Analyzing rainforest ciliate diversity in Panama and Ecuador using nascent sequencing technologies and qRT-PCR.
Final Report Abstract
Looking back on the start of the Emmy-Noether project, I did not set out to try to significantly change how we do metabarcoding studies, how we look at microbial diversity in the tropics or how we interpret meiotic gene inventories. Now that I am at the end of the project, I feel that my independent research group has made some significant changes by deeply and broadly advancing on these different fronts. The project resulted in two novel methodological advances. The first was the localclustering- threshold Swarm method, which does not force upon the environmental molecular data preconceived notions about how big OTUs should be, and which is highly scalable so it can handle the biggest environmental metabarcoding datasets. The second was the use of phylogenetic placements to retain most of the environmental molecular data when new environments are sampled where the OTUs do not match references collected elsewhere – such as tropical forests. This project resulted in the novel discovery of an immense amount of protist diversity in lowland Neotropical rainforests. If protists are the most diverse eukaryotes in tropical rainforests, it would not be due to inordinate speciation in just a few clades since the mid- Phanerozoic (for example, the beetles), it would be because of the diversification of rich and functionally complex protist lineages, beginning in the early Proterozoic, that built up the multifaceted and interactive unseen foundation of these now familiar macroscopic terrestrial ecosystems. If my novel hypothesis is correct, this previously unseen protist foundation helped usher in extremely diverse animal communities through density-dependent parasitism. And these hyperdiverse tropical protists exhibit strong biogeographical patterns that mirror the patterns seen in tropical animals and plants. This project resulted in the novel approach to evaluating secretive sexuality of protists (and other eukaryotes), where the presence or absence of meiotic-specific and meiotic-related genes are best explained by the larger context that there are two crossover pathways. Missing genes from one pathway does not preclude meiosis by going down the other. Using such an approach, the Colpodea were shown to have meiotic machinery; such that, they do not violate macro-organismic-derived theories of the maintenance of meiotic sex. These novel findings have set the stage for my future work over the next five to ten years.
Publications
- Evaluating molecular support for and against the monophyly of the Peritrichia and phylogenetic relationships in the Mobilida (Ciliophora, Oligohymenophorea). Zoologica Scripta, Vol. 42. 2013, Issue 2, pp. 213-226.
Zhan, Z., K. Xu, M. Dunthorn
(See online at https://doi.org/10.1111/j.1463-6409.2012.00568.x) - Fossil tintinnids. In: Dolan, J., D.Montagnes, S. Agatha, W. Coats, D. Stoecker (Eds.), Biology and ecology of tintinnid ciliates: models for marine plankton, 2013, pp. 186-197.
Lipps, J.H., T. Stoeck, M. Dunthorn
(See online at https://dx.doi.org/10.1002/9781118358092) - Meiosis gene inventory of four ciliates reveals the prevalence of a synaptonemal complex-independent crossover pathway. Molecular Biology and Evolution, Vol. 31. 2014, Issue 3, pp. 660–672.
Jingyun Chi, Frédéric Mahé, Josef Loidl, John Logsdon, Micah Dunthorn
(See online at https://doi.org/10.1093/molbev/mst258) - Swarm: robust and fast clustering method for amplicon-based tudies. PeerJ 2:e593.
Frédéric Mahé, Torbjørn Rognes, Christopher Quince, Colomban de Vargas1, Micah Dunthorn
(See online at https://doi.org/10.7717/peerj.593) - Comparing High‐throughput Platforms for Sequencing the V4 Region of SSU‐rDNA in Environmental Microbial Eukaryotic Diversity Surveys.
Journal of Eukaryotic Microbiology, Vol. 62. 2015, Issue 3, pp. 338-345.
Mahé F., Mayor J., Bunge J., Chi J., Siemensmeyer T., Stoeck T., Wahl B., Paprotka T., Filker S., Dunthorn M.
(See online at https://doi.org/10.1111/jeu.12187) - Swarm v2: highly-scalable and high-Resolution amplicon clustering.
PeerJ, Vol. 3, Issue 2: e1420.
Mahé, Rognes, Quince, de Vargas, Dunthorn
(See online at https://doi.org/10.7717/peerj.1420) - Benthic protists: the undercharted majority. FEMS Microbiology Ecology, Vol. 92. 2016, Issue 8: fiw120.
Forster, D., M. Dunthorn, F. Mahé, J.R. Dolan, S. Audic, et al.
(See online at https://doi.org/10.1093/femsec/fiw120) - Comparison of three clustering approaches for detecting novel environmental microbial diversity. PeerJ, Vol. 4. 2016: e1692
Forster, D., M. Dunthorn, T. Stoeck, F. Mahé
(See online at https://doi.org/10.7717/peerj.1692) - Meiotic genes in colpodean ciliates Support secretive sexuality. (bioRxiv doi:10.1101/132472) Genome Biology and Evolution, Vol. 9. 2017, Issue 6, pp. 1781–1787.
Micah Dunthorn, Rebecca A. Zufall, Jingyun Chi, Konrad Paszkiewicz, Karen Moore, Frederic Mahe
(See online at https://doi.org/10.1093/gbe/evx125) - Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests. Nature Ecology & Evolution, Vol. 1. 2017: Article Number 0091.
Mahé, de Vargas, Bass, Czech, Stamatakis, Lara, Singer, Mayor, Bunge, Sernaker, Siemensmeyer, Trautmann, Romac, Berney, Kozlov, Mitchell, Seppey, Egge, Lentendu, Wirth, Trueba, Dunthorn
(See online at https://doi.org/10.1038/s41559-017-0091)
