Orlando Group – University of Copenhagen

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GeoGenetics > Research groups > Orlando Group

Research group: The Orlando Group

Background

Main research areas

Recent publications

- Reviews

- Equid evolution

- Molecular approaches

- Computational tools

- Population genetics

Key collaborators

Background

How much major palaeo-environmental changes have shaped the geographic structure and demographic profiles of mammalian populations has been a recurrent theme in our research. Using mainly ancient DNA (aDNA) data, phylogenetic and serial coalescent approaches, we have reconstructed the diversity dynamics of several Megafauna populations over the last 50.000 years.

This work led to the revision of speciation and extinction times of several emblematic extinct species, such as cave bears (Curr Biol 2001, Mol Biol Evol 2002), and woolly rhinos (Mol Phyl Evol 2003). It also revealed recent climatic changes as a key demographic driver for most Megafauna species (Nature 2011), possibly through major remodeling of plant communities (Nature 2014).

Our work has focused on human evolution as well, with special interest in our relationships with our closest relatives, the Neandertals (Curr Biol 2006, Nature 2007, Curr Biol 2007), and more recently, addressing major migration events, such as the founding events of the New World (Nature 2014, 2015), including the New World Arctic (Nature 2010, Science 2014) and also of Eurasia (Science 2014, Nature 2015).

Fossil horsebones extracted for ancient DNA. Photo: Ludovic Orlando.

Main research areasTil toppen

Since we officially started the lab in 2010, we have focused on developing integrative approaches for studying aDNA molecules, promoting the field of palaeomics by the merger of biochemistry, molecular biology, genomics and computational biology.

In particular, we have pioneered the use of true Single Molecule Sequencing (tSMS, Helicos) in aDNA research and thereby discovered important chemical features of aDNA molecules in relation with their degradation trajectory post-mortem (Genome Res 2011, BMC Genomics 2012).

By advancing our understanding of DNA damage processes, we have been able to tune our molecular tools to improve our ability to extract and manipulate ancient DNA molecules.

Similarly, we have contributed to a full series of bioinformatic tools and studies, all tailored to improving the sensitivity, the quality and the accuracy of the analyses underlying next-generation sequence datasets (Bioinformatics 2011, 2013; Nature Protocol 2014).

Our methodological developments have particularly benefitted to the reconstruction of the evolutionary history of one iconic mammal: the horse. We have generated the oldest genome characterized so far, that of a metapodial that has been preserved in the Yukon permafrost for about 700,000 years (Nature 2013). We also have characterized the complete genomes of several Pleistocene horses together with the genomes of a variety of modern domestic breeds (PNAS 2014a). Additionally, we characterized the first de novo assembly of the donkey genome, and genome-wide genetic variation across the whole equine family (PNAS 2014b). Additionally, we characterized the first de novo assembly of the donkey genome, and genome-wide genetic variation across the whole equine family (PNAS 2014). Incidently, this work resulted in the characterization of the complete genome sequence from the extinct quagga zebra, which kick-started ancient DNA research in the mid-eighties.

This represents an unprecedented genome sequence dataset for equids. We are currently scanning those genomes in order to identify the genetic changes that were specifically selected during horse domestication. Those changes contributed to major changes in human history, as mounted riding revolutionized warfare and, together with chariotry, facilitated the transportation of goods, people, languages, ideas and religion.

'We have also devised methods to track epigenetic changes over evolutionary times, either directly targeting DNA methylation marks (Sci Rep 2015) or exploiting indirect proxies of DNA methylation and nucleosome positioning (Genome Research 2014). This
resulted in the characterization of the first genome-wide nucleosome and methylation maps from an ancient human individual, paving the way for investigating the role of epigenetic changes in evolution (Science 2014).

Our research has been funded from AXA, the French-Danish Co-operation program from the French Embassy, Marie-Curie initiatives (FP7 CIG, FP7 IEF, H2020 IF, FP7 ITN), the Danish National Research Foundation (DNRF), the Danish Council for Independent Research (FNU), the Danish Agency for Research and Innovation (DASI), the Villum Kann Foundation, and the International Research Group Program from the King Saud University, Saudi Arabia.

Head of the group is Ludovic Orlando.

Recent publications

Reviews

Orlando L, Gilbert MT, Willerslev E. 2015. Reconstructing ancient genomes and epigenomes. Nat Rev Genet. 16:395-408.

Perry GH, Orlando L. 2015. Ancient DNA and human evolution. J Hum Evol. 79:1-3.

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.

Orlando L, Cooper A. 2014. Using ancient DNA to understand evolutionary and
ecological processes. Annual Reviews of Ecology, Evolution, and Systematics.
45:573-598.

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Ancient DNA and human evolution

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.

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.

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.

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

Equid evolution

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.

Librado P, Der Sarkissian C, Ermini L, Schubert M,  Jónsson H, Albrechtsen A, Fumagalli M, Yang MA, Gamba C, Seguin-Orlando A, Mortensen CD, Petersen B, Hoover CA, Lorente-Galdos B, Nedoluzhko A, Boulygina E, Tsygankova S, Neuditschko M, Jagannathan V, Thèves C, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Sicheritz-Ponten T, Popov R, Grigoriev S, Alekseev AN, Rubin EM, McCue M, Rieder S, Leeb T, Tikhonov A, Crubézy E, Slatkin MW,  Marques-Bonet T, Nielsen R, Willerslev E, Kantanen J, Prokhortchouk E, Orlando L. 2015. Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments. PNAS 112:E6889-97

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.

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

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.

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.

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

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 quids despite extensive chromosomal
plasticity. PNAS, 111:18655-60

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 D, 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:doi:10.1038/nature12323.

Vilstrup JT, Seguin-Orlando A, Stiller M, Ginolhac A, Raghavan M, Nielsen SC, 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.

Molecular approaches

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.

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.

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.

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.

Seguin-Orlando A, Schubert M, Clary J, Stagegaard J, Alberdi MT, et al. (2013). Ligation Bias in Illumina Next-Generation DNA Libraries: Implications for Sequencing Ancient Genomes. PLoS ONE 8(10): e78575. doi:10.1371/journal.pone.0078575

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

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

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: True single-molecule DNA sequencing of a Pleistocene horse bone. Genome Res 2011, 21:1705-19.

Computational toolsTil toppen

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.

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

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 2014 May;9(5):1056-82. doi: 10.1038/nprot.2014.063. Epub 2014 Apr 10. PubMed PMID: 24722405.

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

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

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

Population genetics

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.

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.

Mourier T, Ho S, Gilbert MTP, Willerslev E, Orlando L: Statistical guidelines for detecting past population shifts using ancient DNA. Mol Biol Evol 2012, 19:2241-51.

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

Ancient epigenomics

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, Article number: 11826 doi:10.1038/srep11826

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

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. 2014, 24:454-66.

Key collaboratorsTil toppen

Pr. Arnaud Zucker, University Nice-Sofia Antipolis, France.

Dr. Stavros Lazaris, University of Strasbourg, France.

Dr. Marjan Mashkour, Natural History Museum MNHN, Paris, France.

Dr. Emmanuelle Vila, Maison de l'Orient, Lyon, France.

Pr. Tomas Marques-Bonet, Universitat Pompeu Fabra

Pr. Khaled Al-Rasheid, King Saud University

Pr. Rasmus Nielsen, Berkeley University

Dr. Beth Shapiro, University of California, Santa Cruz

Pr. Michi Hofreiter, University of York

Pr. Duane Froese, University of Alberta

Dr. Leif Andersson, University of Uppsala

Dr. James McLeod, University of Kentucky

Dr. Molly McCue, University of Minnesota

Dr. Anders Albrechtsen, University of Copenhagen

Pr. Egor Prokhortchouk, Kurchatov Institute

Pr. Eric Crubezy, University of Toulouse

Dr. Olivier Tenaillon, Medicine Faculty Bichat 

Pr. Christophe Douady, University of Lyon

Dr. Christine Paillard, University of Brest

Danish High-Troughput DNA Sequencing Centre, University of Copenhagen

Pr. Laurent Excoffier, University of Bern

(Last updated 06.05.2016)Til toppen