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Niels Raes

Dr. N. (Niels) Raes, Research fellow - Biodiversity Dynamics

Contact

Email: niels.raes@naturalis.nl
Phone: +31(0)71 751 9272
Room number: 3.02, Darwinweg 4
“Key to global food security is biodiversity.”

As scholar and student, I was fascinated by the variety of life, especially that in tropical jungles and on coral reefs. Soon I figured out that primary producers, plants, determine much of the existence of other life forms, which motivated me to study botanical ecology. After having inventoried many hectare plots of tropical rainforest in Guyana and Bolivia during my MSc. studies and thereafter I gained a thorough understanding of liana ecology and - biodiversity, and how liana communities are impacted by selective logging. Then, during my Ph.D. the opportunity arose to scale up my biodiversity studies to the entire island of Borneo. During this period, I developed my skills on species distribution modelling, spatial analyses and biodiversity informatics that I use in many of my current research projects. Being social, creative  and open minded has led to many collaborations in various fields of ecology where species distribution models have an added and unique value.

Recently, I have embarked on climate change proofing and selecting crop wild relatives (CWR), or species evolutionary related to crops, for climate-smart agriculture applications. Cross-breeding of food crops with CWR that have evolved to cope with future climatic conditions will increases the agricultural efficiency, relief the pressure on natural vegetation for arable land, and thereby conserves biodiversity and its wealth of genetic information.

Career

I studied Biology at Universiteit Utrecht, where I graduated in 1998. Between 1999 and 2003 I worked as research associate at Utrecht University, as botanist on an expedition to the Kaw Mountains in French Guiana, and as botanical ecologist at Proyecto Bolfor in Bolivia where I studied liana diversity in relation to selective logging. From 2003-2008 I conducted my Ph.D. research on the botanical diversity and phytogeography of Borneo at the National Herbarium of the Netherlands, Leiden University. After having been project coordinator 'Ecology' at a Dutch conservation NGO (Landschap Noord-Holland) for 1 year (2009), I started my research fellow position on the botanical biodiversity patterns of Sundaland at the National herbarium of the Netherlands (2010-2013). Currently, I hold a research fellow position at Naturalis Biodiversity Center on ecological niche profiling for climate smart agriculture applications.

Research

Research interest

My research is centred around species' ecological niches and their reciprocal geographical distributions, a.k.a. ecological niche modelling or species distribution modelling. Currently, I use ecological niche models (ENMs) to identify species that are evolutionary adapted to future climatic conditions as well as closely related to crop species, crop wild relatives. This allows safeguarding their germ plasm for future use in crop breeding programmes that potentially results in increased agricultural efficiency under global climate change conditions. Given that the global human population is expected to grow to 11 billion this century it is urgently needed that agricultural efficiency is increased to prevent the conversion of the remaining area of natural habitat in arable land, which in turn leads to the loss of biodiversity and its solution to global food security.

Together with several PhD and MSc students we also use SDMs to develop high spatial resolution biodiversity and biogeographic maps under current, future and past climatic conditions for various regions in the world. These analyses shed light on the dynamics of biodiversity under changing climatic conditions through time. Furthermore, the maps inform policy makers and NGOs in their conservation strategies to conserve biodiversity.

Keywords

ecology, biodiversitybiodiversity, biodiversity informatics, climate-smart agriculture, species distribution model, conservation, macroecology, spatial statistics, climate change

Current research topics

Ecological niche profiling for "climate-smart agriculture" applications

Using all botanical collections of the genus Cucumis combined with spatial data on climate and soil properties we define the ecological niche profile of all species with sufficient records (>5) that are phylogenetically related to melons and cucumber. With these niche profiles we can identfy species that have evolved to grow under warm and/or dry conditions and therefor are candidates for cross-breeding with these commercially important crops in order to improve and safeguard their harvest under future climate change.

Climate change proofing of WWF-NL priority conservation areas

WWF-NL has identified nine conservation priority areas for which I assess to what extent climate change based on various global climate models will likely affect the conservation targets. For this purpose I use multivariate analyses of climate anomalies, multivariate environmental similarity surfaces and species distribution modelling techniques.

Taxonomic and phylogenetic botanical diversity of Sundaland

For a large number of species representative for the flora of Sundaland I develop species distribution models and derive taxonomic diversity patterns. At the spatial scale of 5 arc-minutes this also allows the reconstruction of local communities for which we calculated the phylogenetic diversity using the APG III phylogeny. This will results in patterns of phylogenetic clustering and overdispersion, indicative for recent speciation or accumulation of species through time respectively.

Diversity and Phytogeography of Gabon

Ph.D. student Andre van Proosdij works on the diversity and phytogeography of Gabon using species distribution modelling techniques. He also furthers the understanding of the required number of unique collection records to build a reliable species distribution model. For that purpose we use artificial (generated non-existing) species. I am co-promotor in this project.

Orchid diversity and phytogeography of Papua New Guinea

Msc. Julien Vollering has developed diversity maps of orchidaceae on Papua New Guinea (PNG). For this purpose we used the identifications of over 7500 live specimens that were collected by Ed de Vogel and Andre Schuiteman and grown in the Hortus botanicus Leiden. This is arguably the largest dataset available of orchids on PNG and the first quatitative analysis of Orchid diversity and phytogeography on PNG.

Diversity and phytogeography of the herbaceous flora of the Cerrado, Brazil

Ph.D. student Aryanne Amaral from the University of Brasília (UnB), Brazil, has conducted the research for the third chapter in her thesis on the diversity and phytogeography of the herbaceous flore in the Cerrado biome in Brazil at Naturalis Biodiversity Center. We were able to develop species distribution models for over 5000 species by combining GBIF and SpeciesLink data which were subsequently used to develop biodiversity and phytogeographic patterns of the herbaceous flora of the Cerrado.

Badger habitat requirements in the Netherlands

MSc. Carme Piza Roca has conducted her MSc. research at Naturalis Biodiversity Center on the distribution of badgers in the Netherlands and the underlying factors that determine their occurrence. This is a collaboration with Radboud University Nijmegen and the 'Zoogdiervereninging'.

Collaborations

Spatial Analyses

  • Robert Hijmans - UC Davis
  • E. Emiel van Loon - IBED University of Amsterdam

Biodiversity Analyses

  • J.W. Ferry Slik - Universiti Brunei Darussalam
  • Saw Leng Guan - Forest Research Institute Malaysia (FRIM)
  • Tetsukaza Yahara - Kyushu University
  • Tiina Sarkinen - Edinburgh Botanical Gardens
  • Charles Cannon - Texas Tech University
  • Marc Sosef - Botanic Garden Meise

Climate-Smart Agriculture

  • Douwe de Boer - Genetwister
  • Joep Lambalk - ENZA zaden

Teaching

Courses

  • Methods of Biodiversity Analyses; Naturalis Biodiversity Center - section Botany 
  • Introduction to ArcGIS 10 – Part 2; Naturalis GeoPortal & Voyager GIS
  • Introduction to ArcGIS 10 – Part 1; Plotting species distributions on a map
  • Biodiversity: Trends in time and space; National Herbarium of the Netherlands, Leiden University
  • Richness of the World; Naturalis Biodiversity Center, Leiden
Available student projects

Public outreach

Publications

2017

Journals SCI, peer-reviewed

Wicaksono C.Y., Aguirre-Guiterrez J., Nouhra E., Pastor N., Raes N., Pacheco S., Geml J. 2017. Contracting montane cloud forests: a case study of the Andean alder (Alnus acuminata) and associated fungi in the Yungas. Biotropica 49: 141–152.
Go to website (DOI)

Chapters in books

Soudzilovskaia N.A., Vaessen S., Zelfde M. van ’t, Raes N. 2017. Global Patterns of Mycorrhizal Distribution and Their Environmental Drivers. Ecological Studies In: Tedersoo, L. (ed.). Biogeography of Mycorrhizal Symbiosis: 223-235 230: 223-235: Springer International Publishing,
Go to website (DOI)

2016

Journals SCI, peer-reviewed

Proosdij A.S.J. van, Sosef M.S.M., Wieringa J.J., Raes N. 2016. Minimum required number of specimen records to develop accurate species distribution models. Ecography 39: 542-552.
Go to website (DOI)

Schwallier R., Raes N., de Boer H.J., Vos R.A., van Vugt R., Gravendeel B. 2016. Phylogenetic analysis of niche divergence reveals distinct evolutionary histories and climate change implications for tropical carnivorous pitcher plants . Diversity and Distributions 22: 97-110.
Go to website (DOI)

Vollering J., Schuiteman A., Vogel E. de, Vugt R. van, Raes N. 2016. Richness patterns and phytogeographic regions of New Guinea as derived from species distribution models of orchids. Journal of Biogeography 43: 204-214.
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Proosdij A.S.J. van, Raes N., Wieringa J.J., Sosef M.S.M. 2016. Unequal Contribution of Widespread and Narrow-Ranged Species to Botanical Diversity Patterns. PLOS ONE 11: e0169200.
Go to website (URI)

2015

Journals SCI, peer-reviewed

Andel T.R. van, Croft S., Loon E.E. van, Quiroz D., Towns A.M., Raes N. 2015. Prioritizing West African medicinal plants for conservation and sustainable extraction studies based on market surveys and species distribution models. Biological Conservation 181: 173-181.
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Aguirre-Gutiérrez J., Serna-Chavez H.M., Villalobos-Arámbula A.R., Pérez de la Rosa J.A., Raes N. 2015. Similar but not equivalent: ecological niche comparison across closely related Mexican white pines. Diversity and Distributions 21: 245-257.
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Burridge A.K., Goetze E., Raes N., Huisman J., Peijnenburg K.T.C.A. 2015. Global biogeography and evolution of Cuvierina pteropods. BMC Evolutionary Biology 15: 1-16.
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Murray J., Grenyer R., Wunder S., Raes N., Jones J. 2015. Spatial patterns of carbon, biodiversity, deforestation threat and REDD+ projects in Indonesia. Conservation Biology 29: 1434-1445.
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Journals non-SCI, peer-reviewed

Heerlien M., Leusen J. van, Schnörr S., Jong-Kole S. de, Raes N., Hulsen K. van 2015. The natural history production line: an industrial approach to the digitization of scientific collections. Journal on Computing and Cultural Heritage 8: 3-11.
Go to website (URI)

2014

Journals SCI, peer-reviewed

Zhang M.-G., Zhou Z.-K., Chen W.-Y., Cannon C.H., Raes N., Slik J.W.F. 2014. Major declines of woody plant species ranges under climate change in Yunnan, China. Diversity and Distributions 20: 405-415.
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Geml J., Gravendeel B., Neilen M., Lammers Y., Raes N., Semenova T.A., Noordeloos M.E. 2014. The Contribution of DNA Metabarcoding to Fungal Conservation: Diversity Assessment, Habitat Partitioning and Mapping Red-Listed Fungi in Protected Coastal Salix repens Communities in the Netherlands. PLOS ONE 9: e99852.
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Welker F., Duijm E., Gaag K. van der, Geel B. van, Knijff P. de, Leeuwen J. van, Mol D., Plicht J. van der, Raes N., Reumer J., Gravendeel B. 2014. Analysis of coprolites from the extinct mountain goat Myotragus balearicus. Quaternary Research 81: 106-116.
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Budiharta S., Slik F., Raes N., Meijaard E., Erskine P.D., Wilson K.A. 2014. Estimating the Aboveground Biomass of Bornean Forest. Biotropica 46: 507-511.
Go to website (DOI)

Raes N., Cannon C.H., Hijmans R.J., Piessens T., Saw L.G., Welzen P.C. van, Slik J.W.F. 2014. Historical distribution of Sundaland’s Dipterocarp rainforests at Quaternary glacial maxima. Proceedings of the National Academy of Sciences of the United States of America 111: 16790-5.
Go to website (URI)

Chapters in books

Murray J.P., Grenyer R., Wunder S., Raes N., and Jones J.P.G. 2014. Can REDD+ deliver biodiversity co-benefits in Indonesia?. 442-443: Center for International Forestry Research (CIFOR), Bogor, Indonesia. ISBN 978-602-1504-55-0.
Go to website (URI)

2013

Journals SCI, peer-reviewed

Yahara T., Javadi F., Onoda Y., Queiroz L.P. de, Faith D.P., Prado D.E., Akasaka M., Kadoya T., Ishihama F., Davies S., Slik J.W.F., Yi T., Ma K., Bin C., Darnaedi D., Pennington R.T., Tuda M., Shimada M., Ito M., Egan A.N., Buerki S., Raes N., Kajita T., Vatanparast M., Mimura M., Tachida H., Iwasa Y., Smith G.F., Victor J.E., Nkonki T. 2013. Global legume diversity assessment: Concepts, key indicators, and strategies. Taxon 62: 249-266.

Aguirre Gutierrez J., Carvalheiro L.G., Polce C., Loon E.E. van, Raes N., Reemer M., Biesmeijer J.C. 2013. Fit-for-Purpose: Species Distribution Model Performance Depends on Evaluation Criteria - Dutch Hoverflies as a Case Study. PLOS ONE 8: e63708.
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Raes N., Sam L.G., Welzen P.C. van, Yahara T. 2013. Legume diversity as indicator for botanical diversity on Sundaland, South East Asia. South African Journal of Botany 38: 265-272.
Go to website (URI)

Chapters in books

Raes N., Filer D., Farjon A. 2013. Modelled conifer diversity; a pilot study. 483-486:

2012

Journals SCI, peer-reviewed

Raes N. 2012. Partial versus full species distribution models. Natureza & Conservação 10: 127-138.
Go to website (DOI)

Hsu R.C.-C., Tamis W.L.M., Raes N., Snoo G.R. de, Wolf J.H.D., Oostermeijer G., Lin S.-H. 2012. Simulating climate change impacts on forests and associated vascular epiphytes in a subtropical island of East Asia. Diversity and Distributions 18: 334-347.
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Zhang M.-G., Zhou Z.-K., Chen W.-Y., Slik J.W.F., Cannon C.H., Raes N. 2012. Using species distribution modeling to improve conservation and land use planning of Yunnan, China. Biological Conservation 153: 257-264.
Go to website (DOI)

Andel T. van, Mitchell S., Volpato G., Vandebroek I., Swier J., Ruysschaert S., Rentería Jiménez C.A., Raes N. 2012. In search of the perfect aphrodisiac: Parallel use of bitter tonics in West Africa and the Caribbean. Journal of Ethnopharmacology 143: 840-50.
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Wielstra B., Beukema W., Arntzen J.W., Skidmore A.K., Toxopeus A.G., Raes N. 2012. Corresponding mitochondrial DNA and niche divergence for crested newt candidate species. PLOS ONE 7: e46671.
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2011

Journals SCI, peer-reviewed

Slik J.W.F., Aiba S.-I., Bastian M., Brearley F.Q., Cannon C.H., Eichhorn K.A.O., Fredriksson G., Kartawinata K., Laumonier Y., Mansor A., Marjokorpi A., Meijaard E., Morley R.J., Nagamasu H., Nilus R., Nurtjahya E., Payne J., Permana A., Poulsen A.D., Raes N., Riswan S., Schaik C.P. van, Sheil D., Sidiyasa K., Suzuki E., Valkenburg J.L.C.H. van, Webb C.O., Wich S., Yoneda T., Zakaria R., Zweifel N. 2011. Soils on exposed Sunda Shelf shaped biogeographic patterns in the equatorial forests of Southeast Asia. Proceedings of the National Academy of Sciences of the United States of America 108: 12343-12347.
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Hoang V.S., Baas P., Kessler P.J.A., Slik J.W.F., Steege H. ter, Raes N. 2011. Human and environmental influences on plant diversity and composition in Ben En National Park, Vietnam. Journal of Tropical Forest Science 23: 328-337.

Journals non-SCI, peer-reviewed

Welzen P.C. van, Raes N. 2011. The floristic position of Java. Gardens’ Bulletin Singapore 63 (1&2): 329-339.

Chapters in books

Welzen P.C. van, Madern P.A. , Raes N., Parnell J.A.N., Simpson D.A., Moat J, Chayamarit K., Chantaranothai P., Boyce P.C., Bygrave P., Curtis T., Dransfield S., Esser H.-J, Jebb M.H.P., Kirkup D.W., Larsen K, Larsen S.S., Macklin J., Meade C. , Middleton D.J., Muasya A.M., Nielsen I., Prajaksood A., Pendry C.A., Pooma R., Suddee S., Sungkaew S., Teerawatananon A., Trias Blasi A., Wilkin P. 2011. The Current and Future Status of Floristic Provinces in Thailand. Information Science Reference, Hershey, PA, USA. ISBN 9781609606190.

Welzen P.C. van, Madern A., Raes N., Parnell J.A.N., Simpson D.A., Byrne C., Curtis T., Macklin J., Trias-Blasi A., Prajaksood A., Bygrave P., Dransfield S., Kirkup D.W., Moat J., Wilkin P., Couch C., Boyce P.C., Chayamarit K., Chantaranothai P., Esser H.-J., Jebb M.H.P., Larsen K., Larsen S.S., Nielsen I., Meade C., Middleton D.J., Pendry C.A., Muasya A.M., Pattharahirantricin N., Pooma R., Sudde S., Staples G.W., Sungkaew S., Teerawatananon A. 2011. The Current and Future Status of Floristic Provinces in Thailand. Information Science Reference (IGI Global), Hershey (PA).

2010

Journals SCI, peer-reviewed

Kruijer H.J.D, Raes N., Stech M. 2010. Modelling the distribution of the moss species Hypopterygium tamarisci (Hypopterygiaceae, Bryophyta) in Central and South America. Nova Hedwigia 91: 399-420.
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Schilthuizen M., Raes N., Linder P., Triantis K., Fernandez-Palacios J.M., Whittaker R.J. 2010. Special Issue: Evolutionary Islands - 150 Years After Darwin. Journal of Biogeography 37: 983-983.
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Hovenkamp P., Raes N. 2010. Indicators of endemism. Cladistics 26: 213-213.

Slik J.W.F., Aiba S.-I., Brearley F.Q., Cannon C.H., Forshed O., Kitayama K., Nagamasu H., Nilus R., Payne J., Paoli G., Poulsen A.D., Raes N., Sheil D., Sidiyasa K., Suzuki E., Valkenburg J.L.C.H. van 2010. Environmental correlates of tree biomass, basal area, wood specific gravity and stem density gradients in Borneo's tropical forests. Global Ecology and Biogeography 19: 50-60.
Go to website (DOI)

2009

Journals SCI, peer-reviewed

Raes N., Welzen P. C. van 2009. The demarcation and internal division of Flora Malesiana: 1857-present. Blumea: Journal of Plant Taxonomy and Plant Geography 54: 6-8.
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Slik J.W.F., Raes N., Aiba S.-I., Brearley F.Q., Cannon C.H., Meijaard E., Nagamasu H., Nilus R., Paoli G., Poulsen A.D., Sheil D., Suzuki E., Valkenburg J.L.C.H. van, Webb C.O., Wilkie P., Wulffraat S. 2009. Environmental correlates for tropical tree diversity and distribution patterns in Borneo. Diversity and Distributions 15: 523-532.
Go to website (DOI)

Raes N., Mols J.B., Willemse L.P.M., Smets E.F. 2009. Georeferencing specimens by combining digitized maps with SRTM digital elevation data and satellite images: a Bornean case study. Blumea: Journal of Plant Taxonomy and Plant Geography 54: 162-165.
Go to website (DOI)

Raes N., Roos M.C., Slik J.W.F., Loon E.E. van, Steege H. ter 2009. Botanical richness and endemicity patterns of Borneo derived from species distribution models. Ecography 32: 180-192.
Go to website (DOI)

Chapters in books

Haripersaud P.P., Steege H. ter, Raes N., Granville J.-J. de, Chevillotte H., Hof M. 2009. Using species distribution models to determine species richness and endemism patterns for the Guianas. 75-94:

2007

Journals SCI, peer-reviewed

Raes N., Steege H. ter 2007. A null-model for significance testing of presence-only species distribution models. Ecography 30: 727-736.
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Journals non-SCI, peer-reviewed

Raes N. 2007. Digitisation and georegistration of old expedition maps. Flora Malesiana Bulletin 14 (1&2): 30-31.

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