Teaching staff and internships Master Biological Sciences, Track Ecology and Evolution

Patrick Meirmans, Joost Duivenvoorden IBED, Universiteit van Amsterdam, [email protected] August 2014 Teaching staff and internships UvA master Biological Sciences: track Ecology and Evolution

Guidelines for students:

1. Match your research interests with those of each staff member listed below 2. Evaluate the internship options*, recent internships and Selected publications of matched staff 3. Make an appointment with those staff members that do research of your interest

*NB Remember that all staff members have many more internship options than you will find in this overview, for example outside the university

Research interest by general theme:

Evolution and Biodiversity: Acarology; Amphibians; Arthropods ; Arthropod-symbiont interactions; Chemical communication; Chemoecology; Community ecology; Crustaceans; Demography; Diversity patterns; Ecological speciation; Evolutionary Biology; Evolutionary convergence; Evolutionary ecology; Evolutionary genetics; Fishes; Flatworms: Systematics, Biogeography, Phylogeny, Taxonomy, Evolution; Insect-plant interactions; Molecular ecology; Nature conservation and management; Phenotypic plasticity; Plant conservation biology; Plant evolution; Polyploidy; Population biology; Quantitative genetics; Reproductive biology; Reptile conservation; Reptile ecology and population genetics; Sensory Physiology; Sexual selection; Mate choice; Sympatric speciation; Vegetation ecology; Wildlife monitoring

Community dynamics: Adaptive dynamics; Behavioural ecology; Biological Control; Chemical Ecology; Community ecology; Ecological Acarology; Evolution of altruism; Evolution of specialisation; Evolutionary Ecology of Tritrophic Systems involving Mites and Insects on Plants; Ecogenomics; Evolutionary Epidemiology; Food web interactions; Herbivore adaptation; Induced plant defense; Mathematical modeling; Molecular Ecology; Multitrophic interactions; Plant- herbivore interactions; Plant-Predator Mutualisms; Population dynamics; Spatial Models in Ecology and Evolution; Theoretical biology; Virus Dynamics

Geo-Ecology (Landscape ecology): Alpine Geomorphology; Application of Geographical Information Systems and Remote Sensing in Geo-Ecology; Biodegradation of xenobiotic compounds; Bird migration; Foraging ecology; Chemistry of emerging water contaminants; Climate reconstructions; Confronting models with observations; Drugs of abuse; Environmental chemistry; eScience infrastructure for ecological research; Fate of natural and anthropogenic compounds in terrestrial ecosystems; Hazard zonation; Human impact; Hydrology; Influence of atmospheric dynamics on bird movement; Land-sea-ice correlations; LiDAR; Long continental records; Marine palynology; Meteorology; Molecular dynamics of soil organic matter; Non-Pollen Palynomorphs (a.o. fungal and algal spores as paleo-environmental indicators); Nutrient availability; Ornithology; Paleoclimatology; Paleoecology; palaeolimnology; Perfluorinated alkylated substances; Persistent and polar organics; Plant-soil interactions; Pleistocene neotropical biogeography; Quantitative palaeoecology; Restoration ecology; Soil chemistry; Soil science; Solar forcing of climate change; Sorption and bioavailability of organic compounds; Statistics for the natural sciences; subfossil chironomids; Animal tracking technology; Tropical ecology and biodiversity

2 Evolution and Biodiversity

3 Hans (J.A.J.) Breeuwer

IBED, University of Amsterdam.  [email protected].  http://home.medewerker.uva.nl/j.a.j.breeuwer

Research interest: Arthropod-symbiont interactions; Molecular ecology; Evolutionarygenetics; acarology

Titles of recent internships as superviser/examinator

Host race formation in the two-spotted spidermite: Hybrid incompatibility and genetic population structure. Host specificity and fitness effects of intestinal bacteria of thrips (Frankliniella occidentalis). On the phylogeny and phylogeography of Tetillidae in Indonesia. Fingerprinting the Bili apes. Sequencing and DNA methylation of the delta-11-desaturase gene of common ‘high’ and uncommon ‘low’ Heliothis virescens.

Selected publications

Peijnenburg, T.C.A., Fauvelot, C., Breeuwer, J.A.J. and Menken, S.B.J. (2006). Spatial and temporal genetic structure of the planktonic Sagitta setosa (Chaetognatha) in European seas as revealed by mitochondrial and nuclear DNA markers. Molecular Ecology 15 (11): 3319-3338. Ros, VID; Breeuwer, JAJ; Menken, SBJ (2008). Origins of asexuality in Bryobia mites (Acari : Tetranychidae). BMC Evolutionary Biology, 8: Art. No. 153. Ros, VID; Breeuwer, JAJ (2009). The effects of, and interactions between, Cardinium and Wolbachia in the doubly infected spider mite Bryobia sarothamni. Heredity, 102 (4): 413-422. Ros, VID; Fleming, VM; Feil, EJ; Breeuwer JAJ. (2009). How diverse is the genus Wolbachia? multiple-gene sequencing reveals a putatively new Wolbachia supergroup recovered from spider mites (Acari: Tetranychidae). Applied and Environmental Microbiology, 75 (4): 1036-1043. Xavier, JR; Rachello-Dolmen, PG; Parra-Velandia, F; Breeuwer JAJ. (2010). Molecular evidence of cryptic speciation in the "cosmopolitan" excavating sponge Cliona celata (Porifera, Clionaidae). Molecular Phylogenetics and Evolution, 56 (1): 13-20.

4 Edo Goverse

RAVON Monitoring Network.  [email protected].  http://www.ravon.nl/Monitoring/tabid/62/Default.aspx.

Research interests: amphibians, reptiles, fishes, monitoring, nature conservation, nature management

Internship options

Students with interests in doing internships concerning amphibians or fishes not listed on our website can visit me (Sciencepark C4.169) to determine a suitable internship. Also contact: [email protected], tel. 024-7410600

Titles of recent internships as superviser/examinator

Natterjacks in the port of Amsterdam - status, distribution and ecology in 2010. The development of the moor frog Rana arvalis in the national amphibian monitoring program in the Netherlands 1997 - 2007.

Selected publications

Goverse, E., 2009. Hyla arborea (Tree Frog). Blowfly parasitism. Herpetological Review 40(1): 71. Hilterman, M.L. & E. Goverse, 2007. Nesting and nest success of the leatherback turtle (Dermochelys coriacea) in Suriname, 1999-2005. Chelonian Conservation and Biology 6(1): 87-100. Spikmans, F. W. Bosman, A. Spitzen, E. Goverse, M. de Zeeuw & T. van der Meij, 2012. Vuursalamanderdrama: soort op rand van uitsterven in Nederland. RAVON 46(3): 50-56. Van der Meij, T., A. van Strien, G. Smit & E. Goverse, 2009. Trendberekening bij het Meetnet Amfibieën. RAVON 31 10(4): 57-62.

5 Astrid Groot

IBED, University of Amsterdam.  [email protected].  www.science.uva.nl/ibed-eb

Research interests: Evolutionary ecology; Chemical ecology; Molecular ecology; Sexual selection; Mate choice; Sympatric speciation

Internship options

Depending on the currently running projects, there are possibilities for behavioral (observational) studies, usually with chemical (gas chromatographic) analysis and/or molecular projects.

Titles of recent internships as superviser/examinator

The recent host expansion of the diamondback moth, Plutella xylostella and its effect on the female pheromone production – male sensitivity system Sequencing and DNA methylation of the delta-11-desaturase gene of common ‘high’ and uncommon ‘low’ Heliothis virescens Effects of larval food on female sex pheromone of the generalist feeder Heliothis virescens Mating preferences and development of two pheromone types of the moth Heliothis virescens

Selected publications

Hagström AK, Liénard MA, Groot AT, Hedenström E, Löfstedt C. 2012. Semi–selective fatty acyl reductases from four heliothine moths influence the specific pheromone composition. PLoS One 7(5), e37230. Groot AT, Classen A, Inglis O, Blanco CA, Lopez J Jr, Teran Vargas A, Schal C, Heckel DG, Schoefl G. 2011. Genetic differentiation across North America in the generalist moth Heliothis virescens and the specialist H. subflexa. Mol. Ecol. 20: 2676-2692. Henniges-Janssen K, Reineke A, Heckel DG, Groot AT. 2011. Complex inheritance of larval adaptation in Plutella xylostella to a novel host plant. Heredity 107: 421-432. Schöfl G, Dill A, Heckel DG, Groot AT. 2011. Allochronic separation vs. mate-choice: nonrandom patterns of mating between fall armyworm host-strains. Am. Nat., 177(4), 470-485 Gould F, Estock M, Hillier NK, Powell B, Groot AT, Ward CM, Emerson JL, Schal C, Vickers NJ. 2010. Sexual isolation of male moths explained by a single pheromone response QTL containing four receptor genes. PNAS, 107, 8660-8665. Groot AT, Claßen A, Staudacher H, Schal C, Heckel DG. 2010. Phenotypic plasticity in sexual communication signal of a noctuid moth. J. Evol. Biol., 23, 2731-2738. Groot AT, Marr M, Heckel DG, Schöfl G. 2010. The roles and interactions of reproductive isolation mechanisms in fall armyworm (Lepidoptera: Noctuidae) host strains. Ecol. Entomol., 35, 105-118. Lassance JM, Groot AT, Liénard MA, Binu A, Borgwardt C, Andersson F, Hedenström E, Heckel DG, Löfstedt C. 2010. Allelic variation in a fatty-acyl reductase gene causes divergence in moth sex pheromones. Nature, 466, 486-489.

6 Cees Hof

Netherlands Biodiversity Information Facility (NLBIF). [email protected].  www.uva.nl/profiel/c.h.j.hof.

Research interests: Biodiversity databases; digitization of biodiversity data, facilitate free and open access to biodiversity data.

Internship options

Millions and millions of our planet's living plant, animal, and microbiological species have been observed, listed and collected. Throughout the last couple of centuries information has been captured in museum collections, herbaria, expedition reports and living collections and cultures. Digitization and mobilization of this information is now crucial. As the world's biodiversity is dramatically changing due to man-induced climate alterations and the increasing pressure on the use of land, water and air, we need fast and easy access to all data available in order to analyze and understand the changes in temporal and spatial biodiversity patterns and the underlying processes. Biodiversity data are our assets. My scientific and sociatal mission is to facilitate free and open access to biodiversity data by means of standardised ICT facilities. Students with interests in doing internships concerning the use of digitalized biodiversity data can visit me (Sciencepark C4.169) to determine a suitable internship.

Selected publications

Hof, C.H.J., 2008. The virtues of digitised biodiversity data in a global information infrastructure. EAZA-news, 64: 28. Cunningham, J.A., C.H.J. Hof and S.J.Braddy, 2008.Lenisquilla Californiensis, a new species of Stomatopod Crustacean. Journal of Paleontology, 82(2): 431-435. Los, W., and C.H.J. Hof, 2007.The European Network for Biodiversity Information. In, Biodiversity Databases: Technique, Politics, and Applications (G.B. Curry and C. Humphries, eds.), Taylor & Francis, pp. 5-12. Schram, F.R., C.H.J. Hof, R.H. Mapesand P. Snowden, 2003. Paleozoic cumaceans (Crustacea, Malacostraca, Peracarida) from North America. Contributions to Zoology, 72: 1-16. Schram, F.R., and C.H.J. Hof, 1998. Fossils and the Interrelationships of Major Crustacean Groups. In, Arthropod Fossils and Phylogeny (G.D. Edgecombe, ed.), Columbia Univ. Press, New York, pp. 233-302. Hof, C.H.J., 1998. Fossil Stomatopods (Crustacea: Malacostraca) and their phylogenetic impact. Journal of Natural History, 32: 1567-1576. Hof, C.H.J., 1998. Late Cretaceous stomatopods (Crustacea, Malacostraca) from Israel and Jordan. Contributions to Zoology, 67: 257-266.

7 Ingo Janssen

RAVON, division Herpetology.  [email protected].  www.ravon.nl.

Research interests: Reptile conservation; Reptile ecology; Reptile (population) genetics; Nature management; Wildlife monitoring;

Internship options

See http://www.ravon.nl/RAVON/Stages/tabid/89/Default.aspx. Students with interests in doing internships concerning reptiles not listed on our website can visit me (Sciencepark C4.169) to determine a suitable internship.

Titles of recent internships as superviser/examinator

The origin of Natrix natrix in the Netherlands: Phylogenetic and phylogeographic analyses Multiple paternity in the grass snake Natrix natrix Population structure of Natrix natrix around Amsterdam

Selected publications

Janssen, I.A.W., 2009. Ringslang, Natrix natrix. In: H.J.M. van Buggenum et al. (red.), Herpetofauna van Limburg. Verspreiding en ecologie van amfibieën en reptielen in de periode 1980-2008. Stichting Natuurpublicaties Limburg, Maastricht: 332-343 Janssen, I., 2008. Verbreitung und Bestandssituation der Ringelnatter (Natrix natrix) in den Niederlande. In: Blanke, I., A. Borgula & T. Brandt (Hrsg) Verbreitung, Ökologie und Schutz der Ringelnatter (Natrix natrix Linnaeus, 1758). Mertensiella nr. 17, Supplement zu Salamandra: 31-37 Janssen, I. & W. Völkl, 2008. Gibt es räumlich und zeitlich getrennte Teilhabitate der Ringelnatter (Natrix natrix linnaeus, 1758)? In: Blanke, I., A. Borgula & T. Brandt (Hrsg) Verbreitung, Ökologie und Schutz der Ringelnatter (Natrix natrix Linnaeus, 1758). Mertensiella nr. 17, Supplement zu Salamandra: 162-172 Strien, A.J. van, A. Zuiderwijk, B. Daemen, I. Janssen, M. Straver, 2007. Adder en levendbarende hagedis hebben last van versnippering en verdroging. De Levende Natuur nummer 208(2007)2, pag. 44-48

8 Daniel Kissling

IBED, University of Amsterdam.  [email protected]  http://www.danielkissling.de

Research interests: macroecology & biogeography, spatial modelling, species interactions, global change.

Titles of recent internships as superviser/examinator

Selected publications

Kissling, W.D., Dalby, L., Fløjgaard, C., Lenoir, J., Sandel., B., Sandom, C., Trøjelsgaard, K. & Svenning, J.-C. (2014): Establishing macroecological trait datasets: digitalisation, extrapolation and validation of diet preferences in terrestrial mammals worldwide. Ecology and Evolution 4: 2913–2930. Barnagaud, J.-Y., Kissling, W.D., Sandel, B., Eiserhardt, W.L., Sekercioglu, C.H., Enquist, B.J., Tsirogiannis, C. & Svenning, J.-C. (2014): Ecological traits influence the phylogenetic structure of bird species co-occurrences worldwide. Ecology Letters 17: 811–820. Kissling, W.D. & Schleuning, M. (2014): Multispecies interactions across trophic levels at macroscales: retrospective and future directions. Ecography in press. Kissling, W.D., Pattemore, D.E. & Hagen, M. (2014): Challenges and prospects in the telemetry of insects. Biological Reviews Early View. Kissling, W.D., Dormann, C.F., Groeneveld, J., Hickler, T., Kühn, I., McInerny, G.J., Montoya, J.M., Römermann, C., Schiffers, K., Schurr, F.M., Singer, A., Svenning, J.-C., Zimmermann, N.E. & O’Hara, R.B. (2012): Towards novel approaches to modelling biotic interactions in multispecies assemblages at large spatial extents. Journal of Biogeography 39: 2163– 2178.

9 Patrick Meirmans

IBED, University of Amsterdam.  [email protected].  http://www.patrickmeirmans.com.

Research interests: Population genetics, plant mating systems, hybridization, polyploidy, statistics, plant evolution.

Internship options

Hybridization at several spatial scales: do white and red campions hybridize across the Netherlands, despite having different pollinators? Genetic divergence between two ecotypes of sow thistle: from salty dry dunes to moist nutrient- rich roadsides Determing the limits of population genetics analyses: using simulations to see how well statistical analyses of genetic data work when their assumptions are violated.

Titles of recent internships as superviser/examinator

The genetic variation in Parnassia palustris in The Netherlands. The effects of autopolyploidy on the measurement of population structure. On edge effects and the urban green spaces of London. Monitoring and explaining the steady increase of the sand lizard in the Netherlands. The effect of metals and altitude on the genetic population structure of the Aster Werneria nubigena in the Peruvian Andes

Selected publications

Ellstrand N.C., Meirmans P.G., Rong J. et al. (2013), Introgression of crop alleles into wild or weedy populations. Annual Review of Ecology Evolution and Systematics. 44 p. 325-345. Rong J., Xu, S., Meirmans P.G. & Vrieling K. (2013), Dissimilarity of contemporary and historical gene flow in a wild carrot (Daucus carota) metapopulation under contrasting levels of human disturbance: implications for risk assessment and management of transgene introgression. Annals of Botany. 112 p. 1361-1370. Meirmans P.G. & Van Tienderen P.H. (2013), The effects of inheritance in tetraploids on genetic diversity and population divergence. Heredity. 110 p. 131-137. Meirmans P.G. (2012), AMOVA-based clustering of population genetic data. Journal of Heredity. 103 p. 744-750. Meirmans P.G. (2012), The trouble with isolation by distance. Molecular Ecology. 21 p. 2839-2846. Meirmans S., P.G. Meirmans & L.R. Kirkendall (2012), The costs of sex: Facing real-world complexities. Quarterly Review Of Biology. 87 p. 19-40. Hengstum, T., S. Lachmuth, J.G.B. Oostermeijer, J.C.M. Den Nijs, P.G. Meirmans & P.H. Tienderen. (2012), Human-induced hybridization among congeneric endemic plants on Tenerife, Canary Islands. Plant Systematics and Evolution. 298 p. 1119-1131.

10 Steph (S.B.J.) Menken

IBED, University of Amsterdam.  [email protected].  http://www.science.uva.nl/ibed-eb.

Research interests: Insect-plant interactions; Chemical communication; Ecological speciation; Diversity patterns

Titles of recent internships as superviser/examinator

Adaptive Radiation and Ecomorphology in Salamanders and Lizards The role of polyploidizaion in the adaptive evolution of Saccharomyces cerevisiae Are marine lakes laboratories or conservatories of evolution? Population divergence of Brachidontes (Bivalvia, Mytilidae) and Nerita (Gastropoda, Neritidae) from Indonesia Subterranean aquatic planarians of Maryland, U.S.A: new records and new species Do males of Yponomeuta cagnagellus (Lepidoptera: Yponomeutidae) have sex pheromones?

Selected publications

Cleary, D.F.R., C. Fauvelot, M.J. Genner, S.B.J. Menken & A.O. Mooers. Parallel responses of species and genetic diversity to ENSO-induced environmental destruction. Ecology Letters 9: 301-307 (2006). Peijnenburg, K.T.C.A., C. Fauvelot, J.A.J. Breeuwer & S.B.J. Menken. Spatial and temporal structure of the planktonic Sagitta setosa (Chaetognatha) in European seas as revealed by mitochondrial and nuclear DNA markers. Molecular Ecology 15: 3319-3338 (2006). Ros, V.I.D., J.A.J. Breeuwer and S.B.J. Menken. The origin of asexuality in Bryobia mites (Acari: Tetranychidae). BMC Evolutionary Biology 8 # 153 (2008). Menken, S.B.J., J.J. Boomsma & E. van Nieukerken. Large-scale evolutionary patterns of host plant associations in the Lepidoptera. Evolution 64: 1098-1119 (2010). Turner, H., N. Lieshout, W. van Ginkel & S.B.J. Menken. Molecular phylogeny of the small ermine moth genus Yponomeuta (Lepidoptera, Yponomeutidae). PLoS ONE vol. 5(3) (2010).

11 Gerard (J.G.B.) Oostermeijer

IBED, University of Amsterdam.  [email protected]. http://home.medewerker.uva.nl/j.g.b.oostermeijer.

Research interests: Plant conservation biology; Population biology; Demography; Vegetation ecology; Community ecology; Reproductive biology

Titles of recent internships as superviser/examinator

The Effect of Environmental Change on the Demography of the Grassland Perennial Succisa pratensis Effects of invasive plants on the invertebrate community on surrounding species Metapopulation dynamics and landscape genetics of a coastal dune slack species

Selected publications

Volis, S., G. Bohrer, J.G.B. Oostermeijer, and P.H. van Tienderen. 2005. Regional consequences of local population demography and genetics in relation to habitat management in Gentiana pneumonanthe. Conserv Biol 19:357-367. Hooftman, D.A.P., J.G.B. Oostermeijer, M.M.J. Jacobs, and J.C.M. den Nijs. 2005. Demographic vital rates determine the performance advantage of crop-wild hybrids in lettuce. J Appl Ecol 42:1086-1095. Cascante-Marin, A., J.H.D. Wolf, J.G.B. Oostermeijer, J.C.M. den Nijs, O. Sanahuja, and A. Duran- Apuy. 2006. Epiphytic bromeliad communities in secondary and mature forest in a tropical premontane area. Basic Appl Ecol 7:520-532. Hooftman, D.A.P., J.G.B. Oostermeijer, E. Marquard, and J.C.M. den Nijs. 2008. Modelling the consequences of crop-wild relative gene flow: a sensitivity analysis of the effects of outcrossing rates and hybrid vigour breakdown in Lactuca. J Appl Ecol 45:1094-1103. Stift, M., R. Bregman, J.G.B. Oostermeijer, and P.H. van Tienderen. 2010. Other tetraploid species and conspecific diploids as sources of genetic variation for an autotetraploid. Am J Bot 97:1858–1866. ;

12 Katja Peijnenburg

Naturalis / IBED, University of Amsterdam.  [email protected].  www.science.uva.nl/ibed-eb.

Research interests: Marine biology, phylogeography, evolution, zooplankton, molecular evolution.

Titles of recent internships as superviser/examinator

Are marine lakes laboratories or conservatories of evolution? Population divergence of Brachidontes (Bivalvia, Mytilidae) and Nerita (Gastropoda, Neritidae) from Indonesia.

Selected publications

K.T.C.A. Peijnenburg & E. Goetze (2013). High evolutionary potential of marine zooplankton. Ecology and Evolution, 3(8), 2765-2781. 10.1002/ece3.644 T. Swierts, K. Peijnenburg, C. de Leeuw, D.F.R. Cleary, C. Hörnlein, E. Setiawan, G. Wörheide, D. Erpenbeck & N.J. de Voogd (2013). Lock, Stock and two different barrels: comparing the genetic composition of morphotypes of the Indo-Pacific sponge Xestospongia testudinaria. PLoS One, 8(9), e74396. 10.1371/journal.pone.0074396 L.E. Becking, D. Erpenbeck, K. Peijnenburg & N.J. de Voogd (2013). Phylogeography of the sponge Suberites diversicolor in Indonesia: insights into the evolution of marine lake populations. PLoS One, 8(10), e75996. 10.1371/journal.pone.0075996 P.C. Luttikhuizen, J. Drent, K.T. Peijnenburg, H.W. van der Veer & K. Johannesson (2012). Genetic architecture in a marine hybrid zone: comparing outlier detection and genomic clines analysis in the bivalve Macoma balthica. Molecular Ecology, 21(12), 3048-3061. 10.1111/j. 1365-294X.2012.05586.x S. Mariani, K.T.C.A. Peijnenburg & D. Weetman (2012). Independence of neutral and adaptive divergence in a low dispersal marine mollusc. Marine Ecology - Progress Series, 446, 173-187. 10.3354/meps09507

13 Peter Roessingh

IBED, University of Amsterdam.  [email protected].  www.science.uva.nl/ibed-eb.

Research interests: Chemoecology; Sensory Physiology; Evolutionary Biology

Titles of recent internships as superviser/examinator

The recent host expansion of the diamondback moth, Plutella xylostella and its effect on the female pheromone production – male sensitivity system Differential expression of Gustatory Receptors in Bombyx mori The effects of an arbuscular mycorrhiza on Plantago lanceolata plant defense and generalist caterpillar performance The Role of Male Pheromone in the Mating Behaviour of Phytophagous Moths Do males of Yponomeuta cagnagellus (Lepidoptera: Yponomeutidae) have sex pheromones?

Selected publications

Hora, K. H., P. Roessingh, et al. (2005). Inheritance and plasticity of adult host acceptance in Yponomeuta species: implications for host shifts in specialist herbivores. Entomologia Experimentalis Et Applicata 115(1): 271-281. Roessingh, P., S. Xu, et al. (2007). Olfactory receptors on the maxillary palps of small ermine moth larvae: evolutionary history of benzaldehyde sensitivity. Journal of Comparative Physiology A-Neuroethology Sensory Neural and Behavioral Physiology 193(6): 635-647. Bakker, A. C., P. Roessingh, et al. (2008). Sympatric speciation in Yponomeuta: no evidence for host plant fidelity. Entomologia Experimentalis Et Applicata 128(1): 240-247. Bakker, A. C., W. E. van Ginkel, et al. (2008). Differences in mating strategies in two closely related small ermine moth species (Lepidoptera : Yponomeutidae). European Journal of Entomology 105(2): 219-226.

14 Peter (P.H.) van Tienderen

IBED, University of Amsterdam.  [email protected].  http://home.medewerker.uva.nl/p.h.vantienderen.

Research interests: Plant evolution; Polyploidy; Quantitative genetics; Phenotypic plasticity

Titles of recent internships as superviser/examinator

Genes underlying the genetic diversity of Aethionema arabicum (Brassicaceae)

Selected publications

Volis, S., Bohrer, G, Oostermeijer, G. & Van Tienderen, P.H. (2005) Regional consequences of local population demography and genetics in relation to habitat management in Gentiana pneumonanthe. Conservation Biology 19: 357-367. Luttikhuizen, P.C., Stift, M., Kuperus, P. & Van Tienderen, P.H. (2007) Genetic diversity in diploid vs. tetraploid Rorippa amphibia (Brassicaceae). Molecular Ecology 16: 3544-3553. Van Asch, M., Tienderen, P.H. Holleman, L.J.M. & Visser, M.E. (2007) Predicting adaptation of phenology in response to climate change, an insect herbivore example. Global Change Biology 13: 1596-1604. Stift ,M., Berenos, C., Kuperus, P. & Van Tienderen, P.H. (2008) Segregation models for disomic, tetrasomic and intermediate inheritance in tetraploids: A general procedure applied to Rorippa (Yellow cress) microsatellite data. Genetics 179: 2113-2123. Stift M., Luttikhuizen, P.C., Visser E.J.W. & Van Tienderen, P.H. (2008) Different flooding responses in Rorippa amphibia and Rorippa sylvestris, and their modes of expression in F-1 hybrids. New Phytologist 180: 229-239.

15 Ronald Vonk

Naturalis Biodiversity Center  [email protected]; [email protected];  http://science.naturalis.nl/research/people/cv/vonk

Research interests: arthropods; crustaceans; evolution; evolutionary convergence

Internship options

Subterranean life; an exercise in modesty: One of the processes shaping and determining subterranean biodiversity is the well-known evolutionary mechanism of convergence. Crustaceans are a large group of arthropods that have successfully invaded the underground habitat of caves, sand interstices and ocean floor sediments. Some groups have colonised terrestrial and marine groundwater environments and show a remarkable versatility in adapting to subterranean conditions. Here, life becomes slower and reductive forces cause functions and connected organs to disappear. As a result, genera with species that are morphologically quite similar can be found in this milieu, spread out over large distances and different continents. We will collect pioneer species that must have invaded the underground of the brackish/freshwater lake recently. Two paths can be chosen: 1) identifying species, setting up quantitative sampling methods, and describing a groundwater species community. Or 2) an in-depth description of interstitial crustaceans with an open eye for convergent structures.

Titles of recent internships as superviser/examinator

The effects of 4 kHz octave-band noise and pile-driving playback sound on the hearing and behaviour of the harbour seal (Phoca vitulina) Duration of primary moult in birds Biogeography and Conservation of Catfish in the Guianas (Pisces, Siluriformes, Callichthyidae)

Selected publications

Brehier F, Vonk R, Jaume D. 2010. First South American phreatogammarid, with comments on the arrangement of coxal and sternal gills, and on the biramous condition of the seventh pereiopod in amphipods. Journal of Crustacean Biology, 30(3): 503-520 Irham M. Schram FR, Vonk R. 2010. A new species of Pygocephalomorpha (Eumalacostraca, Peracarida) from the Leitchfield Formation, Lower Carboniferous (Mississippian) of Grayson County, Kentucky, U.S.A. In: Studies on Malacostraca: Lipke Bijdeley Holthuis Memorial Volume. Eds: Charles Fransen, Sammy de Grave and Peter Ng. Crustaceana Monographs, 14: 343 - 355. Vonk R, Jaume D. 2010. Glyptogidiella omanica gen. et sp. nov., an inland groundwater bogidiellid from Oman with enlarged coxal plate V (Crustacea, Amphipoda). Zootaxa 2657: 55–65. Vonk R, Hoeksema BW, Jaume D. 2011. A new marine interstitial Psammogammarus (Crustacea, Amphipoda, Melitidae) from Gura Ici Island, off western Halmahera (North Moluccas, Indonesia), and an overview of the genus, ZooKeys 128: 53–73 (2011) Jaume D, Vonk R. 2012 Discovery of Metacrangonyx in inland groundwaters of Oman (Amphipoda: Gammaridea: Metacrangonyctidae). Zootaxa 3335: 54–68 (2012)

16 Community dynamics

17 Maarten (M.C.) Boerlijst

IBED, University of Amsterdam.  [email protected].  http://home.medewerker.uva.nl/m.c.boerlijst

Research interests: Evolutionary Epidemiology; Spatial Models in Ecology and Evolution; Virus Dynamics

Titles of recent internships as superviser/examinator

Collapse without warning: The ambiguity of early warning signals in stage-structured population models

Selected publications

Bogaards JA, van Ballegooijen WM, Weverling GJ, Boerlijst, MC & J Goudsmit (2005) Is population-level perversity a likely outcome of mass vaccination against HIV? Lancet Infectious Diseases 5(5), 254. van Opijnen T, Boerlijst MC, Berkhout B (2006) Effects of random mutations in the human immunodeficiency virus type 1 transcriptional promoter on viral fitness in different host cell environments, Journal of Virology 80(13), 6678-6685. van Opijnen, T., de Ronde, A., Boerlijst M.C., B. Berkhout (2007) “Adaptation of HIV-1 Depends on the Host-Cell Environment”, PloS One 2, e271. Bezemer D, de Wolf F, Boerlijst MC, et al. (2008) A resurgent HIV-1 epidemic among men who have sex with men in the era of potent antiretroviral therapy, AIDS 22(9) , 1071-1077. Boerlijst MC, van Ballegooijen WM (2010) Spatial Pattern Switching Enables Cyclic Evolution in Spatial Epidemics, PloS Computational Biology 6(12), e1001030.

18 Hal Caswell

IBED, University of Amsterdam.  [email protected].  http://www.uva.nl/profiel/h.caswell.

Research interests: Mathematical ecology and demography; matrix population models; stochastic population dynamics; sensitivity analysis; applications to conservation biology and evolutionary demography; plants, animals, humans.. ! ! Internship options

Putting density and environment effects into life table analysis, by linking individual life cycles and population dynamics. Quantifying individual variance in longevity; the effects of heterogeneity and stochasticity. Population genetics in stage-structured populations (This one may not be ready yet) Markov chain models for human diseases and their animal analogues.

Titles of recent internships that I supervised

Variance in lifetime reproduction: theoretical developments and applications to plants, animals, and humans.

Selected publications

Jenouvrier, S., M. Holland, J. Stroeve, M. Serreze, C. Barbraud, H. Weimerskirch, and H. Caswell. 2014. Climate change and continent-wide declines of the emperor penguin. Nature Climate Change. DOI:10.1038/NCLIMATE2280. Caswell, H. and R. Salguero-Gomez. 2013. Age, stage, and senescence in plants. Journal of Ecology 101:585-595. Shyu, E., E. Pardini, T. Knight, and H. Caswell. 2013. A seasonal, density-dependent model for the management of an invasive weed. Ecological Applications 23:1893-1905. Caswell, H. and E. Shyu. 2012. Sensitivity analysis of periodic matrix population models. Theoretical Population Biology. 82:329-339. Caswell, H. 2011. Beyond R0: Demographic calculation of variability in lifetime reproductive output. PLoS ONE 6(6): e20809. Caswell, H. Stage, age, and individual stochasticity in demography. 2009. The Per Brinck Oikos Award Lecture 2008. Oikos 118:1763-1782. Caswell, H. Perturbation analysis of nonlinear matrix population models. 2008. Demographic Research 18:59-116. Caswell, H. 2001. Matrix Population Models: Construction, Analysis, and Interpretation. Second edition. Sinauer Associates, Sunderland MA. 722pp.

19 Martijn (C.J.M.) Egas

IBED, University of Amsterdam.  [email protected].  http://home.medewerker.uva.nl/c.j.m.egas.

Research interests: Plant-herbivore interactions; Adaptive dynamics; Evolution of altruism; Evolution of specialisation

Titles of recent internships as superviser/examinator

Germination, Priming, Preference, Poop: The effect of herbivory and herbivore odours on germination and priming of Brassica oleracea and Brassica nigra. The effects of environmental noise on the population dynamics of selectively harvested populations A study of personality in a migratory shorebird, the Red Knot (Calidris canutus islandica) Spring migration strategy and reproductive success in Svalbard Barnacle geese Branta leucopsis Habitat selection and density dependence of Brent Geese Branta b. bernicla breeding on an arctic island Habitat requirements for the settlement of bearded vultures during the post fledging dispersal

Selected publications

Rueffler C., Egas M. & Metz J.A.J. (2006). Evolutionary predictions should be based on individual- level traits. American Naturalist 168: E148-E162. Egas M. & Riedl A. (2008). The economics of altruistic punishment and the maintenance of cooperation. Proceedings of the Royal Society London B Biological Sciences 275: 871-878. Magalhaes, S., Blanchet E., Egas M. & Olivieri I. (2009). Are adaptation costs necessary to build up a local adaptation pattern? BMC Evolutionary Biology 9: 182. Tien, N.S.H., Sabelis M.W. & Egas, M. (2010). The maintenance of genetic variation for oviposition rate in two-spotted spider mites: inferences from artificial selection. Evolution 64: 2547– 2557. Van Veelen, M., Garcia J., Sabelis M.W., & Egas M. (2010). Call for a return to rigour in models. Nature 467: 661.

20 Arne (A.R.M.) Janssen

IBED, University of Amsterdam.  [email protected].  http://home.medewerker.uva.nl/a.r.m.janssen.

Research interests: Population dynamics; Behavioural ecology; Food web interactions

Titles of recent internships as superviser/examinator

Tasty Natives and Nasty Exotics? On the track of differences in invertebrate community impact on exotic and native plants The response of a predatory mite to herbivore-induced volatiles of plants with multiple pests

Selected publications

Belliure, B, Janssen, A., Maris, P.C., Peters, D., Sabelis, M.W., 2005. Herbivore arthropods benefit from vectoring plant-viruses. Ecol. Lett. 8: 70-79. Magalhães, S., Janssen, A., Montserrat, M., Sabelis, M.W. 2005. Prey attack and predators defend: counterattacking prey trigger parental care in predators. P. Roy. Soc. B. 272: 1929-1933. Janssen, A., Sabelis, M.W., Magalhães, S., Montserrat, M., & van der Hammen, T., 2007. Habitat structure affects intraguild predation. Ecology 88: 2713-2719. Grosman, A.H., Janssen, A., de Brito, E.F., Cordeiro, E.G., Colares, F., Oliveira Fonseca, J., Lima, E.R., Pallini, A., Sabelis, M.W., 2008. Parasitoid increases survival of its pupae by inducing hosts to fight predators. PLoS ONE 3 (6): e2276. Montserrat, M., Magalhães, S., Sabelis, M.W., de Roos, A.M., Janssen, A., 2008. Patterns of exclusion in an intraguild predator-prey system depend on initial conditions. J. Anim. Ecol. 77: 624-630.

21 Merijn (M.R.) Kant

IBED, University of Amsterdam.  [email protected].  http://home.medewerker.uva.nl/m.kant.

Research interests: Chemical Ecology; Molecular Ecology; Ecogenomics; Plant-herbivore interactions; Induced plant defense; Herbivore adaptation

Titles of recent internships as superviser/examinator

Nutrient signaling: genomics underlying lipid metabolism pathways in the parasitoid wasp Nasonia vitripennis The role of glandular trichomes in pest management on tomato: introducing Amblyseius swirskii on tomato by reducing glandualr trichome density Indirect interaction between two herbivore species on tomato

Selected publications:

Kant MR. & Baldwin IT. (2007). The ecogenetics and ecogenomics of plant–herbivore interactions: rapid progress on a slippery road. Cur. Opin. Gen. Dev. 17(6): 519-524. Schweighofer, A., Kazanaviciute,V., Scheikl, E., Teige, M., Doczi, R., Hirt, H., Schwanninger, Kant, M., Schuurink, R., Mauch, F., Buchala, A., Cardinale, F., Meskiene I. (2007). AP2C1, a PP2C phosphatase, is a novel component of MAPK-mediated stress signalling that regulates disease resistance and ethylene/jasmonate production in Arabidopsis. Plant Cell 19: 2213-2224. Paschold, A., Bonaventure, G., Kant MR. & Baldwin IT. (2008). Jasmonate perception regulates jasmonate biosynthesis and JA-Ile metabolism: the case of COI1 in Nicotiana attenuata. Plant Cell Physiol. 49(8): 1165–1175. Kant, MR., Sabelis, MW., Haring, MA., Schuurink, RC. (2008). Intraspecific variation in a generalist herbivore accounts for induction and impact of host-plant defenses. Proc. Royal Soc. B: 275: 443–452. Kant, MR., Bleeker, PM., Van Wijk, M., Schuurink., RC., Haring, MA. (2009). Plant volatiles in defence. Adv. Bot. Res. 51, 613-666.

22 Thomas van Leeuwen

IBED, University of Amsterdam.  [email protected].

Research interests: molecular toxicology, acaricide resistance, plant-mite interactions, genetics and genomics of xenobiotic resistance, horizontal gene transfer !

Internship options

The role of horizontal gene transfer in the evolution of polyphagous mites. Using advanced genomic mapping tools to uncover resistance genes in Tetranychus urticae. Assessing fitness cost of resistance genes in spider mites. Studying mite spit: the role of salivary proteins in plant interactions. Albinism in spider mites: is there a common factor involved ?

Selected publications:

Wybouw N, Dermauw W, Tirry L, Stevens C, Grbić M, Feyereisen R, Van Leeuwen T (2014) A gene horizontally transferred from bacteria protects arthropods from host plant cyanide poisoning . eLife 10.7554/eLife.02365 Dermauw W, Wybouw N, Rombauts S, Menten B, Vontas J, Grbic M, Clark RM, Feyereisen R, &Van Leeuwen T (2013) A link between host plant adaptation and pesticide resistance in the polyphagous spider mite Tetranychus urticae. Proceedings of the National Academy of Sciences of the United States of America 110: E113-E122 Van Leeuwen T, Demaeght P, Osborne EJ, Dermauw W, Gohlke S, Nauen R, Grbic M, Tirry L, Merzendorfer H & Clark RM (2012) Population bulk segregant mapping uncovers resistance mutations and the mode of action of a chitin synthesis inhibitor in arthropods. Proceedings of the National Academy of Sciences of the United States of America 109: 4407-4412 Grbic M, Van Leeuwen T, Clark RM et al. (2011) The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature 479: 487-492 Van Leeuwen T, Vanholme B, Van Pottelberge S, Van Nieuwenhuyse P, Nauen R, Tirry L & Denholm I (2008) Mitochondrial heteroplasmy and the evolution of insecticide resistance: Non-Mendelian inheritance in action. Proceedings of the National Academy of Science of the United States of America 105: 5980-5985

23 André (A.M.) de Roos

IBED, University of Amsterdam.  [email protected].  http://home.medewerker.uva.nl/a.m.deroos.

Research interests: Theoretical biology; Population dynamics; Community ecology; Multitrophic interactions; Mathematical modeling

Titles of recent internships as superviser/examinator

On the evolution of ontogenetic diet shifts: How a diet shift evolves in a stage-structured biomass model What limits food intake of a long-distance migrant (the red knot Calidris canutus) in its wintering area in the Banc d'Arguin, Mauritania? Can size-selective resource partitioning explain patterns of alternating abundances in two small pelagic fish? Coexistence of predator and prey in intraguild predation systems with ontogenetic niche shifts Collapse without warning: The ambiguity of early warning signals in stage-structured population models Effects of nutrients and plot size on foraging site utilization of major herbivores in a woodland savanna system

Selected publications

L. Persson, P.A. Amundsen, A.M. de Roos, A. Klemetsen, R. Knudsen & R. Primicerio, 2007. Culling prey promotes predator recovery - Alternative states in a whole-lake experiment. Science 316: 1743-1746. A.M. de Roos, T. Schellekens, T. van Kooten, K. van de Wolfshaar, D. Claessen & L. Persson, 2007. Food-dependent growth leads to overcompensation in stage- specific biomass when mortality increases: the influence of maturation versus reproduction regulation. American Naturalist 170: E59-E76. A.M. de Roos, T. Schellekens, T. van Kooten & L. Persson, 2008. Stage-specific predator species help each other to persist while competing for a single prey. Proc. Natl. Acad. Sciences 105(37): 13930-13935. A.M. de Roos, 2008. Demographic analysis of continuous-time life-history models. Ecol. Lett. 11(1): 1-15. A. Schröder, L. Persson & A.M. de Roos, 2009. Culling experiments demonstrate size-class specific biomass increases with mortality. Proc. Natl. Acad. Sciences 106(8): 2671-2676.

24 Maurice (M.W.) Sabelis

IBED, University of Amsterdam.  [email protected].  http://home.medewerker.uva.nl/m.w.sabelis

Research interests: Evolutionary Ecology of Tritrophic Systems involving Mites and Insects on Plants; Plant-Predator Mutualisms; Biological Control; Ecological Acarology

Titles of recent internships as superviser/examinator

Does varying host quality affect competitive dynamics between different arbuscular mycorrhizal fungi? Personality and cooperative breeding in the Seychelles warbler Roost area choice of Red Knots in the face of diurnal predation risk – the role of body mass

Selected publications

Belliure, B., A. Janssen, P.C. Maris, D. Peters & M.W. Sabelis (2005). Herbivore arthropods benefit from vectoring plant viruses. Ecology Letters 8: 70–79. Egas, M., M.W. Sabelis & U. Dieckmann (2005). Evolution of specialization and ecological character displacement of herbivores along a gradient of plant quality. Evolution 59: 507– 520. Janssen A., M.W. Sabelis, S. Magalhães, M. Montserrat & T. van der Hammen (2007). Habitat structure affects intraguild predation. Ecology 88: 2713-2719. Kant, M.R., M.W. Sabelis, M.A. Haring & R.C. Schuurink (2008). Intraspecific variation in a generalist herbivore accounts for differential induction and impact of host-plant defences. Proceedings of the Royal Society of London Series B-Biological Sciences 275: 443-452. Tien, N.S.H., M.W. Sabelis & M. Egas (2010). The maintenance of genetic variation for oviposition rate in two-spotted spider mites: inferences from artificial selection. Evolution 64-9: 2547– 2557.

25 Isabel Smallegange

IBED, University of Amsterdam.  [email protected].  www.uva.nl/profiel/i.smallegange.

Research interests: Population biology, demography, dynamic energy budget theory, eco-evolutionary dynamics, behavioural ecology. ! Internship options

Do differences in energy budgets explain why the two male morphs in the bulb mite can coexist? This project involves lab work (life history assays using the bulb mite Rhizoglyphus robini) The impact of environmental noise on male morph expression. This project involves lab work (life history assays using the bulb mite Rhizoglyphus robini) Can changing explain why mites shrink? This is a theoretical project using Dynamic Energy Budget theory and the software MatLab

Titles of recent internships as superviser/examinator

The effects of environmental noise on the population dynamics of harvested populations Diet matters: The impact of variation in developmental diet on the dimorphic bulb mite (Rhizoglyphus robini) Pharaoh's ants and foraging signals Size does matter: contest dynamics in fiddler crabs, Uca perplexa Alternative reproductive phenotype expression in the bulb mite Rhizoglyphus robini (Claparède): the influence of genetic variation The influence of conspecific and heterospecific cues on bumblebee foraging behaviour

Selected publications

(S) Leigh DM, Smallegange IM. 2014. Effects of variation in nutrition on male morph development in the bulb mite Rhizoglyphus robini. Experimental and Applied Acarology. Smallegange, IM, Deere JA, Coulson T. 2014. Consistent eco-evolutionary response to changing environmental stochasticity in a model organism. American Naturalist, 186: 784-797. Smallegange IM, Coulson T. 2013. Towards a general, population-level understanding of eco- evolutionary change. Trends in Ecology and Evolution, 28: 143-148. (S) Smallegange IM, Thorne N, Charalambous M. 2012. Fitness trade-offs and the maintenance of alternative male morphs in the bulb mite (Rhizoglyphus robini). Journal of Evolutionary Biology, 25:972-980 Smallegange IM. 2011. Complex environmental effects on the expression of alternative reproductive phenotypes in the bulb mite. Evolutionary Ecology 25: 857-873. Smallegange IM, Coulson T. 2011. The stochastic demography of two coexisting male morphs. Ecology 92: 755-764. (S) Godsall B, Smallegange IM. (2011). Assessment games in the mangrove tree-dwelling crab, Selatium brockii (De Man, 1887). Crustaceana 84:1697-1718.

26 Geo-Ecology (Landscape Ecology)

27 Willem Bouten

IBED, University of Amsterdam.  [email protected].  http://home.medewerker.uva.nl/w.bouten

Research interests: Confronting models with observations; Soil science; Hydrology; Meteorology; Ornithology; e-Science

Titles of recent internships as superviser/examinator

Can speed and tri-axial acceleration measured by biologgers be used to classify Oystercatcher behaviour?

Selected publications

Vrugt, J.A., C.G.H. Diks, W. Bouten, H.V. Gupta and J.M. Verstraten, 2005, Towards a complete treatment of uncertainty in hydrologic modelling: combining the strengths of global optimisation and data assimilation. Water Resources Research Vol. 41, No. 1, W01017, 10.1029/2004WR003059. Shamoun-Baranes, J., van Gasteren, H., van Belle, J., van Loon, E., Bouten, W., Buurma, L. 2006. A comparative analysis of the influence of weather on the flight altitudes of birds. Bul. Am. Meteorol. Soc. 87 (1): 47-61. Van Belle, J, W. Bouten, J. Shamoun-Baranes and E. Emiel van Loon, 2007, An operational model predicting autumn bird migration intensities for flight safety. Journal of Applied Ecology 44(4): 864-874. Vrugt, J.A., J. van Belle, and W. Bouten, 2007, Pareto front analysis of flight time and energy-use in long distance bird migration. Journal of Avian Biology 38(4):432-442. Shamoun-Baranes, J., W. Bouten, L. Buurma, R. DeFusco, A. Dekker, H. Sierdsema, F. Sluiter, J. Van Belle, H. Van Gasteren and E. van Loon. 2008. Avian Information Systems: Developing Web-Based Bird Avoidance Models. Ecology and Society 13 (2): 38.

28 Joost (J.F.) Duivenvoorden

IBED, University of Amsterdam.  [email protected].  http://home.medewerker.uva.nl/j.f.duivenvoorden.

Research interests: Tropical ecology and biodiversity (emphasis on Amazonian and Andean ecosystems)

Internship options

Trait-based study of páramo recovery: Within the context of her PhD study Marian Cabrera will study the recovery of páramo vegetation after manipulative disturbances in different areas in Colombia. Internships (including substantial fieldwork in páramo) for UvA students will be developed to study the functional role of plants traits and their diversity in this process.

Titles of recent internships as superviser/examinator

Testing new pre-release methods to improve the reintroduction of the Philippine crocodile (Crocodylus mindorensis) in north Luzon, Philippines Soil type determines the influence of large herbivores on nitrogen mineralization rates Effect of two agroecological management strategies on ant diversity in Southwest Colombian coffee plantations Identifying Land Use and Land Cover changes from Landsat imagery using a hybrid pixel- and object-based classification method in a mountainous area in Mexico Forest loss and the impact of the patch’s properties on the woody plant species’ richness and diversity: a case study in three forest types in Mexico Maxent modeling of the geographic distribution range of Trithemis dragonflies in Africa

Selected publications

Duivenvoorden, J.F. & Cuello A, N.L. (2012) Functional trait state diversity of Andean forests in Venezuela changes with altitude. Journal of Vegetation Science 23: 1105–1113. Tovar-Sanchez, A., Duivenvoorden, J.F., Sánchez-Vega, I. & Seijmonsbergen, A.C. (2012) Recent Changes in Patch Characteristics and Plant Communities in the Jalca Grasslands of the Peruvian Andes. Biotropica, 44(3), 321-330. Aguirre, J., Seijmonsbergen, A.C. & Duivenvoorden, J.F. (2012) Optimizing land cover classification accuracy for change detection, a combined pixel-based and object-based approach in a mountainous area in Mexico. Applied Geography 34: 29-37. Benavides, A, Vasco, A., Duque, A.J. & Duivenvoorden, J.F. (2011) Association of vascular epiphytes with landscape units and phorophytes in humid lowlands of Colombian Amazonia. Journal of Tropical Ecology 27: 223-237. (Editors Choice Science 332 - 6 May 2011)

29 Stefan Engels

IBED, University of Amsterdam.  [email protected].  http://home.medewerker.uva.nl/s.engels.

Research interests: Quantitative palaeoecology; climate reconstructions; subfossil chironomids; palynology; palaeolimnology; human impact

Internship options

Late-Glacial temperatures at Uddelermeer: a tale of two cores. Keywords: Palaeoecology, Holocene, Chironomids, Climate reconstruction Pollenrain as an indicator of sedimentation rates: what happened at 850 BC? Keywords: Palaeoecology, Holocene, Palynology, Vegetation reconstruction, Sedimentation rates The pollution history of Uddelermeer – a novel approach for the reconstruction of the former algal and cyanobacterial communities Keywords: Pollution history, restoration, cyanobacteria, new method, palaeoecology

Titles of recent internships as superviser/examinator

Climate change and the role of the Sun: an underestimated factor? Late-Glacial Chironomid-based Temperature Reconstruction of lake Hämelsee, Germany

Selected publications

S. Engels, A.E. Self, T.P. Luoto, S.J. Brooks & K.F. Helmens (2014). A comparison of three Eurasian chironomid–climate calibration datasets on a W–E continentality gradient and the implications for quantitative temperature reconstructions. Journal of Paleolimnology, 51, 529-547. DOI 10.1007/s10933-014-9772-8 V. van den Bos, O. Brinkkemper, I.D. Bull, S. Engels, T. Hakbijl, M. Schepers, M. van Dinter, G. van Reenen & B. van Geel (2014). Roman impact on the landscape near castellum Fectio, The Netherlands. Vegetation History and Archaeobotany, 23, 277-298. 10.1007/ s00334-013-0424-0 E.J. de Boer, H. Hooghiemstra, F.B.V. Florens, C. Baider, S. Engels, V. Dakos, M. Blaauw & K.D. Bennett (2013). Rapid succession of plant associations on the small ocean island of Mauritius at the onset of the Holocene. Quaternary Science Reviews, 68, 114-125. 10.1016/j.quascirev.2013.02.005[go to publisher's site] E.J. de Boer, H. Hooghiemstra, F.B.V. Florens, C. Baider, M. Blaauw, S. Engels & K.D. Bennett (2013). Regime shift at Lateglacial-Holocene transition show climate change driven forest response in a tropical oceanic island. Quaternary Science Reviews, 68, 114-125. B. van Geel, S. Engels, C. Martin-Puertas & A. Brauer (2013). Ascospores of the parasitic fungus Kretzschmaria deusta as rainstorm indicators during a late Holocene beech-forest phase around lake Meerfelder Maar, Germany. Journal of Paleolimnology, 50(1), 33-40. 10.1007/ s10933-013-9701-2

30 Bas van Geel

IBED (retired), University of Amsterdam.  [email protected].  http://home.medewerker.uva.nl/b.vangeel.

Research interests: Paleoecology; Paleoclimatology; Solar forcing of climate change; Non-Pollen Palynomorphs (a.o. fungal and algal spores as paleo-environmental indicators)

Internship options

Paleoecological landscape reconstruction of West-Friesland: During the Bronze Age (ca 1500 – 800 BC) farmers were living in West-Friesland. A decline of solar activity around 850 BC caused a climate shift to cooler wetter conditions that made the area inhabitable. Extensive wetlands developed, resulting in peat deposits. In medieval time (from ca 1000 AD on) the area became inhabited again. Peat deposits, prehistoric ditch fills and infills of medieval wells from archeological excavations are available for paleoecological study (microfossils, macroremains). Goal of the project: detailed reconstructions of natural vegetation successions, prehistoric and medieval land use and landscape ecology. This is a cooperation project with local archeologists.

Titles of recent internships as superviser/examinator

Reconstructing the land of the Dodo: The vegetation and climate of Mauritius since the last Ice Age Reconstruction of a potential coastal dodo environment in Mauritius Palynological study of a brook valley fill buried by River IJssel deposits (Keizerswaard, Deventer, The Netherlands) Vegetational history of the ‘Stobbenven’ near Roderwolde (the Netherlands)

Selected publications van Geel, B. et al., 2012. Biologisch onderzoek van Bronstijd-greppels en middeleeuwse waterputten in Bovenkarspel. Jaarboek Westfries Genootschap 79: 125-137. Martin-Puertas, C. et al., 2012. Regional atmospheric circulation shifts induced by a grand solar minimum. Nature Geoscience 5: 397-401. van Geel, B., 2010. De klimaatcrisis van 850 v. Chr. Jaarboek Westfries Genootschap 77: 88-101.de Jager, C., Duhau, S. and van Geel, B., 2010. Quantifying and specifying the solar influence on terrestrial surface temperature. Journal of Atmospheric and Solar- Terrestrial Physics 72: 926-937. van Geel, B., Guthrie, R.D., Altmann, J.G., Broekens, P., Bull, I.D., Gill, F.L., Gravendeel, B., Jansen, B., Nieman, A.M. 2010. Mycological evidence of coprophagy from the feces of an Alaskan Late Glacial mammoth. Quaternary Science Reviews doi:10.1016/j.quascirev. 2010.03.008. van Geel, B., Aptroot, A., Baittinger, C., Birks, H.H., Bull, I.D., Cross, H.B., Evershed, R.P., Gravendeel, B., Kompanje, E.J.O., Kuperus, P., Mol, D., Nierop, K.G.J., Pals, J.P., Tikhonov, A.N., van Reenen, G. and van Tienderen, P.H., 2008. The ecological implications of a Yakutian mammoth’s last meal. Quaternary Research 69: 361-376.

31 Henry Hooghiemstra

IBED, University of Amsterdam.  [email protected].  http://home.medewerker.uva.nl/h.hooghiemstra

Research interests: Paleoecology (tropics); Paleoclimatology (tropics); Long continental records; Pleistocene neotropical biogeography; Marine palynology; Land-sea-ice correlations

Internship options

Mauritius since the last ice-age: how did biodiversity respond to climate change on a tropical island? Grand Basin is a swamp inside an extinct volcanic crater located in the flat uplands of Mauritius (650 m elevation). Here, a four meter long sediment core was taken reflecting the last ca. 14,000 years. Palynological analysis of this core will provide valuable information on vegetation dynamics in the Mauritian uplands from last-glacial to Holocene times. Our goal is to produce a reliable pollen record with ample radiocarbon dates. The ‘stage report’ on this high- quality reconstruction may be written in the format of a research paper to be submitted to an international journal. The student is invited to co-author this paper and to obtain experience in paper writing. We also ask to produce a ‘poster’ on the results to be distributed internationally, to NGOs, the University of mauritius, and Governmental institutions in particular.

Titles of recent internships as superviser/examinator

Reconstructing the land of the Dodo: The vegetation and climate of Mauritius since the last Ice Age Reconstruction of a potential coastal dodo environment in Mauritius Late Quaternary fire history of the Bolivian Pantanal: A high resolution macroscopic charcoal record from the last 20,000 years

Selected publications

Torres, V., Vandenberghe, J., Hooghiemstra, H., 2005. An environmental reconstruction of the sediment infill of the Bogotá basin (Colombia) during the last 3 million years from abiotic and biotic proxies. Palaeogeography Palaeoclimatology Palaeoecology 226, 127-148. ; Hooghiemstra, H., Wijninga, V.M., Cleef, A.M., 2006. The paleobotanical record of Colombia: implications for biogeography and biodiversity. Ann. Missouri Bot. Gard. 93, 297-324. Flantua, S.G.A., van Boxel;, J.H., Hooghiemstra, H., van Smaalen, J., 2007. Application of GIS and logistic regression to fossil pollen data in modelling present and past spatial distribution of the Colombian savanna. Clim. Dynam. 29, 697-712. Bakker, J., Moscol-Olivera, M., Hooghiemstra, H., 2008. Holocene environmental change at the upper forest line in northern Ecuador. The Holocene 18, 877-893. Hoorn, C., Wesselingh, F.P., terSteege, H., Bermudez, M.A., Mora, A., Sevink, J., Sanmartin, I., Sanchez-Meseguer, A., Anderson, C.L., Figueiredo, J.P., Jaramillo, C., Riff, D., Negri, F.R., Hooghiemstra, H., Lundberg, J., Stadler, T., Sarkinen, T., Antonelli, A., 2010. Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity. Science 330, 927-931.

32 Boris Jansen

IBED, University of Amsterdam.  [email protected].  http://home.medewerker.uva.nl/b.jansen.

Research interests: Soil chemistry; Molecular dynamics of soil organic matter; Fate of natural; and anthropogenic compounds in terrestrial ecosystems

Titles of recent internships as superviser/examinator

Selected publications

B. Jansen, K.G.J. Nierop and J.M. Verstraten, (2005). Mechanisms controlling the mobility of dissolved organic matter, Al and Fe in podzol B horizons. Eur. J. Soil Sci. 56: 537-550. B. Jansen, K.G.J. Nierop, J.A. Hageman, A.M. Cleef and J.M. Verstraten, (2006). The straight- chain lipid biomarker composition of plant species responsible for the dominant biomass production along two altitudinal transects in the Ecuadorian Andes, Org. Geochem. 37: 1514-1536. B. Jansen, K.G.J. Nierop, F.H. Tonneijck, F.W. van der Wielen, and J.M. Verstraten, (2007). Can isoprenoids in leaves and roots of plants along altitudinal gradients in the Ecuadorian Andes serve as biomarkers?, Plant Soil, 291: 181-198. K.G.J. Nierop and B. Jansen, (2009). Extensive transformation of organic matter and excellent lipid preservation at the upper, superhumid Guandera páramo, Geoderma, 151: 357-369. B. Jansen, E.E. van Loon, H. Hooghiemstra and J.M. Verstraten, (2010). Improved reconstruction of palaeo-environments through unravelling of preserved vegetation biomarker patterns, Palaeogeogr. Palaeocl. 285: 119-130.

33 Annemieke (A.M.) Kooijman

IBED, University of Amsterdam.  [email protected].  http://www.science.uva.nl/ibed-ple.

Research interests: Plant-soil interactions; Nutrient availability; Restoration ecology

Titles of recent internships as superviser/examinator

Selected publications

Kooijman, A.M., Kooijman-Schouten, M.M.and Martinez-Hernandez, G.B. 2008. Alternative strategies to sustain N-fertility in acid and calcaric Beech forests: low microbial N-demand versus high biological activity. Basic and Applied Ecology 9: 410-421. Kooijman, A.M. and Martinez-Hernandez, G.B. 2009. Effects of litter quality and parent material on organic matter characteristics and N-dynamics in Luxembourg beech and hornbeam forests. Forest Ecology and Management 257: 1732-1739. Kooijman, A.M., Lubbers, I. and Til, M. van 2009. Iron-rich dune grasslands: Relations between soil organic matter and sorption of Fe and P. Environmental Pollution: 157: 3158-3165. Kooijman, A.M. and Hedenäs, L. 2009. Changes in nutrient availability from calcareous to acid wetland habitats with closely related brownmoss species: increase instead of decrease in N and P. Plant and Soil 324: 267-278. Kooijman, A.M. and Cammeraat, L.H. 2010. Biological control of beech and hornbeam on species richness via changes in the organic layer, pH and soil moisture characteristics. Functional Ecology, 24: 469-477.

34 Emiel (E.E.) van Loon

IBED, University of Amsterdam  [email protected]  http://home.medewerker.uva.nl/e.e.vanloon/

Research interests: Statistics for the natural sciences, including Bayesian modeling, geo-statistics, time series analysis, model identification and selection, dimension reduction

Internship options

Understanding changes in plant diversity on the basis of vegetation monitoring data: One of the flora monitoring projects in The Netherlands comprises observations on +/- 11000 vegetation plots that are revisited each 4 years (this project is called LMF). In this research, relations between environmental factors and plant diversity will be investigated on the basis of LMF data. The aim is to develop a modeling procedure by which plant diversity on plots can be modelled, and to predict selected plant diversity indices as a function of suitable environmental co-variates. A simulation approach to discover important features in gull trajectories: In order to translate animal movement data (e.g. trajectories for GPS-tagged birds) into behaviour, key properties of these trajectories (so-caled features) need to be identified and described quantitatively. It is often very hard to identify robust features through inductive techniques like cluster analysis. In this research, a deductive route is followed to obtain insight in the key-features of animal movement data: simulation. Stochastic simulation models of gull movement are created, with as only aim: to generate movement trajectories which are indistinguishable from those that have been measured for real birds. The quality of the artificially generated data is evaluated in a Turing-like test, by providing experts with a mixed set of real and artificial trajectories to be labelled.

Titles of recent internships as superviser/examinator

Hourly travel speed during different times of the day: Comparing the autumn migration of Marsh Harrier and Osprey in Europe and Africa Niche complexity and the bird population changes in the Netherlands Modeling interactions and competition between Accipiter gentilis and Buteo buteo at the individual level

Selected publications

Shamoun-Baranes, J., J. Leyrer, E. van Loon, P. Bocher, F. Robin, F. Meunier, T. Piersma (2010). Stochastic atmospheric assistance and the use of emergency staging sites by migrants. Proceedings of the Royal Society of London. Series B-Biological Sciences, 277, 1505-1511. Loon, E.E. van, J. Shamoun-Baranes, W. Bouten & S.L. Davis (2011). Understanding soaring bird migration through interactions and decisions at the individual level. Journal of Theoretical Biology, 270(1), 112-126. Kemp, M.U., E.E. van Loon, J. Shamoun-Baranes & W. Bouten (2012). RNCEP: global weather and climate data at your fingertips. Methods in Ecology and Evolution, 3, 65-70. Shamoun-Baranes J., B. Bom, E.E. van Loon, B.J. Ens, K. Oosterbeek & W. Bouten (2012). From sensor data to animal behaviour: an oystercatcher example. PLoS One, 7(5), e37997.

35 John (J.R.) Parsons

IBED, University of Amsterdam.  [email protected].  http://home.medewerker.uva.nl/j.r.parsons.

Research interests: Environmental chemistry; Biodegradation of xenobiotic compounds; Sorption and bioavailability of organic compounds

Titles of recent internships as superviser/examinator

Screening of persistent organic pollutants (POPs) in migrating waterfowl; barnacle goose Branta leucopsis and pink-footed goose Anser brachyrhynchus

Selected publications

Cornelissen, G., J. Haftka, J. Parsons, and O. Gustafsson. 2005. Sorption to black carbon of organic compounds with varying polarity and planarity. Environ. Sci. Technol. 39:3688-3694. Botton, S., and J. R. Parsons. 2006. Degradation of BTEX compounds under iron-reducing conditions in contaminated aquifer microcosms. Environ. Toxicol. Chem. 25:2630-2638. Botton, S., M. van Harmelen, M. Braster, J. R. Parsons, and W. F. M. Röling. 2007. Dominance of Geobacteraceae in BTX-degrading enrichments from an iron-reducing aquifer. FEMS Microbiol. Ecol. 62:118-130. Haftka, J. J. H., J. R. Parsons, H. A. J. Govers, and J.-J. Ortega-Calvo. 2008. Enhanced kinetics of solid-phase microextraction and biodegradation of polycyclic aromatic hydrocarbons in the presence of dissolved organic matter. Environ. Toxicol. Chem. 27:1526-1532. van Noort, P. C. M., J. J. H. Haftka, and J. R. Parsons. 2010. Updated Abraham solvation parameters for polychlorinated biphenyls. Environ. Sci. Technol. 44:7037-7042.

36 Kenneth Rijsdijk

IBED, University of Amsterdam.  [email protected].  http://home.medewerker.uva.nl/k.f.rijsdijk.

Research interests: the role of deep time, dynamics of geodiversity and interaction with island biodiversity; quantifying the impacts of humans on island ecosystems; seeking ways in realising sustainable futures for mankind to live in harmony with geo- eco- systems.

Titles of recent internships as superviser/examinator

Detecting the genetic signature of population contraction: improvements and drawbacks

Selected publications

Rijsdijk K.F., Kroon I.C., Meijer T., Passchier S., Van Dijk T.A.G.P., Bunnik F.P.M., and Janse A.C. 2013. Reconstructing Quaternary Rhine-Meuse dynamics in the southern North Sea: architecture, seismo-lithofacies associations and malacological biozonation. Journal of Quaternary Science, 28, 453-466. De Boer E.J., Slaikovska M, Hooghiemstra H, Rijsdijk K.F., Vélez M.I.; Prins M., Baider C., Florens F.B.V. 2013. Multi-proxy reconstruction of environmental dynamics and colonization impacts in the Mauritian uplands. Palaeogeography, Palaeoclimatology, Palaeoecology, 383–384, 42–51. Meijer, H. J. M., Gill, A., de Louw, P. G. B., Van Den Hoek Ostende, L. W., Hume, J. P., and Rijsdijk, K. F. 2012. Dodo remains from an in situ context from Mare aux Songes, Mauritius. Die Naturwissenschaften , 99, 177-84. Van der Meer, J.J.M, Thomas G.P.S., Chiverrell R.C., Lee, J.L., Phillips, E., Rijsdijk K.F. and Warren W.P. 2011. Macrostructural Analysis: unravelling polyphase glacitectonic histories. In: Phillips E. Lee J.R. and Evans H.M. (Eds.) Glacitectonics- Field Guide. Quaternary Research Association,MWL Printers, Pontypool. pp. 53-58. Van der Meer, J.J.M, Rijsdijk K.F. and Warren W.P. 2011. Polyphase deformation at Ireland. In: Phillips E. Lee J.R. and Evans H.M. (Eds.) Glacitectonics - Field Guide. Quaternary Research Association, MWL Printers, Pontypool. pp. 79-100. Rijsdijk, K.F. , Zinke J., de Louw P.G.B., Hume J.P., van der Plicht H.J., Hooghiemstra H., Meijer H.J.M, Vonhof H.J., Porch N.,Florens F.B.V., Baider C., van Geel B., Brinkkemper J., Vernimmen T., Janoo A. 2011 . Mid-Holocene (4200 yr BP) mass mortalities in Mauritius (Mascarenes): Insular vertebrates resilient to climatic extremes but vulnerable to human impact. The Holocene 21 : 1179 - 1194.

37 Harry (A.C.) Seijmonsbergen

IBED, University of Amsterdam.  [email protected].  http://home.medewerker.uva.nl/a.c.seijmonsbergen.

Research interests: Alpine Geomorphology; Hazard zonation; Application of Geographical Information Systems and Remote Sensing in Geo-Ecology; LiDAR

Titles of recent internships as superviser/examinator

Identifying Land Use and Land Cover changes from Landsat imagery using a hybrid pixel- and object-based classification method in a mountainous area in Mexico Forest loss and the impact of the patch’s properties on the woody plant species’ richness and diversity: a case study in three forest types in Mexico Spatial and temporal pattern dynamics of tropical alpine ecosystems: A degradation process in a naturally fragmented ecosystem, south Cajamarca, Peru Identification of transient productive gyres in semi-enclosed seas through GIS analysis of microwave and infrared satellite imagery

Selected publications

Asselen van S., Seijmonsbergen, A.C. 2006. Expert-driven semi-automated geomorphological mapping for a mountainous area using a laser DTM. Geomorphology 78, 309-320. Gustavsson M., Seijmonsbergen, A.C., Kolstrup E., 2008. Structure and contents of a new geomorphological GIS database linked to a geomorphological map - with an example from Liden, central Sweden. Geomorphology 95, 335-349. Anders, N.S., Seijmonsbergen, A.C., Bouten, W., 2009. Modeling channel incision and alpine hillslope development using laser altimetry data. Geomorphology 113, 35-46. De Jong, M.G.G., Nio D.S., Böhm, A.R., Seijmonsbergen, H.C., de Graaff, L.W.S., 2009. Resolving climate change in the period 15–23 ka in Greenland ice cores: a new application of spectral trend analysis. Terra Nova 21, 137–143. Seijmonsbergen A.C., J. Sevink, L.H. Cammeraat, Recharte, J., 2010. A potential geoconservation map of the Las Lagunas area, northern Peru. Environmental Conservation 37 (2), 107-115.

38 Judy (J.) Shamoun-Baranes

IBED, University of Amsterdam.  [email protected].  http://home.medewerker.uva.nl/j.z.shamoun-baranes.

Research interests: Bird migration; Foraging ecology; Influence of atmospheric dynamics on bird movement; Animal tracking technology

Internship options

Diverse options are available for research topics and should be discussed individually. Research topics can roughly be divided into two themes: 1. Migratory behaviour (diverse species) and the response of birds to environmental conditions. These studies can be based on GPS tracking data, simulation models or a combination of both; 2. Foraging ecology of birds (most studies focus on lesser black backed gulls) throughout their annual routine, these studies are based on GPS tracking data and concurrent field measurements. Studies may focus on behaviour at different scales in space and time and may be conducted in collaboration with partners outside of UvA.

Titles of recent internships as superviser/examinator

Individual variability in foraging strategies of Lesser Black-backed gulls (Larus fuscus) during different breeding phases Can speed and tri-axial acceleration measured by biologgers be used to classify Oystercatcher behaviour? A study of bird movement in the military airfield of Leeuwarden. Quantifying the metrics of gull movements (Larus fuscus) using high resolution GPS measurements. Hourly travel speed during different times of the day: Comparing the autumn migration of Marsh Harrier and Osprey in Europe and Africa Growth in chicks of lesser black-baced gulls (Larus fuscus) and herring guls (Larus argentatus) in the Kelderhusipolder colony, Texel. Interspecific variation in foraging preferences of Herring Gulls (Larus argentatus) and Lesser Black-backed gulls (Larus fuscus) during the breeding season.

Selected publications

Shamoun-Baranes, J., W. Bouten, & E. E. van Loon, 2010. Integrating meteorology into research on migration. Integrative and Comparative Biology 50: 280-292. Shamoun-Baranes, J., J. Leyrer, E. van Loon, P. Bocher, F. d. r. Robin, F. Meunier and T. Piersma. 2010. Stochastic atmospheric assistance and the use of emergency staging sites by migrants. Proceedings of the Royal Society B 277: 1505-1511. Shamoun-Baranes, J. and H. van Gasteren. 2011. Atmospheric conditions facilitate mass migration events across the North Sea. Animal Behaviour, 81(4), 691-704. Shamoun-Baranes J, Dokter AM, van Gasteren H, van Loon EE, Leijnse H, Bouten W. 2011. Birds flee en mass from New Year's Eve fireworks. Behavioral Ecology, 22, 1173-1177 Doi: 10.1093/beheco/arr102

39 Pim (W.P.) de Voogt

IBED, University of Amsterdam.  [email protected].  http://home.medewerker.uva.nl/w.p.devoogt.

Research interests: Environmental Chemistry; Chemistry of emerging water contaminants; Persistent and polar organics; Perfluorinated alkylated substances; Drugs of abuse

Titles of recent internships as superviser/examinator

Ordination analysis in ecotoxicology wildlife studies: polar bear Ursus maritimus as a model Screening of persistent organic pollutants (POPs) in migrating waterfowl; barnacle goose Branta leucopsis and pink-footed goose Anser brachyrhynchus

Selected publications

Jonkers N, Laane RWPM, de Voogt P (2005) Sources and fate of nonylphenol ethoxylates and their metabolites in the Dutch coastal zone of the North Sea. Marine Chem. 96, 115-135 Eschauzier C, Haftka JJH, Stuyfzand PJ, De Voogt P (2010) Perfluorinated compounds in infiltrated river Rhine water and infiltrated rain water in coastal dunes Environ. Sci. Technol. 44, 7450–7455. Schriks M, van Leerdam JA, van der Linden SC, van der Burg B, Heringa MB, van Wezel AP, de Voogt P (2010) High resolution mass spectrometric identification and quantification of glucocorticogenic compounds in various wastewaters in The Netherlands, Environ. Sci. Technol. 44, 4766-4774. Möller A, Ahrens L, Surm R, Westerveld J, van der Wielen F, Ebinghaus R, de Voogt P (2010) Distribution and sources of polyfluoroalkyl substances in the River Rhine watershed, Environ. Pollut. 158, 3243-3250. De Voogt P, Emke E, Helmus R, Panteliadis P, van Leerdam JA (2010) Determination of illicit drugs in the water cycle by LC-Orbitrap MS. In Castiglioni S, Zuccato E, Fanelli R (Eds.) Illicit drugs in the environment: occurrence, analysis, and fate using mass spectrometry. Wiley, New York. p. 85-114.

40 Serge Wich

IBED, University of Amsterdam.  [email protected].  http://www.sergewich.com  http://www.conservationdrones.org

Research interests: great apes, primates, conservation, vocal communication, land cover, oil palm.

Internship options

Studies on great ape behavioural ecology and conservation studies at various field sites in Asia and Africa with the aim to provide scientific support to great ape conservation. Analyses of existing datasets of great ape vocalizations to study vocal communication with the aim to better understand great ape social systems and human language evolution. There are also options to collect more data in zoos and in the wild. Analyses of existing images from drones for a variety of projects that deal with land cover mapping and animal surveys. This work can be linked to data collection at some of the fieldsites.

Selected publications

Wich SA, Garcia-Ulloa J, Kühl HS, Humle T, Lee JS, Koh LP. 2014. Will Oil Palm's Homecoming Spell Doom for Africa's Great Apes?. Current biology : CB, vol. 24(14), 1659-1663. Vogel ER, Zulfa A, Hardus M, Wich SA, Dominy NJ, Taylor AB. 2014. Food mechanical properties, feeding ecology, and the mandibular morphology of wild orangutans. Journal of human evolution. Paneque-Galvez J, McCall MK, Napoletano BM, Wich SA, Koh LP. 2014. Small Drones for Community-Based Forest Monitoring: An Assessment of Their Feasibility and Potential in Tropical Areas. FORESTS, vol. 5(6), 1481-1507. Lameira AR, De Vries H, Spruijt BM, Sterck EHM, Hardus ME, Kowalsky B, Shumaker RW, Wich SA. 2013. Orangutan (Pongo spp.) whistling and implications for the emergence of an open-ended call repertoire: A replication and extension. Journal of the Acoustical Society of America, vol. 134(3), 2326-2335. Lameira AR, Nouwen KJJM, Topelberg E, Spruijt BM, Sterck EHM, Hardus ME, Delgado RA, Knott CD, Wich SA. 2013. Population-Specific Use of the Same Tool-Assisted Alarm Call between Two Wild Orangutan Populations (Pongo pygmaeus wurmbii) Indicates Functional Arbitrariness. PLoS ONE, vol. 8(7).

41 42 Outside the UvA Note that for your first research project your supervisor needs to be afiliated with the UvA

43 Naturalis

Naturalis Biodiversity Center, Leiden  https://science.naturalis.nl/en/education/

Research interests: see list below

Internship options

Here is a list of the expertise of Naturalis research staff per department. Tenured staff and research fellows only.

Marine Zoology

Dr. B.W. Hoeksema Senior Researcher. Head of the department, marine biodiversity, marine biogeography, marine conservation, stony coral taxonomy, coral phylogeny, coral symbionts, reef coral ecology Dr. C.H.J.M. Fransen Senior Researcher. Crustacea, Decapoda, Caridea, taxonomy, phylogeny, historical biogeography, phylogenetic ecology Dr. L.P. van Ofwegen Senior Researcher. Octocoral taxonomy, phylogeny, marine biodiversity Dr. M.J.P. van Oijen Senior Researcher. Fish eating and shrimp eating haplochromine cichlids, natural history collections Dr. R. Vonk Senior Researcher. Stygofauna, shallow marine interstitial and fossil crustaceans, fishes, island biogeography, subterranean habitats Dr. N.J. de Voogd Senior Researcher. Marine biodiversity, marine biogeography, sponge taxonomy, sponge symbionts, reef coral ecology, marine lakes Dr. D.S.J. Groenenberg Senior Researcher. DNA, phylogeny, natural history collections, taxonomy, evolution, identification Dr. K.T.C.A. Peijnenburg Research Fellow. Marine zooplankton, chaetognaths, pteropods, marine invertebrates, phylogeography, phylogeny, marine lakes, morphometrics, molecular markers, mitogenomics, ocean acidification, molecular evolution

Terrestrial Zoology

Dr. J. van TolAssociate DirectorHead of the department, Odonata, Platystictidae, phylogeny, biogeography, Southeast Asia, DNA barcoding, biodiversity informatics, zoological nomenclature Prof.dr. J.C. BiesmeijerScientific DirectorPollination, bees, crops, ecosystem services, identification keys, tropical forest, pollinators, fragmentation, invasive species, social insects, honeybees, social behavior Prof.dr. M. Schilthuizen Senior Researcher. Speciation, land snails, beetles, left-right asymmetry, chirality, genitalia, predator-prey-interactions, Cepaea, Cholevidae, Diplommatinidae, Albinaria, Borneo, Malaysia, Crete, The Netherlands, invasive species

44 Dr. J.W. Arntzen Senior Researcher. European amphibians, systematics, biogeography and hybrid zones, evolutionary biology, master control (Hox) genes, gene flow Mr. T. Hakbijl Senior Researcher. Entomoarchaeology, palaeo-ecology, stored product arthropods, cultural entomology Dr. H. de Jong Senior Researcher. Systematic entomology, Diptera, Tipulidae, biogeography Mr. R.M.J.C. Kleukers Senior Researcher. European Invertebrate Survey, faunistics and taxonomy of European Orthoptera Dr. J.A. Miller Senior Researcher. Araneae, spiders, biodiversity, cybertaxonomy, impact of land use on invertebrate ecosystems Dr. E.J. van Nieukerken Senior Researcher. Lepidoptera, leaf miners, systematics, webbased taxonomy, biogeography, insect-plant relationships Dr. R. Sluys Senior Researcher. Platyhelminthes, Tricladida, systematics, phylogeny, biogeography, biodiversity, birds Dr. S.A. Ulenberg Senior Researcher. Biosystematics of Lepidoptera, Hymenoptera: Chalcidoidea, pest risk assessment, speciation, natural history Dr. A.J. de Winter Senior Researcher. Non-marine Mollusca, taxonomy, biogeography, Africa, slugs, Arionidae, Streptaxidae, invasive species, anatomy, phylogeny, Europe, Atlantic Islands, Dr. R.A. Vos Senior Researcher. Phyloinformatics, genomics, bioinformatics, computational biology, software engineering Dr. T.M. De Meulemeester Postdoc. Systematics of bee cryptic taxa and bee fossils, morphometrics, bumblebee nest architecture, tools for identification and monitoring of bees, wing shape Dr. F.J. Vonk Postdoc. Venom, reptiles, snakes, accessory gland, genome, evolution Dr. L.G. Carvalheiro Postdoc. Community ecology, food webs, plant-insect interactions, biodiversity dynamics, ecosystem services, pollinators Dr. H. Kappes Postdoc. Biodiversity, community assembly, detritivores, habitat heterogeneity, invasive species, land use change, leaf-litter- dwelling invertebrates, macroecology, microclimate, Mollusca: Gastropoda, species traits,

Botany

Prof.dr. E.F. SmetsScientific DirectorHead of the department (since 1-1-2014), systematics, phylogeny, morphology, anatomy, floral development (incl. evo-devo), biogeography, Ericales, Gentianales, Dioscoreales, Poales Dr. M.C. Roos Senior Researcher. Education coordinator, systematics, phylogeny, biogeography, biodiversity, Tree of Life, Malesia Prof.dr. P.C. van Welzen Senior Researcher. Malesia, Euphorbiaceae, Sapindaceae, phylogeny, biogeography Dr. H. Duistermaat Senior Researcher. Plant taxonomy, Flora, Netherlands, Poaceae, Amischotolype, SE Asia, Peninsular Malaysia

45 Dr. B. Gravendeel Senior Researcher. Ancient DNA, evo-devo, next generation sequencing, comparative genomics, orchids, wildlife forensics Dr. R.W.J.M. van der Ham Senior Researcher. Pollen, plant macrofossils, oak galls, drifting seeds, Dutch ferns, bee plants, simplicia, fossil echinoids, Bathonian fossils Dr. P.H. Hovenkamp Senior Researcher. Pteridophytes, systematics, historical biogeography, phylogeny Dr. J.J. Wieringa Senior Researcher. Biosystematics, geography, phytogeography, plant taxonomy, biodiversity, zoology, Fabaceae, West Africa, Gabon, Caesalpinioideae, Begonia, Fabales, Orthoptera Dr. J. Geml Tenure Tracker. DNA metabarcoding, phylogeography, root- associated fungi, soil community ecology, climate change Dr. F.R. Lens Tenure Tracker. Secondary woodiness, species distribution modeling, structure-function relationships, wood anatomy, xylem hydraulics Dr. M. Stech Tenure Tracker. Bryology, systematics, phylogenetics, biogeography Dr. D.C. Thomas Tenure Tracker. Alpha-taxonomy, phylogenetics, historical biogeography, molecular divergence time analyses, ancestral area reconstructions Dr. H. Stegenga Postdoc. Phycology, life histories and systematics of the Acrochaetiaceae, the Netherlands, red algae, eutrophication Dr. T. van der Niet Research Fellow. Speciation, pollination, phenotype, sapromyophily, phylogenetics, natural history, flower shape Dr. S. Mota de Oliviera Postdoc. Bryophytes, epiphytes, Amazon, canopy, Guianas Dr. H. ter Steege Research Fellow. Tree-diversity, Amazon, functional traits, carbon, dynamics, conservation Dr. T.R. van Andel Postdoc. African diaspora, medicinal plants, ritual plants, women’s health, traditional medicine, West Africa, Guianas, non-timber forest products, migrant ethnobotany Dr. V.S.F.T. Merckx Research Fellow. Mycoheterotrophy, evolution, biogeography, phylogenetics, mycorrhizal interactions Dr. N. Raes Postdoc. Biodiversity, biogeography, macroecology, ecology, species distribution modeling, evolution, vegetation classification, GIS, global climate change, palaeoclimate Dr. J. Nuytinck Postdoc. Lactarius, Lactifluus, Russulaceae, Russulales, Fungi, taxonomy, systematics, nomenclature, phylogeny, phylogeography, species delimitation, evolution, morphology, microscopy, ectomycorrhiza Dr. H.J. de Boer Postdoc. DNA barcoding, plant trade, ethnobotany, systematics, Cucurbitaceae, women’s health, molecular identification, tropical botany Dr. E. Tetetla Rangel Postdoc. Biodiversity patterns, landscape ecology, ecological niche modeling, tropical biomes Dr. E. Boer Postdoc. Remote sensing, GIS, spatial modeling, webdatabasing, identification keys

46 Dr. S.E.C. Sierra Daza Postdoc. Biodiversity, data mobilization, e-taxonomy, floras, faunas, infrastructure and collaboration projects interoperability, legacy literature, technical and semantic interoperability, sustainability, systematics, taxonomy

Geology

Dr. L.M. Kriegsman Senior Researcher. Head of the department, metamorphic geology, petrology, tectonics, geodynamics, volcanology Dr. S.K. Donovan Senior Researcher. Palaeozoic and Mesozoic invertebrates, Echinodermata, Crinoidea, UK, Antilles, Jamaica, trace fossils, crabs, barnacles, history of geology Dr. L.W. van den Hoek OstendeSenior Researcher. Fossil microvertebrates, the fossil insectivores of the Neogene, and mainly the Miocene Dr. W. Renema Senior Researcher. Fossil foraminifera, stratigraphy, palaeoenvironment, biogeography Dr. A.S. Schulp Senior Researcher. Mesozoic macrovertebrates, Mosasaurs, dinosaurs, dinosaur tracks, stable isotopes, biomechanics, palaeopathology, Maastrichtian Dr. I. van Waveren Senior Researcher. Permian, Carboniferous, fossil plant taphonomy, early conifers, differential growth Dr. F.P. Wesselingh Senior Researcher. Fossil Mollusca, fossil mollusks, Cenozoic, biodiversity, landscape evolution, taxonomy, turnover, extinction, immigration. Dr. J.C. Zwaan Senior Researcher. Mineralogy, natural history, geology, gemmology, emerald, pearls Dr. M. Rücklin Research Fellow. Palaeozoic fishes, developmental evolution, assembly of body plans, vertebrates, palaeontology Dr. L.J. Cotton Postdoc. Marine tropical biodiversity hotspots during the Eocene – Oligocene

47 NIOO

Netherlands Institute of Ecology, Wageningen  http://www.nioo.knaw.nl/en

Department Animal Ecology

The Department of Animal Ecology (AnE) has as its unifying theme of research the behavioural and evolutionary ecology of animals and it carries out fundamental ecological research with an open eye to society’s needs. In our research we aim to understand the causes and consequences of the average and the variance in life-history traits, such as timing or reproduction, parental care and aging. Animal Ecology has a long-standing tradition of field based studies on individually known animals, using hole-breeding passerines and water birds as model species. In recent years, this work has been complemented with detailed studies of birds in our excellent aviary and water bird facilities. Furthermore, we have recently started genomics work on wild birds. Our experimental work is complemented with modelling and finally, all our data are stored in a unique relational data warehouse.

Department Aquatic Ecology

Research within the department of Aquatic Ecology (AqE) aims to elucidate how ecological mechanisms, eco-evolutionary processes and abiotic factors govern the dynamics and structure of aquatic food webs. We link different levels of biological organization, ranging from microevolutionary change in plankton populations, through trophic and indirect interactions of food web modules, to the biotic and abiotic factors that structure aquatic communities in entire lakes. From 2005-2009 our aquatic research was based on three research themes: Consumer-resource interactions, Food web dynamics and Restoring and enhancing ecosystem services. From 2009 onwards, with the start of two new tenure track positions, a new research theme (Meta)community dynamics has been introduced. All four research themes are now strongly interconnected through exchange of concepts, ideas and data, involvement of staff and shared research methodologies. In fact, many of our projects and publications cover more than one theme.

Department Microbial Ecology

The microbial world contains an enormous metabolic potential that is fundamental to sustaining key ecosystem processes, such as the cycling of nutrients and primary production, across the breadth of the Earth’s diverse ecosystems. In order to understand these systems and to solve the major problems that are associated with human impact on their functioning, comprehensive knowledge of the microbiology of these systems is required. The primary focus of the department is on understanding the patterns and mechanisms of interactions among microbes and between microbes and their environment, how these interactions shape the structure and affect the functioning of microbial communities and, consequently, of ecosystems.

Department Terrestrial Ecology

The scientists of the department Terrestrial Ecology are experts in the ecology, physiology and chemistry of plants, and in soil ecology, entomology and behavioural biology. They investigate the interactions between plants, the animals and diseases that damage plants above and below the ground, and the natural enemies of these attackers. Central to researching how these interactions between the soil and aboveground affect biodiversity and ecosystem functioning are two questions: 1) How do plants in the wild defend themselves? 2) How do the interactions evolve? These questions are investigated in relation to altered land use, loss of biodiversity, biological invasions and climate change.

48 49