Orlando Group – University of Copenhagen

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GeoGenetics > Research groups > Orlando Group

Research group: The Orlando Group

Background

Main research areas

10 latest publications from the Orlando Group

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 and woolly rhinos. It also revealed recent climatic changes as a key demographic driver for most Megafauna species, possibly through major remodeling of plant communities.

Our work has focused on human evolution as well, with special interest in our relationships with our closest relatives, the Neandertals, and the reconstruction of major migration events as anatomically modern human spread out of Africa.

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

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

Main research areas: Ancient DNA, horses and domesticationTil 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 in aDNA research and thereby discovered important chemical features of aDNA molecules in relation with their degradation trajectory post-mortem.

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. All our computational tools are distributed under open source licenses, in order to facilitate technology transfer to the community (see PALEOMIX, epiPALEOMIX, gargammel, mapDamage, and metaBIT).

Our methodological developments have particularly benefited 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. We also have characterized the complete genomes of several Pleistocene horses together with the genomes of a variety of modern domestic breeds. Additionally, we characterized the first de novo assembly of the donkey genome, and genome-wide genetic variation across the whole equine family. 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 or exploiting indirect proxies of DNA methylation and nucleosome positioning. 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.

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 (DASTI), the Villum Foundation, the International Research Group and the International Highly cited Research Group Programs from the King Saud University, Saudi Arabia, the Initiative d'Excellence Chaires d'attractivité, Université de Toulouse (OURASI), and the European Research Council (ERC).

Head of the group is Ludovic Orlando.

10 latest publications from the Palaeomix GroupTil toppen

1) 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.

2) 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.

3) Leonardi M, Librado P, Der Sarkissian C, Schubert M, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Gamba C, Willerslev E, Orlando L. 2017. Evolutionary Patterns and Processes: Lessons from Ancient DNA. Syst Biol 66:e1-e29.

4) Schubert M, Mashkour M, Gaunitz C, Fages A, Seguin-Orlando A, Sheikhi S, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Chuang R, Ermini L, Gamba C, Weinstock J, Vedat O, Orlando. 2016. Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages. J Arc Sci 78:147-157.

5) MacHugh DE, Larson G, Orlando L. 2017. Taming the Past: Ancient DNA and the Study of Animal Domestication. Annu Rev Anim Biosci 5:329-351.

6) Renaud G, Hanghøj K, Willerslev E, Orlando L. 2017. gargammel: a sequence simulator for ancient DNA. Bioinformatics 33:577-579.

7) Boessenkool S, Hanghøj K, Nistelberger HM, Der Sarkissian C, Gondek AT, Orlando L, Barrett JH, Star B. 2016. Combining bleach and mild predigestion improves ancient DNA recovery from bones. Mol Ecol Resour, in press. doi: 10.1111/1755-0998.12623.

8) 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. 2016. The Evolutionary Origin and Genetic Makeup of Domestic Horses. Genetics 204:423-434.

9) Hanghøj K, Seguin-Orlando A, Schubert M, Madsen T, Pedersen JS, Willerslev E, Orlando L. 2016. Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX. Mol Biol Evol 33:3284-3298.

10) 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. 2016. Experimental conditions improving in-solution target enrichment for ancient DNA. Mol Ecol Resour, in press. doi: 10.1111/1755-0998.12595.

Key collaborators

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

Dr. Stavros Lazaris, College de France, Paris, France.

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

Dr. Sebastien Lepetz, Natural History Museum MNHN, Paris, France.

Dr. Benoit Clavel, Natural History Museum MNHN, Paris, France.

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

Pr. Alan Outram, Exeter University, UK.

Pr. Tomas Marques-Bonet, Universitat Pompeu Fabra, Barcelona, Spain.

Pr. Arne Ludwig, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.

Pr. Rasmus Nielsen, Berkeley University

Dr. Beth Shapiro, University of California, Santa Cruz

Pr. Michi Hofreiter, Postdam University, Germany.

Dr. Anders Albrechtsen, University of Copenhagen, Denmark.

Pr. Eric Crubezy, University of Toulouse

Danish High-Troughput DNA Sequencing Centre, University of Copenhagen

Pr. Laurent Excoffier, University of Bern

(Last updated 26.04.2017)Til toppen