We present a method of targeted ancient DNA sequence retrieval, which we used to reconstruct the complete mitochondrial genomes of five Neandertal individuals. Comparison of these sequences with present day humans suggests that Neandertals had a long term low effective population size.
The PEC method is simple, quick, sensitive and specific. Therefore we the authors envisage multiple applications outside ancient DNA, such as capture of small RNA fragments from an RNA library, interrogation of structural variation in a pooled sample or capture of 16S (or other loci) diversity from a metagenomic sample. One point to mention is that the sensitivity of capture becomes lower as the number of PEC primers in a multiplex capture reaction increases. PEC is therefore not ideally suited for capture of very large (e.g. a megabase or more) capture regions, but is extremely well suited for capture of small target regions or even SNP positions from many individuals in a rapid fashion.
The authors have nothing to disclose.
We thank M. Meyer for advice; 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. J.M.G. was supported by an NSF international postdoctoral fellowship (OISE-0754461). Sequences are deposited at the EBI nucleotide database with accession numbers: Neandertal 1 (Feldhofer 1) FM865407, Neandertal 2 (Feldhofer 2) FM865408, Sidron 1253 FM865409, Vindija 33.25 FM865410, Mezmaiskaya 1 FM865411
Material Name | Typ | Company | Catalogue Number | Comment |
---|---|---|---|---|
AmpliTaq Gold polymerase with GeneAmp PCR buffer II and MgCl2 | Applied Biosystems | N8080241 | ||
QIAGEN MinElute PCR purification kit | Qiagen | 28004 | ||
M-270 streptavidin beads | Invitrogen | 653.05 | ||
Tween-20 | Sigma-Aldrich | P2287 | ||
DynaMag-2 magnetic particle separator | Invitrogen | 120.02D |