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. 2019 Jan 9;5(1):63–73. doi: 10.1038/s41477-018-0337-0

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© The Author(s), under exclusive licence to Springer Nature Limited 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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Fig. 1 — a, Number of heterozygous biallelic SNPs per 100-kb non-overlapping windows is plotted along the largest 12 scaffolds. Indels were excluded. b, The history of effective population size was inferred using the PSMC method. One hundred bootstraps were performed and the margins are shown in light red. c, For every non-overlapping 100-kb window, the distribution is shown from top to bottom: gene density (percentage of nucleotides with predicted model), transcriptome (percentage of nucleotides with evidence of transcriptome mapping) and three different classes of repetitive sequences (percentage of nucleotides with transposable element annotation). The red T letter denotes the presence of a telomeric repeat cluster at the scaffold end. LINE, long interspersed nuclear element.