Fig. 3
From: GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species
Results from the downstream analyses for historical and modern Sumatran rhinoceros samples from the test dataset. a Principal component analysis (PCA) of historical and modern Sumatran rhinoceros samples using the Sumatran rhinoceros reference. Historical samples: JvS008, JvS009, JvS022. Modern samples: JvS033, JvS034, JvS035. See “PCA” in Additional file 3. b Maximum likelihood estimates of genome-wide heterozygosity (θ) and 95% confidence intervals from mlRho in historical and modern Sumatran rhinoceros samples using the Sumatran rhinoceros reference. See “mlRho” in Additional file 3. c Inbreeding coefficient estimated as the proportion of the genome in runs of homozygosity (FROH) for ROH of length > = 2 Mb in historical and modern Sumatran rhinoceros samples. Parameter settings in the configuration file: homozyg-snp: 25; homozyg-kb: 100; homozyg-window-snp: 250; homozyg-window-het: 3; homozyg-window-missing: 15; homozyg-het: 750. See “ROH” in Additional file 3. d Number of variants in each impact category in historical and modern Sumatran rhinoceros samples as estimated by snpEff and using the white rhinoceros reference with 253 protein-coding gene annotations. Note that none of the samples contained any high impact variants which are therefore not shown. See “snpEff” in Additional file 2. e Relative mutational load estimated from GERP scores for historical and modern Sumatran rhinoceros samples using the white rhinoceros reference. GERP scores were estimated using 30 outgroup species from across the tree of mammals. Only derived alleles from sites with GERP scores above the 99th percentile were included (corresponding to GERP > 0.00048928). See “GERP” in Additional file 2