Master thesis topics 2020-2021 Department of Biology - Laboratory of Biodiversity and Evolutionary Genomics
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Master thesis topics
2020-2021
Department of Biology
Laboratory of Biodiversity and Evolutionary Genomics
Prof. Filip Volckaert
The VOLCKAERT
Team
Evolution
Ecology
LBEG performs
fundamental research
at the interface of ecology & evolution
Our output has applications in fisheries, aquaculture, human
biology and conservation biology
Topics for master
theses
Trophic ecology
of Arctic fish Genomic
differentiation of
Antarctic fish
A quick tool
for seafood
identification Snails as intermediate
hosts of
schistosomiasis
Monitoring non-
indigenous
marine species
Topics Master in Biology Four topics are open to students following the English taught Master in Biology or Dutch taught Master in de Biologie. The fifth topic (Blue Biotech) is for students of the Master of Biochemistry/ Biotechnology.
Evolutionary ecology –
Understanding the ecological diversification
of high-Antarctic fishes through genomics
Promoter Prof. Dr. Filip Volckaert (filip.volckaert@kuleuven.be, 016 32 39 72)
Supervisor Henrik Christiansen(henrik.christiansen@kuleuven.be, 016 37 66 92)
Aim
Highly adapted icefish (Notothenioidei) inhabit the Southern Ocean which
surrounds Antarctica. Several species of Trematomus have evolved to fill
different ecological niches – in the water column as well as on the seafloor.
Their genomes seem to be highly diverse as well, with diploid chromosome
numbers ranging between 24 and 58. It is unknown how the genomic
background has shaped the evolution of these unique fishes. Therefore we
want to investigate genomic differentiation within and between Antarctic
fishes in relation to their ecological characteristics.
Application
Antarctic marine ecosystems are among the
fastest warming regions on Earth. With no colder
place left to migrate to, it is crucial to under-stand
the evolution and adaptation of these fishes to
advance conservation actions, that may help
these species to persist despite global change.
Evolutionary ecology –
Understanding the ecological diversification
of high-Antarctic fishes through genomics
This project involves population genomic and/or phylogenomic analysis and -
depending on interest, fish dissections and/or molecular laboratory techniques.
Bald notothen
Striped rockcod
This is a great opportunity for students with interest in polar biology & genomics!
Evolutionary
Evolutionary ecology – ecology –
Metabarcoding of
Metabarcoding
polar fish: microbiome ofcomposition
polar fish: in a
microbiome coposition
changing in a changing Arctic
Arctic
Promoter Prof. Dr. Filip Volckaert (filip.volckaert@kuleuven.be, 016 32 39 72)
Supervisor Sarah Maes (sarah.maes@kuleuven,be)
Aim
Climate-induced changes put an increasing pressure on the Arctic ecosystem and
its populations, including the abundant circumpolar fish polar cod (Boreogadus
saida). Changes in the abundance and distribution of this keystone species will
impact the entire Arctic food web. Therefore, good knowledge of polar cod’s
genetics and ecology is essential. Gut microbiota of fish can be sensitive to dietary
changes. Moreover, microbiota diversity and composition can vary among
populations. In this project, we aim to investigate microbiome composition of polar
cod and the link between diet and microbiome.
Application
Global fisheries are expanding towards the poles and put
increasing pressure on the ecosystems Solid understand-
ding of local populations is needed to advance conser-
vation measures and sensible management.
Evolutionary ecology – Metabarcoding of
polar fish: microbiome composition in a
changing Arctic
This project involves molecular laboratory techniques (DNA extraction and
sequencing), statistical examination and interpretation of the gut microbiome.
Boreogadus saida
This is a great opportunity for students with interest in marine polar biology & genetics!
DNA-based monitoring of non-indigenous
Title
marine species in harbours
Promoter Prof. Dr. Filip Volckaert (Filip.Volckaert@kuleuven.be, 016 32 39 72)
Co-Promoter Dr. Pascal Hablützel (pascal.hablutzel@vliz.be)
Aim
Ships transport non-indigenous species (NIS) over long distances which may
find suitable habitats in the heavily anthropogenized harbours. Traditionally,
invasive species are monitored using morphological identification. However,
genetic methods such as DNA-metabarcoding are potentially more accura-
te, more sensitive, cheaper and faster than the traditional approaches. Within
the international project GEANS, we test the application of molecular techni-
ques to a wide array of marine monitoring studies. One of the pilot studies
focuses on NIS in harbours of several European countries. The student will col-
lect samples in Belgium and conduct the laboratory work as well as the bioin-
formatic analysis in collaboration with external partners. The aim of this master
thesis is to test and streamline the workflow for real-world applications.
Application
The research is part of an international research project that aims to improve
DNA-based monitoring in marine environments.
https://northsearegion.eu/geans/
DNA-based monitoring of non-indigenous
marine species in harbours
Specific tasks
• Sample collection
• DNA extraction and preparation for
next-generation sequencing
• Quality control of raw sequence
data
• Statistical analysis and
interpretation
• Trouble shooting of work-flow and
verification of results
Actual work will be conducted at KU
Leuven and VLIZ (Ostend).Evolutionary ecology – IRO
Spatio-temporal distribution of freshwater snails that
transmit the tropical disease bilharzia in Congo.
Promotor: Dr. Tine Huyse (tine.huyse@bio.kuleuven.be, 02 769 57 63)
Prof. Dr. Filip Volckaert (filip.volckaert@kuleuven.be, 016 32 39 72)
Mentor: Tim Maes
Aim: Bilharzia, or schistosomiasis, is a neglected disease that affects more than 200 mil-
lion people worldwide, especially in Africa. Chronic infection leads to stunted
growth, infertility, liver fibrosis and bladder cancer, with an estimated 18,000 deaths
per year Scientists have realized that mass drug administration is not sufficient to
combat the disease and the WHO recommends to complement treatment with
targeted snail control. In order to support snail control, reliable knowledge is
needed on the distribution of snails both in time and space. This will allow to con-
struct reliable species distribution models that can guide snail control. In this thesis
we will use recently collected data from 25 villages in Bas Congo that take part in
the ATRAP project coordinated by the Royal Museum for Central Africa. Your
contribution involves (1) fieldwork, snail sampling and shedding experiments (Congo)
and (2) analysis and writing at the Royal Museum for Central Africa and KU Leuven
(Belgium)
Justification: to identify hotspots of disease transmission to guide control.Evolutionary ecology – IRO
Spatio-temporal distribution of freshwater snails that
transmit the tropical disease bilharzia in Congo.
Life cycle Schistosoma Schistosome parasite Bulinus snails infection experimentsBlue biotech
Developing a methodology for the fast
identification of (sea)food products
Promotor: Prof. Dr. Filip Volckaert (filip.volckaert@kuleuven.be, 016 32 39 72)
Dr. Johan Robbens (johan.robbens@ilvo.vlaanderen.be)
Mentor: Dumas Deconinck
Aim: The most commonly used techniques to identify morphologically unrecognisable
(sea)food products involve DNA. However, DNA barcoding and species-specific
real-time PCR require lengthy extraction, DNA amplification (PCR) and visualisation
procedures. In addition, DNA barcoding requires Sanger sequencing. These steps
are complex requiring machines and skilled labour, making the use of these techni-
ques in the field almost impossible. Here we aim at reducing the time of the identifi-
cation process by replacing every step with a faster and more easily applicable
method. We will replace liquid DNA extraction, which takes 1 to 2 h, with a novel
dipstick method, which would takeBlue biotech
Developing a methodology for the fast
identification of (sea)food products
You will identify seafood mixtures by their DNA in a novel way in a short time span.Good to remember
Research includes :
- field sampling (when possible) Trophic
- lab work ecology of Genomic
- collaborative research Arctic fish differentiation of
- excellent tutoring Antarctic fish
- international contacts
A quick tool
- societal applications for seafood Snails as
identification intermediate hosts
of schistosomiasis
Monitoring
non-
indigenous
marine
species
For more information consult bio.kuleuven.be/eeb/lbeg.
Please drop by at our lab in the Kolenmuseum!You can also read
