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Dick Groenenberg

Dick Groenenberg

Species evolve and so does the way we study them. In this era of high-throughput DNA sequencing there are virtually no limitations on obtaining data, but analyses of these datasets increasingly require computational skills. Since 2002 I have been working for Naturalis as a lab-techinician, researcher and currently as a bioinformatician. I obtained my PhD on "Molecular Taxonomy and Natural History Collections" in Leiden in 2012.

Keywords

Bioinformatics, Phylogenetics, Stylommatophora, Next Generation Sequencing, Mitogenomics, ancient DNA, Galaxy, Scripting

Dr. D.S.J. (Dick) Groenenberg

Bioinformatician
lab
L.01-08

dick.groenenberg@naturalis.nl

+31 (0)71 751 1911

Research
interest

"Changes in DNA allow us to witness evolution and to reconstruct genealogical trees. The relation between genetics, morphology and taxonomy has never been more measurable."

During my MSc internship I learned that copse snails ('heesterslakken') exist in two forms; either with globular or depressed shells. The former is widespread and consists of only one species, whereas the latter is restricted to montane areas and has many (sub)species. In agreement with the morphology (outgroup comparision), our DNA study showed that a depressed shell represented the ancestral (plesiomorphic) condition. This demonstrated that mountain tops (or 'nunataks') can act as evolutionary islands and that the size of a distribution area ('commonness') doesn't have to be indicative of the age of a group. So my interest in molecules, cladistics and landsnails (especially Ariantinae) started.

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Key
publications

  • Gittenberger E., Groenenberg D.S.J., Kokshoorn B., Preece R.C. 2006. Molecular trails from hitch-hiking snails. Nature 439: 409-409.
  • 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(3): e1835. 
  • 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. 3 Molecular Phylogenetics and Evolution 61: 914-923.
  • 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.
  • 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. 1 Hereditas 154: 10 p. 1-10.

All publications

Publications

2021

Journals SCI, peer-reviewed

Saenko S.V., Groenenberg D.S.J., Davison A., Schilthuizen M. 2021. The draft genome sequence of the grove snail Cepaea nemoralis. Genes, Genomes, Genetics 11 (2) : jkaa071. DOI https://doi.org/10.1093/g3journal/jkaa071
2019

Journals SCI, peer-reviewed

Gittenberger E., Reijnen B.T., Groenenberg D.S.J. 2019. Terrestrial gastropods of the Maldives, all of which invasive? Journal of Conchology 43 (4) : 31 p. 353-383.
Groenenberg D.S.J., Duijm E. 2019. The complete mitogenome of the Roman snail Helix pomatia Linnaeus 1758 (Stylommatophora: Helicidae). MITOCHONDRIAL DNA PART B-RESOURCES 4 (1) : 1494-1495. DOI https://doi.org/10.1080/23802359.2019.1601512
Kunihiro S., Farenzena Z., Hoeksema B.W., Groenenberg D.S.J., Hermanto B., Reimer J. 2019. Morphological and phylogenetic diversity of Waminoa and similar flatworms (Acoelomorpha) in the western Pacific Ocean. Zoology 136: 13 p. 125692. Elsevier. DOI https://doi.org/10.1016/j.zool.2019.06.002
2018

Journals non-SCI, peer-reviewed

Vriend S. de, Heijboer S., Groenenberg D.S.J., Langeveld B., Gravendeel B. 2018. 3D bone analysis for improving species identification: a case study on scapulae of selected small toothed whales occurring along the Dutch coast. Lutra 61 (2) : 283-296.

Journals SCI, peer-reviewed

Bogarín D., Perez-Escobar O.A., Groenenberg D., Holland S.D., Karremans A.P., Lemmon E.M., Lemmon A.R., Pupulin F., Smets E., Gravendeel B. 2018. Anchored hybrid enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex. Molecular Phylogenetics and Evolution 129: 27-47. DOI https://doi.org/10.1016/j.ympev.2018.07.014
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 2018. A multidisciplinary study of a late Pleistocene arctic ground squirrel (Urocitellus parryii) midden from Yukon, Canada. Quaternary Research 89 (1) : 333-351. DOI https://doi.org/10.1017/qua.2017.93
2017

Journals SCI, peer-reviewed

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 p. 1-10. Springer. DOI https://doi.org/10.1186/s41065-017-0028-2
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 (2) : 18 p. 87-104. DOI https://doi.org/10.1080/14772000.2016.1226978
2016

Journals SCI, peer-reviewed

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 (592) : 11 p. 27-37. Pensoft. DOI https://doi.org/10.3897/zookeys.592.7907
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 (2) : 17 p. 93-109.
Lammers Y., Kremer D., Brakefield P.M., Groenenberg D.S.J., Pirovano W., Schilthuizen M. 2013. SNP genotyping for detecting the 'rare allele phenomenon' in hybrid zones. Molecular Ecology Resources 13 (4) : 237-242. DOI https://doi.org/10.1111/1755-0998.12044
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. DOI https://doi.org/10.1186/1471-2164-13-114
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) : 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 (13) : 91-95. DOI https://doi.org/10.1016/j.forsciint.2011.02.003
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 (2) : 95-106.
http://dpc.uba.uva.nl/cgi/t/text/get-pdf?c=ctz%3Bidno%3D8002a01
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 (3) : 914-923. DOI https://doi.org/10.1016/j.ympev.2011.08.024
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 (13) : 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. DOI https://doi.org/10.1093/mollus/eyp032
2008

Journals SCI, peer-reviewed

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 (3) : e1835. DOI https://doi.org/10.1371/journal.pone.0001835
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 (1) : 21-32.
2007

Journals SCI, peer-reviewed

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 (3) : 153-178.
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 (1316) : 925-936. DOI https://doi.org/10.1080/00222930701300147
2006

Journals SCI, peer-reviewed

Gittenberger E., Groenenberg D.S.J., Kokshoorn B., Preece R.C. 2006. Molecular trails from hitch-hiking snails. Nature 439 (7075) : 409-409. DOI https://doi.org/10.1038/439409a
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 (2) : 155-164.
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 (1) : 64-73. DOI https://doi.org/10.1016/S1055-7903(03)00182-9