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. 2023 Feb 6;6:153. doi: 10.1038/s42003-023-04514-w

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© The Author(s) 2023

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. 6 — a Variation of heterozygosity levels (He) across a randomly chosen chromosome, for a random subset of samples, depicting He-levels of non-overlapping 20 kb windows, with grey segments highlighting the genomic regions which are marked as run of homozygosity (ROH) by the newly developed ROH-detection software Darwindow. Values along the y-axis represent sample and chromosome-specific F_ROH-values (proportion of chromosome marked as ROH). b Standard deviation of sample-specific F_ROH-values across chromosomes versus genome-wide mean F_ROH-values. High standard deviations are indicative of recent inbreeding events. c Mantel plot showing, for all (25 ∙ 24/2=) 300 brown bear population pairs, mean genome-wide genetic distance (D_XY) versus geographic distance. d D_XY-values against mean genome wide He-estimates, for all possible 300 population pairs. Population pairs involving bears from Middle East and North America affect the significance of the linear regression model. e Boxplots depicting sample-specific ROH-length and genome-wide He estimates, with samples grouped according to sample origin. Centre lines indicate median, and box limits indicate upper and lower quartiles. f SLIM2 genetic forward-in-time simulations indicate that following a population size reduction (from an initial Ne of 5000 individuals), and given sufficient time, ROH-distributions converge to a new equilibrium, with the relationship between F_ROH and number of ROHs depending on the new Ne. Shown are the number of generations since the population size reduction. g, h Sample specific ROH-distributions. The colour bar above the stacked barplot indicates population assignment.