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Dick Groenenberg

Dr. D.S.J. (Dick) Groenenberg, Bioinformatics - Endless forms

Contact

Email: dick.groenenberg@naturalis.nl
Phone: +31 (0)71-75 11 910
Room number: 6.4.15.B, Sylviusweg 70

Research

Research interest

My research ambition is to utilize Next Generation Sequencing (NGS) for testing biological hypotheses. NGS is a powerful technique for acquiring large amounts of data from biological samples, including museum collections (museomics). Amongst others NGS data can be used to obtain more robust phylogenies (mitogenomcis), study biological mixtures (e.g. environmental DNA, stomach contents) and evolutionary processes (e.g. mitochondrial introgression, studies on gene arrangement).

One of the advantages of NGS obviously is the amount of data that can be generated (e.g. sequencing of amplicons from multiple markers, Long Range PCR products or entire genomes), but also the ability to obtain sequence data without PCR (which is often a bottleneck in ancient DNA studies) or prior sequence knowledge. These new sequencing techniques are likely to supersede traditional barcoding initiatives soon. My foremost interest is the evolution and phylogeny of terrestrial snails (Stylommatophora and terrestrial Caenogastropods), though these new techniques are not restricted to any group of organsims, or any biological hypothesis in particular.

PhD Thesis

Molecular Taxonomy and Natural History Collections

Keywords

museomics, next generation sequencing

Current research topics

Collaborations

Teaching

Courses

Evolutiebiologie1 2017 - assisted with wet-lab and computer practicums, wrote part of the manual and gave a lecture on sequence analysis.

Molecular Biological Techniques course 2016 - assisted with computer practicum barcoding / phylogeny reconstruction.

Molecular Biological Techniques course 2015 - assisted with computer practicum barcoding / phylogeny reconstruction.

Supervision MSc Students

2013 Cessa Rauch - A closer look; the secret kleptoplastic life of Elysia viridis
2012 Zoi Ferenzena - Host specificity and evolutionary relationships of Acoel flatworms living in association with corals
2010 Nicole Webster - Phylogenetic reconstruction and shell evolution of the Diplommatinidae (Gastropoda: Caenogastropoda)
2010 Cindy Scholte, Renske van Wijk, Jessy Dommershuizen, Devi van der Horst, Melanie Meijer zu Schlochtern, Rik Lievers - Using DNA-barcoding to make the necrobiont beetle family Cholevidae accessible for forensic entomology
2010 Paul Hoekstra - Phylogenetic relationships between isolated populations of the limestone-dwelling microsnail Gyliotrachela hungerfordiana (Gastropoda: Vertiginidae)

Supervision BSc Students

2017 Josine Meijer - Optimization of Long Range (LR) Polymerase Chain Reaction (PCR)
2017 Sebastiaan de Vriend & Sjors Heijboer - 3D Anlyses of scapulae of Dutch whales and dolphins
2016 Marten Hoogenveen -short internship - Bioinformatics of Great Apes (Pongo and Gorilla)
2015 Sebastiaan de Vriend, Ilke van den Hoek, Mark uit het Broek, Sebastiaan Klein - Museomics of Gorilla gorilla
2015 Laura Bouw, Sharon Bouw - Potyviridae: alignment of LVA (Lily Virus A) sequences
Available student projects

Publications

2017

Journals SCI, peer-reviewed

Voelker G., Tobler M., Prestridge H.L., Duijm E., Groenenberg D.S.J., Hutchinson M.R., Martin A.D., Nieman A., Rooselaar C.S., Huntley J.W. 2017. Three new species of Stiphrornis (Aves: Muscicapidae) from the Afro-tropics, with a molecular phylogenetic assessment of the genus. Systematics and Biodiversity 15: 87-104.
Go to website (DOI)

Groenenberg D.S.J., Harl J., Duijm E., Gittenberger E. 2017. The complete mitogenome of Orcula dolium (Draparnaud, 1801); ultra-deep sequencing from a single long-range PCR using the Ion-Torrent PGM. Hereditas 154: 1-10.
Go to website (DOI)

Langeveld B.W., Mol D., Zazula G.D., Gravendeel B., Eurlings M., McMichael C.N.H., Groenenberg D., Reenen G.B.A. van, Palmeira M., Vogel J., Geel B. van 2017. A multidisciplinary study of a late Pleistocene arctic ground squirrel (Urocitellus parryii) midden from Yukon, Canada. Quaternary Research: pending.
Go to website (DOI)

2016

Journals SCI, peer-reviewed

Groenenberg D.S.J., Subai P., Gittenberger E. 2016. Systematics of Ariantinae (Gastropoda, Pulmonata, Helicidae), a new approach to an old problem. Contributions to Zoology 85: 37-65.
Go to website (URI)

Gittenberger E., Kokshoorn B., Bößneck U., Reijnen B., Groenenberg D.S.J. 2016. Granopupa in Iran, monophyly, and the fossil Granariinae (Gastropoda, Pulmonata, Chondrinidae). ZooKeys 592: 27-37.
Go to website (DOI)

2015

Journals non-SCI, peer-reviewed

Zallot E., Groenenberg D.S.J., Mattia W. de, Fehér Z., Gittenberger E. 2015. Genera, subgenera and species of the Cochlostomatidae (Gastropoda, Caenogastropoda, Cochlostomatidae). Basteria 78: 63-88.

2013

Journals SCI, peer-reviewed

Gravendeel B., Groot A. de, Kik M., Beentjes K.K., Bergman H., Caniglia R., Cremers H., Fabbri E., Groenenberg D., Grone A., Groot Bruinderink G., Font L., Hakhof J., Harms V., Jansman H., Janssen R., Lammertsma D., Laros I., Linnartz L., Marel D. van der, Mulder J.L., Mije S. van der, Nieman A.M., Nowak C., Randi E., Rijks M., Speksnijder A., Vonhof H.B. 2013. The first wolf found in the Netherlands in 150 years was the victim of a wildlife crime. Lutra 56: 93-109.

2012

Journals SCI, peer-reviewed

Groenenberg D.S.J., Pirovano W., Gittenberger E., Schilthuizen M. 2012. The complete mitogenome of Cylindrus obtusus (Helicidae, Ariantinae) using Illumina next generation sequencing. BMC Genomics 13: 114.
Go to website (DOI)

Groenenberg D.S.J., Courcy C. de, Linnie M., Oosterweghel L. 2012. On the identity of the first rhinoceros owned by of the Dublin Zoo (Dagger 1865); genetic characterisation of a poorly preserved museum specimen. Biology and Environment-Proceedings of the Royal Irish Academy 112B: 285-291.
Go to website (DOI)

Nieukerken E.J. van, Doorenweerd C., Stokvis F.R., Groenenberg D.S.J. 2012. DNA barcoding of the leaf-mining moth subgenus Ectoedemia s. str. (Lepidoptera: Nepticulidae) with COI and EF1-alpha: two are better than one in recognising cryptic species. Contributions to Zoology 81: 1-24.

2011

Journals SCI, peer-reviewed

Schilthuizen M., Scholte C., Wijk R.E.J. van, Dommershuijzen J., Horst D. van der, Schlochtern M.M.Z., Lievers R., Groenenberg D.S.J. 2011. Using DNA-barcoding to make the necrobiont beetle family Cholevidae accessible for forensic entomology. Forensic Science International 210: 91-95.
Go to website (DOI)

Groenenberg D.S.J., Dekker R.W.R.J. 2011. A mouse's tail: How to settle an insurance dispute. Forensic Science International 207: E24-E27.
Go to website (DOI)

Groenenberg D.S.J., Neubert E., Gittenberger E. 2011. Reappraisal of the "Molecular phylogeny of Western Palaearctic Helicidae s.l. (Gastropoda: Stylommatophora)": When poor science meets GenBank. Molecular Phylogenetics and Evolution 61: 914-923.
Go to website (DOI)

Groenenberg D.S.J., Wesselingh F.P., Rajagopal S., Jansen J.M., Bos M.M., Velde G. van der, Gittenberger E., Hoeksema B.W., Raad H., Hummel H. 2011. On the identity of broad-shelled mussels (Mollusca, Bivalvia, Mytilus) from the Dutch delta region. Contributions to Zoology 80: 95-106.
Go to website (URI)

2010

Journals non-SCI, peer-reviewed

Breure A.S.H., Groenenberg D.S.J., Schilthuizen M. 2010. New insights in the phylogenetic relations within the Orthalicoidea (Gastropoda, Stylommatophora) based on 28S sequence data. Basteria 74: 25-31.

2009

Journals SCI, peer-reviewed

Groenenberg D.S.J., Goud J., Heij A. de, Gittenberger E. 2009. Molecular phylogeny of North Sea Sepiolinae (Cephalopoda: Sepiolidae) reveals an overlooked Sepiola species. Journal of Molluscan Studies 75: 361-369.
Go to website (DOI)

2008

Journals SCI, peer-reviewed

Reemer M., Groenenberg D.S.J., Achterberg C. van, Peeters T.M.J. 2008. Taxonomic assessment of Andrena rosae and A stragulata by DNA-sequencing (Hymenoptera : Apoidea : Andrenidae). Entomologia Generalis 31: 21-32.

Groenenberg D.S.J., Beintema A.J., Dekker R.W.R.J., Gittenberger E. 2008. Ancient DNA elucidates the controversy about the Flightless Island Hens (Gallinula sp.) of Tristan da Cunha. PLOS ONE 3: e1835.
Go to website (DOI)

2007

Journals SCI, peer-reviewed

Arntzen J.W., Groenenberg D.S.J., Alexandrino J., Ferrand N., Sequeira F. 2007. Geographical variation in the golden-striped salamander, Chioglossa lusitanica Bocage, 1864 and the description of a newly recognized subspecies. Journal of Natural History 41: 925-936.
Go to website (DOI)

Ofwegen L.P. van, Groenenberg D.S.J. 2007. A centuries old problem in nephtheid taxonomy approached using DNA data (Coelenterata : Alcyonacea). Contributions to Zoology 76: 153-178.

2006

Journals SCI, peer-reviewed

Weerd D.R. uit de, Groenenberg D.S.J., Schilthuizen M., Gittenberger E. 2006. Reproductive character displacement by inversion of coiling in clausiliid snails (Gastropoda, Pulmonata). Biological Journal of the Linnean Society 88: 155-164.

Gittenberger E., Groenenberg D.S.J., Kokshoorn B., Preece R.C. 2006. Molecular trails from hitch-hiking snails. Nature 439: 409-409.
Go to website (DOI)

2004

Journals SCI, peer-reviewed

Gittenberger E., Piel W.H., Groenenberg D.S.J. 2004. The Pleistocene glaciations and the evolutionary history of the polytypic snail species Arianta arbustorum (Gastropoda, Pulmonata, Helicidae). Molecular Phylogenetics and Evolution 30: 64-73.
Go to website (DOI)