title: Targeted investigation of the Neandertal genome by array-based sequence capture.
abstract: It is now possible to perform whole-genome shotgun sequencing as well as capture of specific genomic regions for extinct organisms. However, targeted resequencing of large parts of nuclear genomes has yet to be demonstrated for ancient DNA. Here we show that hybridization capture on microarrays can successfully recover more than a megabase of target regions from Neandertal DNA even in the presence of approximately 99.8% microbial DNA. Using this approach, we have sequenced approximately 14,000 protein-coding positions inferred to have changed on the human lineage since the last common ancestor shared with chimpanzees. By generating the sequence of one Neandertal and 50 present-day humans at these positions, we have identified 88 amino acid substitutions that have become fixed in humans since our divergence from the Neandertals.
authors.affiliation: Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
authors.forename: Hernán A
authors.initials: HA
authors.lastname: Burbano
authors.forename: Emily
authors.initials: E
authors.lastname: Hodges
authors.forename: Richard E
authors.initials: RE
authors.lastname: Green
authors.forename: Adrian W
authors.initials: AW
authors.lastname: Briggs
authors.forename: Johannes
authors.initials: J
authors.lastname: Krause
authors.forename: Matthias
authors.initials: M
authors.lastname: Meyer
authors.forename: Jeffrey M
authors.initials: JM
authors.lastname: Good
authors.forename: Tomislav
authors.initials: T
authors.lastname: Maricic
authors.forename: Philip L F
authors.initials: PL
authors.lastname: Johnson
authors.forename: Zhenyu
authors.initials: Z
authors.lastname: Xuan
authors.forename: Michelle
authors.initials: M
authors.lastname: Rooks
authors.forename: Arindam
authors.initials: A
authors.lastname: Bhattacharjee
authors.forename: Leonardo
authors.initials: L
authors.lastname: Brizuela
authors.forename: Frank W
authors.initials: FW
authors.lastname: Albert
authors.forename: Marco
authors.initials: M
authors.lastname: de la Rasilla
authors.forename: Javier
authors.initials: J
authors.lastname: Fortea
authors.forename: Antonio
authors.initials: A
authors.lastname: Rosas
authors.forename: Michael
authors.initials: M
authors.lastname: Lachmann
authors.forename: Gregory J
authors.initials: GJ
authors.lastname: Hannon
authors.forename: Svante
authors.initials: S
authors.lastname: Pääbo
mesh_terms: D019943:Amino Acid Substitution; D000818:Animals; D005580:Fossils; D005796:Genes; D016678:Genome; D015894:Genome, Human; D015186:Hominidae / Q000235:genetics*; D006801:Humans; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D002679:Pan troglodytes / Q000235:genetics; D011506:Proteins / Q000737:chemistry / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D011506:Proteins
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