Background info Ludovic Orlando – University of Copenhagen

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Background information: Ludovic Orlando

Contact

Upcoming events

Invited seminars (> December 2010)

Publications

- Peer reviewed articles

2017

2016

2015

2014

2013 and <2013

- Books, chapter books

- Reviews 

Background information: Ludovic OrlandoTil toppen

Ludovic Orlando is a former student from the Ecole Normale Superieure of Lyon (ENS, 1996-2000), one of the top-5 French universities. First trained as a molecular biologist, he got more recently interested in computational biology and programming.

He received his PhD in molecular genetics from the University of Lyon, France in 2003, almost twenty years after the first ancient DNA molecule was ever sequenced. Trained in phylogenomics as a postdoc (CNRS EA 3781), he was rapidly appointed as a permanent Associate Professor at the prestigious ENS Lyon, where he taught and performed research between 2005 and 2010. He moved to the Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, in April 2010 to start his own research group. He was appointed as a full Professor in Molecular Archaeology in March 2016 and started in December 2016 a five year, ERC-funded project on horse evolution.

His group develops integrative approaches in ancient DNA research, promoting the field of palaeomics by the merger of biochemistry, molecular biology, genomics and computational biology.

Ludovic has been part of several organizing and scientific boards of international meetings, including the prestigious international meeting for the Society of Molecular Biology and Evolution, the International Symposium on Biomolecular Archaeology and the International Union for Quaternary Research. He has been acting as an Academic Editor for the journal PLoS One since January 2012, for Scientific Reports since September 2016, and for Peer J since April 2017.

He is one of the four Editors-in-Chief for the journal 'Science and Technology of Archeological Research'. He was expert member of the committee of the French National Research Agency (ANR, panel SVSE7 for Biodiversity, Evolution, Ecology and Agronomy) in 2012 and 2013, and an expert member of the Junior Committee of the ‘Institut Universitaire de France’ in 2015 and 2016.

ContactTil toppen

Dr. Ludovic Orlando, Professor.
Email: orlando.ludovic@gmail.com, Lorlando@snm.ku.dk
Ph: +45 353 21 231
Skype: lorlando1369
Researcher ID: A-8932-2013
Orcid ID: http://orcid.org/0000-0003-3936-1850
Twitter:@LudovicLorlando

Upcoming eventsTil toppen

July 16th 2017. An ancient genomic perspective on the horse domestication process. In: International Society for Animal Genetics Conference. Dublin, Ireland.

May 19th 2017. Reconstructing ancient environmental and microbial communities. In:
CNRS Environmental DNA workshop. Lautaret, France.

May 17th 2017. The Genomic History of Horse Domestication: In: Young
Researchers in Life Sciences Conference. Paris, France.

Invited seminars Til toppen

March 10th 2017. The Genomic History of Horse Domestication. In: Illumina Nordic User Group Meeting. Stockholm, Sweden.

December 17th 2016. An ancient DNA perspective on horse domestication and horsebreeding. Ferrara, Italy.

December 17th 2016. Methods for reconstructing ancient epigenomes and microbiomes. Ferrara, Italy.

November 30th 2016. How early nomad riders shaped the modern horse. Videnskabgalla, Copenhagen, Denmark.

November 16th 2016. Traveling the past in ancient DNA time capsules. Vienna, Austria.

October 13th 2016. Reconstructing whole genomes, epigenomes and microbiota from ultra-short ancient DNA fragments. ENS Paris, France.

October 6th 2016. Ancient DNA in the bid data era. Reykjavik, Iceland.

October 3rd 2016. Reconstructing whole genomes, epigenomes and microbiota from ultra-short ancient DNA fragments. Reykjavik, Iceland.

September 20th 2016. Ancient DNA 2.0: from short molecules to genomes and ecosystems. ENS Lyon, France.

June 1st 2016. Ancient DNA. Univ. Lausanne, Switzerland.

May 29th 2016. Spring School in Bioinformatics and Population Genomics. Leukerbad, Switzerland.

May 23rd 2016. Reconstructing the domestication of horses, the noblest conquest of mankind. Melbourne, Australia.

May 10-14th 2016. Co-chair Evolutionary and Non-human Genomics. The Biology of Genome 2016. Cold Spring Harbor, US.

May 9th 2016. Traveling the past in ancient DNA time capsules. Baker Institute, Cornell University, US

April 29th 2016. Reconstructing whole genomes, epigenomes and microbiota from ultrashort ancient DNA fragments. Warwick, UK.

April 7th 2016. Tracking evolutionary changes with ancient DNA time capsules, Pasteur Institute, Paris, France.

2006-2016: The paleogenomic revolution, National Natural History Museum, Paris, France.

March 17th 2016. Computational approaches in ancient Genomics and Metagenomics, Jena, Germany.

March 5th 2016. Tracking recent changes in the genomes, epigenomes and microbiota. Riyadh, Saudi Arabia.

February 12th 2016. Darwin Day at the Centre for Ecological and Evolution Synthesis. Oslo, Norway.

February 1st 2016. Workshop on Population and Speciation Genomics, Český Krumlov, Czech Republic.

November 6th 2015. The origins of domestic horses: a tale from DNA. In: Horse breeds and morphotypes: a multidisciplinary approach based on zootechnical, historical, litterary, environmental and genetic data. Nice, France (Zoomathia group).

October 27th 2015. Keynote speaker. Environmental Genomics Workshop. Montpellier, France.

October 14th 2015. The genetic foundation of the modern horse: a tale from ancient DNA. Max Planck Institute for Developmental Biology and the Friedrich Miescher Laboratory. Tuebingen, Germany.

October 11th 2015. Deciphering the domestication and genetic makeup of the modern horse, the noblest conquest of man. King Saud University, Riyadh, Saudi Arabia.

October 2nd 2015: PS. Travelling the past in ancient DNA time capsules, Pasteur Institute, Paris, France.

September 28th 2015-October 1st. Plenary speaker. 10th International Conference on Behaviour, Physiology and Genetics of Wildlife. Conservation Genetics session.

July 12-16th 2015. Keynote speaker. SMBE meeting, session "Ancient genomes: a time machine for investigating natural selection". Vienna, Austria.

June 2015. Keynote speaker. Mathematical and Computational Evolutionary Biology. Ancient DNA: from very old molecules to genomes and epigenomes. Workshop, Porquerolles, France.

May 17-20 2015. Studying human evolution from ancient DNA. Jerusalem, Israel.

May 7th 2015. Talk: Reconstructing ancient genomes, epigenomes and metagenomes: hunting for the molecular past. National University of Mongolia, Department of Ecology.

April 29th, 2015, UCD School of Agriculture and Food Science Research Seminar Series. Dublin, Ireland.

February 9th, 2015. Molecular paleontology: hunting for the molecular past. Lyon, France.

January 11th 2015. International Plant and Animal Genome XXIII. Ancient DNA::
from genomes to epigenomes. San Diego, USA.

January 10th 2015. International Plant and Animal Genome XXIII. Prehistoric
genomes reveal the genetic foundation and cost of horse domestication. San
Diego, USA.

January 8th 2015. Illuminating the last 4 million years of equine evolution. Louisville, USA.

January 6th 2015. Ancient genomes, proteomes and epigenomes unlock our evolutionary past. Lexington, USA.

September 23rd, 2014. Speciation, Adaptation and Domestication: An Evolutionary Genomics History of the Equine Lineage. Biologie Intégrative et de Génomique Equine, INRA, Jouy-en-Josas, France.

September 10th-12th, 2014. Ancient DNA: from small DNA pieces to very old genomes and epigenomes. In: Next-Generation Genomics Symposium. Helsinki, Finland.

August 26th, 2014. The genomics of equine speciation and domestication. Basel, Switzerland. In: ISBA6 conference.

April 24th 2014. Evolutionary genomics: a tale from really ancient proteomes, genomes and epigenomes. Geneva, Switzerland.

March 27th 2014. 6th ICAZ Archaeozoology Genetics and Morphometrics Working Group Meeting. Lisbon Portugal.

March 6th, 2014. Middle-Pleistocen-omics: towards really old genomes, proteomes and epigenomes. Riyadh, Saudi Arabia.

February 13th, 2014. Evolutionary genomics of living and extinct equis. Basel, Switzerland.

January 11th, 2014. Speciation, adaptation and domestication: an evolutionary genomics history of the equine lineage. San Diego, US.

Workshop: December 9th-13th, 2013. Introduction to the bioinformatics of NGS. Toulouse, France.

Conference: November 18-19 2013. Ancient DNA: the first three decades. The Royal Society, London, UK.

Workshop: November 11-15 2013. Adelaide Bioinformatics Workshop. Australian Centre for Ancient DNA, Adelaide, Australia.

Conference: October 17th 2013. RECOMB satellite meeting on Comparative Genomics. Lyon, France.

Conference: September 17th-20th 2013. Ancient DNA perspectives on past climatic changes. Sevilla, Spain.

Conference: July 10-13th 2013. 10th Dorothy Russell Havemeyer Foundation International Equine Genome Workshop. Horse evolutionary genomics: insights from ancient genomes. Azorres, Portugal. 

Conference: July 7th 2013. FEBS 2013. Sequencing ancient and really ancient genomes illuminates horse evolution. St Petersburg, Russian federation.

Press conference: June 25th 2013. World Conference of Science Journalists. Helsinki, Finland.

March 15th 2013. Horse evolutionary genomics: insights from modern, ancient and really ancient genomes. Trinity College, Smurfit Institute, Dublin, Ireland.

January 13th 2013. Ancient DNA: from molecules to genomes. San Diego, USA.

January 2013. The evolutionary genomics of pre-domesticated horses. San Diego, USA.

December 18th 2012. The evolutionary genomics of pre-domesticated horses. Uppsala, Sweden.

December 10th 2012. The genomics of ancient humans: revisiting our origins and dispersals. Paris, France.

November 23th 2012. From the wild to domestication: horse evolutionary genomics. 3rd International Scientific Conference “Post-Genome Methods of Analysis in Biology and Laboratory and Clinical Medicine”, University of Kazan, Russian Federation.

November 22th 2012. Cracking genomes from fossils. Moscow, Russia.

November 7th 2012. The last million years of horse evolution. Adelaide, Australia.

October 24th 2012. The future of ancient DNA. Avignon, France.

October 22nd 2012. From the wild to domestication: horse evolutionary genomics. Lyon, France

September 28th 2012. From the wild to domestication: comparative genomics of ancient and modern horses reveals specific demographic, admixture and selective signatures. Biodiversity Institute Symposium, Oxford.

September 25th 2012. Genome archaeaologists: the molecular life science of pre-domesticated horse genomes. in Horizon in Molecular Life Science. Oslo, Norwegian Academy of Science and Letters, Norway.

June 4th 2012. Ancient DNA: from molecules to genomes and population dynamics. Instituto Gulbenkian de Ciencia. Lisbonn, Portugal.

May 7th 2012. Ancient DNA in the next-next generation sequencing era. Copenhagen, Denmark.

March 22nd 2012. Horse paleogenomics: From fossils to genomes. Firenze, Italy.

January 14th 2012. International Plant and Animal Genome XX. Ancient horse genomics. San Diego, USA.

December 6th 2011. Ancient DNA. Panum Institute (Population studies and Bio-banks course), Copenhagen, Denmark.

November 9th 2011. Symposium for Biotech Research. Ancient genomes in the next-next generation sequencing era - the case of horse domestication. Copenhagen, Denmark.

October 17th-19th 2011. CNRS RTP Paleogenomics summer school. Serial coalescent: basics, methods and power; Third gen- sequencing of ancient DNA templates: what is different from 2nd gen?; BWA mapping: evaluating different strategies for 2nd and 2rd gen sequencing. Cargese, France.

November 4th 2011. Think Alternative: fossils as unconventional sources of genomic data. Vienna, Austria.

July 28th 2011. True single molecule sequencing of ancient genomes. SMBE meeting, Kyoto, Japan.

Ancient DNA datasets and methods. INQUA congress, 21-27 July 2011, Bern, Switzerland 

July 25th 2011. Palaeogenomics and true single molecule sequencing. INQUA meeting, Bern, Switzerland.

May 24th 2011. TBA. European Research Council, Brussels

April 18th 2011. Ancient DNA genomics. Washington DC, National Museum of Natural History. Next Generation Sequencing: Transformative Technology for Biodiversity Science. Host: Pr. Robert Fleischer (download program in pdf)

February 9th 2011. Ancient DNA: telling something new about the past. Aarhus University, Bioinformatics Research Centre. Host: Dr. Thomas Bataillon

December 8th 2010. Ancient DNA: from molecules to genomes and populations. Paris, Institut Pasteur. Host: Dr. Lluis Quintana-Murci

December 7th 2010. The 1001 genomes and human evolution: a tale from ancient DNA. Paris, Institut Pasteur. Host: Dr. Odile Oziez-Kalogeropoulos.

October, 2010. Profiling ancient DNA damage using true Single DNA molecule Sequencing. Shenzen, China.

9th October 2010. Ancient DNA: from damage characterization to repair. International Symposium on Biomolecular Archaeology, Copenhagen, Denmark

8th December 2009. Taxonomic and population inference: what differences it makes to get ancient DNA data. University of Uppsala, Sweden.

22-23. October 2009. Is Homo sapiens just a Neanderthal guy? Insights from ancient DNA. Darwin’s legacy, new insights into human evolution, Institut Jacques Monod, Paris, France

14-16the September 2009. Inferring the past history of populations in the paleogenomic era. International meeting of the CNRS Research Network in paleogenetics, Paris, France

02nd July 2007. Geographic Distribution of an Extinct Equid (E. hydruntinus, Mammalia, Equidae) Revealed by Morphological and Genetical Analysis of Fossils. 8th meeting of Archeology of South Eastern Asia, Maison de l’Orient, Lyon, France

Publications

Peer-reviewed articlesTil toppen

2017

Librado P, Gamba C, Gaunitz C, Der Sarkissian C, Pruvost M, Albrechtsen A, Fages A, Khan N, Schubert M, Jagannathan V, Serres A, Kuderna LFK, Povolotskaya I, Seguin-Orlando S, Lepetz S, Neuditschko M, Theves C, Alquaraishi S, Alfarhan AH, Al-Rasheid K, Rieder S, Samashev Z, Francfort HP, Beneccke N, Hofreiter M, Ludwig A, Keyser C,
Marques-Bonet T, Ludes B, Crubezy E, Leeb T, Willerslev E, Orlando L. 2017. Ancient
Genomic Changes Associated with Domestication of the Horse.
Science, in
press.

Der Sarkissian C, Pichereau V, Dupont C, Ilsøe PC, Perrigault M, Butler P, Chauvaud L, Eiríksson J, Scourse J, Paillard C, Orlando L. 2017. Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past. Mol Ecol Resour, in press. doi: 10.1111/1755-0998.12679.

Lefebure T, Morvan C, Malard F, Francois C, Konecky-Dupre L, Gueguen L, Weiss-Gayet M, Seguin-Orlando A, Ermini L, Der Sarkissian C, Charrier PN, Eme D, Mermillord-Blondin F, Duret L, Vieira C, Orlando L, Douady CJ. 2017. Less effective selection leads to larger genome. Genome Res, in press. [doi:10.1101/gr.212589.116.

Cucchi T, Mohaseb A, Peigne S, Debue K, Orlando L, Mashkour M. 2017. Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies. R Soc Open Sci 4:160997.

Fabre PH, Upham NS, Emmons LH, Justy F, Leite YL, Carolina Loss A, Orlando L, Tilak MK, Patterson BD, Douzery EJ. 2017. Mitogenomic Phylogeny, Diversification, and Biogeography of South American Spiny Rats. Mol Biol Evol 34:613-633.

Llamas B, Willerslev E, Orlando L. 2017. Human evolution: a tale from ancient genomes. Phil Trans Roy Soc B. 372(1713). pii: 20150484.

2016Til toppen

Boessenkool S, Hanghøj K, Nistelberger HM, Der Sarkissian C, Gondek A, Orlando L, Barrett JH, Star B. Combining bleach and mild pre-digestion improves ancient DNA recovery from bones. Mol Ecol Resour. 2016 Oct 28. doi: 10.1111/1755-0998.12623.

Soubrier J, Gower G, Chen K, Richards SM, Llamas B, Mitchell KJ, Ho SY, Kosintsev P, Lee MS, Baryshnikov G, Bollongino R, Bover P, Burger J, Chivall D, Crégut-Bonnoure E, Decker JE, Doronichev VB, Douka K, Fordham DA, Fontana F, Fritz C, Glimmerveen J, Golovanova LV, Groves C, Guerreschi A, Haak W, Higham T,  Hofman-Kamińska E, Immel A, Julien MA, Krause J, Krotova O, Langbein F, Larson G, Rohrlach A, Scheu A, Schnabel RD, Taylor JF, Tokarska M, Tosello G, van der Plicht J, van Loenen A, Vigne JD, Wooley O, Orlando L, Kowalczyk R, Shapiro B, Cooper A. Early cave art and ancient DNA record the origin of European bison. Nat Commun. 2016 Oct 18;7:13158. doi: 10.1038/ncomms13158.

Hanghøj K, Seguin-Orlando A, Schubert M, Madsen T, Pedersen JS, Willerslev E, Orlando L. Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX. Mol Biol Evol. 2016 Sep 13. pii: msw184.

Librado P, Fages A, Gaunitz C, Leonardi M, Wagner S, Khan N, Hanghøj K, Alquraishi SA, Alfarhan AH, Al-Rasheid KA, Der Sarkissian C, Schubert M, Orlando  L. The Evolutionary Origin and Genetic Makeup of Domestic Horses. Genetics. 2016  Oct;204(2):423-434.

Cruz-Dávalos DI, Llamas B, Gaunitz C, Fages A, Gamba C, Soubrier J, Librado P, Seguin-Orlando A, Pruvost M, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Scheu A,  Beneke N, Ludwig A, Cooper A, Willerslev E, Orlando L. Experimental conditions improving in-solution target enrichment for ancient DNA. Mol Ecol Resour. 2016 Aug 27. doi: 10.1111/1755-0998.12595.

Pedersen MW, Ruter A, Schweger C, Friebe H, Staff RA, Kjeldsen KK, Mendoza ML, Beaudoin AB, Zutter C, Larsen NK, Potter BA, Nielsen R, Rainville RA, Orlando L,  Meltzer DJ, Kjær KH, Willerslev E. Postglacial viability and colonization in North America's ice-free corridor. Nature. 2016 Aug 10;537(7618):45-49. doi: 10.1038/nature19085.

Wutke S, Andersson L, Benecke N, Sandoval-Castellanos E, Gonzalez J, Hallsson  JH, Lõugas L, Magnell O, Morales-Muniz A, Orlando L, Pálsdóttir AH, Reissmann M,  Muñoz-Rodríguez MB, Ruttkay M, Trinks A, Hofreiter M, Ludwig A. The origin of ambling horses. Curr Biol. 2016 Aug 8;26(15):R697-9. doi: 10.1016/j.cub.2016.07.001.

Metcalf JL, Turney C, Barnett R, Martin F, Bray SC, Vilstrup JT, Orlando L, Salas-Gismondi R, Loponte D, Medina M, De Nigris M, Civalero T, Fernández PM, Gasco A, Duran V, Seymour KL, Otaola C, Gil A, Paunero R, Prevosti FJ, Bradshaw CJ, Wheeler JC, Borrero L, Austin JJ, Cooper A. Synergistic roles of climate warming and human occupation in Patagonian megafaunal extinctions during the Last Deglaciation. Sci Adv. 2016 Jun 17;2(6):e1501682. doi: 10.1126/sciadv.1501682.

Leonardi M, Librado P, Der Sarkissian C, Schubert M, Alfarhan AH, Alquraishi  SA, Al-Rasheid KA, Gamba C, Willerslev E, Orlando L. Evolutionary Patterns and Processes: Lessons from Ancient DNA. Syst Biol. 2016 Jul 5. pii: syw059.

Louvel G, Der Sarkissian C, Hanghøj K, Orlando L. metaBIT, an integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data. Mol Ecol Resour. 2016 Nov;16(6):1415-1427. doi: 10.1111/1755-0998.12546.

Orlando L. Back to the roots and routes of dromedary domestication. Proc Natl Acad Sci U S A. 2016 Jun 14;113(24):6588-90. doi: 10.1073/pnas.1606340113.

Schubert M, Lindgreen S, Orlando L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res Notes. 2016 Feb 12;9:88. doi: 10.1186/s13104-016-1900-2.

Bayerova Z, Janova E, Matiasovic J, Orlando L, Horin P. Positive selection in the SLC11A1 gene in the family Equidae. Immunogenetics. 2016 May;68(5):353-64. doi: 10.1007/s00251-016-0905-2.

Imsland F, McGowan K, Rubin CJ, Henegar C, Sundström E, Berglund J, Schwochow D, Gustafson U, Imsland P, Lindblad-Toh K, Lindgren G, Mikko S, Millon L, Wade C, Schubert M, Orlando L, Penedo MC, Barsh GS, Andersson L. Regulatory mutations in  TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage color in  horses. Nat Genet. 2016 Feb;48(2):152-8. doi: 10.1038/ng.3475.

Guillot G, Jónsson H, Hinge A, Manchih N, Orlando L. Accurate continuous geographic assignment from low- to high-density SNP data. Bioinformatics. 2016 Apr 1;32(7):1106-8. doi: 10.1093/bioinformatics/btv703..

Renaud G, Hanghøj K, Willeslev E, Orlando L. gargammel: a sequence simulator for ancient DNA. Bioinformatics. 2016 Oct 29. pii: btw670.

Bayerova Z, Janova E, Matiasovic J, Orlando L, Horin P. (2016). Positive selection in the SLC11A1 gene in the family Equidae. Immunogenetics 68:353-64.

Imsland F, McGowan K, Rubin CJ, Henegar C, Sundström E, Berglund J, Schwochow D, Gustafson U, Imsland P, Lindblad-Toh K, Lindgren G, Mikko S, Millon L, Wade C, Schubert M, Orlando L, Penedo MC, Barsh GS, Andersson L. (2016). Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage color in horses. Nat Genet. 48:152-8.

MacHugh DE, Larson G, Orlando L. Taming the Past: Ancient DNA and the Study of Animal Domestication. Annu Rev Anim Biosci. 2016 Oct 28.

Schubert M, Lindgreen S, Orlando L. (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res Notes. 9:88.

Gamba C, Hanghøj K, Gaunitz C, Alfarhan A, Alquraishi S, Al-Rashed K, Bradley D, Orlando L. 2015. Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing. Molecular Ecology Resources, Volume 16,  Issue 2, pages 459–469, March 2016. Article first published online: 15 Oct 2015, DOI: 10.1111/1755-0998.12470

Fernandez R, Schubert M, Vargas AM, Brownlow A, Vikingsson GA, Siebert U, Jensen LF, Øien N, Wall D, Rogan E, Mikkelsen B, Dabin W, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Guillot G, Orlando L. 2016. A genome-wide catalogue of single nucleotide polymorphisms in white-beaked and atlantic white-sided dolphins. Mol Ecol Resour, Volume 16, Issue 1,  pages 266–276, January 2016. Article first published online 29 May 2015, DOI: 10.1111/1755-0998.12427.

2015Til toppen

Orlando L. 2015. Equids. Curr Biol 25:R973-8.

Ermini L, Der Sarkissian C, Willerslev E, Orlando L. 2015. Major transitions in
human evolution revisited: a tribute to ancient DNA. J Hum Evol. 79:4-20.

Der Sarkissian C, Allentoft ME, Ávila-Arcos MC, Barnett R, Campos PF, Cappellini E, Ermini L, Fernández R, da Fonseca R, Ginolhac A, Hansen AJ, Jónsson H, Korneliussen T, Margaryan A, Martin MD, Moreno-Mayar JV, Raghavan M, Rasmussen M, Velasco MS, Schroeder H, Schubert M, Seguin-Orlando A, Wales N, Gilbert MT, Willerslev E, Orlando L. 2015. Ancient genomics. Philos Trans R Soc Lond B Biol Sci. 370:20130387.

Guillot G, Jónsson H, Hinge A, Manchih N, Orlando L. 2015. Accurate continuous geographic assignment from low- to high-density SNP data. Bioinformatics pii: btv703.

Librado P*, Sarkissian DC*, Ermini L, Schubert M, Jónsson H, Albrechtsen A, Fummagalli M, Yang MA, Gamba C, Ginolhac A, Seguin-Orlando A, Mortensen CD, Petersen B, Hoover C, Lorente B, Nedoluzhko A, Boulougina E, Neuditschko M, Jagannathan V, Thèves C, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Sicheritz-Ponten T, Popov R, Alekseev AN, Rubin E, McCue M, Rieder S, Leeb T, Tikhonov A, Crubézy E, Slatkin M, Marques-Bonet T, Nielsen R, Willerslev E,  Kantanen J, Prokhortchouk E, Orlando L. Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments. Proceedings of the National Academy of Sciences. doi:10.1073/pnas.1513696112.

Orlando L. 2015. The first aurochs genome revisits the breeding history of British and European cattle. Genome Biol., Genome Biology 16:225, DOI:10.1186/s13059-015-0793-z

Der Sarkissian C, Ermini L, Schubert M, Yang MA, Librado P, Fumagalli M, Jonsson H, Bar-Gal GK, Albrechtsen A, Vieira FG, Petersen B, Ginolhac A, Seguin-Orlando A, Magnussen K, Fages A, Gamba C, Lorente-Galdos B, Polani S, Steiner C, Neuditschko M, Jagannathan V,
Feh C, Greenblat CL, Ludwig A, Abramson NI, Zimmermann W, Schafberg R, Tikhonov
A, Sicheritz-Ponten T, Willerslev E, Marques-Bonet T, Ryder OA, McCue M, Rieder
S, Leeb T, Slatkin M, Orlando L. 2015. Evolutionary genomics and conservation of
the endangered Przewalski’s horse. Current Biology, Volume 25, Issue 19, p2577–2583, 5 October 2015.

Wales N, Carøe C, Sandoval-Velasco M, Gamba C, Barnett R, Samaniego JA,
Madrigal JR, Orlando L, Gilbert MTP. 2015. New insights on single-stranded vs.
double-stranded DNA library preparation for ancient DNA. BioTechniques, Vol. 59, No. 6, December 2015, pp. 368–371.

Madsen CL, Vilstrup JT, Fernandez R, Marchi N, Hakansson B, Krog M, Asferg T,
Baagøe H, Orlando L. 2015. Mitochondrial Genetic Diversity of Eurasian Red
Squirrels (Sciurus vulgaris) from Denmark. J Hered, Volume 106, Issue 6, pp. 719-727.

Seguin-Orlando A, Gamba C, Der Sarkissian C, Ermini L, Louvel G, Boulygina E, Sokolov A, Nedoluzhko A, Lorenzen E, Lopez P, McDonald HG, Scott E, Tikhonov A, Stafford TW, Shapiro B, Willerslev E, Prokhortchouk E, Orlando L. 2015. Pros and cons of methylation-based enrichment methods for ancient DNA. Scientific Reports 5,11826. doi:10.1038/srep11826

Seguin-Orlando A, Hoover CA, Vasiliev SK, Ovodov ND, Shapiro B, Cooper A, Rubin EM, Willerslev E, Orlando L. 2015. Amplification of TruSeq ancient DNA libraries with Accuprime Pfx: consequences on nucleotide mis-incorporation and methylation patterns. STAR 1:STAR2015112054892315Y.0000000005.

Wilting A, Courtiol A, Christiansen P, Niedballa J, Scharf AK, Orlando L,
Balkenhol N, Hofer H, Kramer-Schadt S, Fickel J, Kitchener AC. 2015. Planning
tiger recovery: Understanding intraspecific variation for effective
conservation. Sci Advances 1:e1400175

Rebolledo-Mendez J, Hestand MS, Coleman SJ, Zeng Z, Orlando L, MacLeod JN, Kalbfleisch T. 2015. Comparison of the Equine Reference Sequence with Its Sanger Source Data and New Illumina Reads. PLoS One 10:e0126852

Hestand MS, Kalbfleisch TS, Coleman SJ, Zeng Z, Liu J, Orlando L, MacLeod JN. 2015. Annotation of the Protein Coding Regions of the Equine Genome. PLoS One 10:e0124375.

Rasmussen M, Sikora M, Albrechtsen A, Korneliussen TS, Moreno-Mayar JV, Poznik GD, Zollikofer CP, Ponce de León MS, Allentoft ME, Moltke I, Jónsson H, Valdiosera C, Malhi RS, Orlando L, Bustamante CD, Stafford TW Jr, Meltzer DJ, Nielsen R, Willerslev E. 2015. The ancestry and affiliations of Kennewick Man. Nature doi: 10.1038/nature14625.

Damgaard PB, Margaryan A, Schroeder H, Orlando L, Willerslev E, Allentoft ME. 2015 Improving access to endogenous DNA in ancient bones and teeth. Sci Rep. 5:11184.

Allentoft ME, Sikora M, Sjögren KG, Rasmussen S, Rasmussen M, Stenderup J, Damgaard PB, Schroeder H, Ahlström T, Vinner L, Malaspinas AS, Margaryan A, Higham T, Chivall D, Lynnerup N, Harvig L, Baron J, Della Casa P, Dąbrowski P, Duffy PR, Ebel AV, Epimakhov A, Frei K, Furmanek M, Gralak T, Gromov A, Gronkiewicz S, Grupe G, Hajdu T, Jarysz R, Khartanovich V, Khokhlov A, Kiss V, Kolář J, Kriiska A, Lasak I, Longhi C, McGlynn G, Merkevicius A, Merkyte I, Metspalu M, Mkrtchyan R, Moiseyev V, Paja L, Pálfi G, Pokutta D, Pospieszny Ł, Price TD, Saag L, Sablin M, Shishlina N, Smrčka V, Soenov VI, Szeverényi V, Tóth G, Trifanova SV, Varul L, Vicze M, Yepiskoposyan L, Zhitenev V, Orlando L, Sicheritz-Pontén T, Brunak S, Nielsen R, Kristiansen K, Willerslev E. 2015. Population genomics of Bronze Age Eurasia. Nature. 522:167-72. 

Welker F, Collins MJ, Thomas JA, Wadsley M, Brace S, Cappellini E, Turvey ST, Reguero M, Gelfo JN, Kramarz A, Burger J, Thomas-Oates J, Ashford DA, Ashton PD, Rowsell K, Porter DM, Kessler B, Fischer R, Baessmann C, Kaspar S, Olsen JV, Kiley P, Elliott JA, Kelstrup CD, Mullin V, Hofreiter M, Willerslev E, Hublin JJ, Orlando L, Barnes I, MacPhee RD. 2015. Ancient proteins resolve the evolutionary history of Darwin's South American ungulates. Nature. 522:81-4.

Der Sarkissian C, Vilstrup JT, Schubert M, Seguin-Orlando A, Eme D, Weinstock J, Alberdi MT, Martin F, Lopez PM, Prado JL, Prieto A, Douady CJ, Stafford TW, Willerslev E, Orlando L. 2015. Mitochondrial genomes reveal the extinct Hippidion as an outgroup to all living equids. Biol Lett. 11:20141058

Orlando L, Gilbert MT, Willerslev E. Reconstructing ancient genomes and epigenomes. Nat Rev Genet. 2015 Jun 9. doi: 10.1038/nrg3935.

Schroeder H, Ávila-Arcos MC, Malaspinas AS, Poznik GD, Sandoval-Velasco M, Carpenter ML, Moreno-Mayar JV, Sikora M, Johnson PL, Allentoft ME, Samaniego JA, Haviser JB, Dee MW, Stafford TW Jr, Salas A, Orlando L, Willerslev E, Bustamante CD, Gilbert MT. Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean. 2015. PNAS. pii: 201421784.

Ersmark E, Orlando L, Sandoval-Castellanos E, Barnes I, Barnett R, Stuart A, Lister A, Dalén L. 2015. Population Demography and Genetic Diversity in the Pleistocene Cave Lion. Open Quaternary, 1:1-14.

Perry GH, Orlando L. 2015. Ancient DNA and human evolution. J Hum Evol, S0047-2484(14)00299-1. doi: 10.1016/j.jhevol.2014.12.002

2014Til toppen

Schubert M, Jónsson H, Chang D, Der Sarkissian C, Ermini L, Ginolhac A, Albrechtsen A, Dupanloup I, Foucal A, Petersen B, Fumagalli M, Raghavan M, Seguin-Orlando A, Korneliussen TS, Velazquez AM, Stenderup J, Hoover CA, Rubin CJ, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, MacHugh DE, Kalbfleisch T, MacLeod JN, Rubin EM, Sicheritz-Ponten T, Andersson L, Hofreiter M, Marques-Bonet T, Gilbert MT, Nielsen R, Excoffier L, Willerslev E, Shapiro B, Orlando L. 2014. Prehistoric genomes reveal the genetic foundation and cost of horse domestication. PNAS 111:E5661-9. 

Jónsson H, Schubert M, Seguin-Orlando A, Ginolhac A, Petersen L, Fumagalli M, Albrechtsen A, Petersen B, Korneliussen TS, Vilstrup JT, Lear T, Myka J, Lundquist J, Miller DC, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Stagegaard J, Strauss G, Bertelsen MF, Sicheritz-Ponten T, Antczak DF, Bailey E, Nielsen R, Willerslev E, Orlando L. 2014. Speciation with gene flow in equids despite extensive chromosomal plasticity. PNAS, 111:18655-60

Seguin-Orlando A, Korneliussen TS, Sikora M, Malaspinas A-S, Manica A, Moltke I, Albrechtsen A, Ko A, Margaryan A, Moiseyev V, Goebel T, Westaway M, Lambert D, Khartanovich V, Wall JD, Nigst PR, Foley RA, Lahr MM, Nielsen R,  Orlando L, Willerslev E. Genomic structure in Europeans dating back at least 36,200 years. Science 28 November 2014: Vol. 346 no. 6213 pp. 1113-1118, DOI: 10.1126/science.aaa0114. Published Online November 6 2014

Ermini L, Der Sarkissian C, Willerslev E, Orlando L. 2014. Major transitions in human evolution revisited: a tribute to ancient DNA. J Hum Evol, 79:4-20

Fabre PH, Vilstrup J, Raghavan M, Der Sarkissian C, Willerslev E, Douzery E, Orlando L. Rodents of the Caribbean: origin and diversification of hutias unravelled by next-generation museomics. Biol Letters, 10, doi:10.1098/rsbl.2014.0266.

Der Sarkissian C, Allentoft ME, Ávila-Arcos MC, Barnett R, Campos PF, Cappellini E, Ermini L, Fernández R, da Fonseca R, Ginolhac A, Hansen AJ, Jónsson H, Korneliussen T, Margaryan A, Martin MD, Moreno-Mayar JV, Raghavan M, Rasmussen M, Sandoval Velasco M, Schroeder H, Schubert M, Seguin-Orlando A, Wales N, Gilbert MTP, Willerslev E, Orlando L.. 2014. Ancient Genomics. Philos Trans R Soc Lond B Biol Sci 370:20130387.

Guillot G, Orlando L. Population Structure.  Oxford Bibliographies, Evolutionary Biology, in press. (PR)

Orlando L, Cooper A. Using ancient DNA to understand evolutionary and ecological processes. Annual Reviews of Ecology, Evolution, and Systematics. First published online as a Review in Advance on October 6, 2014. DOI: 10.1146/annurev-ecolsys-120213-091712. (PR)

Orlando L, Willerslev E. 2014. Evolution. An epigenetic window into the past? Science 345:511-512.

Orlando L. 2014. A 400,000-year-old mitochondrial genome questions phylogenetic relationships amongst archaic hominins. Bioessays, Volume 36, Issue 6, pages 598–605, June 2014.

Der Sarkissian C*, Ermini L*, Jonnson H, Alekseev A, Crubezy E, Shapiro B, Orlando L. 2014. Shotgun Microbial Profiling of Fossil Remains. Mol Ecol, 23:1780-98. (doi:10.1111/mec.12690)

Raghavan M, DeGiorgio M, Albrechtsen A, Moltke I, Skoglund P, Korneliussen TS, Grønnow B, Appelt M, Gulløv HC, Friesen TM, Fitzhugh W, Malmström H, Rasmussen S, Olsen J, Melchior L, Fuller BT, Fahrni SM, Stafford Jr. T, Grimes V, Renouf MAP, Cybulski J, Lynnerup N, Lahr MM, Britton K, Knecht R, Arneborg J, Metspalu M, Cornejo OE, Malaspinas A-S, Wang Y, Rasmussen M, Raghavan V, Hansen TVO,  Khusnutdinova E, Pierre T, Dneprovsky K, Andreasen C, Lange H, Hayes MG, Coltrain J, Spitsyn VA, Götherström A, Orlando L, Kivisild T,  Villems R, Crawford MH, NielsenFC, Dissing J, Heinemeier J, Meldgaard M, Bustamante C, O’Rourke DH, Jakobsson M, Gilbert MTP, Nielsen R, Willerslev E. The genetic prehistory of the New World Arctic. Science 29 August 2014: Vol. 345 no. 6200. DOI: 10.1126/science.1255832

Schubert M, Ermini L, Der Sarkissian C, Jonnson H, Ginolhac A, Schaeffer R, Martin MD, Fernandez R, Kircher M, McCue M, Willerslev E, Orlando L. 2014. Characterizing of ancient and modern genomes by sequencing, SNP detection, phylogenomic and metagenomic analysis. Nature Protocols, 9, pp. 1056–1082, Published online 10 April 2014.doi:10.1038/nprot.2014.063.

Liu S, Lorenzen ED, Fumagalli M, Li B, Harris K, Xiong Z, Zhou L, Korneliussen TS, Somel M, Babbitt C, Wray G, Li J, He W, Wang Z, Fu W, Xiang X, Morgan CC, Doherty A, O'Connell MJ, McInerney JO, Born EW, Dalén L, Dietz R, Orlando L, Sonne C, Zhang G, Nielsen R, Willerslev E, Wang J. Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. Cell. 2014. 157:785-94.

Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M, Stafford TW Jr, Rasmussen S, Moltke I, Albrechtsen A, Doyle SM, Poznick GD, Gudmundsdottir V, Yadav R, Malaspinas AS, Stockton White SV, Allentoft ME, Cornejo OE, Tambets K, Eriksson A, Heintzman PD, Karmin M, Korneliussen TS, Meltzer DJ, Pierre TL, Stenderup J, Saag L, Warmuth VM, Lopes MC, Malhi RS, Brunak S, Sicheritz-Ponten T, Barnes I, Collins M, Orlando L, Balloux F, Manica A, Gupta R, Metspalu M, Bustamante CD, Jakobsson M, Nielsen R, Willerslev E. 2014. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 506:225-229

Willerslev E, Davidson J, Moora M, Zobel M, Coissac E, Edwards ME, Lorenzen ED, Vestergard M, Gussarova G, Haile J, Craine J, Bergmann G, Gielly L, Boessenkool S, Epp LS, Pearman PB, Cheddadi R, Murray D, Brathen KA, Yoccoz N, Binney H, Cruaud C, Winckler P, Goslar T, Aslos IG, Bellemain E, Brysting AK, Elven R, Sonstebo JH, Murton J, Sher A, Rasmussen M, Ronn R, Mourier T, Cooper A, Austin J, Moller P, Froese D, Zazula G, Pompanon F, Rioux D, Niderkorn V, Tikhonov A, Savvinov G, Roberts RG, MacPhee RDE, Gilbert MTP, Kjaer KH, Orlando L, Brochmann C, Taberlet P. 2014. Fifty thousand years of arctic vegetation and megafaunal diet. Nature 506:47-51

2013Til toppen

Pedersen JS, Valen E, Vargas Velazquez AM, Parker BJ, Rasmussen M, Lindgreen S, Lilje B, Tobin DJ, Kelly TK, Vang S, Andersson R, Jones PA, Hoover CA, Tikhonov A, Prokhortchouk E, Rubin EM, Sandelin A, Gilbert MT, Krogh A, Willerslev E, Orlando L.  Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome. Genome Res. Published online on Dec 3rd 2013.

Raghavan M, Skoglund P, Kelly E. Graf, Metspalu M, Albrechtsen A, Moltke I, Rasmussen S, Stafford Jr TW, Orlando L, Metspalu E, Karmin M, Tambets K, Rootsi S, Mägi R, Campos PF, Balanovska E, Balanovsky O, Khusnutdinova E, Litvinov S, Osipova LP, Fedorova SA, Voevoda MI, DeGiorgio M, Sicheritz-Ponten T, Brunak S, Demeshchenko S, Kivisild T,  Villems R, Nielsen R, Jakobsson M, Willerslev E. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature, 20. November 2013.

Overballe-Petersen S, Harms K, Orlando L, Mayar JVM, Rasmussen S, Dahl TW, Rosing MT, Poole AM, Sicheritz-Ponten T, Brunak S, Inselmann S, de Vries J, Wackernagel W, Pybus OG, Nielsen R, Johnsen PJ, Nielsen KM, Willerslev E. Bacterial natural transformation by highly fragmented and damaged DNA. PNAS 2013; published ahead of print November 18, 2013.

Seguin-Orlando A, Schubert M, Clary J, Stagegaard J, Alberdi MT, et al. Ligation Bias in Illumina Next-Generation DNA Libraries: Implications for Sequencing Ancient Genomes. PLoS ONE 8(10): e78575. 2013

Zhang H, Paijmans JL, Chang F, Wu X, Chen G, Lei C, Yang X, Wei Z, Bradley DG, Orlando L, O'Connor T, Hofreiter M. Morphological and genetic evidence for early Holocene cattle management in northeastern China. Nature Communications  4, Article number: 2755 doi:10.1038/ncomms3755. Published 08 November 2013.

Martin MD, Cappellini E, Samaniego JA, Zepeda ML, Campos PF, Seguin-Orlando A, Wales N, Orlando L, Ho SYW, Dietrich FS, Mieczkowski PA, Heitman J, Willerslev E, Krogh A, Ristaino JB, Gilbert MTP. Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. Nature Communications, 2013/07/18/online.

Cardoso JL, Vilstrup JT, Eisenmann V, Orlando L. First evidence of Equus asinus L. in the Chalcolithic disputes the Phoenicians as the first to introduce donkeys into the Iberian Peninsula. Journal of Archaeological Science (2013) 40:4483–4490. http://dx.doi.org/10.1016/j.jas.2013.07.010

Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, Johnson PLF, Fumagalli M, Vilstrup JT, Raghavan M, Korneliussen T, Malaspinas AS, Vogt J, Szklarczyk S, Kelstrup CD, Vinther J, Dolocan A, Stenderup J, Velazquez AMV, Cahill J, Rasmussen M, Wang X, Min J, Zazula GD, Seguin-Orlando A, Mortensen C, Magnussen K, Thompson JF, Weinstock J, Gregersen K, Røed KH, Eisenmann V, Rubin CJ, Miller DC, Antczak DF, Bertelsen MF, Brunak S, Al-Rasheid KAS, Ryder O, Andersson L, Mundy J, Krogh A, Gilbert MTP, Kjær K, Sicheritz-Ponten T, Juhl Jensen L, Olsen JV, Hofreiter M, Nielsen R, Shapiro B, Jun W, Willerslev E: Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature (2013) doi:10.1038/nature12323.

Winther Pedersen M, Ginolhac A, Orlando L, Olsen J, Andersen K, Holm J, Funder S, Willerslev E, Kjær KH: A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa. Quaternary Science Rev, Volume 75, 1 September 2013, Pages 161–168.

Jónsson H, Ginolhac A, Schubert M, Johnson P, Orlando L: mapDamage2.0: Fast approximate Bayesian estimates of ancient DNA damage parametersBioinformatics 2013, doi: 10.1093/bioinformatics/btt193. First published online: April 23, 2013. GutHub repository, with expedient documentation available at http://ginolhac.github.io/mapDamage/.

Vilstrup JT, Seguin-Orlando A, Stiller M, Ginolhac A, Raghavan M, Nielsen SCA, Weinstock J, Froese D, Vasiliev SK, Ovodov ND, Clary J, Helgen KM, Fleischer RC, Cooper A, Shapiro B, Orlando L. Mitochondrial phylogenomics of modern and ancient equids. PLoS ONE 2013, 8:e55950.

2012

Biagini P, Thèves C, Balaresque P, Géraut A, Cannet C, Keyser C, Nikolaeva D, Gérard P, Duchesne S, Orlando L, Willerslev E, Alekseev AN, de Micco P, Ludes B, Crubézy E. 2012. Variola virus in a 300-year-old Siberian mummy. N Engl J Med 367:2057-9.

Foote AD, Thomsen PF, Sveegaard S, Wahlberg M, Kielgast J, Kyhn LA, Salling AB, Galatius A, Orlando L, Gilbert MT. 2012. Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals. PLoS One 7:e41781.

Sánchez-Quinto F, Schroeder H, Ramirez O, Avila-Arcos MC, Pybus M, Olalde I, Velazquez AM, Marcos ME, Encinas JM, Bertranpetit J, Orlando L, Gilbert MT, Lalueza-Fox C. 2012. Genomic affinities of two 7,000-year-old Iberian hunter-gatherers. Curr Biol 22:1494-9.

Yoccoz N, Brathen KA, Gielly L, Haile J, Edwards M, Goslar Tm von Stedingk J, Brysting A, Coissac E, Pompanon F, Sonstebo J, Miquel C, Valentini A, De Bello F, Chave J, Thuillier W, Wincker P, Craud C, Gavory F, Rasmussen M, Gilbert MTP, Orlando L, Brochmann C, Willerslev E, Taberlet P. 2012. DNA from soil mirrors plant taxonomic and growth form diversity. Mol Ecol 2:3647-55.

Schubert M, Ginolhac A, Lindgreen S, Thompson JF, Al-Rasheid KA, Willerslev E, Krogh A, Orlando L. 2012. Improving ancient DNA read mapping against modern reference genomes. BMC Genomics 13:178.

Ginolhac A, Vilstrup J, Stenderup J, Rasmussen M, Stiller M, Shapiro B, Zazula G, Froese D, Steinmann KE, Thompson JF, Al-Rasheid K, Gilbert TMP, Willerslev E, Orlando L. 2012. Improving the performance of true-Single Molecule Sequencing for ancient DNA. BMC Genomics 13:177.

Overballe-Petersen S, Orlando L, Willerslev E. 2012. Next-generation sequencing offers new insights into DNA degradation. Trends Biotechnol 30:364-8.

Jacobsen MW, Hansen MM, Orlando L, Bekkevold D, Bernatchez L, Willerslev E, Gilbert MT. 2012. Mitogenome sequencing reveals shallow evolutionary histories and recent fivergence time between morphologically and ecologically distinct European whitefish (Coregonus spp.). Mol Ecol 21:2727-42.

Mourier T, Ho SY, Gilbert MT, Willerslev E, Orlando L. 2012. Statistical guidelines for detecting past population shifts using ancient DNA. Mol Biol Evol 29:2241-51.

Parducci L, Jorgensen T, Tollesfrud MM, Elverland E, Alm T, Fontana SL, Bennett KD, Haile J, Matetovici I, Suyama Y, Edwards ME, Andersen K, Rasmussen M, Boessenkool S, Coissac E, Brochmann C, Taberlet P, Houmark-Nielsen M, Larsen NK, Orlando L, Gilbert MT, Kjaer KH, Alsos IG, Willerslev E. 2012. Glacial survival of boreal trees in northern Scandinavia. Science 335:1083-6.

Dalen L, Orlando L, Shapiro B, Brandstrom-Durling M, Quam R, Gilbert MT, Diez Fernandez-Lomana JC, Willerslev E, Arsuaga JL, Gotherstrom A. 2012. Partial genetic turnover in Neandertals: continuity in the East and population replacement in the West. Mol Biol Evol 29:1893-7.

Thomsen PF, Kielgast J, Iversen LL, Wiuf C, Rasmussen M, Gilbert MT, Orlando L, Willerslev E. 2012. Monitoring endangered freshwater biodiversity using environmental DNA. Mol Ecol 21:2565-73.

Jorgensen T, Haile J, Moller P, Kjaer KH, Andreev Andrei, Boessenkool S, Rasmussen M, Kienast F, Coissac E, Taberlet P, Brochmann C, Bigelow NH, Andersen K, Orlando L, Gilbert MTP, Willerslev E. 2012. A comparative study of macrofossils, pollen and ancient plant DNA from permafrost sediments of northern Siberia reveals long-term vegetational stability. Mol Ecol 21:1989-2003.

Jorgensen T, Kjaer KH, Haile J, Rasmussen M, Boesenkool S, Andersen K, Coissac E, Taberlet P, Orlando L, Gilbert MTP, Willerslev E. 2012. Islands in the ice: detecting past vegetation on Greenlandic Nunataks using historical records and sedimentary DNA meta-barcoding. Mol Ecol 21:1980-8.

Andersen K, Bird KL, Rasmussen M, Haile H, Breuning-Madsen H, Kjaer K, Orlando L, Gilbert MTP, Willerslev E. 2012. Meta-barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity. Mol Ecol 21:1966-79.

Cappelini E, Jensen L, Szklarczyk D, Ginolhac A, da Fonseca R, Stafford T, Holven S, Collins M, Orlando L, Willerslev E, Gilbert MTP, Olsen JV. 2012. Proteomic analysis of a Pleistocene mammoth femur reveals more than one hundred ancient bone proteins. J Proteome Res 11:917-926.

2011

Lorenzen ED*, Nogués-Bravo D*, Orlando L*, Weinstock J*, Binladen J*, Marske KA*, Ugan A, Borregaard MK, Gilbert MT, Nielsen R, Ho SY, Goebel T, Graf KE, Byers D, Stenderup JT, Rasmussen M, Campos PF, Leonard JA, Koepfli KP, Froese D, Zazula G, Stafford TW Jr, Aaris-Sørensen K, Batra P, Haywood AM, Singarayer JS, Valdes PJ, Boeskorov G, Burns JA, Davydov SP, Haile J, Jenkins DL, Kosintsev P, Kuznetsova T, Lai X, Martin LD, McDonald HG, Mol D, Meldgaard M, Munch K, Stephan E, Sablin M, Sommer RS, Sipko T, Scott E, Suchard MA, Tikhonov A, Willerslev R, Wayne RK, Cooper A, Hofreiter M, Sher A, Shapiro B, Rahbek C, Willerslev E. 2011: Species-specific responses of Late Quaternary magefauna to climate and humans. Nature 479:359-64. * contributed equally

Foote AD, Morin PA, Burba JW, Willerslev E, Orlando L, Gilbert MTP. 2011. Out of the Pacific and back again: insights into the matrilineal history of Pacific killer whale ecotypes. PLoS One 6:e24980.

Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, Albrechtsen A, Skotte L, Lindgreen S, Metspalu M, Jombart T, Kivisild T, Zhai W, Eriksson A, Manica A, Orlando L, De La Vega F, Tridico S, Metspalu E, Nielsen K, Ávila-Arcos MC, Moreno-Mayar JV, Muller C, Dortch J, Gilbert MTP, Lund O, Wesolowska A, Karmin M, Weiner LA, Wang B, Li J, Tai S, Xiao F, Hanihara T, van Driem G, Jha AR, Ricaut F-X, de Knijff P, Migliano AB, Gallego-Romero I, Kristiansen K, Lambert DM, Brunak S, Forster P, Brinkmann B, Nehlich O, Bunce M, Richards M, Gupta R, Bustamante C, Krogh A, Foley RA, Lahr MM, Balloux F, Sicheritz-Pontén T, Villems R, Nielsen R, Jun W, Willerslev E. 2011. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 334:94-98.

Orlando L, Ginolhac A, Raghavan M, Vilstrup J, Rasmussen M, Magnussen K, Steinmann K, Kapranov P, Thompson JF, Zazula G, Froese D, Moltke I, Shapiro B, Hofreiter M, Al-Rasheid KA, Gilbert MT, Willerslev E. 2011. True Single Molecule DNA Sequencing of a Pleistocene horse bone. Genome Res 21:1705-19.

Ginolhac A, Rasmussen M, Gilbert MT, Willerslev E, Orlando L. 2011. mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics 27:2153-5.

Vilstrup JT, Ho Sym Foote AD, Morin PA, Kreb D, Krutzen M, Parra GJ, Robertson KM, de Stephanis R, Verborgh P, Willerslev E, Orlando L, Gilbert ME. 2011. Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae. BMC Evol Biol 11:65.

Orlando L, Hanni C. 2011. Twelve years of Neandertal genetic discoveries: state-of-the-art and future challenges. In: Condemi S., Weiniger G. & Schrenk F. (eds) Continuity and Discontinuity in the Peopling of Europe: One Hundred and Fifty Years of Neanderthal Study. Vertebrate Paleobiology and Paleoanthropology Book Series, Springer Press, 223-238. 

2010

Campos PF, Kristensen T, Orlando L, Sher A, Kholodova M, Gotherstrom A, Hofreiter M, Drucker D, Kosintsev P, Tikhonov A, Baryshnikov G, Willerslev E, Gilbert MT. 2010. Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene. Mol Ecol 19:4863-75.

Lari M, Rizzi E, Milani L, Corti G, Balsamo C, Vai S, Catalano G, Pilli E, Longo L, Condemi S, Giunti P, Hanni C, De Bellis G, Orlando L, Barbujani G, Caramelli D. 2010. The microcephalin ancestral allele in a Neanderthal individual. PloS One 5:e10648.

Campos PF, Willerslev E, Sher A, Orlando L, Axelsson E, Tikhonov A, Aaris-Sorensen K, Greenwood AD, Kahlke RD, Kosintsev P, Krakhmalnaya T, Kuznetsova T, Lemey P, MacPhee R, Norris CA, Shepherd K, Suchard MA, Zazula GD, Shapiro B, Gilbert MT. 2010. Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics. PNAS 107:5675-80.

Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, Bertalan M, Nielsen K, Gilbert MT, Wang Y, Raghavan M, Campos PF, Kamp HM, Wilson AS, Gledhill A, Tridico S, Bunce M, Lorenzen ED, Binladen J, Guo X, Zhao J, Zhang X, Zhang H, Li Z, Chen M, Orlando L, Kristiansen K, Bak M, Tommerup N, Bendixen C, Pierre TL, Grunnow B, Meldgaard  M, Andreasen C, Fedorova SA, Osipova LP, Higham TF, Ramsey CB, Hansen TV, Nielsen FC, Crawford MH, Brunak S, Sicheritz-Ponten T, Villems R, Nielsen R, Krogh A, Wang J, Willerslev E. 2010. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463:757-62.

2009

Orlando L, Metcalf JL, Alberdi MT, Telles-Antunes M, Bonjean D, Otte M, Martin F, Eisenmann V, Mashkour M, Morello F, Prado JL, Salas-Gismondi R, Shockey BJ, Wrinn PJ, Vasil'ev SK, Ovodov ND, Cherry MI, Hopwood B, Male D, Austin JJ, Hanni  C, Cooper A. 2009. Revising the recent evolutionary history of equids using ancient DNA. PNAS 106:21754-9.

Depaulis F, Orlando L, Hanni C. 2009. Using classical population genetics tools with heterochroneous data: time matters! PLoS One 4:e5541. 

2008

Orlando L, Calvignac S, Schnebelen C, Douady CJ, Godfrey LR, Hanni C. 2008. DNA from extinct giant lemurs links archaeolemurids to extant indriids. BMC Evol Biol 8:121.

Orlando L, Male D, Alberdi MT, Prado JL, Prieto A, Cooper A, Hanni C. 2008. Ancient DNA clarifies the evolutionary history of American Late Pleistocene equids. J Mol Evol 66:533-8.

Valdiosera CE, Garcia-Garitagoitia JL, Garcia N, Doadrio I, Thomas MG, Hanni C, Arsuaga JL, Barnes I, Hofreiter M, Orlando L, Gotherstrom A. 2008. Surprising migration and population size dynamics in ancient Iberian brown bears (Ursus arctos). PNAS 105:5123-8.

2007

Krause J, Lalueza-Fox C, Orlando L, Enard W, Green RE, Burbano HA, Hublin JJ,  Hanni C, Fortea J, de la Rasilla M, Bertranpetit J, Rosas A, Paabo S. 2007. The derived FOXP2 variant of modern humans was shared with Neandertals. Curr Biol 17:1908-12.

Levasseur A, Orlando L, Bailly X, Milinkovitch MC, Danchin EG, Pontarotti P. 2007. Conceptual bases for quantifying the role of the environment on gene evolution: the participation of positive selection and neutral evolution. Biol Rev Camb Phil Soc 82:551-72.

Krause J, Orlando L, Serre D, Viola B, Prufer K, Richards MP, Hublin JJ, Hanni C, Derevianko AP, Paabo S. 2007. Neanderthals in central Asia and Siberia. Nature 449:902-4.

Orlando L, Pages M, Calvignac S, Hughes S, Hanni C. 2007. Does the 43 bp sequence from an 800,000 year old cretan dwarf elephantid really rewrite the textbook on mammoths? Biol Lett 3:57-9.

Orlando L, Hanni C, Douady CJ. 2007. Mammoth and elephant phylogenetic relationships: Mammut americanum, the missing outgroup. Evolutionary Bioinform Online 3:45-51.

2006

Orlando L, Mashkour M, Burke A, Douady CJ, Eisenmann V, Hanni C. 2006. Geographic distribution of an extinct equid (Equus hydruntinus: Mammalia, Equidae) revealed  by morphological and genetical analyses of fossils. Mol Ecol 15:2083-93.

Orlando L, Darlu P, Toussaint M, Bonjean D, Otte M, Hanni C. 2006. Revisiting Neandertal diversity with a 100,000 year old mtDNA sequence. Curr Biol 16:R400-2.

2003

Orlando L, Eisenmann V, Reynier F, Sondaar P, Hanni C. 2003. Morphological convergence in Hippidion and Equus (Amerhippus) South American equids elucidated by ancient DNA analysis. J Mol Evol 57 Suppl 1:S29-40.

Orlando L, Leonard JA, Thenot A, Laudet V, Guerin C, Hanni C. 2003. Ancient DNA analysis reveals woolly rhino evolutionary relationships. Mol Phylogenet Evol 28:485-99.

Orlando L, Mauffrey JF, Cuisin J, Patton JL, Hanni C, Catzeflis F. 2003. Napoleon Bonaparte and the fate of an Amazonian rat: new data on the taxonomy of Mesomys hispidus (Rodentia: Echimyidae). Mol Phylogenet Evol 27:113-20.

2002

Orlando L, Bonjean D, Bocherens H, Thenot A, Argant A, Otte M, Hanni C. 2002. Ancient DNA and the population genetics of cave bears (Ursus spelaeus) through space and time. Mol Biol Evol19:1920-33.

2001

Loreille O, Orlando L, Patou-Mathis M, Philippe M, Taberlet P, Hanni C. 2001. Ancient DNA analysis reveals divergence of the cave bear, Ursus spelaeus, and brown bear, Ursus arctos, lineages. Curr Biol 11:200-3.

* Books, Chapter booksTil toppen

Orlando L, Hanni C. 2014. Neandertal evolution and human origins: a tale from the Scladina child. In: The juvenile Neandertal facial remains from Scladina Cave. Etudes et Recherches Archeologiques de l’Universite de Liege.

Orlando L. 2010. L’evolution, c’est tout simple. Preface. Florian Douam and Louis-Marie Bobay. Vuibert. Pp. 128. ISBN: 2311002201.

Orlando L. 2005. L'anti-Jurassic Park. Faire parler l'ADN fossile. Editions Belin- Pour la Science, Collection Regards sur la science, pp. 271. ISBN: 2701141362

Orlando L. 2005. L’ADN des fossiles néandertaliens : un éclairage nouveau sur l’origine de l’humanité. Chapitre lauréat du concours Le Monde de la recherche universitaire (9ème édition). In Sur les chemins de la découverte, ouvrage collectif sous la direction de N. Farouki, Editions Presses Universitaires de France, Collection Partage du savoir, pp. 241. ISBN: 2130547583

Ginolhac A, Orlando L, Thénot, A., Hänni, C. 2003. Détermination du sexe de la "Dame" de Vix in La tombe princière de Vix, ouvrage collectif sous la direction de C. Rolley. Editions Picard, pp. 383. ISBN: 2708406973

* ReviewsTil toppen

Orlando L. 2013. Decoding genomes of the past. Biofutur 349:28-30.

Orlando L. 2006. Des tests ADN aux énigmes de l'Histoire. Pour la Science, n° spécial, Hors-Série Janvier-Mars (Les maux de nos ancêtres), pp. 57-62

Orlando L. 2006. La Princesse de Vix était-elle une Princesse? Pour la Science, n° spécial, Hors-Série Janvier-Mars (Les maux de nos ancêtres), pp. 86-87

Orlando L, Hänni C. 2001. La génétique néndertalienne et l'origine de l'homme. Médecine/Sciences 17 : 273-277

Orlando L, Hänni C. 2000. De l'ADN fossile à l'ARN ancien : le cas du virus de la grippe espagnole. Médecine/Sciences 11, 1269-1270

Orlando L, Hänni, C. 2000. Du nouveau pour l'ADN ancien. Médecine/Sciences 8-9: I-XVI.

(Updated 26.04.2017)