Targeted retrieval and analysis of five neandertal mtDNA genomes

4 pages, 2 figures, 1 table.-- Supporting information available (Materials and Methods, Suppl. figs S1-S14, Suppl. tables S1-S8, Suppl refs, 1 appendix, 37 pages) at: http://science-mag.aaas.org/cgi/data/325/5938/318/DC1/1Sequences 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.Comment on the paper by Martín Cagliani (Spanish lang.) available at 'Mundo Neandertal': http://neanderthalis.blogspot.com/2009/07/la-eva-neandertal-vivio-hace-110-mil.htmlAnalysis 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.We thank 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 Sidrón" 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).Peer reviewe