Fig. 4: Characterization of inbreeding and genetic loads in B. insignis.
From: Decoding the genome of Brainea insignis reveals insights into fern evolution and conservation
Population genetic characteristics of three lineages (YN: n = 21, VN: n = 5, SC: n = 42 individuals). For all box plots, the box represents the 25th–75th percentiles, the center line indicates the median, and whiskers show the minimum and maximum values. Different lowercase letters (a, b) indicate significant differences between lineages. a Genome-wide heterozygosity estimates of three lineages. Exact P values: YN vs. VN = 0.00003, YN vs. SC = 0.00063, VN vs. SC = 0.77612. b Inbreeding levels (FROH) based on medium-length segments ( > 100 kb). Exact P values: YN vs. VN = 0.85, YN vs. SC = 0.014, VN vs. SC = 0.7. c Inbreeding levels (FROH) based on long segments ( > 1 Mb). Exact P values: YN vs. VN = 0.71, YN vs. SC = 0.45, VN vs. SC = 0.27. d Regression of genome-wide heterozygosity against FROH. e Genetic load measured by the ratio of homozygous DEL (2*homo) to the sum of homozygous and heterozygous deleterious (homo + hete). Exact P values: YN vs. VN = 0.0152, YN vs. SC = 0.0015, VN vs. SC = 0.9854. f Genetic load measured by the ratio of homozygous LOF (2*homo) to the sum of homozygous and heterozygous LOF (homo + hete). Exact P values: YN vs. VN = 0.52, YN vs. SC = 0.04, VN vs. SC = 0.72. g Regression of the fraction of homozygous DEL alleles in against FROH. h Regression of the fraction of homozygous LOF alleles against FROH. i Comparison of homozygous LOF variant sites within ROH regions vs. outside ROH regions. The dot box plot shows the number of homozygous LOF variants in ROH and non-ROH regions. Statistical notes: For a–c, e, f, and i significant differences between lineages were assessed using two-sided Wilcoxon rank-sum tests. For the regression analyses (d, g, and h), the significance of the regression coefficients was evaluated using two-sided tests, and the shaded areas represent the 95% confidence intervals (CIs) of the regressions. Source data are provided as a Source Data.
