title: Computational challenges in the analysis of ancient DNA.
abstract: High-throughput sequencing technologies have opened up a new avenue for studying extinct organisms. Here we identify and quantify biases introduced by particular characteristics of ancient DNA samples. These analyses demonstrate the importance of closely related genomic sequence for correctly identifying and classifying bona fide endogenous DNA fragments. We show that more accurate genome divergence estimates from ancient DNA sequence can be attained using at least two outgroup genomes and appropriate filtering.
authors.affiliation: Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. pruefer@eva.mpg.de
authors.forename: Kay
authors.initials: K
authors.lastname: Prüfer
authors.forename: Udo
authors.initials: U
authors.lastname: Stenzel
authors.forename: Michael
authors.initials: M
authors.lastname: Hofreiter
authors.forename: Svante
authors.initials: S
authors.lastname: Pääbo
authors.forename: Janet
authors.initials: J
authors.lastname: Kelso
authors.forename: Richard E
authors.initials: RE
authors.lastname: Green
mesh_terms: D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004247:DNA / Q000032:analysis* / Q000235:genetics*; D030561:Databases, Nucleic Acid; D053476:Extinction, Biological; D014644:Genetic Variation; D006801:Humans; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA