Additional file 1: of Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

Supplemental information. Additional details on methods and results, including additional tables (Tables S1–S37) and figures (Figures S1–S45). Section 1: Samples, libraries and sequencing. Section 2: Genome assembly. Section 3: Genome annotation. Section 4: Functional annotation. Section 5: Manual annotation and comparative analysis of lynx protease genes. Section 6: Transcriptome characterization. Section 7: Evolutionary profiling and expression of lncRNAs. Section 8: Lynx orphan genes. Section 9: Eurasian and Iberian lynx divergence Section 10: Demographic history. Section 11: Karyotype. Section 12: Genome alignments and synteny analysis. Section 13: Phylogenomics. Section 14: Positive selection. Section 15: Transposable elements dynamics. Section 16: Substitution patterns. Section 17: Segmental duplications. Section 18: Variant discovery and genotype calling. Section 19: Runs of homozygosity (ROH) and individual inbreeding. Section 20: Genomic averages of population genetics parameters. Section 21: Variation and divergence at coding sequences. Section 22: X chromosome versus autosomes genetic diversity. Section 23: Patterns of diversity across the genome. Section 24: Linkage disequilibrium. Section 25: The Iberian lynx genome browser. Section 26: References. (PDF 10 MB)