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Rutger Vos

Rutger Vos

I want to help understand where biodiversity comes from and where it might be going in a changing world. To understand the outcomes of evolutionary diversity in the broad scale we have to represent it in silico, and develop the data sets, tools, algorithms, hypotheses and tests to make sense of it all. 

Keywords

comparative genomics, big data, computational biology, open source, emergent characters, phyloinformatics, comparative analysis

Dr. Rutger Vos

Researcher / Bioinformatician
Understanding evolution

rutger.vos@naturalis.nl
+31 (0)6 27 08 5806

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Research
interest

My main research interest is to understand the processes that generate patterns of biodiversity in space and time across large groups of species.

I seek to use open data integration, phylogenetic inference, divergence data estimation, and the comparative analysis of complex data to characterize the patterns of diversity and test hypotheses of the underlying processes of evolution. I do this in collaborative settings where I contribute my expertise in open source scientific software development, algorithm development, and high performance computing.

tunicaat
Budding plant

Current
topics

A selection of the topics I am working on currently.

En Tibi herbarium of tomato

Ancient tomato genomics

Past processes that shaped the current genetic diversity of the domesticated tomato are still largely unknown. Using Illumina HiSeq, we sequenced and compared full genomes from tomato accessions stored worldwide in genebanks and herbaria up to 182 years…
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ARISE logo

ARISE: knowing Nature in the Netherlands

In the ARISE project, Naturalis, together with the Westerdijk Fungal Biodiversity Institute and the universities of Amsterdam and Twente, is building an infrastructure that knows and recognizes all (multicellular) Dutch species. Every species, every sample…
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Key
publications

All publications

Publications

2024

Journals SCI, peer-reviewed

Padfield D., Kay S., Vos R., Quince C., Vos M. 2024. Macroevolutionary dynamics in micro-organisms: generalists give rise to specialists across biomes in the ubiquitous bacterial phylum Myxococcota.. Molecular Biology and Evolution 41 (5) DOI https://doi.org/10.1093/molbev/msae088.
2023

Journals SCI, peer-reviewed

Macher J-N., Coots N.L., Poh Y-P., Girard E.B., Langerak A., Muñoz-Gómez S.A., Sinha S.D., Jirsová D., Vos R., Wissels R., Gile G.H., Renema W., Wideman J.G. 2023. Single-Cell Genomics Reveals the Divergent Mitochondrial Genomes of Retaria (Foraminifera and Radiolaria).. MBIO 14 (2) : e0030223. DOI https://doi.org/10.1128/mbio.00302-23
2022

Journals SCI, peer-reviewed

Andel T. van, Vos R.A., Michels E., Stefanaki A. 2022. Sixteenth-century tomatoes in Europe: who saw them, what they looked like, and where they came from.. PeerJ – the Journal of Life & Environmental Sciences 10: e12790. DOI https://doi.org/10.7717/peerj.12790
2021

Journals SCI, peer-reviewed

Macher J.-N., Wideman J.G., Girard E.B., Langerak A., Duijm E., Jompa J., Sadekov A., Vos R., Wissels R., Renema W. 2021. First report of mitochondrial COI in foraminifera and implications for DNA barcoding.. Scientific Reports 11: 22165. DOI https://doi.org/10.1038/s41598-021-01589-5
Hooft van Huysduynen A., Janssens S., Merckx V., Vos R., Valente L., Zizka A., Larter M., Karabayir B., Maaskant D., Witmer Y., Fernández-Palacios J.M., Nascimento L. de, Jaén-Molina R., Caujapé Castells J., Marrero-Rodríguez Á., Arco M. del, Lens F. 2021. Temporal and palaeoclimatic context of the evolution of insular woodiness in the Canary Islands.. Ecology and Evolution 11 (17) : 12220-12231. DOI https://doi.org/10.1002/ece3.7986
https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.7986
2020

Journals non-SCI, peer-reviewed

Bennett D., Hettling H., Silvestro D., Vos R.A., Antonelli A. 2020. outsider: Install and run programs, outside of R, inside of R. Journal of Open Source Software 5 (45) DOI https://doi.org/10.21105/joss.02038
Tennant J., Agarwal R., ... Vos R., Worthington S., Yarkoni T. 2020. A tale of two 'opens': intersections between Free and Open Source Software and Open Scholarship. SocArXiv DOI https://doi.org/10.31235/osf.io/2kxq8

Journals SCI, peer-reviewed

Bochove K. van, Bakker F.T., Beentjes K.K., Hemerik L., Vos R.A., Gravendeel B. 2020. Organic matter reduces the amount of detectable environmental DNA in freshwater. Ecology and Evolution 10 (8) : 3647-3654. DOI https://doi.org/10.1002/ece3.6123
Schwallier R., Wely V. van, Baak M., Vos R., Heuven B.J. van, Smets E.F., Vugt R.R. van, Gravendeel B. 2020. Ontogeny and anatomy of the dimorphic pitchers of Nepenthes rafflesiana Jack. Plants 9 (11) : 1603. DOI https://doi.org/10.3390/plants9111603
2019

Journals non-SCI, peer-reviewed

Vos R.A., Emmanuel N.N., Aguiyi J.C. 2019. WGS2NCBI - Toolkit for preparing genomes for submission to NCBI. Journal of Open Source Software 4 (36) : 1364. Open Journals. DOI https://doi.org/10.21105/joss.01364

Journals SCI, peer-reviewed

Vos R. 2019. DBTree ‐ Very large phylogenies in portable databases. Methods in Ecology and Evolution 11 (3) : 457-463.
2018

Journals non-SCI, peer-reviewed

Bennett D., Hettling H., Silvestro D., Vos R.A., Antonelli A. 2018. restez: Create and Query a Local Copy of GenBank in R. Journal of Open Source Software 3 (31) : 1102. DOI https://doi.org/10.21105/joss.01102
Bennett D.J., Hettling H., Silvestro D., Zizka A., Bacon C.D., Faurby S., Vos R.A., Antonelli A. 2018. phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R. Life 8 (2) : 11 p. 20. DOI https://doi.org/10.3390/life8020020

Journals SCI, peer-reviewed

Eiserhardt W.L., Antonelli A., Bennett D.J., Botigué L.R., Burleigh J.G., Dodsworth S., Enquist B.J., Forest F., Kim J.T., Kozlov A.M., Leitch I.J., Maitner B.S., Mirarab S., Piel W.H., Pérez‐Escobar O.A., Pokorny L., Rahbek C., Sandel B., Smith S.A., Stamatakis A., Vos R.A., Warnow T., Baker W.J. 2018. A roadmap for global synthesis of the plant tree of life. American Journal of Botany 105 (3) : 614-622. DOI https://doi.org/10.1002/ajb2.1041
2017

Journals SCI, peer-reviewed

Antonelli A., Hettling H., Condamine F.L., Vos K., Nilsson R.H., Sanderson M.J., Sauquet H., Scharn R., Silvestro D., Töpel M., Bacon C.D., Oxelman B., Vos R.A. 2017. Towards a self-updating platform for estimating rates of speciation and migration, ages, and relationships of taxa (SUPERSMART). Systematic Biology 66: 152-166. DOI https://doi.org/10.1093/sysbio/syw066
Essens T., Langevelde F. van, Vos R.A., Swaay C.A.M. van, Vries M.F.W. de 2017. Ecological determinants of butterfly vulnerability across the European continent. Journal of Insect Conservation 21 (3) : 439-450. DOI https://doi.org/10.1007/s10841-017-9972-4
Langevelde F. van, Braamburg-Annegarn M., Huigens M.E., Groendijk R., Poitevin O., Deijk J.R. van, Ellis W.N., Grunsven R.H.A. van, Vos, R. de, Vos R.A., Franzén M., Wallis DeVries M.F. 2017. Declines in moth populations stress the need for conserving dark nights. Global Change Biology: pending. DOI https://doi.org/10.1111/gcb.14008
Pentinsaari M., Vos R., Mutanen M. 2017. Algorithmic single-locus species delimitation: effects of sampling effort, variation and non-monophyly in four methods and 1870 species of beetles. Molecular Ecology Resources 17 (3) : 393-404. DOI https://doi.org/10.1111/1755-0998.12557
Stoltzfus A., Rosenberg M., Lapp H., Budd A., Cranston K., Pontelli E., Oliver S., Vos R.A. 2017. Community and Code: Nine Lessons from Nine NESCent Hackathons. F1000Research 6: 19 p. 786-805. DOI https://doi.org/10.12688/f1000research.11429.1
Dirks-Mulder A., Butot R., Schaik P. van, Wijnands J.W.P.M., Berg R. van den, Krol L., Doebar S., Kooperen K. van, Boer H. de, Kramer E.M., Smets E.F., Vos R.A., Vrijdaghs A., Gravendeel B. 2017. Exploring the evolutionary origin of floral organs of Erycina pusilla, an emerging orchid model system. BMC Evolutionary Biology 17: 89. DOI https://doi.org/10.1186/s12862-017-0938-7
2016

Journals SCI, peer-reviewed

Boettiger C., Chamberlain S., Vos R., Lapp H. 2016. RNeXML: a package for reading and writing richly annotated phylogenetic, character and trait data in r. Methods in Ecology and Evolution 7 (3) : 352–357. DOI https://doi.org/10.1111/2041-210X.12469
Lens F., Vos R., Charrier G., Niet T. van der, Merckx V., Baas P., Aguirre Gutierrez J., Jacobs B., Chacon Doria L., Smets E., Delzon S., Janssens S. 2016. Scalariform-to-simple transition in vessel perforation plates triggered by differences in climate during the evolution of Adoxaceae. Annals of Botany 118 (5) : 1043-1056. DOI https://doi.org/10.1093/aob/mcw151
Hardisty A.R., Bacall F., Beard N., Balcázar-Vargas M.-P., Balech B., Barcza Z., Bourlat S.J., Giovanni R. De, Jong Y. de, Leo F. De, Dobor L., Donvito G., Fellows D., Fernandez Guerra A., Ferreira N., Fetyukova Y., Fosso B., Giddy J., Goble C., Güntsch A., Haines R., Ernst V.H., Hettling H., Hidy D., Horváth F., Ittzés D., Ittzés P., Jones A., Kottmann R., Kulawik R., Leidenberger S., Lyytikäinen-Saarenmaa P., Mathew C., Morrison N., Nenadic A., Nieva de la Hidalga A., Obst M., Oostermeijer G., Paymal E., Pesole G., Pinto S., Poigné A., Quevedo Fernandez F., Santamaria M., Saarenmaa H., Sipos G., Sylla K.-H., Tähtinen M., Vicario S., Vos R.A., Williams A.R., Yilmaz P. 2016. BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology. BMC Ecology 16 (49) : 49. DOI https://doi.org/10.1186/s12898-016-0103-y
Schilthuizen M., Santos Pimenta L.P., Lammers Y., Steenbergen P.J., Flohil M., Beveridge N.G.P., Duijn, P.T. van, Meulblok M.M., Sosef N., Ven R. van de, Werring R., Beentjes K.K., Meijer K., Vos R.A., Vrieling K., Gravendeel B., Choi Y., Verpoorte R., Smit C., Beukeboom L.B. 2016. Incorporation of an invasive plant into a native insect herbivore food web. PeerJ 4: e1954. DOI https://doi.org/10.7717/peerj.1954
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 (1) : 97-110. DOI https://doi.org/10.1111/ddi.12382
Mutanen M., Kivelä S.M., Vos R.A., Doorenweerd C., Ratnasingham S., Hausmann A., Huemer P., Dincă V., Nieukerken E.J. van, Lopez-Vaamonde C., Vila R., Aarvik L., Decaëns T., Efetov K.A., Hebert P.D.N., Johnsen A., Karsholt O., Pentinsaari M., Rougerie R., Segerer A., Tarmann G., Zahiri R., Godfray C.J. 2016. Species-Level Para- and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera. Systematic Biology 65: 1024-1040. DOI https://doi.org/10.1093/sysbio/syw044
Hoehndorf R., Alshahrani M., Gkoutos G., Gosline G., Groom Q., Hamann T., Kattge J., Mota de Oliveira S., Schmidt M., Sierra S., Smets E., Vos R.. Weiland C. 2016. The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. Journal of Biomedical Semantics 7: 65. DOI https://doi.org/10.1186/s13326-016-0107-8
2015

Journals non-SCI, peer-reviewed

Journals SCI, peer-reviewed

Thessen A.E., Bunker D.E., Buttigieg P.L., Cooper L.D., Dahdul W.M., Domisch S., Franz N.M., Jaiswal P., Lawrence-Dill C.J., Midford P.E., Mungall C.J., Ramírez M.J., Specht C.D., Vogt L., Vos R.A., Walls R.L., White J.W., Zhang G., Deans A.R., Huala E., Lewis S.E., Mabee P.M. 2015. Emerging semantics to link phenotype and environment. PeerJ 3: 39 p. e1470. DOI https://doi.org/10.7717/peerj.1470
2014

Journals non-SCI, peer-reviewed

Vos R.A., Biserkov J.V., Balech B., Beard N., Blissett M., Brenninkmeijer C., Dooren T. van, Eades D., Gosline G., Groom Q.J., Hamann T.D., Hettling H., Hoehndorf R., Holleman A., Hovenkamp P., Kelbert P., King D., Kirkup D., Lammers Y., DeMeulemeester T., Mietchen D., Miller J.A., Mounce R., Nicolson N., Page R., Pawlik A., Pereira S., Penev L., Richards K., Sautter G., Shorthouse D.P., Tähtinen M., Weiland C., Williams A.R., Sierra S. 2014. Enriched biodiversity data as a resource and service. Biodiversity Data Journal 2: 15 p. 1-15. Pensoft. DOI https://doi.org/10.3897/BDJ.2.e1125
http://bdj.pensoft.net/articles.php?id=1125

Journals SCI, peer-reviewed

Geel B. van, Protopopov A., Bull I., Duijm E., Gill F., Nieman A., Rudaya N., Trofimova S., Tikhonov A., Vos R.A., Zhilich S., Gravendeel B. 2014. Multiproxy diet analysis of the last meal of an early Holocene Yakutian Bison. Journal of Quaternary Science 29 (3) : 261-268. DOI https://doi.org/10.1002/jqs.2698
Katayama T., Wilkinson M.D., Aoki-Kinoshita K.F., Kawashima S., Yamamoto Y., Yamaguchi A., Okamoto S., Kawano S., Kim J.-D., Wang Y., Wu H., Kano Y., Ono H., Bono H., Kocbek S., Aerts J., Akune Y., Antezana E., Arakawa K., Aranda B., Baran J., Bolleman J., Bonnal R.J.P., Buttigieg P.L., Campbell M.P., Chen Y., Chiba H., Cock P.J.A., Cohen K.B., Constantin A., Duck G., Dumontier M., Fujisawa T., Fujiwara T., Goto N., Hoehndorf R., Igarashi Y., Itaya H., Ito M., Iwasaki W., Kalas M., Katoda T., Kim T., Kokubu A., Komiyama Y., Kotera M., Laibe C., Lapp H., Lütteke T., Marshall M.S., Mori T., Mori H., Morita M., Murakami K., Nakao M., Narimatsu H., Nishide H., Nishimura Y., Nystrom-Persson J., Ogishima S., Okamura Y., Okuda S., Oshita K., Packer N.H., Prins P., Ranzinger R., Rocca-Serra P., Sansone S., Sawaki H., Shin S.-H., Splendiani A., Strozzi F., Tadaka S., Toukach P., Uchiyama I., Umezaki M., Vos R., Whetzel P.L., Yamada I., Yamasaki C., Yamashita R., York W.S., Zmasek C.M., Kawamoto S., Takagi T. 2014. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. Journal of Biomedical Semantics 5 (1) : 5. DOI https://doi.org/10.1186/2041-1480-5-5
Lammers Y., Peelen T., Vos R.A., Gravendeel B. 2014. The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data. BMC Bioinformatics 15 (44) : 44. DOI https://doi.org/10.1186/1471-2105-15-44
Aflitos S., Schijlen E., Finkers R., Smit S., Wang J., Zhang G., Li N., Mao L., Jong H. de, Bakker F., Gravendeel B., Breit T., Dirks R., Huits H., Struss D., Swanson-Wagner R., Leeuwen H. van, Ham R.C.H.J. van, Fito L., Guignier L., Sevilla M., Ellul P., Ganko E., Kapur A., Reclus E., Geus B. de, Geest H. van de, Lintel Hekkert B. te, Haarst J. van, Smits L., Koops A., Sanchez-Perez G., Heusden A.W. van, Visser R., Quan Z., Min J., Liao L., Wang X., Wang G., Yue Z., Yang X., Xu N., Schranz E., Smets E., Vos R.A., Rauwerda J., Ursem R., Schuit C., Kerns M., Berg J. van den, Vriezen W., Janssen A., Jahrmann T., Moquet F., Bonnet J., Peters S. 2014. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant Journal 80 (1) : 136-148. DOI https://doi.org/10.1111/tpj.12616
Gravendeel B., Protopopov A., Bull I., Duijm E., Gill F., Nieman A., Rudaya N., Tikhonov A.N., Trofimova S., Reenen G.B.A. van, Vos R., Zhilich., Geel B. van 2014. Multiproxy study of the last meal of a mid-Holocene Oyogos Yar horse, Sakha Republic, Russia. Holocene 24 (9) : 1-9. DOI https://doi.org/10.1177/0959683614540953
2013

Journals SCI, peer-reviewed

Maryam P., Sheth A.P., Ranabahu A., Vos R.A., Leebens-Mack J. 2013. Advancing data reuse in phyloinformatics using an ontology-driven Semantic Web approach. BMC Medical Genomics 6 (3) : S5. DOI https://doi.org/10.1186/1755-8794-6-S3-S5
Katayama T., Wilkinson M.D., Micklem G., Kawashima S., Yamaguchi A., Nakao M., Yamamoto Y., Okamoto S., Oouchida K., Chun H.-W., Aerts J., Afzal H., Antezana E., Arakawa K., Aranda B., Belleau F., Bolleman J., Bonnal R.J., Chapman B., Cock P., Eriksson T., Gordon P., Goto N., Hayashi K., Horn H., Ishiwata R., Kaminuma E., Kasprzyk A., Kawaji H., Kido N., Kim Y.J., Kinjo A.R., Konishi F., Kwon K.-H., Labarga A., LamprechtA.-L., Lin Y., Lindenbaum P., McCarthy L., Morita H., Murakami K., Nagao K., Nishida K., Nishimura K., Nishizawa T., Ogishima S., Ono K., Oshita K., Park K.-J., Prins P., Saito T.L., Samwald M., Satagopam V.P., Shigemoto Y., Smith R., Splendiani A., Sugawara H., Taylor J., Vos R., Withers D., Yamasaki C., Zmasek C.M., Kawamoto S., Okubo K., Asai K., Takagi T. 2013. The 3rd DBCLS BioHackathon: improving life science data integration with semantic Web technologies. Journal of Biomedical Semantics 4: 6. DOI https://doi.org/10.1186/2041-1480-4-6
Vonk F.J., Casewell N.R., Henkel C.V., Heimberg A., Jansen H.J., McCleary R.J., Kerkkamp H., Vos R.A., Guerreiro I., Calvette J., Wuster W., Woods A.E., Logan J., Harrison R.A., Castoe T.A., Koning A.J. de, Pollock D.D., Yandell M., Calderon D., Renjifo C., Currier R.B., Salgado D., Pla D., Sanz L., Hyder A.S., Ribeiro J.M.C., Arntzen J.W., Thillart G.E.E.J.M. van den, Boetzer M., Pirovano W., Dirks R., Spaink H.P., Duboule D., McGlinn E., Kini R.M., Richardson M.K. 2013. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proceedings of the National Academy of Sciences of the United States of America 110 (51) : 20651-20656. DOI https://doi.org/10.1073/pnas.1314702110
Stoltzfus A., Lapp H., Matasci N., Deus H., Sidlauskas B., Zmasek C.M., Vaidya G., Pontelli E., Cranston K., Vos R., Webb C.O., Harmon L.J., Pirrung M., O'Meara B., Pennell M.W., Mirarab S., Rosenberg M.S., Balhoff J.P., Bik H.M., Heath T., Midford P., Brown J.W., McTavish E.J., Sukumaran J., Westneat M., Alfaro M.E., Steele A. 2013. Phylotastic! Making Tree-of-Life knowledge accessible, re-usable and convenient. BMC Bioinformatics 14: 158. DOI https://doi.org/10.1186/1471-2105-14-158
2012

Journals SCI, peer-reviewed

Bonnal R.J.P., Aerts J., Githinji G., Goto N., MacLean D, Miller C.A., Mishima H., Pagani M., Ramirez-Gonzalez R., Smant G., Strozzi F., Syme R., Vos R., Wennblom T.J., Woodcroft B.J., Katayama T., Prins P. 2012. Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics. Bioinformatics 28 (7) : 1035-1037. DOI https://doi.org/10.1093/bioinformatics/bts080
Vos R.A., Balhoff J.P., Caravas J.A., Holder M.T., Lapp H., Maddison W.P., Midford P.E., Priyam A., Sukumaran J., Xia X., Stoltzfus A. 2012. NeXML: rich, extensible, and verifiable representation of comparative data and metadata. Systematic Biology 61 (4) : 675-689. DOI https://doi.org/10.1093/sysbio/sys025
2011

Journals SCI, peer-reviewed

2010

Journals SCI, peer-reviewed

Hipfner J.M., Gorman K.B., Vos R.A., Joy J.B. 2010. Evolution of embryonic developmental period in the marine bird families Alcidae and Spheniscidae: roles for nutrition and predation? BMC Evolutionary Biology 10: 179. DOI https://doi.org/10.1186/1471-2148-10-179
2008

Journals SCI, peer-reviewed

Bininda-Emonds O.R.P., Cardillo M., Jones K.E., MacPhee R.D.E., Beck R.M.D., Grenyer R., Price S.A., Vos R.A., Gittleman J.L., Purvis A. 2008. The delayed rise of present-day mammals (vol 446, pg 507, 2007). Nature 456 (7219) : 274-274. DOI https://doi.org/10.1038/nature07347
2007

Journals SCI, peer-reviewed

Lapp H., Bala S., Balhoff J.P., Bouck A., Goto N., Holder M., Holland R., Holloway A., Katayama T., Lewis P.O., Mackey A.J., Osborne B.I., Piel W.H., Kosakovsky Pond S.L., Poon A.F.Y., Qiu W.-G., Stajich J.E., Stoltzfus A., Thierer T., Vilella A.J., Vos R.A., Zmasek C.M., Zwickl D.J., Vision T.J. 2007. The 2006 NESCent Phyloinformatics Hackathon: A Field Report. Evolutionary Bioinformatics 3: 287-296.
2006

Journals SCI, peer-reviewed

Vries E.J. de, Vos R.A., Jacobs G., Breeuwer H.A.J. 2006. Western flower thrips (Thysanoptera : Thripidae) preference for thrips-damaged leaves over fresh leaves enables uptake of symbiotic gut bacteria. European Journal of Entomology 103 (4) : 779-786. DOI https://doi.org/10.14411/eje.2006.106
2004

Chapters in book

Vos R.A., Mooers A. 2004. Reconstructing divergence times for supertrees: a molecular approach. Phylogenetic supertrees: Combining information to reveal the tree of life.: 550 p. 281--299. Kluwer Academic Publishers, Dordrecht.
2003

Journals SCI, peer-reviewed

2001

Journals SCI, peer-reviewed

Rundle H.D., Breden F., Griswold C., Mooers A., Vos R.A., Whitton J. 2001. Hybridization without guilt: gene flow and the biological species concept - Commentary. Journal of Evolutionary Biology 14 (6) : 868-869. DOI https://doi.org/10.1046/j.1420-9101.2001.00338.x