Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes
Economic Ancient DNA Sequencing
Analysis of ancient DNA is often limited by the availability of ancient material for sequencing. Briggs et al. (p. 318; see the news story by Pennisi) describe a method of ancient DNA sequence retrieval that greatly reduces shotgun sequencing costs while avoiding the many difficulties associated with direct PCR-based approaches. They generated five complete and one near-complete Neandertal mitochondrial DNA genomes, which would have been economically impossible with a simple shotgun approach. Analysis of these genomes shows that Neandertal populations had a much smaller effective population size than modern humans or great apes.
Abstract
Analysis of Neandertal DNA holds great potential for investigating the population history of this group of hominins, but progress has been limited due to the rarity of samples and damaged state of the DNA. We present a method of targeted ancient DNA sequence retrieval that greatly reduces sample destruction and sequencing demands and use this method to reconstruct the complete mitochondrial DNA (mtDNA) genomes of five Neandertals from across their geographic range. We find that mtDNA genetic diversity in Neandertals that lived 38,000 to 70,000 years ago was approximately one-third of that in contemporary modern humans. Together with analyses of mtDNA protein evolution, these data suggest that the long-term effective population size of Neandertals was smaller than that of modern humans and extant great apes.
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Published In
Science
Volume 325 | Issue 5938
17 July 2009
17 July 2009
Copyright
Copyright © 2009, American Association for the Advancement of Science.
Submission history
Received: 3 April 2009
Accepted: 3 June 2009
Published in print: 17 July 2009
Acknowledgments
We thank P. Johnson, M. Knapp, A.-S. Malaspinas, M. Meyer, J. Sullivan, M. Slatkin, and anonymous reviewers for comments; the Croatian Academy of Sciences and Arts and the Berlin-Brandenburg Academy of Sciences for logistic and scientific support; and the Presidential Innovation Fund of the Max Planck Society for financial support. The government of the Principado de Asturias funded excavations at the El Sidron site. C.L.-F. was supported by the Spanish Ministry of Education and Science and J.M.G. by an NSF international postdoctoral fellowship (OISE-0754461). Sequences are deposited at the EBI (European Bioinformatics Institute) nucleotide database with the following accession numbers: Neandertal 1 (Feldhofer 1), FM865407; Neandertal 2 (Feldhofer 2), FM865408; Sidron 1253, FM865409; Vindija 33.25, FM865410; Mezmaiskaya 1, FM865411.
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