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. 2019 Dec 17;9:19297. doi: 10.1038/s41598-019-55253-0

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© The Author(s) 2019

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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Schematic diagram of the methods used in the study. Two distinct approaches are used: one estimates the distances among samples, to form a distance matrix using one of various models (Yang, 2006), and then finds the relationships based on the distances. The other finds the relationship directly from the sequence matrix. Only direct PCA shows the relationships of samples and bases coincidently. Methods that estimate a tree-shaped relationship are coloured in oak.