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. 2022 Aug 4;6(10):1458–1470. doi: 10.1038/s41559-022-01838-4

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 6 — Three examples of transitions detected by the incorporation of short-read data in our phylogenies that would otherwise have been missed. Shades of blue/purple represent marine sequences, while shades of orange/red represent non-marine taxa. (a) A clade of marine centrohelids is detected in purple (including sequences from the Malaspina expedition, Ocean Sampling Day, Tara Oceans, and Mariana Trench datasets). (b) A clade of marine chytrids is detected mainly from Ocean Sampling Day datasets. (c) A clade of non-marine haptophytes is detected mainly from the Swiss Soils and Neotropical soil datasets. Such cases were spread throughout the eukaryotic phylogeny.