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

    Genome Research 21(10):1705 (2011) PMID 21803858 PMCID PMC3202287

    We report the results of the first "true single molecule sequencing" of ancient DNA. We generated 115.9 Mb and 76.9 Mb of DNA sequences from a permafrost-preserved Pleistocene horse bone using the Helicos HeliScope and Illumina GAIIx platforms, respectively. We find that the percentage of endogenous...
  2. Ancient DNA analysis reveals woolly rhino evolutionary relationships.

    Molecular Phylogenetics and Evolution 28(3):485 (2003) PMID 12927133

    We have sequenced the entire 12S rRNA and partial cytochrome b (cyt b) genes of one 60-70,000-year-old sample, and partial 12S rRNA and cyt b sequences of two 40-45,000-year-old samples of the extinct woolly rhinoceros (Coelodonta antiquitatis). Based on these two mitochondrial markers, phylogenetic...
  3. Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA meta-barcoding.

    Molecular Ecology 21(8):1980 (2012) PMID 21951625

    We have investigated the changes in plant composition at these nunataks using both the results of surveys of the flora over the last 130 years and through reconstruction of the vegetation from the end of the Holocene Thermal Maximum (5528 ± 75 cal year BP) using meta-barcoding of plant DNA...
  4. Revisiting Neandertal diversity with a 100,000 year old mtDNA sequence.

    Current Biology 16(11):R400 (2006) PMID 16753548

  5. Glacial survival of boreal trees in northern Scandinavia.

    Science 335(6072):1083 (2012) PMID 22383845

    We show the presence of a rare mitochondrial DNA haplotype of spruce that appears unique to Scandinavia and with its highest frequency to the west-an area believed to sustain ice-free refugia during most of the last ice age. We further show the survival of DNA from this haplotype in lake sediments a...
  6. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome.

    Genome Research 24(3):454 (2014) PMID 24299735 PMCID PMC3941110

    We show that genome-wide epigenetic information can be gathered directly from next-generation sequence reads of DNA isolated from ancient remains. Using the genome sequence data generated from hair shafts of a 4000-yr-old Paleo-Eskimo belonging to the Saqqaq culture, we generate the first ancient nu...
  7. The derived FOXP2 variant of modern humans was shared with Neandertals.

    Current Biology 17(21):1908 (2007) PMID 17949978

    We find that our closest extinct relatives, the Neandertals, share with modern humans two evolutionary changes in FOXP2, a gene that has been implicated in the development of speech and language. We furthermore find that in Neandertals, these changes lie on the common modern human haplotype, which p...
  8. Morphological and genetic evidence for early Holocene cattle management in northeastern China.

    Nature Communications 4:2755 (2013) PMID 24202175

    We provide firmly dated morphological and genetic evidence for early Holocene management of taurine cattle in northeastern China. We describe conjoining mandibles from this region that show evidence of oral stereotypy, dated to the early Holocene by two independent ¹⁴C dates. Using Illumina high-thr...
  9. The microcephalin ancestral allele in a Neanderthal individual.

    PLoS ONE 5(5):e10648 (2010) PMID 20498832 PMCID PMC2871044

    We report the first PCR amplification and high-throughput sequencing of nuclear DNA at the microcephalin (MCPH1) locus from Neanderthal individual from Mezzena Rockshelter (Monti Lessini, Italy). We show that a well-preserved Neanderthal fossil dated at approximately 50,000 years B.P., was homozygou...
  10. Mitogenome sequencing reveals shallow evolutionary histories and recent divergence time between morphologically and ecologically distinct Eu...

    Molecular Ecology 21(11):2727 (2012) PMID 22509795

    We explored an alternate use of such data to recover relationships and population history of closely related lineages with a shallow evolutionary history. Using a GS-FLX platform, we sequenced 106 mitogenomes from the Coregonus lavaretus (Europe) and Coregonus clupeaformis (North America) species co...