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. 2020 Apr 2;10:5805. doi: 10.1038/s41598-020-62362-8

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© The Author(s) 2020

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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A conceptual diagram showing the distribution of SNPs on a chromosome with reference to the reference chromosome: the chromosome is similar to an ecological community, and the number of SNPs on a gene locus is similar to the species abundance in an ecological community. For example, there are three SNPs on the locus of gene-1, assuming the total SNPs on the chromosome is N (or 10 displayed with the first 3 genes displayed), then the relative SNP abundance for gene-1 is equal to 3/N (or 3/10 = 0.3 with the 3 genes displayed). Similarly, p₂, p₃, … can be computed. When the relative abundances of SNPs are available, the diversity (Hill numbers) can be computed based on the diversity definitions [Eqs. (2–15)]. The R-codes computing alpha-diversity, beta-diversity (including similarity) profiles are provided in the OSI.