Supplemental Section S 1 – Genome
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چکیده
Supplemental Section S1 – Genome Sequencing and Assembly........................................... 2 Supplemental Section S2 – Indel Assessment With the Neutral Indel Model ................11 Supplemental Section S3 – Great Ape Divergence Estimate via WGS Read Mapping..11 Supplemental Section S4 – Short Read Sequencing................................................................13 Supplemental Section S5 – The Orangutan Ensembl Gene Set ...........................................13 Supplemental Section S6 – Ancestral Reconstruction ...........................................................15 Supplemental Section S7 – The Genomic Distribution of Genic Evolution Rates .........18 Supplemental Section S8 – Cytogenetic Characterization....................................................22 Supplemental Section S9 – Highcopy Repeat Assessment ..................................................28 Supplemental Section S10 – Processed Pseudogene Formation........................................31 Supplemental Section S11 – Segmental Duplications and Structural Variation...........33 Supplemental Section S12 – Great Ape Gene Family Expansion ........................................39 Supplemental Section S13 – Protease Gene Families ............................................................41 Supplemental Section S14 – Evolution of Orangutan Alpha and Theta Defensins.......52 Supplemental Section S15 – Genic Positive Selection............................................................57 Supplemental Section S16 – Bornean/Sumatran Divergence.............................................62 Supplemental Section S17 – HMM Estimate of Bornean/Sumatran Divergence Time, Speciation Time and Effective Population Size........................................................................63 Supplemental Section S18 – Bornean/Sumatran Duplication Comparison...................64 Supplemental Section S19 – Retroelement Polymorphisms ...............................................70 Supplemental Section S20 – SNP Calling and Ancestral Base Reconstruction ..............72 Supplemental Section S21 – Demographic Inference Using DaDi .....................................72 Supplemental Section S22 – References.....................................................................................86 SUPPLEMENTARY INFORMATION doi:10.1038/nature09687
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