the Arctic ecosystem and its populations, including the most abundant circumpolar fish polar cod. As a keystone species, changes in its abundance and distribution will impact the entire Arctic food web. However, intra-specific genetic differentiation could mean that some polar cod populations are at greater risk than others. Therefore, you will investigate the genetic population structure of polar cod in space and time. Application Next to global change, also global fisheries are expanding towards the poles, putting more pressure on these ecosystems. Solid understanding of local populations and their genetic make-up is needed, to advance conservation measures and/or sensible management.

6 This is a great opportunity for students with interest in marine polar biology & genetics! Evolutionary ecology Genetic structure of polar cod (Boreogadus saida): connectivity in a changing ecosystem This project involves molecular laboratory techniques (DNA extraction, PCR, gel electrophoresis) and statistical examination of the genotypes. Boreogadus saida

7 Population Ecology Growth in juvenile European plaice based on daily growth rings of otoliths Promoter Prof. Dr. Filip Volckaert Supervisor Dr. Kris Hostens (ILVO, Dr. Ir. Karen Bekaert (ILVO, Aim Estuaries and shallow coastal systems are key habitats for many organisms. They function as nurseries for flatfish where the trade-off between growth and survival is related to the abundance of food resources, predation levels and favorable environmental conditions. Habitat quality features thus have the potential to influence recruitment levels. Growth is a proven index to asses habitat quality. You will study juvenile growth on a small spatial scale based on the analysis of daily growth rings in otoliths of juvenile European plaice Pleuronectes platessa. You will track the inter- and intra-annual variation in individual growth by cohort in the Belgian part of the North Sea. The realized growth will be compared with the potential growth based on a Dynamic Energy Budget Model (DEB), which predicts maximal growth in relation to temperature and fish size. The combination of individual growth (otoliths) and population growth (DEB) will provide an unbiased growth analysis. Application The results will help to calibrate a biophysical dispersal model for flatfish as developed by Lacroix et al. (2013, 2017) and Savina et al. (2016). They will also contribute to the sustainable management of fish stocks of the North Sea.

8 Population Ecology Growth in juvenile European plaice based on daily growth rings of otoliths Research involves the reading of daily growth rings after polishing, microscopy & image analysis of otoliths, statistical analysis (growth vs. habitat quality parameters) & statistical modeling. European plaice Pleuronectes platessa Otoliths in a fish head Yearly growth rings of otoliths (5 yr old plaice) Image analysis of daily growth rings in an otolith Actual length-frequency and simulated DEB growth in juvenile plaice Some equations used in Dynamic Energy Budget (DEB) modelling

9 Molecular ecology Population dynamics of ichthyoplankton of the Eastern English Channel Promoter Prof. Dr. Filip Volckaert ) Co-promoter Aim Christophe Loots Heavy fishing and climate change have critically changed the dynamics of marine communities. As a consequence the fauna of the Eastern English Channel has measurably changed. It is important to continue to document this process in order to fully understand the drivers and consequences. Therefore you will study the ichthyoplankton community at the Gravelines station based on historical and recently collected samples. You will DNA barcode a set of samples collected bimonthly, and correlate the temporal species distribution with the locally collected environmental data and long term databases (such as egg surveys). Application The results will help to calibrate biophysical dispersal models for flatfishes as developed by Lacroix et al. (2013, 2017) and Savina et al. (2016). They will also contribute to the conservation management of the Eastern English Channel.

10 Molecular ecology Population dynamics of ichthyoplankton of the Eastern English Channel This is a great opportunity for students with interest in marine polar biology & genetics! You will identify fish eggs with DNA barcoding and analyse a time series of their population dynamics statistically.. Plaice eggs and yolk sac larvae by Ueberschär

11 Evolutionary ecology Metabarcoding of Antarctic fish: prey item composition in a changing ecosystem Promoter Prof. Dr. Filip Volckaert filip.volckaert@kuleuven.be, phone: Supervisor Franz Maximilian Heindler franzmaximilian.heindler@kuleuven.be Aim Highly adapted icefish (Notothenioidei) inhabit the Southern Ocean surrounding Antarctica. Rapid environmental changes and increasing human impact are not only challenging for these peculiar fish, but also their prey. For many of these species it is even unknown on what they prey. However, this kind of information is important in regulating conservation measures and protecting ecosystem functions. This project involves molecular laboratory techniques (DNA extraction, PCR, gel electrophoresis) and statistical examination of the prey composition of the stomach. This is a great opportunity for students with interest in marine polar biology & genetics! Application Next to global change, also global fisheries are expanding towards the poles, putting more pressure on these ecosystems. Solid understanding of local food webs and their interaction is needed, to advance conservation measures and/or sensible management.

12 Evolutionary Ecology The effect of water quality on the health of three-spined stickleback Promoter Prof. Dr. Filip Volckaert ) Supervisor Io Deflem ) Aim Global biodiversity is declining. The largest biodiversity loss is occurring in freshwater ecosystems. Hence freshwater systems are considered among the most endangered habitats worldwide. In Flanders, the riverine landscape is drastically altered by human activities. Poor water quality, the construction of migration barriers and the introduction of invasive species threatens fish populations and health and in turn alters whole fish communities. Application Three-spined sticklebacks were caught at 40 locations in de Dijle-Demer basin. You will dissect each fish and screen for the presence of parasites. You will perform morphometric analyses to study the impact of water quality on body shape. In a final step, you will study other measures of fish health such as spleen and liver size. All traits will be linked to environmental data (measured by the Flemish Environmental Agency, VMM) to investigate how human-induced pollution affects fish population health.

13 The effect of water quality on the health of three-spined stickleback Sampling locations in the Dijle-Demer basin Stickleback sampling Picture for morphometric analysis Parasite infecting three-spined stickleback

14 Evolutionary ecology Effects of mercury pollution on parasite load in three-spined stickleback Promoter Prof. Dr. Filip Volckaert tel: ) Supervisor Dr. Federico Calboli Supervisor Mr. Vyshal Delahaut Aim Fish are endangered by numerous anthropic effects, such as pollution. Parasites can also have a substantial impact on fish, yet little is known of how these two factors interact in the wild. You will sample rivers in Flanders to assess the level of mercury in the water and in the sediment. You will also measure the parasite load of three-spined sticklebacks caught in the same sites. You will use this data to build statistical models describing the relationship between pollution levels and parasite load, to understand how pollution affects the risk of parasite infection in fish. Application Your thesis will help understand whether increased pollution causes fish to be more vulnerable to parasites. Your results will give a better assessment of the risks our freshwater ecosystems are facing.

15 Evolutionary ecology Effects of of Mercury mercury Pollution pollution on on Parasite parasite Load load in Threespine three-spined Stickleback stickleback This Project has three components Statistical modeling Field work Lab work: parasite and toxicological analyses

16 Evolutionary ecology IRO Life history traits of Tanganyika sardines: scientific input for sustainable management Promoter Prof. Dr. Filip Volckaert tel: Supervisor Els De Keyzer Aim You will work with samples of sardines of Lake Tanganyika in order to understand more of their feeding habits, life cycle and population structure. The much needed information will improve the sustainable management of LT fisheries. You will do lab work, including genetic work or morphometric analyses, and will be responsible for data collection and analysis. If the opportunity arises, the project may involve fieldwork in DR Congo(IRO grant). Application The fisheries of Lake Tanganyika are an important food source for millions of people living near the lake shores. Almost 60% of the catch consists of two sardine species, and these populations now threaten to collapse. To enable effective management, more information about the biology of the two sardine species is much needed.

17 Evolutionary ecology Life history traits of Tanganyika sardines: scientific input for sustainable managment Relevant for management of an indispensable food source Two endemic pelagic clupeids make up most of the fisheries catch DNA barcoding of stomach content to unravel feeding habits Stolothrissa tanganicae Limnothrissa miodon Morphometrics to discover hidden population structure Tanganyika, one of the oldest and biggest lakes in the world

18 Evolutionary ecology IRO Hybridization of Schistosoma species in Zimbabwe and South Africa: Implications for animal and human disease transmission Promotor: Dr. Tine Huyse ) Prof. Dr. Filip Volckaert ) Aim: Schistosomiasis or bilharzia is a major poverty-related disease which affects over 200 million people worldwide. Despite available control strategies the disease continues to re-emerge. One of the possible reasons behind this is the phenomenon of hybridization. Recent molecular studies showed that hybridization between animal and human schistosome species is frequent. This complicates control due to the existence of animal reservoirs that are not included in current control measures. Moreover, hybrid parasites can have an enhanced transmission potential and can have a greater tolerance against drug treatment. A special focus on the identification, distribution and host use of hybrid parasites is therefore warranted. This includes a thorough parasitological study of gastropod snails, to identify their role in disease transmission, and new molecular methods to detect hybrid species in the field. 1. Fieldwork, snail shedding experiments and PCR analysis (Zimbabwe) 2. Statistical analysis & writing at Royal Museum for Central Africa and KU Leuven (Belgium) Justification: to estimate potential threat to human and animal health due to hybrids

19 Evolutionary ecology IRO Hybridization of Schistosoma species in Zimbabwe and South Africa: Implications for animal and human disease transmission. Life cycle Schistosoma Schistosome parasite Bulinus snails infection experiments

20 Topics Master Biology The following two topics can be selected by students following the English taught ICP Master in Sustainable Development

21 Population Ecology Growth in juvenile European plaice based on daily growth rings of otoliths Promoter Prof. Dr. Filip Volckaert Supervisor Dr. Kris Hostens (ILVO, Dr. Ir. Karen Bekaert (ILVO, Aim Estuaries and shallow coastal systems are key habitats for many organisms. They function as nurseries for flatfish where the trade-off between growth and survival is related to the abundance of food resources, predation levels and favorable environmental conditions. Habitat quality features thus have the potential to influence recruitment levels. Growth is a proven index to asses habitat quality. You will study juvenile growth on a small spatial scale based on the analysis of daily growth rings in otoliths of juvenile European plaice Pleuronectes platessa. You will track the inter- and intra-annual variation in individual growth by cohort in the Belgian part of the North Sea. The realized growth will be compared with the potential growth based on a Dynamic Energy Budget Model (DEB), which predicts maximal growth in relation to temperature and fish size. The combination of individual growth (otoliths) and population growth (DEB) will provide an unbiased growth analysis. Application The results will help to calibrate a biophysical dispersal model for flatfish as developed by Lacroix et al. (2013, 2017) and Savina et al. (2016). They will also contribute to the sustainable management of fish stocks of the North Sea.

22 Population Ecology Growth in juvenile European plaice based on daily growth rings of otoliths Research involves the reading of daily growth rings after polishing, microscopy & image analysis of otoliths, statistical analysis (growth vs. habitat quality parameters) & statistical modeling. European plaice Pleuronectes platessa Otoliths in a fish head Yearly growth rings of otoliths (5 yr old plaice) Image analysis of daily growth rings in an otolith Actual length-frequency and simulated DEB growth in juvenile plaice Some equations used in Dynamic Energy Budget (DEB) modelling

23 Conservation Genetics Ex-situ conservation genetics of horned pheasants Promoter Prof. Dr. Filip Volckaert ) Supervisor Dr. Peter Galbusera Ing. Bart Hellemans Aim Three of the five species of horned pheasants (Tragopan caboti, T. temminckii. and T. satyra; Phasianidae) are commonly bred by fowl breeders across Europe. Their native range are the forests of southern and southeastern Asia; several species feature on the IUCN red list as threatened. Since 2005 breeding pairs have been screened with microsatellite markers for species status with the purpose of reducing hybridisation. You will be genotyping new samples with DNA microsatellite markers and analyzing the database for genetic diversity, relatedness and structure. You will be working with fowl and zoo managers, and your results will contribute to the management of genetic biodiversity. Application Your results are guiding hobby breeders to manage their fowl with a conservation perspective.

24 Conservation Genetics Ex-situ conservation genetics of horned pheasants Tragopan satyra Tragopan temminckii Tragopan caboti This project involves literature and database research, sample preparation, genotyping and computational work. Knowledge of numerical computing in R is appreciated. This is a great opportunity for students with an interest in the sustainable management of tropical fowl. Working place will be Leuven.

25 Good to remember Our research involves : - field sampling - lab work - collaborative research - excellent tutoring - international contacts - useful societal applications Adaptation in Fish Human Parasites Ocean Connectivity Marine ecology For information consult bio.kuleuven.be/eeb/lbeg and Please drop by at our lab for more information!