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  1. Reconstructing ancient genomes and epigenomes.

    Nature Reviews: Genetics 16(7):395 (2015) PMID 26055157

    Research involving ancient DNA (aDNA) has experienced a true technological revolution in recent years through advances in the recovery of aDNA and, particularly, through applications of high-throughput sequencing. Formerly restricted to the analysis of only limited amounts of genetic information...
  2. The ancestry and affiliations of Kennewick Man.

    Nature 523(7561):455 (2015) PMID 26087396

    Kennewick Man, referred to as the Ancient One by Native Americans, is a male human skeleton discovered in Washington state (USA) in 1996 and initially radiocarbon dated to 8,340-9,200 calibrated years before present (BP). His population affinities have been the subject of scientific debate and l...
  3. Population genomics of Bronze Age Eurasia.

    Nature 522(7555):167 (2015) PMID 26062507

    The Bronze Age of Eurasia (around 3000-1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We in...
  4. Ancient proteins resolve the evolutionary history of Darwin's South American ungulates.

    Nature 522(7554):81 (2015) PMID 25799987

    No large group of recently extinct placental mammals remains as evolutionarily cryptic as the approximately 280 genera grouped as 'South American native ungulates'. To Charles Darwin, who first collected their remains, they included perhaps the 'strangest animal[s] ever discovered'. Today, much ...
  5. Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean.

    PNAS 112(12):3669 (2015) PMID 25755263 PMCID PMC4378422

    Between 1500 and 1850, more than 12 million enslaved Africans were transported to the New World. The vast majority were shipped from West and West-Central Africa, but their precise origins are largely unknown. We used genome-wide ancient DNA analyses to investigate the genetic origins of three e...
  6. Improving access to endogenous DNA in ancient bones and teeth.

    Scientific reports 5:11184 (2015) PMID 26081994 PMCID PMC4472031

    Poor DNA preservation is the most limiting factor in ancient genomic research. In the majority of ancient bones and teeth, endogenous DNA molecules represent a minor fraction of the whole DNA extract, rendering shot-gun sequencing inefficient for obtaining genomic data. Based on ancient human bo...
  7. Comparison of the Equine Reference Sequence with Its Sanger Source Data and New Illumina Reads.

    PLoS ONE 10(6):e0126852 (2015) PMID 26107638 PMCID PMC4479572

    The reference assembly for the domestic horse, EquCab2, published in 2009, was built using approximately 30 million Sanger reads from a Thoroughbred mare named Twilight. Contiguity in the assembly was facilitated using nearly 315 thousand BAC end sequences from Twilight's half brother Bravo. Sin...
  8. Pros and cons of methylation-based enrichment methods for ancient DNA.

    Scientific reports 5:11826 (2015) PMID 26134828 PMCID PMC4488743

    The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules conta...
  9. Annotation of the Protein Coding Regions of the Equine Genome.

    PLoS ONE 10(6):e0124375 (2015) PMID 26107351 PMCID PMC4481266

    Current gene annotation of the horse genome is largely derived from in silico predictions and cross-species alignments. Only a small number of genes are annotated based on equine EST and mRNA sequences. To expand the number of equine genes annotated from equine experimental evidence, we sequence...
  10. Prehistoric genomes reveal the genetic foundation and cost of horse domestication.

    PNAS 111(52):E5661 (2014) PMID 25512547 PMCID PMC4284583

    The domestication of the horse ∼ 5.5 kya and the emergence of mounted riding, chariotry, and cavalry dramatically transformed human civilization. However, the genetics underlying horse domestication are difficult to reconstruct, given the near extinction of wild horses. We therefore sequenced tw...