Master Biologie

Project description: Anthropogenic nitrogen deposition leads to eutrophication and soil acidification globally, which may change vegetation composition and cause biodiversity loss. This can in turn lead to decreased ecosystem functioning. A possible mitigation measure is the application of rock dust, a slow-release fertilizer that can partially restore lost minerals and enhance soil buffering capacity. One big uncertainty, however, is how ungulates respond to rock dust and how this in turn influences forest regeneration and development. Past experiments focusing on N, P, and/or K fertilization found increased browsing, which may hamper forest regeneration. So, will rock dust be a possible solution to improve forest quality or will we worsen regeneration problems in forest ecosystems? More information can be found on the project page

Possible student projects:

1. How do ungulates use the landscape and how does this influence the forest vegetation? Long-term dataset, exclosures, experiments Best time period: March-June and for vegetation mid-August to October*
2. How do different tree species respond to rock dust? Big full-factorial experiment on 8 tree species Measurements executed March-May and July-August
3. How does rock dust influence the utilization rate of ungulate herbivores? Multiple experiments, camera traps (e.g. Snapshot Hoge Veluwe), etc. Best time period: March-June
4. How does rock dust influence ungulate food preference? Feeding experiments Best time period: March-June
5. Other projects are possible, you can give your own input! Please email Sylvana if you are interested to see what is possible. Open to: Mainly MSc thesis projects, but there might be possibilities for MSc internship/ BSc thesis/ BSc internship.

*We are always looking for multiple students to help with the annual vegetation inventory from mid-August (3rd week) to the end of October. MSc theses using this data will start 1-2 months ahead with proposal writing.

Pre-requisite: knowledge about native flora and the ability to work with Heukels or other reliable flora guides.

Preferably: good general understanding about statistics and basic skills in R

Topic(s): Biodiversity and functional diversity/ Plant-animal interactions/ Population and forest dynamics/ Sustainable forest management/ Forest restoration and succession / Ecosystem services / Agroforestry/ Ecophysiology

Region(s): The Netherlands, forests on sandy soils at the Veluwe, mainly situated in De Hoge Veluwe National Park. Some projects also include other habitat types on sandy soils in Noord-Brabant and Gelderland. Climate(s): Temperate zone Corona proof: Yes

Used skills: Depending on the project: data analysis in R(Studio), possibly Canoco; field work; flora species inventory; working with camera traps; soil and/or leaf chemical analysis (lab work), basic lab work.

Offer to which study programs: BBN (=BSc Forest and Nature Conservation) MFN (=MSc Forest and Nature Conservation BBI (=BSc Bioloy) MBI (=MSc Biology) BPW (=BSc Plant Sciences) MPS (=MSc Plant Sciences)

Contact: Sylvana.harmsen@wur.nl

Severe droughts associated to El Niño Southern Oscillation (ENSO) events are known to have a devastating effect on tropical forest ecosystems in the Americas. High biodiversity is thought to produce more resilient forests. However, quantitative evidence for this assumption is almost nonexistent given the difficulty in gathering high quality, long-term information on the dynamics of forests before and after an ENSO severe drought occurs.

In this study you will take advantage of one of the longest high-temporal resolution datasets of forest dynamics available to date for tropical forests. The study site will be the region of Nizanda, Mexico. Here, the dynamics of old-growth forests have been followed for 18 years on an annual basis. The forest dynamics has been tracked in several plots, which differ in species diversity. You will assess the resilience of this tropical forest to the 2015 ENSO severe drought event and determine the role that species diversity plays on drought resilience.

During this project, you will bring to practice your knowledge about ecological theory and will develop statistical skills required to work with resilience metrics. You will also be working on a very novel and timely topic useful for climate change mitigation and for climate-smart forestry.

If topic is part of research project: found here

If you are interested, send a mail to: ellen.wilderink@wur.nl

and there is more:
Are you interested in Forest Ecology and Forest Management (FEM)? Well, there are some new MSc thesis/internship topics available to you! If you are interested in any of the questions listed below, simply click the link to get some more information about the subject and to get the contact info and the requirements needed.

* Effects of extreme drought on tree species – selecting species and provenances under climate change (MSc/BSc thesis, MSc internship)
* Which oak to choose? Provenance selection for resilient forests (MSc thesis, MSc internship)
* Drought resistance of chestnut growing in Dutch forests (MSc thesis, MSc internship)
* Drought resistance of maple growing under contrasting site conditions in the Netherlands (MSc thesis, MSc internship)
* High resolution tree growth responses to extreme drought events (MSc thesis, MSc internship)

New baby elephant: Our (WEC/BHE) MSc student spent the last months understanding the influence of public, enclosure design, and noise in the daily time budget and social dynamics of a group of elephants in Rotterdam Zoo. Soon, they will welcome a baby elephant. And there is an interest in understanding better the potential changes in social dynamics with this new group composition. The project is basic to repeat and complement the previous thesis using the previous data as a comparison point. – 1 MSc thesis - fieldwork (Zoo). MUST START IN APRIL!

For further information:
Filipe Cunha – Behavioural Ecology Group
filipe.cunha@wur.nl

Dikes are often very varied, relatively nutrient-poor habitats. They can be home to typical grassland vegetation types and can be great habitats for insects. Because of their primary function regarding water safety, dike vegetation is cut regularly, and a tight grass mat is traditionally preferred. Herbaceous species have different rooting structures, which could affect the erosion susceptibility of the dike, but could also affect water availability and thereby drought resistance. Furthermore, more diverse vegetation on dikes could increase flower availability for pollinators. This MSc project assesses the relationship between the management of clay dikes and species richness, flower abundance and erosion resistance of dike vegetation at the water board ‘Hollandsche Delta’, south of Rotterdam. In 2021 the mowing strategy will be adjusted, therefore this project is a great opportunity to study which factors influence the success. The start of the project is preferably in spring 2021 (March/April, before management starts).

We are looking for: Motivated MSc students with an interest in field work and vegetation analysis. Having a drivers licence is a pre. You will develop your own research questions based on your interests and skills.

Interested? Send your motivation to José van Paassen (jose.vanpaassen@wur.nl)

The Tapinoma nigerrimumcomplex is a group of four cryptic ant species, of which currently three are found to be invasive in the Netherlands. Originating in southern Europe, their invasion is thought to be fueled by human action: spreading via plant material (imported exotic plants or secondary infestations at sites of import).Due to its captivating Dutch common name (“Mediterraan draaigatje”) the attention of the media for these invasive ants has been relatively high, resulting in the discovery of at least 29 infestations afterthe first notice in 2016.

These infestations, occurring mostly in urban areas, can have serious consequences for the local flora and fauna (including humans). Colonies experience exponential growth thanks to their hyperpolygynic nature (having many thousands of reproducing queens) and can occupy areas of up to 35,000 m2, suppressing native ants, undermining sidewalks, and invading homes to look for food and shelter. In some cases, people have moved away or threaten to do so.Controlling these invasive antshas thus far been attempted with mixed results, in part by a lack of legally permitted methods.

This poses further risks, as unsanctioned biocide use and “do it yourself” solutions are liable to present larger dangers for the environment than the ants themselves.Activity of these ants is highest between March and September, though areas with problems indoors may experience nuisances all year long. During the active period, ample ants of all life stages are available for sampling outdoors. For several well-visited colonies, we have collection material available at The Dutch Pest & Wildlife Expertise Centre(Kennis-en Adviescentrum Dierplagen –KAD).

 

Aim: In this project, you will be determiningthe exact species of the ants in the Tapinoma nigerrimumcomplex collected throughout The Netherlands. This may provide valuable insight in its spread, possible elucidating the timing and source.Such insights into the biology of a pest can help to designsustainable pest management strategies.

 

Approach: Ants from the T.nigerrimumcomplex will be collected throughout The Netherlands, and in collaboration with Dr. Jitte Groothuisfrom the KAD in Wageningen. Collected samples will be stored at the Laboratory of Genetics after which DNA will be extracted.Using PCR and sequencing of mtDNA COImarkers, we will identify the species status of the sampled colonies andtry to determinethe relationship between them.

• Used skills:Molecular laboratory techniques:DNA extraction, PCR analysis, sequence analysis, data analysis.Field work:insect collecting
• Required skills:Basic knowledge of genetics, evolutionary and molecular biology. For example, obtained through (but not limited to): Molecular and Evolutionary Ecology (GEN20306).
• In addition, an interest in entomological and ecological fieldwork is required.
• Contact: Dr. Bart Pannebakker –Laboratory of Genetics –bart.pannebakker@wur.nl–0317-485330Dr. Jitte Groothuis –Kennis-en Adviescentrum Dierplagen-jgroothuis@kad.nl
• Additional information:Seifert, Bernhard & d’Eustacchio, Dario & Kaufmann, Bernard & Centorame, Massimiliano & Lorite, Pedro & Modica, Maria Vittoria. (2017). Four species within the supercolonial ants of the Tapinoma nigerrimumcomplex revealed by integrative taxonomy (Hymenoptera: Formicidae). Myrmecological News. 24. 123-144.

 

If you are interested in a doing aproject that combines field work with molecular techniques, and work on an invasivespecies that raises a lot of currentinterest,please get into touch.

Human disturbances affect the natural environment both acoustically and visually. Traffic noise and street lights are two of the most prominent environmental pollutants which affecting diurnal activity patterns of wildlife. Birds in urban surroundings have been reported to sing nocturnally and to have an earlier dawn chorus compared to their rural counterparts. This spring, we want to record singing activity of birds throughout the day in both a urban and rural environment. By comparing city birds with rural birds we will get a better view on the effect of urban disturbances on diurnal singing patterns. We are looking for two MSc students who want to conduct sound recordings using automatic sound recorders (March-May) and to analyse the data afterwards. You are encouraged to come up also with your own more specific research questions. Fieldwork can be conducted in the Wageningen area, although other cities are also possible. You need the flexibility to work outside the normal working hours and basic R skills would be desirable. For more information write to Dr. Pim van Hooft (pim.vanhooft@wur.nl), Wildlife Ecology and Conservation Group (WEC), or Prof. Marc Naguib (marc.naguib@wur.nl), Behavioural Ecology Group (BHE).

Welke ecologische kansen denk jij dat er liggen voor de haven van Rotterdam?

 

Wereldwijd staat de natuur sterk onder druk. Met name soorten die zich verplaatsen tussen verschillende ecosystemen worden hard geraakt. Havens bevinden zich op de overgangen tussen deze ecosystemen; de combinatie van zoet- en zoutwater en getijdenwerking zorgt voor een uniek estuarien ecosysteem. Daarmee vormt dit gebied een essentieel onderdeel van de delta (natuur). Echter, havens zijn niet ontworpen met oog voor natuur. De natuurlijke gradiënten ontbreken en er zijn voornamelijk harde overgangen tussen zoet- en zoutwater. Hierdoor blijven grote mogelijkheden voor een robuuster en gezonder ecosysteem onbenut. Daarnaast worden maatregelen ten behoeve van de natuur vaak gezien als kostenpost, terwijl ze juist positief kunnen bijdragen aan het functioneren van de haven. Met aandacht voor zowel deze havenfuncties als ecologische waarden kan een systeemanalyse uitkomst bieden, door kansen voor natuurontwikkeling te identificeren die de havenactiviteiten niet hinderen en zelfs kunnen verbeteren.

 

Witteveen+Bos heeft veel ervaringen met systeemanalyses van verschillende ecosystemen. Sinds een paar jaar is op dit vlak ook een gespecialiseerde mariene en estuariene ecologie groep actief. Daarnaast werken we als ingenieursbureau vaak aan havenontwerpen, -planontwikkeling en maritieme structuren. Hoog tijd om deze werkvelden te integreren in de (eco)systeem analyse havens!

Het doel van dit onderzoek is het ontwikkelen van een (eco)systeem analyse van het havengebied van de haven van Rotterdam. Vanuit (a)biotische gegevens ontwikkel je een model dat de kansen voor de natuur en de haven in kaart brengt. Hierbij maak je gebruik van beschikbare gegevens en kennis van het havenbedrijf en Witteveen+Bos. Deze kennis verwerk je in één model, waarmee een concreet advies kan worden geven voor maatregelen voor de natuur en havenactiviteiten.

 

Je gaat in eerste instantie aan de slag met de ontwikkeling van een conceptueel model van het havengebied. Dit toetst je bij het havenbedrijf en interne experts. De vervolgstap is om deze bevindingen te vertalen naar een kwantitatief model. Hiervoor breng je de (a)biotische processen en de ecologische toestand in beeld. Vervolgens kijk je hoe maatregelen ten behoeve van de natuur de ecologie kunnen versterken en wat de gevolgen zijn voor de haven.

 

Wat wij vragen

We vinden het belangrijk dat je een achtergrond in ecologie hebt en dat je beschikt over programmeerervaring. Wij zoeken iemand die:

• een master opleiding volgt op het vlak van watermanagement, (mariene) biologie, milieuwetenschappen, aquacultuur en visserij of een soortgelijke richting, en;
• kennis en ervaring heeft met GIS en modelleren (bij voorkeur Python, alternatief R, Matlab, of ervaring met high level programmeertaal zoals C++).

Copy the link for more info: Link here

When it comes to insects, developing into a male or female is rarely straightforward. In the insect order Hymenoptera, the overarching principle is that unfertilized eggs develop into haploid males, and fertilized eggs develop into diploid females. However, a variety of mechanisms can be involved in the sex determination pathways, one of which is called complementary sex determination (CSD). In this mechanism two different forms of the csd allele (i.e. heterozygosity) lead to diploid female development, while hemi- and homozygous individuals develop into haploid and diploid males respectively. Lowered genetic diversity and inbreeding in the population can quickly lead to an increase of diploid males and this can wreak havoc on breeding systems. With inbreeding experiments it has been hypothesized to be a sex determination system in many Hymenoptera.

Up until now, the csd gene has only been identified in the honeybee, Apis mellifera, as a duplicated gene of another sex determination gene, feminizer. Our recent work into the parasitoid wasp Bracon brevicornis attempted to identify the csd gene, and our initial results seem promising. We also found a paralog of B. brevicornis feminizer (Bbfem) and named it Bbfem1. Initially, the region was annotated to be a completely different gene product that looked like a fusion of two other genes, but closer inspection shows that the region in interest fulfils the checklist for similar regions related to sex determination. So perhaps similar paralogs/orthologs can be found in closely related species that are known to exhibit CSD?

In this project, which is able to be performed entirely remotely, you will work with existing sequence data from several related species to B. brevicornis, using bioinformatic tools to identify similar regions for further investigation. This project will be fairly independent and computer-based (assistance provided), and outcomes are strengthened by knowledge in bioinformatics, molecular biology, and data management. While aimed at being home-based work, there is a possibility for lab work if desired, as well as possibilities for in-person meetings. Candidate(s) will be based in both the Laboratory of Genetics and the Laboratory of Entomology (Wageningen University), and have access to the online tools necessary for the project. Further consultation with outside experts is probable, introducing candidates to a variety of contacts within Europe.

Used skills:
Experimental work: bioinformatics (strong preference), data management, problem solving
(Optional) Molecular laboratory techniques: DNA extraction, PCR analysis, sequence analysis (in silico and in vivo); data analysis.

Required skills:
Basic knowledge of ecology and molecular biology. For example, obtained through (but not limited to): Molecular and Evolutionary Ecology (GEN20306).

Contact:
Dr. Bart Pannebakker – Laboratory of Genetics – bart.pannebakker@wur.nl
Dr. Eveline Verhulst – Laboratory of Entomology – eveline.verhulst@wur.nl

Additional reading:
Gempe et al. 2009. Sex determination in honeybees: two separate mechanisms induce and maintain the female pathway. PLoS Biology 7, e1000222–e1000222. https://doi.org/10.1371/journal.pbio.1000222
Geuverink and Beukeboom, 2014 Phylogenetic Distribution and Evolutionary Dynamics of the Sex Determination Genes doublesex and transformer in Insects. Sex. Dev. 8: 38–49. https://doi.org/10.1159/000357056.
Ferguson et al. 2020. Bracon brevicornis genome showcases the potential of linked-read sequencing in identifying a putative complementary sex determiner gene. Genes 11(12), 1390. https://doi.org/10.3390/genes11121390.

Updated:
December 16th, 2020, Project available until February 28, 2021 (preferred start date as soon as possible)

Background information
Viral pathogens are widespread in natural insect populations, and can affect
the population dynamics of their host. Though viruses are known to affect host
dynamics, little is known about the evolution of viruses in these systems.
Cyclic population dynamics in Western tent caterpillars ( Malacosoma
californicum pluviale ) in British Columbia, Canada are driven by baculovirus
McplNPV, which infects tent caterpillar populations as they reach high density.
Tent caterpillar populations have been monitored since 1975, and baculovirus
infected larvae have been collected since the 1990s.
The collection of these archived baculovirus samples provides an opportunity
to determine how a baculovirus genome evolves and varies across natural
populations, and over time.

Project outline
Using an Illumina-based approach, we have deep sequenced 111 McplNPV
isolates and uncovered genetic variation both within and between isolates.
Using this dataset, we can determine:
1. Whether different virus genotypes are linked to different stages in the
host population cycle
2. Whether we can observe parallel trends in virus evolution for different
field sites
3. Whether there are signs of directional selection (i.e. adaptive evolution)
in the virus genome.
Within this project, hosted at the Microbial Ecology department at the
Netherlands Institute of Ecology (NIOO), we are looking for an MSc student
with experience with bioinformatics, and preferably a strong background in
(population) genetics and genomics. We offer an exciting thesis opportunity
for an existing, complete deep-sequencing dataset.

For further enquiries contact Dieke Boezen at D.Boezen@nioo.knaw.nl

ReViFES-project
The NWO TTW Project North Sea Reef Vitalization For Ecosystem Services ReViFES focuses on “paving the way for a novel “profitable nature based reefscape'' concept that enables
restoration of ecological valuable North Sea reefs, while simultaneously providing a scientific base for sustainable aquaculture and fisheries in its surroundings.

European flat oyster
The European flat oyster is selected as a key reef building species within the ReViFES Project. It was marked as a potential target species in a number of previous investigative studies triggered
by offshore wind developments. The project aims to contribute to the initiation of flat oyster reef development in the offshore environment, contribution to nature values and to facilitate
sustainable oyster harvesting in the future.

Thesis topic
To initiate oyster reef development in offshore wind farms, human induced outplacement of live
oysters is required, as the dispersion range of oyster larvae is to small to reach the wind farms
naturally. So called broodstock structures’ hosting adult oysters have already been designed by
TU Delft (MSc thesis Van Rie, 2020 and are installed at the scour protection in the innovation
wind farm Borssele V.
This MSc thesis topic focuses on engineering an outplacement mechanism for juvenile oysters
(spat) at the sandy seabed in between the wind turbines.
The outcome of the study is expected to make a significant contribution to oyster reef development at a large scale in the North Sea.

Contact
More information available at:
Prof.dr. ir. Mark van Koningsveld (M.vanKoningsveld@tudelft.nl)
Drs. Remment ter Hofstede (R.terHofstede@tudelft.nl)

Bats are strictly night active species, and suffer from light pollution. The main objective of this project is to study the light intensity dependent habitat loss and fragmentation. The 2021 field season will mostly focus on the barrier effect of infrastructure (bridges, culverts, underpasses) illumination on bats flying over water surface. To do that, a mobile lighting setup with light variation will be applied for light impact assessment. Bat behavior will be studied with acoustic tracking by using microphone arrays. We can estimate the 3D positions of bats and thus their trajectory by recording their echolocation signals. The differences in arrival time of the sound between several microphones are calculated by cross-correlation and then converted into 3D-positions.

 

What are we looking for?

We need two highly motivated and independent students to assist in our fieldwork (from May to August 2021) and to analyze the data afterwards. This topic is more suitable for long-term internships or Master’s thesis (6 months). Students are encouraged to come up with their own research question, but here are some possible lines of research:

• Are bats taking alternative routes if commuting corridors are experimentally lit?

• Do bats alter their flight behavior when approaching lit underpasses (i.e. flight speed, height, tortuosity,…)?

• Does the experimental lighting alter the insect density? Does it affect the foraging effort of bats along the flying routes? This study can be undertaken by placing sticky sheets trap and/or camera traps for insects and by analyzing acoustic data for feeding buzzes.

 

Requirements

• Driving license is essential, you might need to drive 1-2 hours per day to move between sites.

• Fieldwork requires flexibility to work outside the normal working hours (mostly at night).

• Proficiency in R or similar programming language would be desirable.

• Enthusiasm!

 

Duration

6 months – from April/May to September/October 2021 – of course we are mostly dependent on the summer season, but we can talk about different start and end dates

 

Contact

For more information write to dr. Maaike de Jong (maaike.dejong@wur.nl), Plant Ecology and Nature Conservation Group (PEN). Daily supervision by Claire Hermans, PhD candidate at the Netherlands Institute of Ecology (NIOO-KNAW).

 

This student subject is part of the ‘Light on Landscape’ project, which is the immediate continuation of the ‘Light on Nature ‘ project .

The European Association of Zoos and Aquaria (EAZA) has developed population management programmes (so-called EAZA Ex situ Programmes (EEPs)) for a wide variety of species, with the aim of maintenance of vital populations in captivity.

 

In Gibbons, there are at least three EEP populations that have a birth sex-ratio that is skewed towards males. Several attempts have been done to study this for the EEP but the reasons for this remain unclear.

It is difficult to formulate hypotheses because there are no clear evolutionary advantages to producing a male over a female in a particular circumstance, as far as can be assessed. This may be due to the lack of knowledge on the species in the wild. There are much fewer studies done in the wild on gibbons than on other apes. It is also unclear if the way gibbons are being kept could lead to any type of physiological response.

 

This study aims to perform the most comprehensive analysis possible by taking the following steps:

1. Independently formulate clear and detailed hypotheses, based on logic and rationale and on what is known about gibbon biology, physiology and behaviour.
2. Collecting all quality data available on ex situ populations of at least these three species and possibly more.
3. Run multivariable analyses, dissecting the different effects that may influence the birth sex-ratio and that may interact.

 

The results of this study may be used to inform the management of these Gibbon EEPs and SSPs. If this could lead to an increase in female births, this would have a several significant positive effects.

• It may benefit animal welfare. Not all males can currently be paired with a female and groups of males only seem to work (to some extent) for Siamang.
• It will increase demographic stability, which is of particular importance for the smaller populations.
• It may allow more genetic diversity to be maintained, benefitting the populations’ insurance role.
• It has logistic benefits, because it will be easier to house males.
• It may have educational benefits, because showing an exhibit as a pair is more natural.

Contact person: Henri Woelders, Mirte Bosse and Bart Ducro of ABGC

Availability: as from January 2021 

Arthropod-borne (arbo) viruses are transmitted by mosquitoes and ticks and can cause disease in humans. Recently, a new arbovirus was discovered in the Netherlands, transmitted by ticks. How this virus appeared in the Netherlands remains unknown and we still lack knowledge how biotic and abiotic factors influenced the spread of this virus.

 

In this project we will study 1) the role of endosymbionts and other pathogens in ticks on the transmission of arboviruses 2) how climate change can affect the spread of viruses transmitted by ticks and 3) which mice species are important in the transmission of arboviruses.

 

Possible projects:

• How do pathogens influence the transmission of viruses by ticks?

• Ticks are infected with a variety of pathogen such as Lyme disease. If these pathogens influence virus transmission is unknown. You will investigate the effect of these pathogens on the transmission of tick-borne viruses.

• How do abiotic factors influence the transmission and behaviour of ticks?

• Arthropod-borne viruses are on the rise due to the change in climate. How these climatic factors influence virus transmission by ticks remains unknown. You will study the effect of abiotic factors on the behaviour of ticks and the transmission of viruses by ticks.

• Which mice species are important in the transmission of arboviruses?

• The bank vole and the wood mouse are important species in the transmission and maintenance of tick-borne viruses. Whether there are differences between these mice species is unknown. We will study the role of different mice species in the Netherlands in the transmission of viruses to ticks.

 

Used skills: qPCR, cell culture, tick bio-assays, fieldwork (tick collection, rodent sampling), virusinfection, RNA/DNA isolation and cloning. If you are interested you can send an email to: julian.bakker@wur.nl.

Aphids are serious pests in greenhouse vegetable crops. It has recently been found that some aphids carry endosymbionts that can make them resistant to parasitoid wasps. To optimize parasitoid wasp biocontrol and make biological control a better alternative to pesticides, we are studying the effects of endosymbionts on the effectiveness of aphid biocontrol in Dutch greenhouses.

 

We are looking for BSc and MSc students who can do their internship/thesis during 2019 or 2020. Projects can involve field work such as greenhouse sampling and sampling aphids outside, molecular work (DNA extraction, PCR, barcoding, sequencing) on aphids and endosymbionts, and laboratory cage studies on aphid performance or parasitoid wasp virulence. If you are interested, don’t hesitate to contact me at Helena.Donner@wur.nl.

 

Land-use dynamics and ecosystem services in an agro-forest frontier in Mexico

Credits: 36

Examiner: Prof. Dr. F.J.J.M (Frans) Bongers

Supervisors: Madelon Lohbeck, Lucas Carvalho Gomes, Mathieu Decuyper

Contact: Madelon.lohbeck@wur.nl

Begin date: 2019/01/01

End date: 2021/01/01

Requirements: Fem-30306 Forest Ecology and Forest Management; REG-31806 Ecological Methods 1

Used Skills: GIS, programming

This Msc thesis is part of the FOREFRONT program which focuses on agro-forest frontier areas. Agro-forest frontiers are the particularly dynamic borders between forested and agricultural land. The program aims is to link the landscape-transforming strategies of the various actors with landscape changes and resulting ecosystem services. 

In this Msc project you will focus on the La Sepultura region in Mexico, this is a highly dynamic agro-forest frontier area where smallholder farmers depend on agriculture, timber and NTFPs and live adjacent to the La Sepultura biosphere reserve. Demand for agricultural produce and conservation interests are sometimes conflicting although synergistic landuses have also been developed. You will combine different sources of satellite imagery over time (landsat, google earth) with field data on land uses and ecosystem services to respond to the following question:

How has land use changed in the past decades and what are the consequences for balancing agriculture and conservation in the La Sepultura region in Chiapas, Mexico?

 

Methods: classifying land uses in different timesteps using Google Earth Engine, R, ArcGIS/ QGIS (this is designed as a desktop study although if there is keen interest it could be combined with fieldwork). (Spatial) statistics on trends over time in landuses and ecosystem services and evaluating trade-offs and synergies. Possibility of field visits for validation.

 

 

FOREFRONT research programme:

https://www.wur.nl/en/Value-Creation-Cooperation/FOREFRONT-Program.htm

Location:            Netherlands (WUR)

Period:                Between 3 and 7 months, starting any time

Supervision:      Sjouke A. Kingma

 

Bird species differ a lot from each other in appearance and behaviour. What determines this variation? Why do some birds live in groups and others not? Why are some brightly coloured and others not? Why are eggs so different?

 

Comparative studies, based on published data, are a powerful way to help answering these questions. As part of an ongoing project, you will explore how evolution shaped the enormous variety in patterns and behaviours. This project is especially suitable for a student who wants to go deep into macro- evolutionary patterans. We have some exciting plans, but specifically also welcome your ideas!

 

More information? Just contact: sjouke.kingma@wur.nl

 

The social savanna project: a bird study in Swaziland

Location:            Mbuluzi Game Reserve in Swaziland (southern Africa) (www.mbuluzi.com)

Period:                Between 4 and 7 months, starting in June/July or August-October

 

Supervision:      Kat Bebbington & Sjouke A. Kingma (Sjouke.kingma@wur.nl)

Several MSc research projects are available in our ‘Social savanna’ research project. We study the behaviour and physiology of a range of different bird species (speckled mousebirds, arrow-marked babblers, white-crested helmet-shrikes, dark-capped bulbuls and oxpeckers). The projects include 2.5 to 3 months fieldwork (e.g. nest monitoring, observations and catching individuals) in the stunning Mbuluzi Game Reserve, a typical African savanna habitat with amazing wildlife (but no dangerous large animals). The project start date would preferably be either in June/July (when we mainly catch individuals) or in August-October (the start of the breeding season).

 

Specifically, we are currently considering the following questions:

-          Do mousebirds benefit physiologically from group living?

-          How do mousebirds resolve conflict over which group members get to reproduce?

-          How do ‘helpers-at-the-nest benefit reproduction? (possible in all species)

-          Does cooperation reduce parasite infection and lead to a better immune system? (all species)

-          Do helpers in babblers prevent parasitism by cuckoos?

-          Host-preference by oxpeckers: do they prefer certain host species or certain individuals, and why?

-          Begging behaviour in bulbuls: how do siblings compete for food and what is the effect?

 

As you see, plenty of opportunities, and we also welcome own ideas in the field of avian cooperation, competition and other topics. Please just come visit us to have a chat, we can tell you more about the projects, and we can see if there is anything that would suit your interest!

More information? Just contact: sjouke.kingma@wur.nl

Do you love plants and insects? Do ecological interactions fascinate you? Would you like to work with different species of insects that interact with each other by feeding on the same host plant? And are you interested in finding mechanisms that could underlie such interactions?

 

If the answers to the questions above are a firm “Hell yeah!”, then maybe doing a thesis in this project is something for you! We’re studying the effects of leaf feeding herbivores (caterpillars and aphids) on the roots of cabbage plants, and how that affects root feeding herbivores. We focus on greenhouse studies supported by molecular work to unravel the mechanisms behind these interactions, in order to gain new insights in ecology and plant defence in the roots. Since the project is quite broad, students can opt to focus more on the molecular work, or more on greenhouse studies.

 

If you’re interested, please contact Peter Karssemeijer (peter.karssemeijer@wur.nl) for more information.

Master Thesis

33-36 credits

Supervisors: Tessa Visser MSc, and Dr. Sander Koenraadt

Contact: tessa.visser@wur.nl

 

Requirements: at least one of the following courses, ENT-30806, ENT-51306, ENT-30306, ENT-54306

 

Mosquitoes play a key role in the disease transmission of diseases such as dengue, chikungunya and the recently emerged Zika virus. To prevent mosquito-borne disease it is important to gain more knowledge about the behaviour of these pesky biters.

We are looking for an inventive MSc student to help design a new behavioural assay for capturing Aedes aegypti. This mosquito species is vector of all diseases mentioned above. Aedes aegypti is especially dangerous because it’s preference for human blood. This research will contribute to a PhD project in which the final design will be used in a Biosafety level 3 facility to work with real Zika infected mosquitoes. But first we need to design the assay and gain important baseline information. You will work in a team with enthusiastic entomologists!

 

 

Learning outcome: performing behaviour studies, statistical analyses, mosquito rearing, design of experiments

As a Wageningen Biologist (graduated 2005), it is my pleasure to send out this invitation to BVW for internship applications! I am leading the Biodiversity Genomics Team at Guangxi University, hosted at the Plant Ecophysiology and Evolution Group (College of Forestry).

 

Within the Team we conduct research on some of the largest families of tropical trees which are complex clusters of young, closely related species with often poorly defined morphologies. Our goal is to quantify and assess patterns of genomic diversity, to unravel evolutionary relationships, reconstruct historical biogeography, speciation patterns and describe trends in assembly of the tropical forest biome. To this end, we apply the latest NextGen sequencing techniques, bioinformatics and technological advances (e.g. DoveTail, Nanopore). We don’t concern us with PCR-based single marker approaches but focus explicitly on collecting and sequencing on a large scale, targeting organellar genomes and specific whole genomes in key lineages. Our research involves extensive molecular laboratory work, computer analyses and bioinformatics, and periodical fieldwork in protected areas, botanical gardens and the permanent forest plot system of Guangxi University.

The Team has a growing herbarium collection of tropical tree specimens (BGT herbarium) which is under active construction (data basing/digitizing). A taxonomic angle to your internship is certainly possible, in combination with a molecular/genomic component.

 

During your internship, you will be exposed to all the aspects of the work we do, from fieldwork to the lab to learning how to write scripts and analyze data using genomic software. For us as a Team, our goal is to get you to leave at the end of your internship with one submitted article. So far, all Team members have succeeded in publishing in their first year, and given the amount of data available, this is a feasible target!

In principle, multiple positions are available, for periods of 3-6 months. Exact topics can be discussed via email. Housing is available through Guangxi University on our large Nanning City campus. Unfortunately, travel funding to cover your flight is not available. I recommend approaching funding bodies like the Wageningen University Fund, to apply for a travel grant. I was fortunate to obtain this when studying in Wageningen for a Philippines-based MSc.

 

Nanning is a large city (~5 million) and the new subway makes getting around easy. It is nicknamed “the Green City” and has a subtropical climate, with warm-hot summers and mild winters. The new international airport gets you to almost every regional Asian capital. By road, you can get to Hanoi or the coast in about 3-4 hours. Hong Kong is about 2 hours by plane.

 

Guangxi University is based on a very large and green campus, with about 20,000 students. Almost everyone lives on the campus and everything you need for daily life is available on site or near one of the campus gates (restaurants, fast food and coffee). Life in Nanning is not expensive – a meal at one of the 15! canteens on campus will set you back 1-3 euro.

 

The Team currently consists of 4 postdocs, 2 MSc and one PhD student. The College of Forestry is unique in Guangxi University for the cluster of foreign professors leading research teams staring in 2014. Since then, six teams have emerged with different backgrounds, and now we have a stable population of 35-40 (Chinese and foreign) faculty, postdocs, PhD and MSc students. In my team I have people from France, Spain, the US, Serbia, Ecuador, India and China. Other groups have members of Sri Lanka, Indonesia, Colombia, Madagascar, Malaysia and Cyprus, making our community highly diverse and dynamic. Daily language within the teams is English.

 

A picture impression of life on campus and some facilities is available here: http://www.plant-ecophysiology-evolution.com/contact-us/

If you’d like to learn more about coming to China and joining the Team for your internship, please send an email to jsstrijk@hotmail.com , and let’s see what we can do! We look forward to hearing from you.

 

Joeri Sergej Strijk

Associate Professor

Biodiversity Genomics Team

 

Guangxi University, Nanning, China 

 

Population viability of an endangered tree species in tropical China

Parashorea chinensis is a red-listed, endangered tropical forest tree, occurring in Southern China (Yunnan province) and Northern Vietnam. To assist in the conservation of this emergent tree species (which reaches up to 80 m in height), it would be helpful to know the viability of remaining populations. One of these remaining populations is located in Xishuangbanna region, Yunnan. In this area, a research institute (Xishuangbanna Tropical Botanical Garden) of the Chinese Academy of Science has established a 20-ha plot (400 × 500 m). The forest is dominated by Parashorea chinensis and all trees of 1 cm and bigger in diameter at breast height (dbh) in the 20-ha plot were tagged and measured. Repeated measurements have been conducted to estimate rates of growth, surival and recruitment. In this project you will answer the following questions: (1) what are estimated ages for this endangered species? (2) is the population in the 20-ha plot projected to increase or decrease over the coming decades? (3) what are the most important stages and vital rates in for the population? You will perform some field work to evaluate tree reproduction, spend time at the Xishuangbanna Tropical Botanical Garden institute and perform matrix modelling analyses at Wageningen University. For more information, see http://tip.wur.nl/Project.php?ProjectID=3774 

Relevant research questions:

o Does multiple paternity occur in placental fish species? And in other live-bearing fish species?

o Is multiple paternity facilitated by superfetation (i.e. multiple broods in different developmental stages)?

o How do environmental pressures (e.g. water visibility, predator regime) influence polyandry in placental fish?

 

For more info see: http://www.wur.nl/en/article/Student-projects-Molecular-Ecology-Live-bearing-fish.htm

Artificial light at night constitutes a serious threat to nocturnal insect populations, with aversive effects on biorhythms, navigation and perception. With the global increase of sky brightness, light pollution might add to the rapid insect decline currently observed. Once nocturnal insects are attracted towards street lamps, around 30% of them die, with rates varying for habitats and lamp systems. A quantitative comparison of insect deaths caused by street lamps of different colour could provide directions for nocturnal insect-friendly lighting systems for the future.

This field study will take place within the framework of the Light on Nature and Light on Landscape project. 4m high lampposts with one of three different light colours (white, green, red) and a control (dark) are placed in grids of 5 lamps per colour over 100m. 3x3 m tarps are placed underneath the light post that is on the edge between forest and grassland. One tarp is placed for each light colour (+ dark control) after sunset (~21:00), resulting in 4 tarps per site. The next day, all tarps will be collected in the morning (after 12 hours), weighed and conserved in ethanol for later identification. The collected insects will be identified to order or genus level in a joint effort taking place either in Konstanz, Germany, or Wageningen, the Netherlands.

The dead weight of nocturnal insects will provide us with an estimate for abundance for each light colour. The order and/or genus information will give insight in insect diversity, which gives valuable insights in spectral sensitivity and susceptibility towards specific lights and provides a guideline towards more insect-friendly night lights.

 

Project should start around April / May 2020 the latest. Funds are available to do part of the project at the University of Konstanz. For more info contact: maaike.dejong@wur.nl

EN. below.

 

Bij het onderzoeksbedrijf waar ik werk (MITOX) zoeken we een stagiaire of thesis-student (MSc) die het (lokale) migratiegedrag van bodemfauna wil bestuderen. Denk hierbij aan de bewegingspatronen van springstaarten, wormen en/of kevers, het ontvluchten van verdroging of juist extreme natheid en hoe snel ze dat kunnen doen. Het is een zeer actueel onderzoeksonderwerp waarbij de resultaten bijvoorbeeld gebruikt kunnen gaan worden om de effecten van pesticiden en het ploegen van akkers te minimalizeren om een gezonde bodemfauna te houden.

 

Wat kan je verwachten:

Samenwerking in een zeer gespecialiseerd internationaal vooruitstrevend team waar je je eigen inbreng kan geven maar ook ondersteuning krijg van ervaren mensen. Met mooie resultaten zullen we je begeleiden met het publiceren van het onderzoek in een vooraanstaande journal.

 

Wat verwachten we van jou:

Creativiteit, enige flexibiliteit en gedrevenheid om in dit zeer slecht onderzochte onderzoeksgebied nieuwe dingen te ontdekken!

 

Geïntresseerd? Stuur een mail naar koenverhoogt@eurofins-mitox.com

 

EN

With our research company (MITOX), a research topic has become available where we want an intern or a MSc thesis student to study the (local) migration patterns of terrestrial fauna such as springtails (Collembola), earthworms and/or beetles. Possible study subjects are the travel patterns of the fauna to escape dry or flooded areas, or how they move in search of food. The results of this study can, for example, be used minimize the effects of the use of pesticides or the ploughing of the field in agricultural fields.

 

What can you expect from us:

You come to work in a very specialised and international team which is leading in these kinds of studies. Your own input is greatly appreciated and you get the liberty to work freely, but also get a lot of support and guidance when needed. If the study results in nice and interesting data we will guide you to publish it in an internationally highly respected journal.

 

What do we expect from you:

Creativity, some flexibility and passion to get some insights in this poorly studies research subject.

 

If you are interested send me an email to koenverhoogt@eurofins-mitox.com

Bats are strictly night active species, and suffer from light pollution. The main objective of this project is to study the light intensity dependent habitat loss and fragmentation. The 2020 field season will mostly focus on the barrier effect of infrastructure (bridges, culverts, underpasses) illumination on bats flying over water surface. To do that, a mobile lighting setup with light variation will be applied for light impact assessment. Bat behavior will be studied with acoustic tracking by using microphone arrays. We can estimate the 3D positions of bats and thus their trajectory by recording their echolocation signals. The differences in arrival time of the sound between several microphones are calculated by cross-correlation and then converted into 3D-positions.

 

We are looking for two highly motivated and independent students to assist in our fieldwork (from June to August 2020) and to analyze the data afterwards. Students are encouraged to come up with their own research question, but there are some possible lines of research:

Are bats taking alternative routes if commuting corridors are experimentally lit?

Do bats alter their flight behavior when approaching lit underpasses (i.e. flight speed, height, tortuosity)? This study can be carried out with the combination of acoustic tracking data and analysis of video footages under the bridges.

Does the experimental lighting alter the insect density? Does it affect the foraging effort of bats along the flying routes? This study can be undertaken by placing sticky sheet traps for insects and by analyzing acoustic data for feeding buzzes.

Requirements:

Driving license is essential, you might need to drive 1-2 hours per day to move between sites.

Fieldwork requires flexibility to work outside the normal working hours (mostly at night).

Proficiency in R or similar programming language, or the willingness to learn R, is highly desirable.

Enthusiasm!

Interested? Contact Maaike de Jong at maaike.dejong@wur.nl.

MFN, MBI or comparable programs; at least 36 ECTS; from April/May to September/October 2020.

Songbirds seem to change their behaviour and timing when nestboxes are exposed to artificial light at night. Compared to white or red light, green light has a much friendlier ring to it. It's used in many places to mitigate 'light pollution'. But does this actually work? Birds have excellent eyesight, and their brains respond strongly to light. That makes them perfect test subjects for a project that studies the gradual disappearance of 'real' darkness from our living environment. Focusing mostly on great tits, blue tits and pied flycatchers, we are interested in whether exposure to artificial light of any colour - be it white, red or green - causes disruption to the birds' timing. In terms of daily timing, e.g. when to become active in the morning, and in terms of seasonal timing, e.g. when to start laying eggs. Even more importantly, do potential effects on behaviour result in effects on fitness? Do reproduction and survival, and ultimately population numbers change? Within the long term, experimental ‘Light on Nature’ set-up (www.lichtopnatuur.org), managed by the Netherlands Institute of Ecology (NIOO-KNAW), we are now looking for motivated and enthusiastic master students to perform their own research project within the above mentioned themes. Good to know: Having a driving license is essential (or team up with a student that has one), field sites are across the Veluwe and in Drenthe. Fieldwork requires flexibility in time, also outside the normal working hours (i.e. during weekends). Interested? Contact Maaike de Jong at maaike.dejong@wur.nl. Thesis or internship within MFN, MBI or comparable programs; starting date and duration open but should include April, May, June 2020.