Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts

  title={Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts},
  author={M. Thomas P. Gilbert and Lynn P. Tomsho and Snjezana Rendulic and Mike Packard and Daniela I. Drautz and Andrei V. Sher and Alexei Tikhonov and Love Dal{\'e}n and Tatyana Kuznetsova and Pavel A Kosintsev and Paula F. Campos and Thomas F.G. Higham and Matthew James Collins and Andrew Wilson and Fyodor Shidlovskiy and Bernard Buigues and Per G. P. Ericson and Mietje Germonpr{\'e} and Anders G{\"o}therstr{\"o}m and Paola Iacumin and V. I. Nikolaev and Malgosia Nowak-Kemp and Eske Willerslev and James R. Knight and Gerard P. Irzyk and Clotilde Perbost and Karin M. Fredrikson and Timothy T. Harkins and Sharon Sheridan and Webb Miller and Stephan C. Schuster},
  pages={1927 - 1930}
Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in… 

Analysis of Whole Mitogenomes from Ancient Samples.

This protocol was designed for enrichment of mitochondrial DNA in ancient or other degraded samples, and can be easily adapted for using for building libraries for shotgun-sequencing of whole genomes, or enrichment of other genomic regions.

True single-molecule DNA sequencing of a pleistocene horse bone.

The first "true single molecule sequencing" of ancient DNA is reported, suggesting that paleogenomes could be sequenced in an unprecedented manner by combining current second- and third-generation sequencing approaches.

Comment on "Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts"

When experimental parameters are carefully controlled for, including adequate sampling, quantitative polymerase chain reaction analysis, and modeling the decay of DNA, the general importance of this claim is not supported.

Response to Comment on "Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts"

The authors are misreading and misinterpreting the conclusions of the study; they claim nothing further than that hair shaft represents an excellent source material for the shotgun sequencing of mitochondrial DNA genomes.

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Mitogenomic analyses from ancient DNA.

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The results on Pleistocene cave bear samples show that DNA yields are quantitatively comparable, and in fact even slightly better than with silica batch extraction, while at the same time the number of samples that can conveniently be processed in parallel increases and both bench time and costs decrease using this method.



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The metagenomic approach used here establishes the feasibility of ancient DNA genome sequencing programs and revealed the evolutionary relationship of cave bear and modern bear sequences.

Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA

The high percentage of endogenous DNA recoverable from this single mammoth would allow for completion of its genome, unleashing the field of paleogenomics.

DNA typing from single hairs

Three different means of DNA typing are used for the determination of amplified DNA fragment length differences, hybridization with allele-specific oligonucleotide probes, and direct DNA sequencing on single human hairs to detect genetically variable mitochondrial and nuclear DNA sequences.

DNA sequences from the quagga, an extinct member of the horse family

Dried muscle from a museum specimen of the quagga, a zebra-like species that became extinct in 1883, is examined, and DNA was extracted in amounts approaching 1% of that expected from fresh muscle, and that the DNA was of relatively low molecular weight.

Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae

The phylogenetic analyses show that the mammoth was more closely related to the Asian than to the African elephant, and the divergence of mammoth, African and Asian elephants occurred over a short time, corresponding to only about 7% of the total length of the phylogenetic tree for the three evolutionary lineages.

Analysis of one million base pairs of Neanderthal DNA

A 38,000-year-old Neanderthal fossil that is exceptionally free of contamination from modern human DNA is identified and it is revealed that modern human and Neanderthal DNA sequences diverged on average about 500,000 years ago.

Human hair histogenesis for the mitochondrial DNA forensic scientist.

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Sequencing and Analysis of Neanderthal Genomic DNA

The characterization of Neanderthals from a new perspective is described, based on the development of a Neanderthal metagenomic library and its high-throughput sequencing and analysis, and the finding that the Neanderthal and human genomes are at least 99.5% identical is found.