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  1. DNA from extinct giant lemurs links archaeolemurids to extant indriids.

    BMC Evolutionary Biology 8:121 (2008) PMID 18442367 PMCID PMC2386821

    We therefore used ancient DNA technology to address the phylogenetic status of the two archaeolemurid genera (Archaeolemur and Hadropithecus). Despite poor DNA preservation conditions in subtropical environments, we managed to recover 94- to 539-bp sequences for two mitochondrial genes among 5 subfo...
  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. 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...
  4. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.

    Nature 499(7456):74 (2013) PMID 23803765

    We present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560-780 thousand years before present (kyr BP). Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the geno...
  5. Rodents of the Caribbean: origin and diversification of hutias unravelled by next-generation museomics.

    Biology Letters 10(7) (2014) PMID 25115033 PMCID PMC4126619

    We used target enrichment and next-generation sequencing of mitochondrial and nuclear genes to infer the phylogenetic relationships of hutias, estimate their divergence ages, and understand their mode of dispersal in the Greater Antilles.We found that Capromyidae are nested within Echimyidae (spiny...
  6. Revisiting Neandertal diversity with a 100,000 year old mtDNA sequence.

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

  7. mapDamage: testing for damage patterns in ancient DNA sequences.

    Journal of Gerontology 27(15):2153 (2011) PMID 21659319

    SUMMARY: Ancient DNA extracts consist of a mixture of contaminant DNA molecules, most often originating from environmental microbes, and endogenous fragments exhibiting substantial levels of DNA damage. The latter introduce specific nucleotide misincorporations and DNA fragmentation signatures in se...
  8. Revising the recent evolutionary history of equids using ancient DNA.

    PNAS 106(51):21754 (2009) PMID 20007379 PMCID PMC2799835

    We examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87-688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and r...
  9. Mammoth and elephant phylogenetic relationships: Mammut americanum, the missing outgroup.

    Evolutionary Bioinformatics 3:45 (2007) PMID 19430604

    We demonstrate here that the three competing topologies have similar likelihood, bayesian and parsimony supports. The analysis further suggests the inadequacy of using Sirenia or Hyracoidea as outgroups. We therefore argue that orthologous sequences from the extinct American mastodon will be require...
  10. Ancient DNA analysis reveals divergence of the cave bear,Ursus spelaeus, and brown bear,Ursus arctos, lineages

    Current Biology 11(3):200 (2001)

    We previously amplified a short DNA fragment of the mitochondrial DNA control region (mt control region) of a 40,000-year-old Ursus spelaeus sample [4]. In this paper, we describe the DNA analysis of two mtDNA regions, the control region and the cytochrome b gene. Control region sequences were obtai...