Computational challenges in the analysis of ancient DNA.
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.
Prüfer
Kay
K
Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany. pruefer@eva.mpg.de
Stenzel
Udo
U
Hofreiter
Michael
M
Pääbo
Svante
S
Kelso
Janet
J
Green
Richard E
RE
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*
D004247:DNA