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The Laboratory of Biodiversity and Evolutionary Genomics
http://bio.kuleuven.be/eeb/lbeg
Fundamental research at the interface of ecology & evolution
with applications in fisheries, aquaculture, human biology and nature conservation
The Volckaert team Ecology Evolution
Human parasites
Adaptation in fish
Dynamics of sea fisheries
Topics for a Master thesis
Human evolution
Dynamics of sea fisheries
Natural fish populations have been impacted measurably by man. The history of fish catches is a well kept secret – a shifting baseline. Much can be learned from written records and the genome ...
-4 -2 0 2 4 6 848.5
50.5
52.5
54.5
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Longitude (°E)
Latit
ude
(°N
)
FRBE
NL
GE
UK
1995-2011
Dynamics of sea fisheries
FV1 - Connectivity of sole in the Southern North Sea
FV2 - Seascape genetics of flatfishes: SNP
development to trace fish and unravel populations
FV3 – Modeling in support of the design of
Marine Protected Areas (MPAs) in the North Sea
B-FishConnect
Dispersal and demography of four commercial flatfishes
Promoter: Prof. Dr. Filip Volckaert ([email protected]) Co-promoter: Dr. Johan Robbens ([email protected]) Supervisor: Andreas Vanden Bavière ([email protected]) Aim: Flatfish are commercially important species in the North Sea fishery. Although they are heavily targeted by the fishing industry, we still don’t have a full understanding of their recruitment and early-life dynamics. We will focus on four commercially important species: sole, plaice, turbot and brill. In this project we will investigate their recruitment and early dynamics by analyzing both zooplankton and fish samples caught at sea and in the nursery areas. You will take part in field and lab work, and learn to analyse data. Application: your research is relevant for marine ecology, fisheries and conservation biology.
Dispersal and demography of four commercial flatfishes
In order to obtain a full understanding of local flatfish dynamics we will apply a set of ecological tools such as indices, spatial analysis, otolith data and biomarkers
This project is a great opportunity for students interested in marine ecology! The project includes field work at sea on RV Simon Stevin.
Nursery grounds Feeding
grounds
Spawning grounds
Movements between habitats
Evolution - Seascape genetic of flatfishes : SNP development to trace fish and unravel populations
Promoter Prof. Dr. Filip Volckaert ([email protected], 016 32 39 72) Dr. Ilaria Coscia ([email protected], 016 32 66 66)
Supervisor Sophie Delerue-Ricard ([email protected], 016 32 39 18)
Background Overfishing and selective fishing reduce genetic diversity and modify life cycles. Conservation efforts have to be made to protect flatfishes, including the connectivity patterns of larvae. We are developing a panel of highly informative Single Nucleotide Polymorphism (SNP) markers to trace individual fish to its origin. By using genetic tools we will highlight dispersal HIGHWAYS and possibly distinct populations. Your task will be to perform biostatistical analyses on DNA sequences to find the most informative SNPs. For this you will use state-of-the-art biostatistical software. You will also join field work on board of a research vessel, and perform DNA extractions and PCR amplifications. The research serves fisheries management and conservation management of fish stocks.
Application Your research will benefit fisheries and conservation management.
Past Future Present
HIGHWAY TO NURSERY
Where do flatfishes come from ?
Evolution - Seascape genetic of flatfishes : SNP development to trace fish and un-ravel populations
Flatfish are caught off the Belgian and French coast. DNA is purified and genotyped. Following a full scale quality-control (sequence, assembly, null alleles, missing genotypes, …), the focus will be on differentiation-, outlier-, clustering-, assignment- and multivariate analyses.
This project is a great opportunity for students with an interest in bio-informatics and genetics!
Sampling points of flatfish larvae, postlarvae and juveniles along the Belgian-French coast.
Sea sampling
Beach sampling
Nursery grounds
Feeding grounds
Spawning grounds
ECOLOGY - Modeling in support of the design of Marine Protected Areas (MPAs) in the North Sea
Promoter Prof. Dr. Filip Volckaert ([email protected], 016 32 39 72) Co-promoter Dr. Geneviève Lacroix ([email protected], 02 773 21 00) Supervisor (MUMM): Leo Barbut ([email protected]) Aim: Overfishing is common in the North Sea and impacts many fish species. MPAs (Marine protected areas) are important instruments to protect biodiversity and fish stocks. This dynamic research field requires research on the design of a network of MPAs to ensure connectivity between populations. This is necessary for the functioning of the ecosystem and the maintenance of gene flow. The goal is to identify priority areas to implant MPAs, using the connectivity matrix obtained from a larval transport model, completed with population genetic data. This study will focus on flatfish. A possible methodology is described in "Optimal selection of marine protected areas based on connectivity and habitat quality" (Berglund et al. 2012). Justification: Fisheries and conservation management
The project requires an interest for modelling and analytical skills. Knowledge of numerical computing software (matlab, scilab, R...) is much appreciated. The thesis requires communication and writing in English.
ECOLOGY - Modeling in support of the design of Marine Protected Areas (MPAs) in the North Sea
-4 -2 0 2 4 6 848.5
50.5
52.5
54.5
56.5
Longitude (°E)
Latit
ude
(°N
)
FRBE
NL
GE
UK
1995-2011
Nurseries Origin (spawning grounds)
# larvae
No
Tha
Spawning sites of sole in the Southern North Sea and English Channel [ICES FishAtlas, 2005]
Larval abundance of sole in the North Sea (Lacroix et al., 2013). Spawning grounds: EC (Eastern Channel), BC (Belgian Coast), Tx (Texel), GB (German Bight), N (Norfolk), Th (Thames). Nurseries: FR (French nursery), BE (Belgian nursery), NL (Dutch nursery), GE (German nursery), No (Norfolk nursery), Tha (Thames nursery).
FR, BE, NL, GE, No, Tha
Adaptation and selection in fish
Organisms have to cope with changing conditions; hence they adapt to abiotic and biotic pressures
The genome and phenotype provide a unique window on the drivers of
this adaptive variation.
Adaptation and selection of fish
FV4 – Niche overlap between two stickleback species
FV5 – PopGenP : an integrated platform for
performing population genomics
Evolutionary ecology – Niche overlap
between two stickleback species
Promoter Prof. Dr. Filip Volckaert ([email protected], 016 32 39 72)
Supervisors Joost Raeymaekers ([email protected])
Blake Matthews ([email protected])
Aim Natural populations are often adapted to their local environment, but have to share it with competitors. In this study, we compare the trophic position and niche overlap of two coexisting and phylogenetically related species, the three- and nine-spined stickleback. Populations of the two species are sampled across a salinity gradient (freshwater to brackish water), and habitat characteristics are quantified. The fish are transported to the laboratory to investigate their diet and trophic morphology. Liver and muscle tissue is sampled for the analysis of stable isotopes, which is indicative for their position in the food web.
Application Understanding adaptation in the context of ecosystems and food webs
This project is a great opportunity for students that want to work this summer in Switzerland!
Evolutionary ecology – Niche overlap
between two stickleback species
Top: the analysis of stable isotopes will be done at Eawag in Kastanienbaum, a famous research center for aquatic ecology based in the Alps, at the shore of Lake Luzern.
Right: fieldwork in Belgium and the Netherlands
nine-spined stickleback
three-spined stickleback
BIOINFORMATICS: PopGenP: An integrated platform for performing
population genomic analyses
Promoter : Prof. Dr. Filip Volckaert ([email protected], 016 32 39 72)
Co-promoter : Prof. Dr. Luc De Meester ([email protected], 016 32 37 08)
Supervisor : Anurag Chaturvedi ([email protected], 016 32 42 96).
Aim:
With the arrival of next generation sequencing (NGS) the cost of sequencing is di-minishing; NGS now includes also non-model organisms. Introduction of approaches such as reduced genome representation e.g., GBS, has opened new venues for uncovering the various processes in evolutionary biology at the population level. There are many platforms available for calling genotypes from sequencing data but there are only bits and pieces available for analyzing population genomics principles confronting a biologist. The aim of this project is to develop a multipurpose population genomics platform utilizing multicore efficiency of a normal desktop and providing basic functions from parsing, graphical user interface for
command line programs up to high user end graphics from the existing resources. This should be done in a comprehensive manner.
This is a topic for a student with a programming background and good
communication skills in English
Justification:
The project involves software development for population genomics. In our lab it is used for analysing next generation sequencing data to assist with evolutionary biology and the conservation of the natural environment.
The candidate will take advantage of object oriented programming (OOP) languages such as JAVA and Python. HDF5 will be used for data storage. The learning outcome will be mastering the OOPs concept such as inheritance and polymorphism with the amalgamation of scripting with latest technologies. The candidate is expected to learn the principles of population genomics as the platform will be validated by real time analysis of experimental data.
BIOINFORMATICS: PopGenP: An integrated platform for performing
population genomic analyses
Human parasites
Flatworms are common macroparasites. Their close association with vertebrate hosts has resulted in distinct
patterns of co-evolution and host-switching. We study their evolution in man (Schistosoma).
Human parasites
FV6 – IRO – The evolutionary epidemiology of the parasite Schistosoma haematobium
FV9 – Human schistosomiasis and the slave trade FV10 – Hybridisation and colonization dynamics of
human schistosoma parasites
EVOLUTIONARY EPIDEMIOLOGY The evolutionary epidemiology of the parasite Schistosoma haematobium
Promoter : Prof. Dr. Filip Volckaert
([email protected], 016 32 39 72)
Co-promotor: Prof. Dr. Katja Polman ([email protected], 03 247 62 04)
Dr. Tine Huyse ([email protected], 02 76 95 63)
Supervisor: Drs. Nele Boon ([email protected], 016 32 45 72)
Aim: You will try to understand the role of parasite genetics in its infectivity
and pathogenicity. Schistosoma is a parasite affecting over 200 million
people worldwide. Your goal is to explore neutral and functional genetic
variation of S. haematobium parasite populations and to relate this genetic
variation to phenotypic data of the human host such as age, gender,
infection intensity, pathology, …
Justification: Neglected Tropical Diseases: improving schistosomiasis
control by studying the genetics of the schistosome parasite
EVOLUTIONARY EPIDEMIOLOGY Schistosomiasis: The role of parasite genetics in human infection and disease
This project involves:
-Lab work: genotyping of parasite samples using microsatellite markers
-Data analysis of (population-)genetic and epidemiological data
- Fieldwork in Senegal/DRCongo: The collection of parasite samples and epidemiological data (optional), if a VLIR-UOS travel grant is obtained and the
conditions in the field are suitable.
Human Schistosomiasis and the slave trade
Promoter: Dr. Tine Huyse ([email protected], 016 32 42 96)
Prof. Dr. Filip Volckaert ([email protected], 016 32 39 72)
Aim: to reconstruct the colonization pathways of Schistosoma mansoni in Brazil with new molecular markers. This parasite affects over 200 million people worldwide and was introduced in South America with the slave trade about 500 years ago. The use of DNA markers will allow us to understand from where in West Africa this parasite was introduced and how it further evolved and spread in Brazil.
The student will:
1. Collect parasites in Senegal or Congo if VLIR travel grant is obtained
2. Genotype individual parasites by means of DNA microsatellites
3. Reconstruct parasite migration and transmission dynamics in Brazilian populations.
Justification: to understand the evolution of an important poverty-related disease
Hybridization and colonization dynamics in
human schistosome parasites
EVOLUTIONARY PARASITOLOGY AND POPULATION GENETICS: Hybridization
and colonization dynamics of human schistosomiasis parasites
Evolutionary parasitology and population genetics
Urine & stool collection schistosome eggs and larvae microsatellite genotyping
Human Schistosomiasis and the slave trade
Hybridization and colonization dynamics in human schistosome parasites
EVOLUTIONARY PARASITOLOGY AND POPULATION GENETICS: Hybridization
and colonization dynamics of human schistosomiasis parasites
Hybridization and colonization dynamics in
human schistosome parasites
Promoter: Dr. Tine Huyse ([email protected], 016 32 42 96)
Prof. Dr. Filip Volckaert ([email protected], 016 32 39 72)
Aim: to study the impact of hybridization between a human and bovine schistosome parasite on the distribution and spread of schistosomiasis in northern Senegal. Moreover, we want to study the impact of hybridization on the molecular level, by sequencing the complete mitochondrial genome and by means of nuclear microsatellite genotyping. This will allow us to understand the patterns of introgression and selection for genes or gene regions that are important in schistosome biology, on a genome wide scale.
The student will:
1. Collect parasites in Northern Senegal if VLIR travel grant is obtained
2. Genotype individual parasites by means of DNA microsatellites
3. Sequence 10 mitochondrial genomes with PacBio RS sequencing
Justification: to understand the role and consequences of hybridization in the epidemiology of a tropical disease
HUMAN EVOLUTIONARY GENETICS: Hybridization and colonization dynamics
of human schistosomiasis parasites
Urine & stool collection schistosome eggs and larvae microsatellite genotyping
HUMAN EVOLUTIONARY GENETICS : Hybridization and colonization dynamics
of human schistosomiasis parasites
Human genetics
Man’s evolution can be traced throughout his biology and culture. Hence hypotheses can be suggested on micro-evolutionary patterns in
Western Europe and Belgium.
Human genetics
FV7 – Optimising human Y-chromosomal phylogeny using whole genome sequence data
FV8 – “The Y-chromosomes of ’t Stad – Genetic- demographic analysis of males with a ‘COR’-
surname in Antwerp
HUMAN EVOLUTIONARY GENETICS
Optimising human Y-chromosomal phylogeny using whole genome sequencing data
Promoters: Prof. dr. Filip Volckaert ([email protected], 016 32 39 72)
Prof. dr. Ronny Decorte ([email protected], 016 33 66 00)
Co-promoter & supervisor: dr. Maarten Larmuseau ([email protected], 0494 39 72 97)
Background:
A state-of-the-art phylogeny of the human Y-chromosome is an essential tool for evolutionary genetics, behavioural ecology and forensic sciences. The explosion of whole genome sequencing (WGS) data due to the rapid progress of next-generation sequencing facilities is useful to optimise and to increase the resolution of the phylogenetic Y-chromosomal tree. In this thesis the student will develop new algorithms in order to optimise the current phylogeny based on WGS data and to select new interesting Y-chromosomal variants for the direct applications of the Y-chromosomal tree.
Applications:
Your research will provide crucial information for Human evolution and biology, Forensic science, Historical demography & Genealogical genetics
HUMAN EVOLUTIONARY GENETICS
Additional information:
1. Van Geystelen A., Wenseleers T., Decorte R., Caspers M., Larmuseau M.H.D. (In press) In silico detection of phylogenetic informative Y-chromosomal SNPs from WGS data. Electrophoresis SCI I.F. 3.2
2. Van Geystelen A., Decorte R. & Larmuseau M.H.D. (2013) AMY-tree: a method to use whole genome SNP calling for Y chromosomal phylogenetic applications. BMC Genomics, 14: 101. SCI I.F. 4.1
Human Evolutionary Genetics
The Y-chromosomes of ’t Stad - Genetic-demographic analysis of males with a ‘COR’-surname in Antwerp
Promoters: Prof. dr. Filip Volckaert ([email protected], 016 32 39 72)
Prof. dr. Ronny Decorte ([email protected], 016 33 66 00)
Co-promoter & supervisor: dr. Maarten Larmuseau ([email protected], 0494 39 72 97)
Background: Historical demographic researchers of the KU Leuven have developed a unique databank of families with a so-called ‘COR’-surname, e.g. Cornelis, Corbeel, Corremans, ... which lived in the province of Antwerp between the years 1800-1900. By studying the Y-chromosomes of these families, we could verify for the first time if evolutionary Y-chromosomal variants are related with demographic characteristics as fertility and life age. As such, we will study whether the observed Antwerp Y-chromosomal variants have an influence on the phenotype of a male.
Applications: This research will provide crucial information for Human evolution and biology, Forensic science, Historical demography & Genealogical genetics
Human Evolutionary Genetics
Aim: 1. Collecting DNA-donors and genealogical data
2. Genotyping Y-chromosomal loci in a Forensic Lab (UZ-Leuven)
3. Analysing historical demography on micro-geographical scale
DNA sampling Y-chromosome amplification Genotyping Data analysis
Materials & Methods:
Nice to remember… Our research involves :
- field sampling
- lab work
- collaborative research
- excellent tutoring
- international contacts
- useful societal applications
For information consult names & addresses in the booklet and Eindwerk-on-line.
See you later!
Human parasites
Adaptation & selection of fish
Dynamics of sea fisheries
Human evolution
http://bio.kuleuven.be/eeb/lbeg
