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3. Diversity, Nomenclature, and Taxonomy of Protists

Author

Adl, Sina M., Leander, Brian S., Simpson, Alastair G. B., Archibald, John M., Anderson, O. Roger., Bass, David, Bowser, Samuel. S., Brugerolle, Guy, Farmer, Mark. A., Karpov, Sergey, Kolisko, Martin, Lane, Christopher E., Lodge, Deborah J., Mann, David G., Meisterfeld, Ralf, Mendoza, Leonel, Moestrup, Øjvind, Mozley-Standridge, Sharon E., Smirnov, Alexey V., and Spiegel, Frederick

Published
2007
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4. Local stability properties of complex, species‐rich soil food webs with functional block structure

Author

Castro, Francisco, primary, Adl, Sina M., additional, Allesina, Stefano, additional, Bardgett, Richard D., additional, Bolger, Thomas, additional, Dalzell, Johnathan J., additional, Emmerson, Mark, additional, Fleming, Thomas, additional, Garlaschelli, Diego, additional, Grilli, Jacopo, additional, Hannula, Silja Emilia, additional, Vries, Franciska, additional, Lindo, Zoë, additional, Maule, Aaron G., additional, Öpik, Maarja, additional, Rillig, Matthias C., additional, Veresoglou, Stavros D., additional, Wall, Diana H., additional, and Caruso, Tancredi, additional

Published
2021
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5. Local stability properties of complex, species-rich soil food webs with functional block structure

Author

de Castro, Francisco, Adl, Sina M., Allesina, Stefano, Bardgett, Richard D., Bolger, Thomas, Dalzell, Johnathan J., Emmerson, Mark, Fleming, Thomas, Garlaschelli, Diego, Grilli, Jacopo, Hannula, Silja Emilia, de Vries, Franciska, Lindo, Zoë, Maule, Aaron G., Öpik, Maarja, Rillig, Matthias C., Veresoglou, Stavros D., Wall, Diana H., Caruso, Tancredi, de Castro, Francisco, Adl, Sina M., Allesina, Stefano, Bardgett, Richard D., Bolger, Thomas, Dalzell, Johnathan J., Emmerson, Mark, Fleming, Thomas, Garlaschelli, Diego, Grilli, Jacopo, Hannula, Silja Emilia, de Vries, Franciska, Lindo, Zoë, Maule, Aaron G., Öpik, Maarja, Rillig, Matthias C., Veresoglou, Stavros D., Wall, Diana H., and Caruso, Tancredi

Abstract

Ecologists have long debated the properties that confer stability to complex, species-rich ecological networks. Species-level soil food webs are large and structured networks of central importance to ecosystem functioning. Here, we conducted an analysis of the stability properties of an up-to-date set of theoretical soil food web models that account both for realistic levels of species richness and the most recent views on the topological structure (who is connected to whom) of these food webs. The stability of the network was best explained by two factors: strong correlations between interaction strengths and the blocked, nonrandom trophic structure of the web. These two factors could stabilize our model food webs even at the high levels of species richness that are typically found in soil, and that would make random systems very unstable. Also, the stability of our soil food webs is well-approximated by the cascade model. This result suggests that stability could emerge from the hierarchical structure of the functional organization of the web. Our study shows that under the assumption of equilibrium and small perturbations, theoretical soil food webs possess a topological structure that allows them to be complex yet more locally stable than their random counterpart. In particular, results strongly support the general hypothesis that the stability of rich and complex soil food webs is mostly driven by correlations in interaction strength and the organization of the soil food web into functional groups. The implication is that in real-world food web, any force disrupting the functional structure and distribution pattern of interaction strengths (i.e., energy fluxes) of the soil food webs will destabilize the dynamics of the system, leading to species extinction and major changes in the relative abundances of species.

Published
2021

10. Journal of Eukaryotic Microbiology / Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

Author

Adl, Sina M., Bass, David, Lane, Christopher E., Lukeš, Julius, Schoch, Conrad L., Smirnov, Alexey, Agatha, Sabine, Berney, Cedric, Brown, Matthew W., Burki, Fabien, Cárdenas, Paco, Čepička, Ivan, Chistyakova, Lyudmila, del Campo, Javier, Dunthorn, Micah, Edvardsen, Bente, Eglit Aaron A. Heiss Mon, Yana, Guillou, Laure, Hampl, Vladimír, Heiss, Aaron A., Hoppenrath, Mona, James, Timothy Y., Karnkowska, Anna, Karpov, Sergey, and Kudryavtsev

Subjects
amoebae, protozoa, taxonomy, Algae, fungus, microbiology, parasite, plankton, ecology, ciliate, systematics, flagellate, biodiversity
Abstract

This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users. (VLID)3393271

Published
2019

11. Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

Author

Adl, Sina M., Bass, David, Lane, Christopher E., Lukes, Julius, Schoch, Conrad L., Smirnov, Alexey, Agatha, Sabine, Berney, Cedric, Brown, Matthew W., Burki, Fabien, Cárdenas, Paco, Cepicka, Ivan, Chistyakova, Lyudmila, del Campo, Javier, Dunthorn, Micah, Edvardsen, Bente, Eglit, Yana, Guillou, Laure, Hampl, Vladimir, Heiss, Aaron A., Hoppenrath, Mona, James, Timothy Y., Karnkowska, Anna, Karpov, Sergey, Kim, Eunsoo, Kolisko, Martin, Kudryavtsev, Alexander, Lahr, Daniel J. G., Lara, Enrique, Le Gall, Line, Lynn, Denis H., Mann, David G., Massana, Ramon, Mitchell, Edward A. D., Morrow, Christine, Park, Jong Soo, Pawlowski, Jan W., Powell, Martha J., Richter, Daniel J., Rueckert, Sonja, Shadwick, Lora, Shimano, Satoshi, Spiegel, Frederick W., Torruella, Guifre, Youssef, Noha, Zlatogursky, Vasily V., Zhang, Qianqian, Adl, Sina M., Bass, David, Lane, Christopher E., Lukes, Julius, Schoch, Conrad L., Smirnov, Alexey, Agatha, Sabine, Berney, Cedric, Brown, Matthew W., Burki, Fabien, Cárdenas, Paco, Cepicka, Ivan, Chistyakova, Lyudmila, del Campo, Javier, Dunthorn, Micah, Edvardsen, Bente, Eglit, Yana, Guillou, Laure, Hampl, Vladimir, Heiss, Aaron A., Hoppenrath, Mona, James, Timothy Y., Karnkowska, Anna, Karpov, Sergey, Kim, Eunsoo, Kolisko, Martin, Kudryavtsev, Alexander, Lahr, Daniel J. G., Lara, Enrique, Le Gall, Line, Lynn, Denis H., Mann, David G., Massana, Ramon, Mitchell, Edward A. D., Morrow, Christine, Park, Jong Soo, Pawlowski, Jan W., Powell, Martha J., Richter, Daniel J., Rueckert, Sonja, Shadwick, Lora, Shimano, Satoshi, Spiegel, Frederick W., Torruella, Guifre, Youssef, Noha, Zlatogursky, Vasily V., and Zhang, Qianqian

Abstract

This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.

Published
2019
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12. Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

Author

Gordon and Betty Moore Foundation, Natural Sciences and Engineering Research Council of Canada, Generalitat de Catalunya, Comunidad de Madrid, European Commission, Science for Life Laboratory, National Institutes of Health (US), Adl, Sina M., Bass, David, Lane, Christopher E., Massana, Ramon, Lukeš, Julius, Schoch, Conrad, Smirnov, A., Agatha, Sabine, Berney, Cédric, Brown, Matthew W., Burki, Fabien, Cárdenas, Paco, Čepička, Ivan, Chistyakova, Lyudmila, Campo, Javier del, Dunthorn, Micah, Edvardsen, Bente, Eglit, Yana, Guillou, Laure, Hampl, Vladimir, Heiss, Aaron A., Hoppenrath, Mona, James, Timothy Y., Karnkowska, Anna, Karpov, Sergey A., Kim, Eunsoo, Kolisko, Martin, Kudryavtsev, Alexander, Lahr, Daniel J.G., Lara, Enrique, Le Gall, Line, Lynn, Denis H., Mann, David G., Mitchell, Edward A.D., Morrow, Christine, Soo Park, Jong, Pawlowski, Jan, Powell, Martha J., Richter, Daniel J., Rueckert, Sonja, Shadwick, Lora, Shimano, Satoshi, Spiegel, Frederick W., Torruella, Guifré, Youssef, Noha, Zlatogursky, Vasily, Zhang, Qianqian, Gordon and Betty Moore Foundation, Natural Sciences and Engineering Research Council of Canada, Generalitat de Catalunya, Comunidad de Madrid, European Commission, Science for Life Laboratory, National Institutes of Health (US), Adl, Sina M., Bass, David, Lane, Christopher E., Massana, Ramon, Lukeš, Julius, Schoch, Conrad, Smirnov, A., Agatha, Sabine, Berney, Cédric, Brown, Matthew W., Burki, Fabien, Cárdenas, Paco, Čepička, Ivan, Chistyakova, Lyudmila, Campo, Javier del, Dunthorn, Micah, Edvardsen, Bente, Eglit, Yana, Guillou, Laure, Hampl, Vladimir, Heiss, Aaron A., Hoppenrath, Mona, James, Timothy Y., Karnkowska, Anna, Karpov, Sergey A., Kim, Eunsoo, Kolisko, Martin, Kudryavtsev, Alexander, Lahr, Daniel J.G., Lara, Enrique, Le Gall, Line, Lynn, Denis H., Mann, David G., Mitchell, Edward A.D., Morrow, Christine, Soo Park, Jong, Pawlowski, Jan, Powell, Martha J., Richter, Daniel J., Rueckert, Sonja, Shadwick, Lora, Shimano, Satoshi, Spiegel, Frederick W., Torruella, Guifré, Youssef, Noha, Zlatogursky, Vasily, and Zhang, Qianqian

Abstract

This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users

Published
2019

14. Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

Author

Adl, Sina M., primary, Bass, David, additional, Lane, Christopher E., additional, Lukeš, Julius, additional, Schoch, Conrad L., additional, Smirnov, Alexey, additional, Agatha, Sabine, additional, Berney, Cedric, additional, Brown, Matthew W., additional, Burki, Fabien, additional, Cárdenas, Paco, additional, Čepička, Ivan, additional, Chistyakova, Lyudmila, additional, Campo, Javier, additional, Dunthorn, Micah, additional, Edvardsen, Bente, additional, Eglit, Yana, additional, Guillou, Laure, additional, Hampl, Vladimír, additional, Heiss, Aaron A., additional, Hoppenrath, Mona, additional, James, Timothy Y., additional, Karnkowska, Anna, additional, Karpov, Sergey, additional, Kim, Eunsoo, additional, Kolisko, Martin, additional, Kudryavtsev, Alexander, additional, Lahr, Daniel J.G., additional, Lara, Enrique, additional, Le Gall, Line, additional, Lynn, Denis H., additional, Mann, David G., additional, Massana, Ramon, additional, Mitchell, Edward A.D., additional, Morrow, Christine, additional, Park, Jong Soo, additional, Pawlowski, Jan W., additional, Powell, Martha J., additional, Richter, Daniel J., additional, Rueckert, Sonja, additional, Shadwick, Lora, additional, Shimano, Satoshi, additional, Spiegel, Frederick W., additional, Torruella, Guifré, additional, Youssef, Noha, additional, Zlatogursky, Vasily, additional, and Zhang, Qianqian, additional

Published
2019
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21. Observations on a Geocentrophora sp. (Lecithoepitheliata) flatworm from forest soils in Nova Scotia

Author

Adl, Sina M., Ruiz-Trillo, Inaki, and Wilson, Melanie L.

Subjects
Biodiversity, Taxonomy
Abstract

Adl, Sina M., Ruiz-Trillo, Inaki, Wilson, Melanie L. (2006): Observations on a Geocentrophora sp. (Lecithoepitheliata) flatworm from forest soils in Nova Scotia. Journal of Natural History 40 (23-24): 1381-1387, DOI: 10.1080/00222930600929285, URL: http://dx.doi.org/10.1080/00222930600929285

Published
2006

24. The Revised Classification of Eukaryotes

Author

Adl, Sina M., Simpson, Alastair G. B., Lane, Christopher E., Lukeš, Julius, Bass, David, Bowser, Samuel S., Brown, Matthew W., Burki, Fabien, Dunthorn, Micah, Hampl, Vladimir, Heiss, Aaron, Hoppenrath, Mona, Lara, Enrique, le Gall, Line, Lynn, Denis H., McManus, Hilary, Mitchell, Edward A. D., Mozley-Stanridge, Sharon E., Parfrey, Laura W., Pawlowski, Jan, Rueckert, Sonja, Shadwick, Laura, Schoch, Conrad L., Smirnov, Alexey, Spiegel, Frederick W., Adl, Sina M., Simpson, Alastair G. B., Lane, Christopher E., Lukeš, Julius, Bass, David, Bowser, Samuel S., Brown, Matthew W., Burki, Fabien, Dunthorn, Micah, Hampl, Vladimir, Heiss, Aaron, Hoppenrath, Mona, Lara, Enrique, le Gall, Line, Lynn, Denis H., McManus, Hilary, Mitchell, Edward A. D., Mozley-Stanridge, Sharon E., Parfrey, Laura W., Pawlowski, Jan, Rueckert, Sonja, Shadwick, Laura, Schoch, Conrad L., Smirnov, Alexey, and Spiegel, Frederick W.

Abstract

This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.

Published
2013

27. Regulation of cell cycle duration, cell size and life history in the ciliate sterkiella histriomuscorum

Author

Adl, Sina M.

Abstract

As eukaryotic cells grow and divide, their size remains within a limited range despite changes in resources available. Understanding cell cycle regulation can help understand how size constancy is achieved and provide the molecular and physiological clues to size regulation. However, it is not always obvious how to reconcile the physiological behaviour of cells with this molecular information. We chose the ciliate Sterkiella histriomuscorum (Oxytrichidae) to obtain new insights into size regulation. This organism re-adjusts its cell dimensions as resources diminish. It exits the cell cycle for conjugation or encystment when resources are scarce. A general model is proposed for ciliate cell cycle regulation and the cell cycle of Sterkiella was described within this context. Conditions for inducing conjugation, encystment and excystment were determined to obtain synchronous cultures, and to describe the timing of each process. Observations on the effect of clonal ageing on each process is described. These allow one to manipulate the organism predictably in the laboratory. The consequences of changes in food particle size, prey species, prey abundance and temperature on the size and cell cycle duration of Sterkiella were explained using Michaelis- Menten kinetics. Two parameters (Pmin and Pdiv) were then described and calculated, that were useful in predicting tendencies of cultures with one or two prey species. Two approaches were taken to understand this regulation of cell size physiologically. First, an attempt was made to find out if cAMP is an important regulator of cell cycle progression and duration of growth. Some ciliate "fat" mutants were rescued by drug treatments with inhibitors of kinases. Second, the c d mutant was rescued by transformation with a partial DNA library from wild type Paramecium. However, the rescuing element was not the c d gene. Finally, cell size regulation in several protists is provided with a unified jargon, from a physiological and molecular perspective. This allowed for the first time, a comparison of regulatory processes between species and the development of several ideas regarding cell size regulation. Several principles are proposed as generalities for testing.

Published
1998
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30. The Revised Classification of Eukaryotes

Author

Adl, Sina M., primary, Simpson, Alastair G. B., additional, Lane, Christopher E., additional, Lukeš, Julius, additional, Bass, David, additional, Bowser, Samuel S., additional, Brown, Matthew W., additional, Burki, Fabien, additional, Dunthorn, Micah, additional, Hampl, Vladimir, additional, Heiss, Aaron, additional, Hoppenrath, Mona, additional, Lara, Enrique, additional, le Gall, Line, additional, Lynn, Denis H., additional, McManus, Hilary, additional, Mitchell, Edward A. D., additional, Mozley‐Stanridge, Sharon E., additional, Parfrey, Laura W., additional, Pawlowski, Jan, additional, Rueckert, Sonja, additional, Shadwick, Laura, additional, Schoch, Conrad L., additional, Smirnov, Alexey, additional, and Spiegel, Frederick W., additional

Published
2012
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40. The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists

Author

ADL, SINA M., primary, SIMPSON, ALASTAIR G. B., additional, FARMER, MARK A., additional, ANDERSEN, ROBERT A., additional, ANDERSON, O. ROGER, additional, BARTA, JOHN R., additional, BOWSER, SAMUEL S., additional, BRUGEROLLE, GUY, additional, FENSOME, ROBERT A., additional, FREDERICQ, SUZANNE, additional, JAMES, TIMOTHY Y., additional, KARPOV, SERGEI, additional, KUGRENS, PAUL, additional, KRUG, JOHN, additional, LANE, CHRISTOPHER E., additional, LEWIS, LOUISE A., additional, LODGE, JEAN, additional, LYNN, DENIS H., additional, MANN, DAVID G., additional, MCCOURT, RICHARD M., additional, MENDOZA, LEONEL, additional, MOESTRUP, OJVIND, additional, MOZLEY-STANDRIDGE, SHARON E., additional, NERAD, THOMAS A., additional, SHEARER, CAROL A., additional, SMIRNOV, ALEXEY V., additional, SPIEGEL, FREDERICK W., additional, and TAYLOR, MAX F. J. R., additional

Published
2005
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