Research
My research focuses on hypothesis-driven questions that evaluate novel theories and observations about protistan ecology and evolution, and that elevate the place of free-living and parasitic protists in our understanding of the functioning of different aquatic and terrestrial ecosystems.
Biodiversity and Biogeography: Our views of species diversity and biological communities are dominated by work on macro-organismic plants and animals, although most of the history of life has been dominated by microbes such as protists. I am interested in expanding our views to include broader microbial perspectives, by evaluating protistan species-, phylogenetic-, and functional-diversity in aquatic communities under multiple stressors and in tropical forests. My approaches include using genomic and morphological methods to uncover microbial diversity, and developing novel bioinformatic methods and databases to handle environmental sequencing datasets.
Meiotic Sex and Crossover Pathways: Our theoretical understanding, and empirical observations, of the maintenance and distribution of meiotic sex within eukaryotes is also dominated by research on plants and animals. While there is a cost to sex, almost all macro-organisms are known to be sexual, allowing them to survive changing environments and to escape their parasites. If macrobial theory applies to all eukaryotes, most protist should also be sexual. However, meiotic sex has not been observed in many protistan species and higher clades. I am interested in evaluating the distribution and maintenance of meiotic sex, and meiotic crossover pathways, in ciliates, chrysophytes and other protists using genomic, metatranscriptomic, and microscopic methods.
Observing Ciliates: My taxonomic expertise focuses on ciliates. Although ciliates have a murky fossil record, they are now everywhere and they often thrive in high abundances. Ciliates are model organisms in the development and testing of hypotheses about microbial biodiversity and biogeography; they are excellent bioindicators for the monitoring of natural and human-stressed environments; and they are the major grazers of bacteria and their biofilms in rivers and other ecosystems. A central aspect in these types of studies is the correct identification of species. I am interested in expanding the microscopic methods used to identify ciliates by moving away from classical silver stains and moving towards using fluorescence stains that can allow for single-cell sorting and observations, which can be subsequently merged with single-cell genomics.
PUBLICATIONS
Ewers, I., L. Rajter, L. Czech, F. Mahé, A. Stamatakis, M. Dunthorn (2023). Interpreting phylogenetic placements for taxonomic assignment of environmental DNA. Journal of Eukaryotic Microbiology 70 (5), e12990Vos, M., D. Hering, M.O. Gessner, F. Leese, R.B. Schäfer, R. Tollrian, J. Boenigk, P. Haase, R. Meckenstock, D. Baikova, H. Bayat, A. Beermann, D. Beisser, B. Beszteri, S. Birk, L. Boden, V. Brauer, M. Brauns, D. Buchner, A. Burfeid-Castellanos, G. David, A. Deep, A. Doliwa, M. Dunthorn, J. Enß, C. Escobar-Sierra, C.K. Feld, N. Fohrer, D. Grabner, U. Hadziomerovic, S.C. Jähnig, M. Jochmann, S. Khaliq, J. Kiesel, A. Kuppels, K.P. Lampert, T.T.Y. Le, A.W. Lorenz, G.M. Madariaga, B. Meyer, J.H. Pantel, I.M. Pimentel, N.S. Mayombo, H.H. Nguyen, K. Peters, S.M. Pfeifer, S. Prati, A.J. Probst, D. Reiner, P. Rolauffs, A. Schlenker, T.C. Schmidt, M. Shah, G. Sieber, T.L. Stach, A.-K. Tielke, A-M. Vermiert, M. Weiss, M. Weitere, B. Sures (2023). The Asymmetric Response Concept explains ecological consequences of multiple stressor exposure and release. Science of The Total Environment 872: 162196
Dubbert, J., A. Höing, N. Graupner, L. Rajter, M. Dunthorn, S.K. Knauer, A. Galstyan, F. Rizzo, J. Voskuhl (2023). Chemistry - A European Journal 29: e202300334
Buchta, A., M. Dunthorn (2023). Moving slime: exploring chemotaxis with slime mould. Science in School 62:1-5
Ekrem, T., T. Baussant, G.J. Dunshea, M. Dunthorn, E.D. Egge, A. Engesmo, F. Fossøy, H. Hansen, S. Kistenich, A. Krolicka, A. Larsen, Q. Mauvisseau, D. Strand, T. Vrålstad, K.B. Westergaard (2023). The use of eDNA and DNA based methods to assess and monitor alien and doorknocker species. Report. Norwegian Environment Agency
Rajter, L., B. Lu, E. Rassoshanska, M. Dunthorn (2022). Future prospects for investigating ciliate biodiversity. Acta Protozoologica 61:35-46
Dunthorn, M. (2022). Report of the 2022 Protistology Nordics meeting. Journal of Eukaryotic Microbiology 69:e12928
Lansac-Tôha, F.M. P.R.B. Buosi, M.T. Baumgartner, M. Progênio, B.R. Meira, A.F. Cabral, B.T. Segovia, M. Dunthorn, G. Lentendu, F.A. Lansac-Tôha, L.F.M. Velho (2022). Molecular insight reveals broad-scale spatial patterns in floodplain ciliate communities, while morphology reflects local environmental controls. Freshwater Science 41:270-283
Czech, L. A. Stamatakis, M. Dunthorn, P. Barbera (2022). Metagenomic analysis using phylogenetic placement--a review of the first decade. Frontiers in Bioinformatics 2:871393
Mahé, F., L. Czech, A. Stamatakis, C. Quince, C. de Vargas, M. Dunthorn, T. Rognes (2022). Swarm v3: towards tera-scale amplicon clustering. Bioinformatics 38:267-269
Bredin, Y.K., L.L. Hess, A.B. Scabin, M. Dunthorn, T. Haugaasen, C.A. Peres, H.R. Nilsson, A. Antonelli, C.D. Ritter (2022). Above- and below-ground biodiversity responses to the prolonged flood pulse in central-western Amazonia, Brazil. Environmental DNA 4: 533-548
Voskuhl, L., A. Akbari, H. Müller, M. Pannekens, D. Brusilova, S. Dyksma, S. Haque, N. Graupner, M. Dunthorn, R.U. Meckenstock, V.S. Brauer (2021). Indigenous microbial communities in heavy oil show a threshold response to salinity. FEMS Microbiology Ecology 97:fiab157
Dunthorn M. (2021). Report of the 2021 meeting of the International Society of Protistologists. Journal of Eukaryotic Microbiology 68:e12873
Ritter, C.D., A.F. Machado, K.F. Ribeiro, M. Dunthorn (2021). Metabarcoding advances for ecology and biogeography of Neotropical protists: what do we know, where do we go? Biota Neotropica 21:20211214
Rajter, L., M. Dunthorn (2021). Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data. Metabarcoding and Metagenomics 5:e69602
Dunthorn, M., N. Graupner (2021). Report of the 2021 meeting of the German Society for Protozoology. European Journal of Protistology 77:125790
Lentendu, G., M. Dunthorn (2021). Phylogenetic relatedness drives protist assembly in marine and terrestrial environments. Global Ecology and Biogeography 30:1532-1544
Ritter, C.D., D. Forster, J.A.R. Azevedo, A. Antonelli, R.H. Nilsson, M.E. Trujillo, M. Dunthorn (2021). Assessing biotic and abiotic interactions of microorganisms in Amazonia through co-occurrence networks and DNA metabarcoding. Microbial Ecology 82:746-760
Doliwa, A., M. Dunthorn, E. Rassoshanska, F. Mahé, D. Bass, C.D. Ritter (2021). Identifying potential hosts of short-branch Microsporidia. Microbial Ecology 82:549-553
Gottschling, M., L. Czech, F. Mahé, S. Adl, M. Dunthorn (2021). The windblown: possible explanations for dinophyte DNA in forest soils. Journal of Eukaryotic Microbiology 68:e12833
Rajter, L., I. Ewers, N. Graupner, P. Vďačný, M. Dunthorn (2021). Colpodean ciliate phylogeny and reference alignments for phylogenetic placements. European Journal of Protistology 77:125747
Singer, D., C.V.W. Seppey, G. Lentendu, M. Dunthorn, D. Bass, L. Belbahri, Q. Blandenier, D. Debroas, G.A. Groot, C. de Vargas, I. Domaizon, C. Ducker, I. Izaguirre, I. Koenig, G. Mataloni, M.R. Schiaffino E.A.D. Mitchell, S. Geisen, E. Lara (2021). Protist taxonomic and functional diversity in soil, freshwater and marine ecosystems. Environment International 146:106262
Hörandl, E. J. Bast, A. Brandt, S. Scheu, C. Bleidorn, M. Cordellier, M. Nowrousian, D. Begerow, A. Sturm, K. Verhoeven, J. Boenigk, T. Friedl, M. Dunthorn (2020). Genome evolution of asexual organisms and the paradox of sex in eukaryotes. In P. Pontarotti (ed.). Evolutionary Biology—A Transdisciplinary Approach. Springer, Cham pp. 133-167
Lynn, D.H., M. Dunthorn (2020). Intramacronucleata. In de Queiroz, K., P.D. Cantino, J.A. Gauthier (eds.) Phylonyms: a companion to the PhyloCode. CRC Press: Boca Raton pp:95-96
Dunthorn, M., D.H. Lynn (2020). Postciliodesmatophora. In de Queiroz, K., P.D. Cantino, J.A. Gauthier (eds.) Phylonyms: a companion to the PhyloCode. CRC Press: Boca Raton pp:93
Dunthorn, M., D.H. Lynn (2020). Ciliophora. In de Queiroz, K., P.D. Cantino, J.A. Gauthier (eds.) Phylonyms: a companion to the PhyloCode. CRC Press: Boca Raton pp:91-92
Simpson, A.G.B., B. S. Leander, M. Dunthorn (2020). Alveolata. In de Queiroz, K., P.D. Cantino, J.A. Gauthier (eds.) Phylonyms: a companion to the PhyloCode. CRC Press: Boca Raton pp:85-89
Simpson, A.G.B., M. Dunthorn (2020). Stramenopila. In de Queiroz, K., P.D. Cantino, J.A. Gauthier (eds.) Phylonyms: a companion to the PhyloCode. CRC Press: Boca Raton pp:55-59
Simpson, A.G.B., M. Dunthorn (2020). Sar. In de Queiroz, K., P.D. Cantino, J.A. Gauthier (eds.) Phylonyms: a companion to the PhyloCode. CRC Press: Boca Raton pp:51-53
Santoferrara, L., F. Burki, S. Filker, R. Logares, M. Dunthorn, G.B. McManus (2020). Perspectives from ten years of protist studies by high-throughput metabarcoding. Journal of Eukaryotic Microbiology 67:612-622
Ritter, C.D., M. Dunthorn, S. Anslan, V. de Lima, L. Tedersoo, R.H. Nilsson, A. Antonelli (2020). Advancing biodiversity assessments with environmental DNA: long-read technologies help reveal the drivers of Amazonian fungal diversity. Ecology and Evolution 10:7509-7524
Lentendua, G., P.R.B. Buosi, A.F. Cabralc, B.T. Segóviad, B.R. de Meirab, F.M. Lansac-Tôhab, L.F.M. Velho, C. Ritter, M. Dunthorn (2019). Protist biodiversity and biogeography in lakes from four Brazilian river-floodplain systems. Journal of Eukaryotic Microbiology 66:592-599
Adl, S.M., D. Bass, C.E. Lane, J. Lukeš, C.L. Schoch, A. Smirnov, S. Agatha, C. Berney, M.W. Brown, F. Burki, P. Cárdenas, I. Čepička, L. Chistyakova, J. del Campo, M. Dunthorn, B. Edvardsen, Y. Eglit, L. Guillou, V. Hampl, A.A. Heiss, M. Hoppenrath, T.Y. James, S. Karpov, E. Kim, M. Kolisko, A. Kudryavtsev, D.J.G. Lahr, E. Lara, L. Le Gall, D.H. Lynn, D.G. Mann, R. Massana i Molera, E.A.D. Mitchell, C. Morrow, J.S. Park, J.W. Pawlowski, M.J. Powell, D.J. Richter, S. Rueckert, L. Shadwick, S. Shimano, F.W. Spiegel, G. Torruella i Cortes, N. Youssef, V. Zlatogursky, Q. Zhang (2019). Revisions to the classification, nomenclature, and diversity of eukaryotes. Journal of Eukaryotic Microbiology 66:4-119
Kraus D., J. Chi, J. Boenigk, D. Beisser, N. Graupner, M. Dunthorn (2019). Putatively asexual chrysophytes have meiotic genes: evidence from transcriptomic data. Peer J 6:e5894
Piredda, R., J.-M. Claverie, J. Decelle, C. de Vargas, M. Dunthorn, B. Edvardsen, W.Eikrem, D. Forster, W.H.C.F. Kooistra, R. Logares, R. Massana, M. Montresor, F. Not, H. Ogata, J. Pawlowski, S. Romac, D. Sarno, T. Stoeck, A. Zingone (2018). Diatom diversity through HTS-metabarcoding in coastal European sea. Scientific Reports 8:18059
Decelle, J., Q. Carradec, X. Pochon, N. Henry, S. Romac, F. Mahé, M. Dunthorn, A.Kourlaiev, C.R. Voolstra, P. Wincker, C. de Vargas (2018). Worldwide occurrence and activity of the reef-building coral symbiont Symbiodinium in the open ocean. Current Biology 28:3625-3633
Gurdebeke, P.R., K.N. Mertens, Y. Takano, A. Yamaguchi, K. Bogus, M. Dunthorn, K.Matsuoka, H. Vrielinck, S. Louwye (2018). The affiliation of Hexasterias problematica and Halodinium verrucatum sp. nov. to ciliate cysts based on molecular phylogeny and cyst wall composition. European Journal of Protistology 66:115-135
Bass, D., L. Czech, B. Williams, C. Berney, M. Dunthorn, F. Mahé, G. Torruella, G.D. Stentiford, T.A. Williams (2018). Clarifying the relationships between Microsporidia and Cryptomycota. Journal of Eukaryotic Microbiology 65:773-782
Lentendu, G., F. Mahé, D. Bass, S. Rueckert, T. Stoeck, M. Dunthorn (2018). Consistent patterns of high alpha and low beta diversity in tropical parasitic and free-living protists. Molecular Ecology 27: 2846-2857
Geisen, S., E.A.D. Mitchell, S. Adl, M. Bonkowski, M. Dunthorn, F. Ekelund, L.D. Fernández, A. Jousset, V. Krashevska, D. Singer, F.W. Spiegel, J. Walochnik, E. Lara (2018). Soil protists: a fertile frontier in soil biology research. FEMS Microbiology Reviews 42:293-323
Dunthorn, M., H. Kauserud, D. Bass, J. Mayor, F. Mahé (2017). Yeasts dominate soilfungal communities in three lowland Neotropical rainforests. Environmental Microbiology Reports 9:668-675
Dunthorn, M., R.A. Zufall, J. Chi, K. Paszkiewicz, K. Moore, F. Mahé (2017). Meiotic genes in colpodean ciliates support secretive sexuality. Genome Biology and Evolution 9:1781-1787
Warren, A., D.J. Patterson, M. Dunthorn, J.C. Clamp, U.E.M. Achilles-Day, E. Aescht, S.A. Al-Farraj, S. Al-Quraishy, K. Al-Rasheid, M. Carr, J.G. Day, M. Dellinger, H.A. El-Serehy, Y. Fan, F. Gao, S. Gao, J. Gong, R. Gupta, X. Hu, K. Kamra, G. Langlois, X. Lin, D. Lipscomb, C.S. Lobban, P. Luporini, D.H. Lynn, H. Ma, M. Macek, J. Mackenzie-Dodds, S. Makhija, R.I. Mansergh, M. Martín-Cerecedax, N. McMiller, S. Nikolaeva, G.O. Ong’ondo, B. Pérez-Uz, J. Purushothaman, P. Quintela-Alonso, J. Rotterová, L. Santoferrara, C. Shao, Z. Shen, X. Shi, W. Song, T. Stoeck, A. La Terza, A. Vallesi, M. Wang, T. Weisse, K. Wiackowski, L. Wu, K. Xu, Z. Yi, R. Zufall, S Agatha (2017). Beyond the “Code”: a guide to the description and documentation of the biodiversity of ciliated protists (Alveolata, Ciliophora). Journal of Eukaryotic Microbiology 64:539-554
Berney, C., A. Ciuprina, S. Bender, J. Brodie, V. Edgcomb, E. Kim, J. Rajan, L.W.Parfrey, S. Adl, S. Audic, D. Bass, D.A. Caron, G. Cochrane, L. Czech, M. Dunthorn, S. Geisen, F. O. Glöckner, F. Mahé, C. Quast, J.Z. Kaye, A.G.B. Simpson, A. Stamatakis, J. del Campo, P. Yilmaz, C. de Vargas (2017). UniEuk: time to speak a common language in protistology! Journal of Eukaryotic Microbiology 64:407-411
Geisen, S., E.A.D. Mitchell, D.M. Wilkinson, S. Adl, M. Bonkowski, M.W. Brown, A.M.Fiore-Donno, T.J. Heger, V.E.J. Jassey, V. Krashevska, D.J.G. Lahr, K. Marcisz, M. Mulot, R. Payne, D. Singer, O.R. Anderson, D.J. Charman, F. Ekelund, B.S. Griffiths, R. Rønn, A. Smirnov, D. Bass, L. Belbahri, C. Berney, Q. Blandenier, A. Chatzinotas, M. Clarholm, M. Dunthorn, A. Feest, L.D. Fernandez-Parra, W. Foissner, B. Fournier, E. Gentekaki, M. Hajek, J. Helder, A. Jousset, R. Koller, S. Kumar, A. La Terza, M. Lamentowicz, Y. Mazei, S.S. Santos, C.V.W. Seppey, F.W. Spiegel, J. Walochnik, A. Winding, E. Lara (2017). Soil protistology rebooted: 30 fundamental questions to start with. Soil Biology and Biochemistry 111:94-103
Mahé, F., C. de Vargas, D. Bass, L. Czech, A. Stamatakis, E. Lara, D. Singer, J. Mayor, J.Bunge, S. Sernaker, T. Siemensmeyer, I. Trautmann, S. Romac, C. Berney, A. Kozlov, E.A.D. Mitchell, C.V.W. Seppey, E. Egge, G. Lentendu, R. Wirth, G. Trueba, M. Dunthorn (2017). Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests. Nature Ecology and Evolution 1:0091
Forster, D., M. Dunthorn, F. Mahé, J.R. Dolan, S. Audic, D. Bass, L. Bittner, C. Boutte,R. Christen, J.-M. Claverie, J. Decelle, B. Edvardsen, E. Egge, W. Eikrem, A.Gobet, W.H.C.F. Kooistra, R. Logares, R. Massana, M. Montresor, F. Not, H. Ogata, J. Pawlowski, M.C. Pernice, S. Romac, K. Shalchian-Tabrizi, N. Simon, T.A. Richards, S. Santini, D. Sarno, R. Siano, D. Vaulot, P. Wincker, A. Zingone, C. de Vargas, T. Stoeck (2016). Benthic protists: the under-charted majority. FEMS Microbiology Ecology 92:fiw120
Forster, D., M. Dunthorn, T. Stoeck, F. Mahé (2016). Comparison of three clustering approaches for detecting novel environmental microbial diversity. PeerJ 4:e1692
Mahé, F., T. Rognes, C. Quince, C. de Vargas, M. Dunthorn (2015). Swarm v2: highly-scalable and high-resolution amplicon clustering. PeerJ 3:e1420
Richards, T., G. Leonard, F. Mahé, J. del Campo, S. Romac, M. D. M. Jones, F. Maguire, M. Dunthorn, C. de Vargas, R. Massana, A. Chambouvet (2015). Molecular diversity and distribution of marine fungi across 130 European environmental samples. Proceedings of the Royal Society B 282:20152243
Massana, R., A. Gobet, S. Audic, D. Bass, L. Bittner, C. Boutte, A. Chambouvet, R.p Christen, J.-M. Claverie, J. Decelle, J. R. Dolan, M. Dunthorn, B. Edvardsen, I. Forn, D. Forster, L. Guillou, O. Jaillon, W.H.C.F. Kooistra, R. Logares, F. Mahé, F. Not, H. Ogata, J. Pawlowski, M. C. Pernice, I. Probert, S. Romac, T. Richards, S. Santini, K. Shalchian-Tabrizi, R. Siano, N. Simon, T. Stoeck, D. Vaulot, A. Zingone, and C. de Vargas (2015). Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing. Environmental Microbiology 17:4035-4049
Dunthorn, M., J.H. Lipps, J.R. Dolan, M. Abboud-Abi Saab, E. Aescht, C. Bachy, M. Sonia Barría de Cao, H. Berger, W.A. Bourland, J.Ki. Choi, J. Clamp, M. Doherty, F. Gao, E. Gentekaki, J. Gong, X. Hu, J. Huang, T. Kamiyama, M.D. Johnson, B. Kammerlander, S.Y. Kim, Y.-O Kim, A. la Terza, M. Laval-Peuto, D. Lipscomb, C.S. Lobban, H. Long, P. Luporini, D.H. Lynn, M. Macek, R.I. Mansergh, M. Martín-Cereceda, G.G. McManus, D.J.S. Montagnes, G.O. Ong'ondo, D.J. Patterson, B. Pérez-Uz, P. Quintela-Alonso, L.S.L. Safi, L.F. Santoferrara, B. Sonntag, W. Song, T. Stoeck, D.K. Stoecker, M.C. Strüder-Kypke, I. Trautmann, L.R.P. Utz, A. Vallesi, P. Vd'ačný, A. Warren, T. Weisse, S.A. Wickham, Z. Yi, W. Zhang, Z. Zhan, R. Zufall, S. Agatha (2015). Ciliates—protists with complex morphologies and ambiguous early fossil record. Marine Micropaleontology 119:1-6
de Vargas C., S. Audic, N. Henry, J. Decelle, F. Mahé, R. Logares, E. Lara, C. Berney, N.Le Bescot, I. Probert, M. Carmichael, J. Poulain, S. Romac, S. Colin, J.-M. Aury, L. Bittner, S. Chaffron, M. Dunthorn, S. Engelen, O. Flegontova, L. Guidi, A. Horak, O. Jaillon, G. Lima-Mendez, J. Lukes, S. Malviya, R. Morard, M. Mulot, E. Scalco, R. Siano, F. Vincent, A. Zingone, C. Dimier, M. Picheral, S. Searson, S Kandels-Lewis, Tara Oceans Coordinators, S. G. Acinas, P. Bork, C. Bowler, F. Gail, G. Gorsky, N. Grimsley, P. Hingamp, D. Iudicone, F. Not, H. Ogata, S. Pesant, J. Raes, M. Sieracki, S. Speich, L. Stemman, S. Sunagawa, J. Weissenbach, P. Wincker, E. Karsenti (2015). Eukaryotic plankton diversity in the sunlit ocean. Science 348:1261605
Mahé, F., J. Mayor, J. Bunge, J. Chi, T. Siemensmeyer, T. Stoeck, B. Wahl, T. Paprotka,S. Filker, M. Dunthorn (2015). Comparing high-throughput platforms for sequencing the hyper-variable V4 region in environmental eukaryotic diversity surveys. Journal of Eukaryotic Microbiology 62:338-345
Filker, S., A. Gimmler, M. Dunthorn, F. Mahé, T. Stoeck (2015). Deep sequencing uncovers high and substantial novel diversity in protistan plankton of solar saltern ponds. Extremophiles 19:283-295
Forster, D., L. Bittner, S. Karkar, M. Dunthorn, S. Romac, S. Audic, P. Lopez, T. Stoeck, E. Bapteste (2015). Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms. BMC Biology 13:16
Dunthorn, M., R. A. Zufall, C. Lobban (2015). Report of the 2014 Joint Workshop of the International Research Coordination Network for Biodiversity of Ciliates and the British Society for Protist Biology. European Journal of Protistology 51:118-119
Mahé, F., T. Rognes, C. Quince, C. de Vargas, M. Dunthorn (2014). Swarm: robust and fast clustering method for amplicon-based studies. PeerJ 2:e593
Dunthorn, M., T. Stoeck, J. Clamp, A. Warren, F. Mahé (2014). Ciliates and the rare biosphere: a review. Journal of Eukaryotic Microbiology 61: 404-409
Dunthorn, M., M. Hall, W. Foissner, T. Stoeck, L.A. Katz (2014). Broad taxon sampling of ciliates using mitochondrial small subunit ribosomal DNA. Acta Protozoologica 53:207-213
Filker, S., M. Kaiser, R. Rosselló-Móra, M. Dunthorn, G. Lax, T. Stoeck. (2014). Candidatus Haloectosymbiotes riaformosensis (Halobacteriaceae), an archaeal ectosymbiont of the hypersaline ciliate Platynematum salinarum. Systematic and Applied Microbiology 37:244-251
Chi, J., M. Parrow, M. Dunthorn (2014). Cryptic sex in Symbiodinium (Alveolata, Dinoflagellata) is supported by an inventory of meiosis genes. Journal of Eukaryotic Microbiology 61:322-327
Stoeck, T., E. Przybos, M. Dunthorn (2014). The D1-D2 region of the large subunit ribosomal DNA as barcode for ciliates. Molecular Ecology Resources 14:458-468
Logares, R., S. Audic, D. Bass, L. Bittner, C. Boutte, R. Christen, J.-M. Claverie, J.Decelle, J. Dolan, M. Dunthorn, B. Edvardsen, A. Gobet, W. Kooistra, F. Mahé, F. Not, H. Ogata, J. Pawlowski, M.C. Pernice, S. Romac, K. Shalchian-Tabrizi,N. Simon, T. Stoeck, S. Santini, R. Siano, P. Wincker, A. Zingone, T. Richards, C. de Vargas, R. Massana (2014). Patterns of rare and abundant marine microbial eukaryotes. Current Biology 24:813-821
Dunthorn, M., J. Otto, S. A. Berger, A. Stamatakis, F. Mahé, S. Romac, C. de Vargas, S. Audic, BioMarKs Consortium (= B. Edvardsen, R. Massana, F. Not, N. Simon, A. Zingone), A. Stock, F. Kauff, T. Stoeck (2014). Placing environmental next generation-sequencing amplicons from microbial eukaryotes into a phylogenetic context. Molecular Biology and Evolution 31:993-1009
Chi, J., F. Mahé, J. Loidl, J. Logsdon, M. Dunthorn (2014). Meiosis gene inventory of four ciliates reveals the prevalence of a synaptonemal complex-independent crossover pathway. Molecular Biology and Evolution 31:660-672
Vďačnýa, P., H.-W. Breiner, V. Yashchenko, M. Dunthorn, T. Stoeck, W. Foissner (2014). The Chaos Prevails: Molecular Phylogeny of the Haptoria (Ciliophora, Litostomatea). Protist 165: 93–111
Foissner, W., W.A. Bourland, K.W. Wolf, T. Stoeck, M. Dunthorn (2014). New SSU-rDNA gene sequences for eleven colpodeans (Ciliophora, Colpodea) and description of Apocyrtolophosis nov. gen. European Journal of Protistology 50:40-46
Zhan, Z., T. Stoeck, M. Dunthorn, K. Xu (2014). Identification of a pathogenic ciliate Pseudocohnilembus persalinus (Oligohymenophorea: Scuticociliatia) by fluorescence in situ hybridization. European Journal of Protistology 50:16-24
Zhan, Z., K. Xu, M. Dunthorn (2013). Evaluating molecular support for and against the monophyly of the Peritrichia and phylogenetic relationships in the Mobilida (Ciliophora, Oligohymenophorea). Zoologica Scripta 42:213-226
Guillou L., D. Bachar, S. Audic, D. Bass, C. Berney, L. Bittner, C. Boutte, G. Burgaud, C. de Vargas, J. Decelle, J. del Campo, J.R. Dolan, M. Dunthorn, B. Edvardsen, M. Holzmann, W.H.C.F. Kooistra, E. Lara, N. Lebescot, R. Logares, F. Mahé, R. Massana, M. Montresor, R. Morard, F. Not, J. Pawlowski, I. Probert, A.-L. Sauvadet, R. Siano, T. Stoeck, D. Vaulot, P. Zimmermann, R. Christen (2013). The protist ribosomal reference database (PR2): a catalog of unicellular eukaryote small subunit rRNA sequences with curated taxonomy. Nucleic Acids Research 41:D597-D604
Lipps, J.H., T. Stoeck, M. Dunthorn (2013). Fossil tintinnids. In Dolan, J., D. Montagnes, S. Agatha, W. Coats, D. Stoecker (Eds.), Biology and ecology of tintinnid ciliates: models for marine plankton, pp. 186-197
Pawlowski, J., S. Audic, S. Adl, D. Bass, L. Belbahri, C. Berney, S.S. Bowser, I. Cepicka, J. Decelle, M. Dunthorn, A.M. Fiore-Donno, G. Gile, M. Holzmann, R. Jahn, M. Jirků, P.J. Keeling, M. Kostka, A. Kudryavtsev, E. Lara, J. Lukeš, D.G. Mann, E.A.D. Mitchell, F. Nitsche, M. Romeralo, G.W. Saunders, A.G.B.
Simpson, A.V. Smirnov, J. Spouge, R.F. Stern, T. Stoeck, J. Zimmermann, D. Schindel, C. de Vargas (2012). CBOL Protist Working Group: barcoding eukaryotic richness beyond the animal, plant and fungal kingdoms. PLoS Biology 10:e1001419
Dunthorn, M., W. Foissner, L.A. Katz, T. Stoeck (2012). Congruence and indifference between two molecular markers for understanding oral evolution in the Marynidae sensu lato (Ciliophora, Colpodea). European Journal of Protistology 48:297-304
Adl, S.M., A.G.B. Simpson, C.E. Lane, J. Lukeš, D. Bass, S.S. Bowser, M.W. Brown, F. Burki, M. Dunthorn, V. Hampl, A. Heiss, M. Hoppenrath, E. Lara, L. Le Gall, D.H. Lynn, H. McManus, E.A.D. Mitchell, S.E. Mozley-Stanridge, L.W. Parfrey, J. Pawloski, S. Rueckert, L. Shadwick, C. Schoch, A. Smirnov, F. W. Spiegel (2012). The revised classification of eukaryotes. Journal of Eukaryotic Microbiology 59:429-493
Dunthorn, M., T. Stoeck, K. Wolf, H.-W. Breiner, W. Foissner (2012). Diversity and endemism of ciliates inhabiting Neotropical phytotelmata. Systematics and Biodiversity 10:195-205
Huang, J., M. Dunthorn, W. Song (2012). Expanding character sampling for the molecular phylogeny of euplotid ciliates (Protozoa, Ciliophora) using three markers, with a focus on the family Uronychiidae. Molecular Phylogenetics and Evolution 63:598-605
Trueba, G., M. Dunthorn (2012). Many neglected tropical diseases may haveoriginated in the Paleolithic or before: new insights from genetics. PLoS Neglected Tropical Diseases 6:e1393
Dunthorn, M., L.A. Katz. (2012). Secretive ciliates and putative asexuality in microbialeukaryotes. In Schaechter, M. (Ed.), Eukaryotic microbes. Academic Press: Amsterdam, pp. 227-233
Dunthorn, M., J. Kleir, J. Bunge T. Stoeck (2012). Comparing the hyper-variable V4 and V9 regions for assessment of ciliate environmental diversity. Journal of Eukaryotic Microbiology 59:185-187
Katz, L.A., J. DeBerardinis, M. Hall, A.M. Kovner, M. Dunthorn, S.V. Muse (2011). Heterogeneous rates of molecular evolution between cryptic species of the ciliate morphospecies Chilodonella uncinata. Journal of Molecular Evolution 73: 266-722
Foissner, W., T. Stoeck, S. Agatha, M. Dunthorn (2011). Intraclass evolution and classification of the Colpodea (Ciliophora). Journal of Eukaryotic Microbiology 58:397-415
Nebel, M., C. Pfabel, A. Stock, M. Dunthorn, T. Stoeck (2011). Delimiting operational taxonomic units for assessing ciliate environmental diversity using small-subunit rRNA gene sequences. Environmental Microbiology Reports 3:154-158
Dunthorn, M., W. Foissner, L.A. Katz (2011). Expanding character sampling in ciliate phylogenetic inference using mitochondrial SSU-rDNA as a molecular marker. Protist 162: 85-99
Yi, Z., M. Dunthorn, W. Song, T. Stoeck (2010). Increasing taxon sampling using both unidentified environmental sequences and identified cultures improves phylogenetic inference in the Prorodontida (Ciliophora, Prostomatea). Molecular Phylogenetics and Evolution 57:937-941
Dunthorn, M., J.H. Lipps, T. Stoeck (2010). Reassessment of the putative ciliate fossils Eotintinnopsis, Wujiangella, and Yonyangella from the Neoproterozoic Doushantuo formation in China. Acta Protozoologica 49:139-144
Dunthorn, M., L.A. Katz. (2010). Secretive ciliates and putative asexuality in microbial eukaryotes. Trends in Microbiology 18:183-188
Dunthorn, M., M. Eppinger, M.V.J. Schwarz, M. Schweikert. J. Boenigk, L.A. Katz, T. Stoeck (2009). Phylogenetic placement of the Cyrtolophosididae Stokes, 1888 (Ciliophora; Colpodea) and neotypification of Aristerostoma marinum Kahl, 1931. International Journal of Systematic and Evolutionary Microbiology 59:167-180
Dunthorn, M. (2009). Foliar anatomy and fiber motifs in Mammea (Clusiaceae). Plant Systematics and Evolution 280: 153-166
Dunthorn, M., L.A. Katz (2008). Richness of morphological hypotheses in ciliate systematics allows for detailed assessment of homology and comparisons with gene trees. Denisia 23:389-394
Dunthorn, M., N. Johnson (2008). Los Mecanismos de la Evolución. In Trueba, G.,C. Montúfar (Eds.), Big Bang a Dolly, 3rd Ed. Universidad San Francisco de Quito Press: Quito (in Spanish; = The Mechanisms of Evolution), pp. 147-154
Dunthorn, M., W. Foissner, L.A. Katz. (2008). Molecular phylogenetic analysis of theclass Colpodea (Phylum Ciliophora) using broad taxon sampling. Molecular Phylogenetics and Evolution 46: 316-327
Parfrey, L.W., E. Barbero, E. Lasser, M. Dunthorn, D. Bhattacharya, D.J. Patterson,L.A. Katz. (2006). Evaluating support for the current classification of eukaryotic diversity. PLoS Genetics 2:e220
Dunthorn, M. (2004). Cryptic dioecy in Mammea (Clusiaceae). Plant Systematics and Evolution 249: 191-196