Ludovic Orlando

Summary

Affiliation: University of Copenhagen
Country: Denmark

Publications

  1. ncbi Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse
    Ludovic Orlando
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, 1350 Copenhagen K, Denmark
    Nature 499:74-8. 2013
  2. pmc True single-molecule DNA sequencing of a pleistocene horse bone
    Ludovic Orlando
    Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen University, Copenhagen DK 1350, Denmark
    Genome Res 21:1705-19. 2011
  3. ncbi Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans
    Maanasa Raghavan
    1 Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, 1350 Copenhagen, Denmark 2
    Nature 505:87-91. 2014
  4. pmc Improving the performance of true single molecule sequencing for ancient DNA
    Aurélien Ginolhac
    Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen University, 5 7 Øster Voldgade, København, 1350, Denmark
    BMC Genomics 13:177. 2012
  5. pmc Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals
    Andrew D Foote
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
    PLoS ONE 7:e41781. 2012
  6. doi The genome of a Late Pleistocene human from a Clovis burial site in western Montana
    Morten Rasmussen
    1 Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, DK 1350 Copenhagen K, Denmark 2
    Nature 506:225-9. 2014
  7. ncbi A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability
    Tina Jørgensen
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
    Mol Ecol 21:1989-2003. 2012
  8. pmc Mitochondrial phylogenomics of modern and ancient equids
    Julia T Vilstrup
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
    PLoS ONE 8:e55950. 2013
  9. pmc Improving ancient DNA read mapping against modern reference genomes
    Mikkel Schubert
    Centre for GeoGenetics Natural History Museum of Denmark, University of Copenhagen, 5 7 Øster Voldgade, 1350, Kobenhavns K, Denmark
    BMC Genomics 13:178. 2012
  10. doi Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene
    Paula F Campos
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, 1350 Copenhagen, Denmark
    Mol Ecol 19:4863-75. 2010

Collaborators

Detail Information

Publications27

  1. ncbi Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse
    Ludovic Orlando
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, 1350 Copenhagen K, Denmark
    Nature 499:74-8. 2013
    ..Such regions could correspond to loci selected early during domestication...
  2. pmc True single-molecule DNA sequencing of a pleistocene horse bone
    Ludovic Orlando
    Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen University, Copenhagen DK 1350, Denmark
    Genome Res 21:1705-19. 2011
    ..Our results suggest that paleogenomes could be sequenced in an unprecedented manner by combining current second- and third-generation sequencing approaches...
  3. ncbi Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans
    Maanasa Raghavan
    1 Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, 1350 Copenhagen, Denmark 2
    Nature 505:87-91. 2014
    ..Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans. ..
  4. pmc Improving the performance of true single molecule sequencing for ancient DNA
    Aurélien Ginolhac
    Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen University, 5 7 Øster Voldgade, København, 1350, Denmark
    BMC Genomics 13:177. 2012
    ..Here, we aim at improving even further the performance of tSMS for ancient DNA by testing two novel tSMS template preparation methods for Pleistocene bone fossils, namely oligonucleotide spiking and treatment with DNA phosphatase...
  5. pmc Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals
    Andrew D Foote
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
    PLoS ONE 7:e41781. 2012
    ..Therefore, with optimization aimed towards processing larger volumes of seawater this method has the potential to compliment current visual and acoustic methods of species detection of marine mammals...
  6. doi The genome of a Late Pleistocene human from a Clovis burial site in western Montana
    Morten Rasmussen
    1 Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, DK 1350 Copenhagen K, Denmark 2
    Nature 506:225-9. 2014
    ..Finally, we find evidence of a deep divergence in Native American populations that predates the Anzick-1 individual. ..
  7. ncbi A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability
    Tina Jørgensen
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
    Mol Ecol 21:1989-2003. 2012
    ....
  8. pmc Mitochondrial phylogenomics of modern and ancient equids
    Julia T Vilstrup
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
    PLoS ONE 8:e55950. 2013
    ....
  9. pmc Improving ancient DNA read mapping against modern reference genomes
    Mikkel Schubert
    Centre for GeoGenetics Natural History Museum of Denmark, University of Copenhagen, 5 7 Øster Voldgade, 1350, Kobenhavns K, Denmark
    BMC Genomics 13:178. 2012
    ....
  10. doi Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene
    Paula F Campos
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, 1350 Copenhagen, Denmark
    Mol Ecol 19:4863-75. 2010
    ..66-77%) following either a demographic bottleneck in the course of the Holocene or late Pleistocene, or a geographic fragmentation (followed by local extinction of one subpopulation) at the Holocene/Pleistocene transition...
  11. pmc Reconstructing genome evolution in historic samples of the Irish potato famine pathogen
    Michael D Martin
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, 1350 Copenhagen K, Denmark
    Nat Commun 4:2172. 2013
    ..At least one of these genotypes encodes a virulent phenotype in modern strains, which helps explain the 20th century's episodic replacements of European P. infestans lineages...
  12. ncbi Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA meta-barcoding
    Tina Jørgensen
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
    Mol Ecol 21:1980-8. 2012
    ..This suggests that even the flora of fairly small and isolated ice-free areas reacts quickly to a changing climate...
  13. pmc mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters
    Hákon Jónsson
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 København K, Denmark
    Bioinformatics 29:1682-4. 2013
    ..The absence of formal statistical modeling of the DNA damage process, however, precluded rigorous quantitative comparisons across samples...
  14. doi Monitoring endangered freshwater biodiversity using environmental DNA
    Philip Francis Thomsen
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, DK 1350 Copenhagen, Denmark
    Mol Ecol 21:2565-73. 2012
    ..Our findings underpin the ubiquitous nature of DNA traces in the environment and establish environmental DNA as a tool for monitoring rare and threatened species across a wide range of taxonomic groups...
  15. doi Next-generation sequencing offers new insights into DNA degradation
    Søren Overballe-Petersen
    Centre for GeoGenetics, University of Copenhagen, Øster Voldgade 5 7, 1350 Copenhagen K, Denmark
    Trends Biotechnol 30:364-8. 2012
    ..In this review, we argue that the latter results from an electron resonance structure unique to guanosine rather than adenosine having an extra resonance structure over guanosine as previously suggested...
  16. pmc Out of the Pacific and back again: insights into the matrilineal history of Pacific killer whale ecotypes
    Andrew D Foote
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
    PLoS ONE 6:e24980. 2011
    ....
  17. pmc Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes
    Andaine Seguin-Orlando
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
    PLoS ONE 8:e78575. 2013
    ..Consequently, we show that models adequate for estimating post-mortem DNA damage levels must be robust to the molecular tools used for building ancient DNA libraries. ..
  18. doi Proteomic analysis of a pleistocene mammoth femur reveals more than one hundred ancient bone proteins
    Enrico Cappellini
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, 1350, Copenhagen, Denmark
    J Proteome Res 11:917-26. 2012
    ..This approach therefore represents a further step into the ongoing integration of different high-throughput technologies for identification of ancient biomolecules, unleashing the field of paleoproteomics...
  19. pmc An Aboriginal Australian genome reveals separate human dispersals into Asia
    Morten Rasmussen
    Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5 7, 1350 Copenhagen, Denmark
    Science 334:94-8. 2011
    ..Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa...
  20. pmc Species-specific responses of Late Quaternary megafauna to climate and humans
    Eline D Lorenzen
    Centre for GeoGenetics, University of Copenhagen, Øster Voldgade 5 7, DK 1350 Copenhagen K, Denmark
    Nature 479:359-64. 2011
    ....
  21. ncbi Statistical guidelines for detecting past population shifts using ancient DNA
    Tobias Mourier
    Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
    Mol Biol Evol 29:2241-51. 2012
    ..In addition, our results suggest that many ancient DNA studies may face power issues in detecting moderate demographic collapses and/or highly dynamic demographic shifts when based solely on mitochondrial information...
  22. ncbi Meta-barcoding of 'dirt' DNA from soil reflects vertebrate biodiversity
    Kenneth Andersen
    Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
    Mol Ecol 21:1966-79. 2012
    ....
  23. doi mapDamage: testing for damage patterns in ancient DNA sequences
    Aurélien Ginolhac
    Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen University, 1350 København K, Denmark
    Bioinformatics 27:2153-5. 2011
    ..The Perl script outputs are further automatically processed in embedded R script in order to detect typical patterns of genuine ancient DNA sequences...
  24. pmc Ancient human genome sequence of an extinct Palaeo-Eskimo
    Morten Rasmussen
    Centre for GeoGenetics, Natural History Museum of Denmark and Department of Biology, University of Copenhagen, Universitetsparken 15, DK 2100 Copenhagen, Denmark
    Nature 463:757-62. 2010
    ..This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit...
  25. ncbi Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX
    Mikkel Schubert
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
    Nat Protoc 9:1056-82. 2014
    ..Applying the PALEOMIX pipeline to the three ancient and seven modern Phytophthora infestans genomes as described here takes 5 d using a 16-core server. ..
  26. pmc Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics
    Paula F Campos
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK 1350 Copenhagen, Denmark
    Proc Natl Acad Sci U S A 107:5675-80. 2010
    ....
  27. pmc Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae
    Julia T Vilstrup
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, 1350 Copenhagen, Denmark
    BMC Evol Biol 11:65. 2011
    ..Further ad hoc tests were then conducted to estimate the support for alternative topologies...