TY - DATA T1 - Additional file 1: of Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx PY - 2016/12/14 AU - Federico Abascal AU - André Corvelo AU - Fernando Cruz AU - José Villanueva-Cañas AU - Anna Vlasova AU - Marina Marcet-Houben AU - Begoña Martínez-Cruz AU - Jade Cheng AU - Pablo Prieto AU - Víctor Quesada AU - Javier Quilez AU - Gang Li AU - Francisca García AU - Miriam Rubio-Camarillo AU - Leonor Frias AU - Paolo Ribeca AU - Salvador Capella-Gutiérrez AU - José Rodríguez AU - Francisco Câmara AU - Ernesto Lowy AU - Luca Cozzuto AU - Ionas Erb AU - Michael Tress AU - Jose Rodriguez-Ales AU - Jorge Ruiz-Orera AU - Ferran Reverter AU - Mireia Casas-Marce AU - Laura Soriano AU - Javier Arango AU - Sophia Derdak AU - Beatriz Galán AU - Julie Blanc AU - Marta Gut AU - Belen Lorente-Galdos AU - Marta Andrés-Nieto AU - Carlos López-Otín AU - Alfonso Valencia AU - Ivo Gut AU - José García AU - Roderic Guigó AU - William Murphy AU - Aurora Ruiz-Herrera AU - Tomas Marques-Bonet AU - Guglielmo Roma AU - Cedric Notredame AU - Thomas Mailund AU - M. Albà AU - Toni Gabaldón AU - Tyler Alioto AU - José Godoy UR - https://springernature.figshare.com/articles/journal_contribution/Additional_file_1_of_Extreme_genomic_erosion_after_recurrent_demographic_bottlenecks_in_the_highly_endangered_Iberian_lynx/4365542 DO - 10.6084/m9.figshare.c.3611990_D2.v1 L4 - https://ndownloader.figshare.com/files/7091648 KW - Conservation genomics KW - Genetic diversity KW - Inbreeding KW - Genetic drift KW - Lynx N2 - 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) ER -