Ludovic Orlando

Summary

Affiliation: University of Copenhagen
Country: Denmark

Publications

  1. doi Equids
    Ludovic Orlando
    Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5 7, 1350K Copenhagen, Denmark Electronic address
    Curr Biol 25:R973-8. 2015
  2. pmc The first aurochs genome reveals the breeding history of British and European cattle
    Ludovic Orlando
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Østervoldgade 5 7, 1350K, Copenhagen, Denmark
    Genome Biol 16:225. 2015
  3. doi 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
  4. 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
  5. pmc 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
  6. 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
  7. 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
  8. pmc 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
  9. 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
  10. pmc Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments
    Pablo Librado
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark
    Proc Natl Acad Sci U S A 112:E6889-97. 2015

Collaborators

Detail Information

Publications48

  1. doi Equids
    Ludovic Orlando
    Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5 7, 1350K Copenhagen, Denmark Electronic address
    Curr Biol 25:R973-8. 2015
    ..Unlike ruminants, they are hindgut fermenters, which digest plant cellulose in their intestines and not in differentiated multiple stomach chambers. ..
  2. pmc The first aurochs genome reveals the breeding history of British and European cattle
    Ludovic Orlando
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Østervoldgade 5 7, 1350K, Copenhagen, Denmark
    Genome Biol 16:225. 2015
    ..The first genome sequence of the extinct European wild aurochs reveals the genetic foundation of native British and Irish landraces of cattle.See related Research article: www.dx.doi.org/10.1186/s13059-015-0790-2. ..
  3. doi 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...
  4. 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...
  5. pmc 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. ..
  6. 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...
  7. 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...
  8. pmc 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. ..
  9. 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
    ....
  10. pmc Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments
    Pablo Librado
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark
    Proc Natl Acad Sci U S A 112:E6889-97. 2015
    ..Finally, we find evidence for convergent evolution with native human populations and woolly mammoths, suggesting that only a few evolutionary strategies are compatible with survival in extremely cold environments. ..
  11. 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
    ....
  12. 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
    ....
  13. pmc Speciation with gene flow in equids despite extensive chromosomal plasticity
    Hákon Jónsson
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK 1350 Copenhagen K, Denmark
    Proc Natl Acad Sci U S A 111:18655-60. 2014
    ....
  14. 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...
  15. 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...
  16. doi 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...
  17. pmc Prehistoric genomes reveal the genetic foundation and cost of horse domestication
    Mikkel Schubert
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark
    Proc Natl Acad Sci U S A 111:E5661-9. 2014
    ..Our work demonstrates the power of ancient genomes to reconstruct the complex genetic changes that transformed wild animals into their domesticated forms, and the population context in which this process took place...
  18. 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...
  19. 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...
  20. 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...
  21. 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
    ....
  22. doi New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA
    Nathan Wales
    Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
    Biotechniques 59:368-71. 2015
    ..Our findings can help researchers determine when to utilize the time- and resource-intensive ssDNA library preparation method. ..
  23. pmc Improving access to endogenous DNA in ancient bones and teeth
    Peter B Damgaard
    Centre for GeoGenetics, Natural History Museum, University of Copenhagen
    Sci Rep 5:11184. 2015
    ..Our presented methods are likely to increase the proportion of ancient samples that are suitable for genome-scale characterization. ..
  24. doi Evolutionary Genomics and Conservation of the Endangered Przewalski's Horse
    Clio Der Sarkissian
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350K, Denmark
    Curr Biol 25:2577-83. 2015
    ..1%. This, together with the identification of ancestry informative markers and corrections to the International Studbook, establishes a framework for evaluating the persistence of genetic variation in future reintroduced populations...
  25. pmc Ancient genomics
    Clio Der Sarkissian
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
    Philos Trans R Soc Lond B Biol Sci 370:20130387. 2015
    ..As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past. ..
  26. pmc Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil
    Anna Sapfo Malaspinas
    Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5 7, 1350 Copenhagen K, Denmark
    Curr Biol 24:R1035-7. 2014
    ..Our findings could either represent genomic evidence of Polynesians reaching South America during their Pacific expansion, or European-mediated transport. ..
  27. doi Population genomics of Bronze Age Eurasia
    Morten E Allentoft
    Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5 7, 1350 Copenhagen K, Denmark
    Nature 522:167-72. 2015
    ....
  28. pmc The ancestry and affiliations of Kennewick Man
    Morten Rasmussen
    1 Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, DK 1350 Copenhagen K, Denmark 2 Department of Genetics, School of Medicine, Stanford University, Littlefield Center, Stanford, California 94305, USA
    Nature 523:455-8. 2015
    ..We therefore conclude based on genetic comparisons that Kennewick Man shows continuity with Native North Americans over at least the last eight millennia...
  29. 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. ..
  30. 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...
  31. 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...
  32. 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
    ....
  33. pmc Ancient and modern environmental DNA
    Mikkel Winther Pedersen
    Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5 7, Copenhagen C 1350, Denmark
    Philos Trans R Soc Lond B Biol Sci 370:20130383. 2015
    ..However, the approach remains marred by biases related to DNA behaviour in environmental settings, incomplete reference databases and false positive results due to contamination. We provide a review of the field. ..
  34. doi The genetic prehistory of the New World Arctic
    Maanasa Raghavan
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, 1350 Copenhagen, Denmark
    Science 345:1255832. 2014
    ..Despite periodic abandonment of major Arctic regions, a single Paleo-Eskimo metapopulation likely survived in near-isolation for more than 4000 years, only to vanish around 700 years ago. ..
  35. pmc Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean
    Hannes Schroeder
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark Faculty of Archaeology, Leiden University, 2300 Leiden, The Netherlands
    Proc Natl Acad Sci U S A 112:3669-73. 2015
    ....
  36. doi 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...
  37. doi 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
    ....
  38. 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...
  39. pmc Pros and cons of methylation-based enrichment methods for ancient DNA
    Andaine Seguin-Orlando
    1 Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5 7, 1350K Copenhagen, Denmark 2 National High throughput DNA Sequencing Centre, Øster Farimagsgade 2D, 1353K Copenhagen, Denmark
    Sci Rep 5:11826. 2015
    ..This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions. ..
  40. doi Major transitions in human evolution revisited: a tribute to ancient DNA
    Luca Ermini
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
    J Hum Evol 79:4-20. 2015
    ....
  41. doi Paleogenomics. Genomic structure in Europeans dating back at least 36,200 years
    Andaine Seguin-Orlando
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, 1350 Copenhagen, Denmark
    Science 346:1113-8. 2014
    ....
  42. 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...
  43. doi 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. ..
  44. 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
    ....
  45. pmc AdapterRemoval v2: rapid adapter trimming, identification, and read merging
    Mikkel Schubert
    Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350, Copenhagen, Denmark
    BMC Res Notes 9:88. 2016
    ..Efficient adapter trimming algorithms are also needed to process the growing amount of data generated per sequencing run...
  46. doi Mitochondrial Genetic Diversity of Eurasian Red Squirrels (Sciurus vulgaris) from Denmark
    Corrie L Madsen
    From the Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, 1350 Copenhagen, Denmark Madsen, Vilstrup, Fernández, Marchi, and Orlando the Eco Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Universite Paris Diderot, Sorbonne Paris Cité, France Marchi the Danmarks Naturfredningsforening, Masnedøgade 20, 2100 Copenhagen, Denmark Håkansson the Naturstyrelsen, Naturstyrelsen på Fyn, Sollerupsvej 22, 5600 Faaborg, Denmark Krog Department of BioScience, Aarhus University, Grenåvej 14, 8410 Rønde, Denmark Asferg and the Zoological Museum, Natural History Museum of Denmark, Universitetsparken 15, 2100 Copenhagen, Denmark Baagøe
    J Hered 106:719-27. 2015
    ..Additional nuclear DNA analyses will be required to determine the precise admixture levels between original Danish and introduced squirrels and to locate unmixed candidate populations for specific conservation efforts. ..
  47. doi Reconstructing ancient genomes and epigenomes
    Ludovic Orlando
    1 Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, Copenhagen 1350C, Denmark 2 Université de Toulouse, University Paul Sabatier UPS, Laboratoire AMIS, CNRS UMR 5288, 37 Allees Jules Guesde, 31000 Toulouse, France
    Nat Rev Genet 16:395-408. 2015
    ..In this Review, we discuss these varied technical challenges and solutions for sequencing ancient genomes and epigenomes. ..
  48. 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...