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BSc and BaSc Projects

Below you will find the recent BSc and BaSc projects at Naturalis. Some of these are applicable both as BSc and MSc level. For more info contact the relevant researcher.

Projects


 

Environmental correlates of body shape in salamanders - Character evolution

Ichthyosuara alpestris

Ichthyosuara alpestris

Supervisor(s): Pim Arntzen

Contact: email: pim.arntzen@naturalis.nl

Period & duration: Negotiable

Study & Level: B.Sc. Biology

Background & context: Reference studies Colleoni et al. (2014), Arntzen et al. (submitted).

Objectives & goals: Salamanders come in a variety of shapes. Some are long and elongated while others are short and sturdy. This study aims to analyse body shape in salamanders of the family Salamandridae from an evolutionary perspective.

Methods: Description of material in the Naturalis collection. Measurements on salamander morphology, if possible supplemented with X-rays to determine the number of vertebrae in the body and in the tail. Evolutionary change in body shape is to be analysed in the framework of an available molecular phylogeny.

Requirements: None special 

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Leaf anatomy of Aporosa (Phyllanthaceae) and relatives or what are the small cavities on the upper leaf surface? -Systematic research

Staminate flowers

Supervisor: Peter van Welzen

Contact: tel.: 071 7517205, email: peter.vanwelzen@naturalis.nl. Nieuwenhuizenweg 19, room 2.03.

Period & duration: start preferably not during Biodiversity courses and after data basing of collections; duration c. 6 months. Please, discuss date of research well in advance.

Study & level: B.Sc.

Background & context: The genus Aporosa can be identified by the presence of small, round cavities in the leaf surface. The cavities are probably caused by the presence of mucilage cells in the epidermis, which are a bit sunken on the surface. Related genera are not checked for this character, perhaps they also have the mucilage cells, which then raises the question: why do they not show the cavities. A brief leaf anatomical study exists (A. Schot, 2004, Systematics of Aporosa (Euphorbiaceae). Blumea supplement 17: 44—47).

Objectives & goals: What is causing these cavities and are they typical for all Aporosa species and are they perhaps also present in related genera?

Methods: Anatomical slides (sampling dried leaves, rehydrating them, making sections, cuticle macerations and cleared leaf fragments, bleaching, colouring, mounting, labelling) will be made, studied and described. Photos (SEM, microscope) will be made.

Results: to be published in a high impact journal. Thus report in form of journal manuscript.

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Revision of Bischofia and Hymenocardia (Euphorbiaceae) - Systematic research

Supervisor: Peter van Welzen

Contact: tel.: 071 7517205, email: peter.vanwelzen@naturalis.nl. Nieuwenhuizenweg 19, room 2.03.

Period & duration: start preferably not during Biodiversity courses and after data basing of collections; duration 5-6 months. Please, discuss date of research well in advance.

Study & Level: B.Sc.

Background & context: Bischofia and Hymenocardia are Euphorbiaceae genera (spurges / wolfsmelkachtigen), each with a single species in the Malay Archipelago. Bischofia is one of the very few Euphorbiaceae with a compound leaf, while Hymenocardia has very typical flat, heart-shaped fruits. Both genera have to be revised for treatment in Flora Malesiana.

Objectives & goals: Which species of Bischofia and Hymenocardia occur in Malaysia and what is their variation.

Results: to be published in a journal, on the Euphorbiaceae website and finally in Flora Malesiana.

Requirements: Courses Biodiversity I+II.

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Revision of the Malaysian species of jatropha (Euphorbiaceae) -Systematic research

Jatropha gossypiifolia

Supervisor: Peter van Welzen

Contact: tel.: 071 7517205, email: peter.vanwelzen@naturalis.nl. Nieuwenhuizenweg 19, room 2.03.

Period & duration: start preferably not during Biodiversity courses and after data basing of collections; duration 5-6 months. Please, discuss date of research well in advance.

Study & level: B.Sc. 

Supervisor: Peter van Welzen

Contact: tel.: 071 7517205, email: peter.vanwelzen@naturalis.nl. Nieuwenhuizenweg 19, room 2.03.

Period & duration: start preferably not during Biodiversity courses and after data basing of collections; duration 5-6 months. Please, discuss date of research well in advance.

Study & level: B.Sc. 

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An identification key to the larvae of Dutch Cholevinae - Character evolution

Supervisor: Menno Schilthuizen

Contact: menno.schilthuizen@naturalis.nl

Period & duration: 5 months

Study & level: Biology, BSc level

Background & context: Cholevinae form a subfamily of beetles that often live on cadavers of mammals. For this reason, they may be relevant in forensic entomology. Although the adults are well-known, identification methods for the larvae are unavailable. This project aims to remedy this, by making use of the extensive collection of cholevine larvae at Naturalis.

Objectives & goals: To produce a photo gallery of all available Cholevinae larvae (all three instars), to produce a list of characters for identification and turn these into an identification key. To write and publish the results together with the supervisor.

Methods, tasks & approach: microscopy, chaetotaxy, photography, web-based taxonomy

Requirements: basic microscopy and entomology; ability to handle digital images and managing a website; able to read scientific German and French.

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Tropical Spider Communities: Biodiversity and Seasonality - Dynamic biodiversity

Supervisor: Jeremy Miller

Contact: jeremy.miller@naturalis.nl

Period & duration: February-June 2015

Study & level: Biology, entomology; MSc or exceptional BSc

Background & context: Seasonal dynamics of arthropod communities are evident in temperate regions, but have rarely been investigated in the tropics. The supervisor of this project has sampled the same two hectares of forest in Vietnam on two occasions separated by 18 months. The baseline (first inventory) samples have been sorted, photographed, DNA barcoded, and all data have been uploaded to online resources (see digitalSpiders.org). For this project, the same procedures will be applied to the second round of samples. This work will take place in an environment focused on biodiversity informatics, open data, and using online resources to build bridges between traditional taxonomy, ecology, and other stakeholders of biodiversity data.

Objectives & goals: The primary objective will be to quantify seasonal change in the tropical spider community. Other analyses will develop ideas about changes in diverse communities over space and time. New data will be contributed to the digitalSpiders.org web site and other online resources. A report will be prepared with the ultimate goal of publication in a peer reviewed scientific journal.

Methods & aims: All adult spider specimens will be sorted to morphospecies and databased. Each one-hectare plot will contain an estimated 700-1000 adult individuals. The web site digitalSpiders.org will be the primary taxonomic reference. Species new to the site will be photographed, DNA barcoded, and assigned a unique species code. Images will be uploaded to Morphbank. Subsamples will be sent to the Naturalis DNA barcoding facility, where they will be sequenced and uploaded to the Barcode of Life database. DNA barcode data will be used to crosscheck morphospecies assignments. The digitalSpiders.org website will be updated and linked to the new content. Inventory completeness will be evaluated using non-parametric extrapolation. Differences between baseline and subsequent inventories will be evaluated using modified beta diversity metrics among other techniques.

Requirements: Experience handling delicate arthropod specimens in alcohol using binocular microscope and forceps; aptitude with data integrity, organization and analysis using Microsoft Excel; interest in quantitative biodiversity analysis; interest in photography; flexibility to meet unexpected challenges; dedication and a willingness to work long hours; comfort working and writing in English. 

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When green leaves are not an option: Barcoding non-green plants -  Systematic Research

Supervisors: Vincent Merckx & Constantijn Mennes

Contact: vincent.merckx@naturalis.nl, constantijn.mennes@naturalis.nl

Period & duration: 2014-2015; 6 months

Study & level: Biology, MSc. or BSc.

Background & context: The establishment of the 2-locus combination of rbcL+matK as the standard barcode for land plants has made DNA barcoding an efficient species identification tool for plants. However, this barcode purely relies on chloroplast data and cannot be effectively used for non-green plants (mycoheterotrophs and holoparasites): these non-photosynthetic species of plants still contain chloroplast genomes, but high substitution rates and gene-losses make amplification of rbcL and matK genes difficult or even impossible. Thus, for about 890 species of flowering plants (c. 390 species of holoparasitic plants and c. 500 species of mycoheterotrophic plants) no universal barcode for species identification currently exists. Many mycoheterotrophs and holoparasites are rare and threatened species that are extremely difficult to identify when they are not flowering. A standard DNA barcode would be a desirable tool for their identification.

Objectives & goals: In this project we will to test the application of the nuclear internal transcribed spacer (nrITS) as a universal barcode for non-green plants. DNA Sequencing and analysis will be tested on a large collection of DNA material of non-green plants, including species of all lineages of mycoheterotrophic plants and a few lineages of holoparasitic plants. This will allow us to evaluate the power nrITS as a tool for plant identification and also test current species delimitation in groups of plants with complex morphologies.

Methods, tasks, and approach: This research project combines modern laboratory methods (PCR, sequencing) and analysis tools (phylogenetic analysis, species-delimitation tools) to develop a tool with broad application potential. The results will be of interest to a broad scientific audience, and may lead to a scientific publication.

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Out of South America? The biogeographic history of Triuridaceae - Dynamic biodiversity

Supervisors: Vincent Merckx & Constantijn Mennes

Contact: vincent.merckx@naturalis.nl, constantijn.mennes@naturalis.nl

Period & duration: 2014-2015; 6 months

Study & level: Biology, MSc. or BSc.

Background & context: Mycoheterotrophic plants obtain all of their carbon requirements through symbiotic associations with mycorrhizal fungi. As a result they are non-green and have very reduced vegetative habits. Many mycoheterotrophic plant species are rare and have very limited distribution ranges, but paradoxally some mycoheterotrophic genera and families are globally widely distributed. A prime example is the Triuridaceae, a family of mycoheterotrophic plants of c. 50 species in 11 genera. Species of Triuridaceae occur in the tropical rainforests of South America, Africa, and Australasia, but the majority of Triuridaceae genera are restricted to the neotropics suggesting that the family may have a South American origin. 

Objectives & goals: The evolutionary relationships of the Triuridaceae were inferred only recently by Mennes et al. (Mol. Phylogenet. Evol. 69: 994, 2013). This evolutionary hypothesis based on nuclear and mitochondrial DNA data now allows testing hypotheses about the biogeographic origin and diversification history of the family. The hypothesis that the early diversification events in the family are caused by the breakup of Gondwana is of particular interest.

Methods, tasks, and approach: In this project we will build a solid phylogeny of Triuridaceae by supplementing the dataset of Mennes et al. with data from additional species. This phylogeny will then be used to study the evolutionary history of the family in a temporal and geographic context.  This research project combines modern laboratory methods (PCR, sequencing) and analysis tools (phylogenetic analysis, ancestral area analyses).

Requirements: None.

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From grassland to tropical forest: Evolutionary trends in Burmanniaceae - Character evolution

Supervisors: Vincent Merckx & Constantijn Mennes

Contact: vincent.merckx@naturalis.nl, constantijn.mennes@naturalis.nl

Period & duration: 2014-2015; 6 months

Study & level: Biology, MSc. or BSc.

Background & context: Burmanniaceae is a family of monocots and comprises 96 species in eight genera. Species of Burmanniaceaeoccur in the tropics of the Old and the New World, and the distribution of some species extends into the subtropics. Interestingly, all species except for a few in the genus Burmannia, are non-green mycoheterotrophic plants. Mycoheterotrophic plants obtain all of their carbon requirements through symbiotic associations with fungi, and, while achlorophyllous, they are not directly parasitic on other plants. Previous evolutionary analyses have indicated that the mycoheterotrophic mode of life has evolved multiple times independently in the family. The evolutionary transition to mycoheterotrophy seems to coincide with a transition from grassland habitats to tropical forest habitats. 

Objectives & goals: In this project you will sequence multiple nuclear and mitochondrial DNA regions of several Burmanniaceaeindividuals, both autotrophs and mycoheterotrophs, from around the world. Using phylogenetic reconstruction methods you will infer a hypothesis of the evolutionary relationships in the family. The resulting phylogeny will provide information about the number of independent origins of the mycoheterotrophic mode of life in Burmanniaceae. In addition this evolutionary tree will be used to investigate the morphological evolution and diversification history of this intriguing family of plants.

Methods, tasks & approach: This research project combines modern laboratory methods (PCR, sequencing) with state-of the-art analysis tools (phylogenetic analysis, ancestral state reconstructions). The phylogenetic results will be used to interpret evolutionary trends in this intriguing group of plants.

Requirements: None.

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Unravelling genetic variation in arctic mosses and liverworts

SupervisorsDr. Michael Stech, Dr. Hans Kruijer (Naturalis Biodiversity Center)

Contact: Dr. Michael Stech, tel. 071-7517219, e-mail: michael.stech@naturalis.nl, Dr. Hans Kruijer, tel. 071-7517221, e-mail: hans.kruijer@naturalis.nl.

Period & duration: 3–6 months. Starting date is flexible. A field trip, if included, must take place in the arctic summer between June and August.

Study & level: This project is suitable for a master’s project but can also be conducted in a shorter version as a bachelor’s project. 

Background: Bryophytes are a significant component of the vegetation cover in arctic terrestrial environments, and well-known for their suitability as bioindicators. However, identification difficulties still hamper the proper use of many moss taxa in biodiversity assessments and biomonitoring. This is especially true for arctic environments, where the harsh conditions can cause extremely deviating morphologies.

Objectives: Providing clear species circumscriptions for applied uses of arctic mosses and liverworts and comparing the genetic and morphological variation of populations from the Arctic with those from non-Arctic regions. Target groups are species complexes from different groups of mosses or liverworts, which can be selected in consideration with the supervisors. The project will be part of the research focus BRYOARCT at Naturalis Biodiversity Center, partly embedded in international research collaboration.

Methods: Sequencing of non-coding DNA markers and molecular phylogenetic analyses. Morphological studies of herbarium specimens collected on Greenland and Spitsbergen by light and scanning electron microscopy. Taking part in a field trip to the High Arctic (e.g., Spitsbergen, Greenland) to collect plant material and to study mosses in their arctic environment is a possibility, depending upon the availability of funding, transport, and facilities in research stations.

Requirements: BSc degree in biology (in case of a bachelor’s project completion of the 1st and 2nd year of the biology programme). 

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Resolving the identity of little known and cryptic species in the Dutch bryophyte flora

Capsule of Schistidium crassipilum (Muurachter­lichtmos). Photo: www.verspreidingsatlas.nl

SupervisorsDr. Michael Stech, Dr. Hans Kruijer (Naturalis Biodiversity Center)

Contact: Dr. Michael Stech, tel. 071-7517219, e-mail: michael.stech@naturalis.nl; Dr. Hans Kruijer, tel. 071-7517221, e-mail: hans.kruijer@naturalis.nl.

Period & duration: 3–6 months. Starting date is flexible.

Study & level: This project is suitable for a master’s project but can also be conducted in a shorter version as a bachelor’s project. 

Background: The bryophyte flora of the Netherlands comprises ca. 600 species and may be considered one of the best known bryophyte floras of the world. However, since bryophyte species are often morphologically variable and difficult to identify,  uncertainties about exact species numbers and the identity of certain species remain. Currently Naturalis is generating DNA sequences of almost all Dutch bryophyte species, in the frame of its DNA barcoding programme and in collaboration with the Dutch Bryological and Lichenological Working Group (BLWG). DNA sequences improve the identification of many bryophyte species, but also reveal the remaining or even new problems of species circumscriptions.  

Objectives: Providing clear species circumscriptions of selected bryophytes where preliminary molecular data indicated the presence of ‘cryptic’ or yet incompletely known species in the Netherlands. Examples are Leptodictyum riparium (in Dutch: Beekmos), Orthotrichum spp. (Haarmuts), or Schistidium spp. (Achterlichtmos). Study taxa can be selected in consideration with the supervisors and BLWG members who are experts in the morphological identification of the respective taxa in the Netherlands and will collaborate in this project. The resulting data will contribute to updating identification keys, distribution maps etc. for a better knowledge and improved uses of the Dutch bryophyte flora in biodiversity assessments.

MethodsCollecting bryophyte specimens in the Netherlands. Sequencing of non-coding DNA markers. Molecular phylogenetic and species delimitation analyses. Morphological studies of the collected specimens by light and scanning electron microscopy.

Requirements: BSc degree in biology (in case of a bachelor’s project completion of the 1st and 2nd year of the biology programme). 

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The importance of mosses as diet for arctic herbivores

Lemming droppings in awinter nest (East Greenland).

SupervisorsDr. Michael Stech, Dr. Hans Kruijer (Naturalis Biodiversity Center)

Contact: Dr. Michael Stech, tel. 071-7517219, e-mail: michael.stech@naturalis.nl, Dr. Hans Kruijer, tel. 071-7517221, e-mail: hans.kruijer@naturalis.nl.

Period & duration: 3–6 months. Starting date is flexible. A field trip, if included, must take place in the arctic summer between June and August.

Study & level: This project is suitable for a master’s project but can also be conducted in a shorter version as a bachelor’s project.

Background: Mosses are generally not eaten by animals because of their low nutrition value. In the High Arctic, however, mosses may form an important part of herbivore diets, especially in spring time when food sources are still limited. However, little is known about which moss species are eaten by the different herbivores and in which amounts, and how this changes during the summer season when more nutrient-rich vascular plants are available.

Objectives: The aim of the project is to characterize the moss component of the diet of the following High Arctic herbivores: Muskox (Ovibos moschatus; Greenland), Svalbard reindeer (Rangifer tarandus platyrhynchus; Spitsbergen), Collared Lemming (Dicrostonyx groenlandicus; Greenland), and Barnacle Goose (Branta leucopsis; Greenland, Spitsbergen). The project will be part of the research focus BRYOARCT at Naturalis Biodiversity Center and is a follow up of a previous student project on Spitsbergen.

Methods: Morphological-anatomical analysis of moss remains in droppings collected on Spitsbergen and Greenland. DNA extraction of faecal material and sequencing of moss DNA from droppings following a DNA barcoding approach. Next generation sequencing of PCR products and data analysis. Taking part in a field trip to the High Arctic (e.g., Spitsbergen, Greenland) to collect droppings and to study mosses and vascular plants in their arctic environment is a possibility, depending upon the availability of funding, transport, and facilities in research stations.

Requirements: BSc degree in biology (in case of a bachelor’s project completion of the 1st and 2nd year of the biology programme).

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Archaeopteris of bear island (late devonian) - Dynamic biodiversity

Supervisor: Dr. Isabel van Waveren

Contact: Dr. Isabel Van Waveren , tel. 071- 7517261, e-mail: isabel.vanwaveren@naturalis.nl

Period & duration: 3 -6 month-2014-2015, in the Naturalis Building. Starting date is flexible.

Study & level: This project is suitable for a master’s project but can also be conducted in a shorter version as a bachelor’s project.

Introduction: Present and past mirror the same biotic and abiotic correlations. Present aridification and past land colonization by plants are inversed processes that reflect inversed climatic processes (Algeo, 1998, Le Hir et al., 2011).  The Devonian represents the earliest phase of land colonization and soil formation

Objective: The naturalis collection holds 5 species of the pro-gymnosperm Archeopteris. Lately research on this collection has demonstrated the occurrence of a new species (Pombo- Geertsema,  2013) some phenotypical variability not encountered anywhere else (Akkermans, 2013). While the Archaeopteris identifications in the collection have been provisional, the detailed first study of this material is needed and may yield new species within this genus and give an insight in biodiversity development in the Late Devonian.

Methods, tasks and approach: Describe and identify the 5 Archaeopteris species, make pictures, drawing, study and compare to other finds, sites and associations.  The earlier studies will be compiled to make a paper on these old Naturalis collections.

RequirementBotany course.

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Middle devonian of elberfeld (germany) - Dynamic biodiversity

Supervisor: Isabel Van Waveren with the help of  emeritus Prof. Dr. J.H.A. van Konijnenburg-van Cittert)

Contact: Dr. Isabel Van Waveren , tel. 071- 7517261, e-mail: isabel.vanwaveren@naturalis.nl

Period & duration: 3 month-6 month Starting date is flexible.

Study & level: This project is suitable for a master’s project but can also be conducted in a shorter version as a bachelor’s project.

Introduction: Present and past mirror the same biotic and abiotic correlations. Present aridification and past land colonization by plants are inversed processes that reflect inversed climatic processes (Algeo, 1998, Le Hir et al., 2011).  The Devonian represents the earliest phase of land colonization and soil formation Understanding the different steps that led to present ecosystems and the climate it induced will help in determining the requirements for a sustainable environment.

Objective: The naturalis collections holds Asteroxylon en Duisbergia als mogelijke wolfsklauwachtigen, Hyenia en Calamophyton als voorlopers van paardenstaarten, en Aneurophyton als vroegste pro-gymnosperm

Methods tasks & Approach: Describe and identify the 5 genera, make pictures, drawing, study and compare to other finds, sites and associations.

Requirement: Biology Botany course.

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Pollen and spores from the early permian of muse (burgundy, france) - Dynamic biodiversity

Supervisor: Isabel Van Waveren

Contact: Dr. Isabel Van Waveren , tel. 071- 7517261, e-mail: isabel.vanwaveren@naturalis.nl

Period & duration: 3 month-6 month Starting date is flexible.

Study & level: This project is suitable for a master’s project but can also be conducted in a shorter version as a bachelor’s project. 

Introduction: An Early Permian (Autunian) Lake has been sampled systematically every few centimeters in a similar way as would be done for a limnic core in a modern lake. These deposits, outcropping in the village of Muse in Burgundy, represent a fresh water lake positioned West of the Variscan mountains separating them from the Paleotethys.  At that time Burgondy, was positioned on the equator and wet tropical monsoons winds crossing the Variscan Mountains fed the Muse Lake and its tributaries.  The Permian is characterized by xerification and increasing patchiness of the vegetation, which results from the increasing colonization of the land through seed plants forming wood and soils. This moment in earth history needs to be fully understood as the reverse situation is presently taking place, and the Muse locality represents a unique data set to analyze climatic changes of local, extra local and global origin.

At first we would like to see if the rich pollen spectrum from the lake yields sufficient data to be able to differentiate between local peatification of the lake, extralocal signals with a Milankovitch signature or a global trend independent of the later. The pollen spectrum can also serve for relative age determination

Methods, tasks & approach: Fifty pollen and spore samples are ready for analysis. All samples will be looked through to analyze how many different types can be identified. The 25 most frequent types will be made pictures of and determined with relevant literature. Their ecology will be determined according to the ecogroups of Abbink et al.,(1998) and Remy and Remy (1974). A pollen diagram will be made using the frequency of each individual pollen species but also the ecogroups. Changes in composition will be analyzed in terms of stratigraphy and frequency.

RequirementsBotany or Geology Introduction.

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Ferns and  spores from the early permian of muse (burgundy, france) - Dynamic biodiversity

Supervisor: Isabel Van Waveren

Contact: Dr. Isabel Van Waveren , tel. 071- 7517261, e-mail: isabel.vanwaveren@naturalis.nl

Period & duration: 3 month-6 month Starting date is flexible.

Study & level: This project is suitable for a master’s project but can also be conducted in a shorter version as a bachelor’s project.

Introduction: The palaeobotanical collections at borrowed from the Natural Museum of Autun comprise a large collection of fossil plants associated with a rich pollen and spore spectrum. Plant fossils are oftre fertile tus offering the possibility to associate plant fossils to the pollen they produce.  This flora is Stephanian (latest Carboniferous) to early Permian in age, a period characterized in Europe by ongoing droughts and climatic warming. Stephanian floras differ considerably from those of the previous stage (Westphalian) in that the large peat-forming mires have disappeared and other plants succeeded the large Lycophytes and Sphenophytes that dominated the swamps.

Objective: To obtain an insight in the relation between plants and their pollen and spores and see if we observed signs of increasing drought, associated to a climatic signal.

MethodsAnalysis and taxonomical revision of the material from Muse borrowed  from the Natural History Museum in Autun. Comparison with other Stephanian (palyno)floras from adjacent areas in Europe. Dissecting  microscopy, cuticular analysis, study of in situ pollen and spores, palaeoecological reconstruction, may be part of the work.

RequirementBSc Botany or Geology, participation to field work during august 2014 or 2015 may be part of the requirements.

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Stangalpe flora from the latest carboniferous of Austria - Dynamic biodiversity

Supervisor: Isabel van Waveren,

Contact: Dr. Isabel Van Waveren , tel. tel. 071- 7517261, e-mail: isabel.vanwaveren@naturalis.nl with the support of emeritus Prof JHC konijnenburg@naturalis.nl

Period & duration: 3 month-6 month Starting date is flexible.

Study & level: This project is suitable for a master’s project but can also be conducted in a shorter version as a bachelor’s project. 

IntroductionThe palaeobotanical collections at Naturalis comprise a large collection of fossil plants from Stangalpe, Austria. This flora is Stephanian (latest Carboniferous) in age, a period characterized in Europe by ongoing droughts and climatic warming. Stephanian floras differ considerably from those of the previous stage (Westphalian) in that the large peat-forming mires have disappeared and other plants succeeded the large Lycophytes and Sphenophytes that dominated the swamps.

Objective:  To obtain an insight in the biodiversity and the palaeoecology during the Stephanian in this part of the world.

MethodsAnalysis and taxonomical revision of the material from Stangalpe present at Naturalis. Comparison with other Stephanian floras from adjacent areas in Europe. Dissecting  microscopy, cuticular analysis, study of in situ pollen and spores, palaeoecological reconstruction.

RequirementBSc Botany or Geology, participation to field work during august 2014 or 2015 may be part of the requirements. 

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Internal structure of the largest extant spiecies of foraminifera, showing the subdivision of the chambers (yellow) and the canaliculation (blue). Segmented image based on synchotron images.

Ultrastructure of Nummulitidae and/or Calcarinidae

Supervisors: Willem Renema & Laura Cotton

Contact: willem.renema@naturalis.nl

Period & duration: Flexible

Study & level: This project is suitable for a bachelor or master project

Background: Despite being unicellular organisms, foraminifera can grow large tests of up to 10 cm. Most of the large foraminifera live in symbiosis with microalgae, similar to zooxanthellate corals. They are are abundant in the fossil record, and are used to reconstruct paleoenvironments. They provide imprtant information about the settings in which reef evolution occurred. They also provide a valuable reference for macro-evolutionary processes in coral reefs. This large size can be achieved due to a number of adaptation to the test, resulting in numerous convergent adaptations. However, these convergent characters have traditionally been used for phylogeny and classification. Modern techniques allow for investigating independent characters, and potentially unravelling the phylogeny of these groups. Two taxa are particularly interesting, the Calcarinidae (or star sands), and the Nummulitidae. The first because of their association with phase shfts in coral reef ecosystems, the latter for their deep evolutionary history and importance for our understanding of macro-evolutionary processes.

Methods: The student will use high resolution computed tomography (microCT) to make a 3D model of the foraminifera. This technique is based on taking repeated X-ray images of a specimen at slightly different angles. From these images an image stack is produced. In the second step the student will label, segment and analyse these images using specialised software for 3D-image analysis. The resulting datasets will be used to test specific hypotheses about the taxa under investigation.

Requirements: Keen interest in paleontology, good insight into 3D geometric patterns, basic levels of computer skills.

These are some ideas about BSc/MSc projects in micropaleontology. These are just ideas, these can be developed further based on the interests and skills of the candidates.

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Temporal dynamics in coral reef ecosystems

Supervisor: Willem Renema

Contact: willem.renema@naturalis.nl

Period & duration: Flexible

Study & level: This project is suitable for a bachelor or master project

Background: Coral reefs are the most diverse marine ecosystems, but are severely affected by direct and indirect environmental changes. Increased frequency of disturbances has reduced the ability of these systems to recover. This has resulted in more and more reefs that underwent a transition to coral depauperate systems, especially in the Caribbean. We are finding a slightly different pattern, in which the reef moat of Indo Pacific reefs is severely affected by similar phase shifts, whereas the upper reef slope itself still is characterised by coral dominated benthic cover. 

However, it is becoming increasingly better understood that reefs are highly dynamic ecosystems, but also that ecosystem change is rooted further in history than previously thought.  The only way to understand these dynamics is by investigating time-series. Naturalis has a long history of investigating reefs systems in Indonesia, especially in Southwest Sulawesi and near Jakarta. In both areas we are building a time-series of both the biota on the reefs and the associated foraminifera assemblages. Furthermore, foraminifera leave a good fossil record, and by using sediment cores these time series can be extended into the past hundred years.

Methods: Samples for 2010 and 2012, and 2013 are available at Naturalis Biodiversity Center. The 2010 and 2012 samples have been analysed, but the 2013 samples not yet. The student will identify the foraminifera in  ~150 samples taken on 10 reefs in the Spermonde Archipelago (Southwest Sulawesi, Indonesia). These will form a direct comparison to the samples taken in the previous year, as well as other areas in the region. Depending on the available time, it is possible to associate fieldwork with this project. This would be in Sulawesi (Indonesia).

Requirements: Interest in coral reef ecosystem functioning and temporal dynamics, interest in paleontology, licensed Skuba diver if fieldwork is associated with this project. 

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Time series analyses of herbivory of selected host plants of the former Beekbergerwoud

Supervision:  Barbara Gravendeel, Camiel Doorenweerd and Eddy Weeda

Contact: barbara.gravendeel@naturalis.nl

Period & duration: minimum of 5 months

Study level: Biology (BSc or MSc); Applied Biology, LifeSciences, Microbiology (BaSc)

Language skills required: you should be capable of reading and interpreting Dutch

Background:

The last original forest of the Netherlands

The former Beekbergerwould was the last original wet forest of the Netherlands. It was destroyed in 1871 to be replaced by agricultural land. During its glory days, the Beekbergerwoud encompassed more than 1 km2 of swamp forest situated in the vicinity of Apeldoorn. Both the botanical (vascular plants, mosses and fungi) and zoological diversity (amphibians, birds, insects) of this former forest were exceptionally high. We know this from literature and from specimens preserved in the collection of Naturalis Biodiversity Center.

Time series analysis of herbivory

We recently discovered that specimens of selected tree and shrub species (Acer pseudoplatanus, Corylus avellana, Ilex aquifolium) collected in the former Beekbergerwoud were surprisingly free of herbivore damage. Leaves of these species in the Netherlands are nowadays frequently covered by galls of Aceria macrorhyncha and mines of Stigmella microtheriella and Phytomyza ilicis, respectively(see photographs above).

Objective: The student will first carry out a database survey to extract Dutch locality data of herbarium specimens made of the selected tree species mentioned above over the past 150 years, then revisit localities of specimens to collect herbivores for identification using DNA barcoding and compare current levels of herbivory (ratio of infected versus non infected leaves) and distribution of functional feeding groups (hole and margin feeding versus galling and mining) with historical data. Finally, a statistical analysis will be carried out to investigate a possible correlation between increase in mean summer month temperatures and herbivory levels over time. This research will help understanding how human induced climate change contributes to the diversity of an important functional group of insects and their associated host trees.

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