The makeup of the modern horse: a history of the biological changes introduced by human management

Publications

Author(s): Ludovic Orlando; Robin Allaby; Pontus Skoglund; Clio Der Sarkissian; Philipp W. Stockhammer; María C. Ávila-Arcos; Qiaomei Fu; Johannes Krause; Eske Willerslev; Anne C. Stone; Christina Warinner
Published in: Nature Reviews Methods Primer, Issue 1, 2021, Page(s) 14, ISSN 2662-8449
Publisher: Nature
DOI: 10.1038/s43586-020-00011-0

Historical management of equine resources in France from the Iron Age to the Modern Period

Author(s): Sebastien Lepetz; Benoit Clavel; Duha Alioglu; Lorelei Chauvey; Stephanie Schiavinato; Laure Tonasso-Calviere; Xuexue Liu; Antoine Fages; Naveed Khan; Andaine Seguin-Orlando; Clio Der Sarkissian; Pierre Clavel; Oscar Estrada; Charleen Gaunitz; Jean-Marc Aury; Maude Barme; Nicolas Boulbes; Alice Bourgois; Franck Decanter; Sylvain Foucras; Stephane Frere; Armelle Gardeisen; Gaëtan Jouanin; Charlo
Published in: Journal of Archaeological Science: Reports, Issue 40, 2021, Page(s) 103250, ISSN 2352-409X
Publisher: Elsevier BV
DOI: 10.1016/j.jasrep.2021.103250

Sex in the city: Uncovering sex-specific management of equine resources from prehistoric times to the Modern Period in France

Author(s): Benoit Clavel; Sebastien Lepetz; Lorelei Chauvey; Stephanie Schiavinato; Laure Tonasso-Calviere; Xuexue Liu; Antoine Fages; Naveed Khan; Andaine Seguin-Orlando; Clio Der Sarkissian; Pierre Clavel; Oscar Estrada; Duha Alioğlu; Charleen Gaunitz; Jean-Marc Aury; Maude Barme; Pierre Bodu; Monique Olive; Olivier Bignon-Lau; Jean-Christophe Castel; Myriam Boudadi-Maligne; Nicolas Boulbes; Alice Bourgoi
Published in: Journal of Archaeological Science: Reports, Issue 41, 2022, Page(s) 103341, ISSN 2352-409X
Publisher: Elsevier BV
DOI: 10.1016/j.jasrep.2022.103341

Uncovering Signatures of DNA Methylation in Ancient Plant Remains From Patterns of Post-mortem DNA Damage

Author(s): Stefanie Wagner, Christophe Plomion, Ludovic Orlando
Published in: Frontiers in Ecology and Evolution, Issue 8, 2020, Page(s) -, ISSN 2296-701X
Publisher: Frontiers in Ecology and Evolution
DOI: 10.3389/fevo.2020.00011

Struct-f4: a Rcpp package for ancestry profile and population structure inference from f4-statistics

Author(s): Pablo Librado; Ludovic Orlando
Published in: Bioinformatics, Issue 38, 2022, Page(s) 2070-2071, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btac046

CASCADE: A Custom-Made Archiving System for the Conservation of Ancient DNA Experimental Data

Author(s): Dirk Dolle; Antoine Fages; Xavier Mata; Stéphanie Schiavinato; Laure Tonasso-Calvière; Lorelei Chauvey; Stefanie Wagner; Clio Der Sarkissian; Aurore Fromentier; Andaine Seguin-Orlando; Ludovic Orlando
Published in: Frontiers in Ecology and Evolution, Vol 8 (2020), Issue 3, 2020, Page(s) -, ISSN 2296-701X
Publisher: Frontiers in Ecology and Evolution
DOI: 10.3389/fevo.2020.00185

Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge

Author(s): Alisa O. Vershinina, Peter D. Heintzman, Duane G. Froese, Grant Zazula, Molly Cassatt‐Johnstone, Love Dalén, Clio Der Sarkissian, Shelby G. Dunn, Luca Ermini, Cristina Gamba, Pamela Groves, Joshua D. Kapp, Daniel H. Mann, Andaine Seguin‐Orlando, John Southon, Mathias Stiller, Matthew J. Wooller, Gennady Baryshnikov, Dmitry Gimranov, Eric Scott, Elizabeth Hall, Susan Hewitson, Irina Kirillova,
Published in: Molecular Ecology, Issue 20210510, 2021, Page(s) -, ISSN 0962-1083
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/mec.15977

The genomic history and global expansion of domestic donkeys

Author(s): Evelyn T. Todd; Laure Tonasso-Calvière; Loreleï Chauvey; Stéphanie Schiavinato; Antoine Fages; Andaine Seguin-Orlando; Pierre Clavel; Naveed Khan; Lucía Pérez Pardal; Laura Patterson Rosa; Pablo Librado; Harald Ringbauer; Marta Verdugo; John Southon; Jean-Marc Aury; Aude Perdereau; Emmanuelle Vila; Matilde Marzullo; Ornella Prato; Umberto Tecchiati; Giovanna Bagnasco Gianni; Antonio Tagliacoz
Published in: Science, Issue 377, 2022, Page(s) 1172-1180, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abo3503

Late Quaternary dynamics of Arctic biota from ancient environmental genomics

Author(s): Y. L. Wang; Y. L. Wang; Mikkel Winther Pedersen; Inger Greve Alsos; Bianca De Sanctis; Fernando Racimo; Ana Prohaska; Eric Coissac; Hannah L. Owens; Marie Kristine Føreid Merkel; Antonio Fernandez-Guerra; Alexandra Rouillard; Youri Lammers; Adriana Alberti; Daniel Money; Anthony Ruter; Hugh McColl; Nicolaj K. Larsen; Anna Cherezova; Anna Cherezova; Mary E. Edwards; Mary E. Edwards; Grigory Fedoro
Published in: 1476-4687, Issue 600, 2021, Page(s) 86-92, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.17863/cam.82534

Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene

Author(s): Mian Gong; Siqi Zhu; Dawei Cai; Naifan Zhang; Jia Wen; Qiyao Liang; Weilu Sun; Xinyue Shao; Yaqi Guo; Yudong Cai; Zhuqing Zheng; Wei Zhang; Songmei Hu; Xiaoyang Wang; He Tian; Youqian Li; Wei Liu; Miaomiao Yang; Jian Yang; Duo Wu; Ludovic Orlando; Yu Jiang
Published in: Crossref, Issue 11, 2022, Page(s) e73346, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.73346

Assessing the predictive taxonomic power of the bony labyrinth 3D shape in horses, donkeys and their F1-hybrids

Author(s): Pierre Clavel, Jean Dumoncel, Clio Der Sarkissian, Andaine Seguin-Orlando, Laure Calvière-Tonasso, Stephanie Schiavinato, Lorelei Chauvey, Aude Perdereau, Jean-Marc Aury, Patrick Wincker, Vedat Onar, Benoît Clavel, Sébastien Lepetz, José Braga, Ludovic Orlando
Published in: Journal of Archaeological Science, Issue 131, 2021, Page(s) 105383, ISSN 0305-4403
Publisher: Academic Press
DOI: 10.1016/j.jas.2021.105383

Grey wolf genomic history reveals a dual ancestry of dogs

Author(s): Anders Bergstrom; David W G Stanton; Ulrike H Taron; Laurent Frantz; Mikkel-Holger S Sinding; Erik Ersmark; Saskia Pfrengle; Molly Cassatt-Johnstone; Ophelie Lebrasseur; Linus Girdland-Flink; Daniel M Fernandes; Morgane Ollivier; Leo Speidel; Shyam Gopalakrishnan; Michael V Westbury; Jazmin Ramos-Madrigal; Tatiana R Feuerborn; Ella Reiter; Joscha Gretzinger; Susanne C Münzel;
Published in: Nature, Issue 607, 2022, Page(s) 313-320, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-022-04824-9

Assessing the impact of USER-treatment on hyRAD capture applied to ancient DNA

Author(s): Tomasz Suchan; Lorelei Chauvey; Marine Poullet; Laure Tonasso-Calviere; Stephanie Schiavinato; Pierre Clavel; Benoit Clavel; Sebastien Lepetz; Andaine Seguin-Orlando; Ludovic Orlando
Published in: Molecular Ecology Resources, Issue 22, 2022, Page(s) 2262-2274, ISSN 1755-098X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1755-0998.13619

The Evolutionary and Historical Foundation of the Modern Horse: Lessons from Ancient Genomics

Author(s): Ludovic Orlando
Published in: Annual Review of Genetics, Issue 54/1, 2020, Page(s) 563-581, ISSN 0066-4197
Publisher: Annual Reviews, Inc.
DOI: 10.1146/annurev-genet-021920-011805

Modern human incursion into Neanderthal territories 54,000 years ago at Mandrin, France

Author(s): Ludovic Slimak; Clement Zanolli; Tom Higham; Marine Frouin; Jean-Luc Schwenninger; Lee J Arnold; Martina Demuro; Katerina Douka; Norbert Mercier; Gilles Guerin; Hélène Valladas; Pascale Yvorra; Yves Giraud; Andaine Seguin-Orlando; Ludovic Orlando; Jason E Lewis; Xavier Muth; Hubert Camus; Segolene Vandevelde; Mike Buckley; Carolina Mallol; Chris Stringer; Laure Metz
Published in: Science Advances, Issue 8, 2022, Page(s) eabj9496, ISSN 2375-2548
Publisher: American Association for the Advancement of Science
DOI: 10.1126/sciadv.abj9496

Late Quaternary dynamics of Arctic biota from ancient environmental genomics

Author(s): Yucheng Wang, Mikkel Winther Pedersen, Inger Greve Alsos, Bianca De Sanctis, Fernando Racimo, Ana Prohaska, Eric Coissac, Hannah Lois Owens, Marie Kristine Føreid Merkel, Antonio Fernandez-Guerra, Alexandra Rouillard, Youri Lammers, Adriana Alberti, France Denoeud, Daniel Money, Anthony H. Ruter, Hugh McColl, Nicolaj Krog Larsen, Anna A. Cherezova, Mary E. Edwards, Grigory B. Fedorov, James Haile
Published in: Nature, Issue 20211020, 2021, Page(s) -, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-021-04016-x

Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages

Author(s): Mikkel Schubert, Marjan Mashkour, Charleen Gaunitz, Antoine Fages, Andaine Seguin-Orlando, Shiva Sheikhi, Ahmed H. Alfarhan, Saleh A. Alquraishi, Khaled A.S. Al-Rasheid, Richard Chuang, Luca Ermini, Cristina Gamba, Jaco Weinstock, Onar Vedat, Ludovic Orlando
Published in: Journal of Archaeological Science, Issue 78, 2017, Page(s) 147-157, ISSN 0305-4403
Publisher: Academic Press
DOI: 10.1016/j.jas.2016.12.005

Evaluating the impact of domestication and captivity on the horse gut microbiome

Author(s): Jessica L. Metcalf, Se Jin Song, James T. Morton, Sophie Weiss, Andaine Seguin-Orlando, Frédéric Joly, Claudia Feh, Pierre Taberlet, Eric Coissac, Amnon Amir, Eske Willerslev, Rob Knight, Valerie McKenzie, Ludovic Orlando
Published in: Scientific Reports, Issue 7/1, 2017, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-017-15375-9

Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds

Author(s): Robert J. Schaefer, Mikkel Schubert, Ernest Bailey, Danika L. Bannasch, Eric Barrey, Gila Kahila Bar-Gal, Gottfried Brem, Samantha A. Brooks, Ottmar Distl, Ruedi Fries, Carrie J. Finno, Vinzenz Gerber, Bianca Haase, Vidhya Jagannathan, Ted Kalbfleisch, Tosso Leeb, Gabriella Lindgren, Maria Susana Lopes, Núria Mach, Artur da Câmara Machado, James N. MacLeod, Annette McCoy, Julia Metzger, Cecilia
Published in: BMC Genomics, Issue 18/1, 2017, ISSN 1471-2164
Publisher: BioMed Central
DOI: 10.1186/s12864-017-3943-8

A new genus of horse from Pleistocene North America

Author(s): Peter D Heintzman, Grant D Zazula, Ross DE MacPhee, Eric Scott, James A Cahill, Brianna K McHorse, Joshua D Kapp, Mathias Stiller, Matthew J Wooller, Ludovic Orlando, John Southon, Duane G Froese, Beth Shapiro
Published in: eLife, Issue 6, 2017, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/eLife.29944

Detecting Signatures of Positive Selection along Defined Branches of a Population Tree Using LSD

Author(s): Pablo Librado, Ludovic Orlando
Published in: Molecular Biology and Evolution, Issue 35/6, 2018, Page(s) 1520-1535, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msy053

Late Quaternary horses in Eurasia in the face of climate and vegetation change

Author(s): Michela Leonardi, Francesco Boschin, Konstantinos Giampoudakis, Robert M. Beyer, Mario Krapp, Robin Bendrey, Robert Sommer, Paolo Boscato, Andrea Manica, David Nogues-Bravo, Ludovic Orlando
Published in: Science Advances, Issue 4/7, 2018, Page(s) eaar5589, ISSN 2375-2548
Publisher: Science Advances
DOI: 10.1126/sciadv.aar5589

Ancient genomic changes associated with domestication of the horse

Author(s): Pablo Librado, Cristina Gamba, Charleen Gaunitz, Clio Der Sarkissian, Mélanie Pruvost, Anders Albrechtsen, Antoine Fages, Naveed Khan, Mikkel Schubert, Vidhya Jagannathan, Aitor Serres-Armero, Lukas F. K. Kuderna, Inna S. Povolotskaya, Andaine Seguin-Orlando, Sébastien Lepetz, Markus Neuditschko, Catherine Thèves, Saleh Alquraishi, Ahmed H. Alfarhan, Khaled Al-Rasheid, Stefan Rieder, Zainolla S
Published in: Science, Issue 356/6336, 2017, Page(s) 442-445, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aam5298

Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies

Author(s): T. Cucchi, A. Mohaseb, S. Peigné, K. Debue, L. Orlando, M. Mashkour
Published in: Royal Society Open Science, Issue 4/4, 2017, Page(s) 160997, ISSN 2054-5703
Publisher: Royal Society Open Science
DOI: 10.1098/rsos.160997

Improved de novo genomic assembly for the domestic donkey

Author(s): Gabriel Renaud, Bent Petersen, Andaine Seguin-Orlando, Mads Frost Bertelsen, Andrew Waller, Richard Newton, Romain Paillot, Neil Bryant, Mark Vaudin, Pablo Librado, Ludovic Orlando
Published in: Science Advances, Issue 4/4, 2018, Page(s) eaaq0392, ISSN 2375-2548
Publisher: Science Advances (American Association for the Advancement of Science)
DOI: 10.1126/sciadv.aaq0392

Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes

Author(s): Jan E. Janečka, Brian W. Davis, Sharmila Ghosh, Nandina Paria, Pranab J. Das, Ludovic Orlando, Mikkel Schubert, Martin K. Nielsen, Tom A. E. Stout, Wesley Brashear, Gang Li, Charles D. Johnson, Richard P. Metz, Al Muatasim Al Zadjali, Charles C. Love, Dickson D. Varner, Daniel W. Bellott, William J. Murphy, Bhanu P. Chowdhary, Terje Raudsepp
Published in: Nature Communications, Issue 9/1, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-05290-6

Improved reference genome for the domestic horse increases assembly contiguity and composition

Author(s): Theodore S. Kalbfleisch, Edward S. Rice, Michael S. DePriest, Brian P. Walenz, Matthew S. Hestand, Joris R. Vermeesch, Brendan L. O′Connell, Ian T. Fiddes, Alisa O. Vershinina, Nedda F. Saremi, Jessica L. Petersen, Carrie J. Finno, Rebecca R. Bellone, Molly E. McCue, Samantha A. Brooks, Ernest Bailey, Ludovic Orlando, Richard E. Green, Donald C. Miller, Douglas F. Antczak, James N. MacLeod
Published in: Communications Biology, Issue 1/1, 2018, ISSN 2399-3642
Publisher: Communications Biology
DOI: 10.1038/s42003-018-0199-z

Early pastoral economies along the Ancient Silk Road: Biomolecular evidence from the Alay Valley, Kyrgyzstan

Author(s): William Taylor, Svetlana Shnaider, Aida Abdykanova, Antoine Fages, Frido Welker, Franziska Irmer, Andaine Seguin-Orlando, Naveed Khan, Katerina Douka, Ksenia Kolobova, Ludovic Orlando, Andrei Krivoshapkin, Nicole Boivin
Published in: PLOS ONE, Issue 13/10, 2018, Page(s) e0205646, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0205646

Late Bronze Age cultural origins of dairy pastoralism in Mongolia

Author(s): Ludovic Orlando
Published in: Proceedings of the National Academy of Sciences, Issue 115/48, 2018, Page(s) 12083-12085, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1817559115

Sexing Viking Age horses from burial and non-burial sites in Iceland using ancient DNA

Author(s): Heidi M. Nistelberger, Albína Hulda Pálsdóttir, Bastiaan Star, Rúnar Leifsson, Agata T. Gondek, Ludovic Orlando, James H. Barrett, Jón Hallsteinn Hallsson, Sanne Boessenkool
Published in: Journal of Archaeological Science, Issue 101, 2019, Page(s) 115-122, ISSN 0305-4403
Publisher: Academic Press
DOI: 10.1016/j.jas.2018.11.007

The first horse herders and the impact of early Bronze Age steppe expansions into Asia

Author(s): Peter de Barros Damgaard, Rui Martiniano, Jack Kamm, J. Víctor Moreno-Mayar, Guus Kroonen, Michaël Peyrot, Gojko Barjamovic, Simon Rasmussen, Claus Zacho, Nurbol Baimukhanov, Victor Zaibert, Victor Merz, Arjun Biddanda, Ilja Merz, Valeriy Loman, Valeriy Evdokimov, Emma Usmanova, Brian Hemphill, Andaine Seguin-Orlando, Fulya Eylem Yediay, Inam Ullah, Karl-Göran Sjögren, Katrine Højholt Iversen
Published in: Science, Issue 360/6396, 2018, Page(s) eaar7711, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aar7711

Decline of genetic diversity in ancient domestic stallions in Europe

Author(s): Saskia Wutke, Edson Sandoval-Castellanos, Norbert Benecke, Hans-Jürgen Döhle, Susanne Friederich, Javier Gonzalez, Michael Hofreiter, Lembi Lõugas, Ola Magnell, Anna-Sapfo Malaspinas, Arturo Morales-Muñiz, Ludovic Orlando, Monika Reissmann, Alexandra Trinks, Arne Ludwig
Published in: Science Advances, Issue 4/4, 2018, Page(s) eaap9691, ISSN 2375-2548
Publisher: Science Advances
DOI: 10.1126/sciadv.aap9691

Spotted phenotypes in horses lost attractiveness in the Middle Ages

Author(s): Saskia Wutke, Norbert Benecke, Edson Sandoval-Castellanos, Hans-Jürgen Döhle, Susanne Friederich, Javier Gonzalez, Jón Hallsteinn Hallsson, Michael Hofreiter, Lembi Lõugas, Ola Magnell, Arturo Morales-Muniz, Ludovic Orlando, Albína Hulda Pálsdóttir, Monika Reissmann, Matej Ruttkay, Alexandra Trinks, Arne Ludwig
Published in: Scientific Reports, Issue 6/1, 2016, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/srep38548

Evolutionary Patterns and Processes: Lessons from Ancient DNA

Author(s): Michela Leonardi, Pablo Librado, Clio Der Sarkissian, Mikkel Schubert, Ahmed H. Alfarhan, Saleh A. Alquraishi, Khaled A. S. Al-Rasheid, Cristina Gamba, Eske Willerslev, Ludovic Orlando
Published in: Systematic Biology, 2017, Page(s) syw059, ISSN 1063-5157
Publisher: Taylor & Francis
DOI: 10.1093/sysbio/syw059

A Robust Framework for Microbial Archaeology

Author(s): Christina Warinner, Alexander Herbig, Allison Mann, James A. Fellows Yates, Clemens L. Weiß, Hernán A. Burbano, Ludovic Orlando, Johannes Krause
Published in: Annual Review of Genomics and Human Genetics, Issue 18/1, 2017, Page(s) 321-356, ISSN 1527-8204
Publisher: Annual Reviews, Inc.
DOI: 10.1146/annurev-genom-091416-035526

The Effects of Captivity on the Mammalian Gut Microbiome

Author(s): Valerie J. McKenzie, Se Jin Song, Frédéric Delsuc, Tiffany L. Prest, Angela M. Oliverio, Timothy M. Korpita, Alexandra Alexiev, Katherine R. Amato, Jessica L. Metcalf, Martin Kowalewski, Nico L. Avenant, Andres Link, Anthony Di Fiore, Andaine Seguin-Orlando, Claudia Feh, Ludovic Orlando, Joseph R. Mendelson, Jon Sanders, Rob Knight
Published in: Integrative and Comparative Biology, Issue 57/4, 2017, Page(s) 690-704, ISSN 1540-7063
Publisher: Oxford University Press
DOI: 10.1093/icb/icx090

Ancient genomes revisit the ancestry of domestic and Przewalski’s horses

Author(s): Charleen Gaunitz, Antoine Fages, Kristian Hanghøj, Anders Albrechtsen, Naveed Khan, Mikkel Schubert, Andaine Seguin-Orlando, Ivy J. Owens, Sabine Felkel, Olivier Bignon-Lau, Peter de Barros Damgaard, Alissa Mittnik, Azadeh F. Mohaseb, Hossein Davoudi, Saleh Alquraishi, Ahmed H. Alfarhan, Khaled A. S. Al-Rasheid, Eric Crubézy, Norbert Benecke, Sandra Olsen, Dorcas Brown, David Anthony, Ken Massy,
Published in: Science, Issue 360/6384, 2018, Page(s) 111-114, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aao3297

Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series

Author(s): Antoine Fages, Kristian Hanghøj, Naveed Khan, Charleen Gaunitz, Andaine Seguin-Orlando, Michela Leonardi, Christian McCrory Constantz, Cristina Gamba, Khaled A.S. Al-Rasheid, Silvia Albizuri, Ahmed H. Alfarhan, Morten Allentoft, Saleh Alquraishi, David Anthony, Nurbol Baimukhanov, James H. Barrett, Jamsranjav Bayarsaikhan, Norbert Benecke, Eloísa Bernáldez-Sánchez, Luis Berrocal-Rangel, Fereid
Published in: Cell, Issue 177/6, 2019, Page(s) 1419-1435.e31, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2019.03.049

Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples

Author(s): Gabriel Renaud, Kristian Hanghøj, Thorfinn Sand Korneliussen, Eske Willerslev, Ludovic Orlando
Published in: Genetics, 2019, Page(s) genetics.302057.2019, ISSN 0016-6731
Publisher: Genetics Society of America
DOI: 10.1534/genetics.119.302057

DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage

Author(s): Kristian Hanghøj, Gabriel Renaud, Anders Albrechtsen, Ludovic Orlando
Published in: GigaScience, Issue 8/4, 2019, ISSN 2047-217X
Publisher: OUP
DOI: 10.1093/gigascience/giz025

DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions

Author(s): Lucie Zinger, Aurélie Bonin, Inger G. Alsos, Miklós Bálint, Holly Bik, Frédéric Boyer, Anthony A. Chariton, Simon Creer, Eric Coissac, Bruce E. Deagle, Marta De Barba, Ian A. Dickie, Alex J. Dumbrell, Gentile Francesco Ficetola, Noah Fierer, Luca Fumagalli, M. Thomas P. Gilbert, Simon Jarman, Ari Jumpponen, Håvard Kauserud, Ludovic Orlando, Johan Pansu, Jan Pawlowski, Leho Tedersoo, Philip F
Published in: Molecular Ecology, Issue 28/8, 2019, Page(s) 1857-1862, ISSN 0962-1083
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/mec.15060

EPAS1 gain-of-function mutation contributes to high-altitude adaptation in Tibetan horses

Author(s): Xuexue Liu, Yanli Zhang, Yefang Li, Jianfei Pan, Dandan Wang, Weihuang Chen, Zhuqing Zheng, Xiaohong He, Qianjun Zhao, Yabin Pu, Weijun Guan, Jianlin Han, Ludovic Orlando, Yuehui Ma, Lin Jiang
Published in: Molecular Biology and Evolution, 2019, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msz158

Origin and Evolution of Deleterious Mutations in Horses

Author(s): Ludovic Orlando, Pablo Librado
Published in: Genes, Issue 10/9, 2019, Page(s) 649, ISSN 2073-4425
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes10090649

Dairy pastoralism sustained eastern Eurasian steppe populations for 5,000 years

Author(s): Shevan Wilkin, Alicia Ventresca Miller, William T. T. Taylor, Bryan K. Miller, Richard W. Hagan, Madeleine Bleasdale, Ashley Scott, Sumiya Gankhuyg, Abigail Ramsøe, S. Uliziibayar, Christian Trachsel, Paolo Nanni, Jonas Grossmann, Ludovic Orlando, Mark Horton, Philipp W. Stockhammer, Erdene Myagmar, Nicole Boivin, Christina Warinner, Jessica Hendy
Published in: Nature Ecology & Evolution, Issue 4/3, 2020, Page(s) 346-355, ISSN 2397-334X
Publisher: Springer Nature
DOI: 10.1038/s41559-020-1120-y

Ancient Genomes Reveal Unexpected Horse Domestication and Management Dynamics

Author(s): Ludovic Orlando
Published in: BioEssays, Issue 42/1, 2019, Page(s) 1900164, ISSN 0265-9247
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/bies.201900164

Animal domestication in the era of ancient genomics

Author(s): Laurent A. F. Frantz, Daniel G. Bradley, Greger Larson, Ludovic Orlando
Published in: Nature Reviews Genetics, 2020, ISSN 1471-0056
Publisher: Nature Publishing Group
DOI: 10.1038/s41576-020-0225-0

Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA

Author(s): Caroline Pont, Stefanie Wagner, Antoine Kremer, Ludovic Orlando, Christophe Plomion, Jerome Salse
Published in: Genome Biology, Issue 20/1, 2019, Page(s) 29, ISSN 1474-760X
Publisher: BMC
DOI: 10.1186/s13059-019-1627-1

Filling Important Gaps in the Genomic History of Southwest Asia

Author(s): Ludovic Orlando
Published in: Cell, Issue 181, ISSUE5, MAY 28 2020, 2020, Page(s) 966-968, ISSN 1097-4172
Publisher: US Cell Press
DOI: 10.1016/j.cell.2020.05.010

Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny

Author(s): Enrico Cappellini, Frido Welker, Luca Pandolfi, Jazmín Ramos-Madrigal, Diana Samodova, Patrick L. Rüther, Anna K. Fotakis, David Lyon, J. Víctor Moreno-Mayar, Maia Bukhsianidze, Rosa Rakownikow Jersie-Christensen, Meaghan Mackie, Aurélien Ginolhac, Reid Ferring, Martha Tappen, Eleftheria Palkopoulou, Marc R. Dickinson, Thomas W. Stafford, Yvonne L. Chan, Anders Götherström, Senthilvel K. S.
Published in: Nature, Issue 574/7776, 2019, Page(s) 103-107, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-019-1555-y

Horse males became over-represented in archaeological assemblages during the Bronze Age

Author(s): Antoine Fages, Andaine Seguin-Orlando, Mietje Germonpré, Ludovic Orlando
Published in: Journal of Archaeological Science: Reports, Issue 31, 2020, Page(s) 102364, ISSN 2352-409X
Publisher: Elsevier BV
DOI: 10.1016/j.jasrep.2020.102364

The origins and spread of domestic horses from the Western Eurasian steppes

Author(s): Pablo Librado, Naveed Khan, Antoine Fages, Mariya A. Kusliy, Tomasz Suchan, Laure Tonasso-Calvière, Stéphanie Schiavinato, Duha Alioglu, Aurore Fromentier, Aude Perdereau, Jean-Marc Aury, Charleen Gaunitz, Lorelei Chauvey, Andaine Seguin-Orlando, Clio Der Sarkissian, John Southon, Beth Shapiro, Alexey A. Tishkin, Alexey A. Kovalev, Saleh Alquraishi, Ahmed H. Alfarhan, Khaled A. S. Al-Rasheid, Ti
Published in: Nature, Issue 598/7882, 2021, Page(s) 634-640, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-021-04018-9

A single-nucleotide mutation within the TBX3 enhancer increased body size in Chinese horses

Author(s): Xuexue Liu; Yanli Zhang; Wujun Liu; Yefang Li; Jianfei Pan; Yabin Pu; Jianlin Han; Ludovic Orlando; Yuehui Ma; Lin Jiang
Published in: Current Biology, Issue 32, 2022, Page(s) 480-487.e6, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2021.11.052

Using paleo-archives to safeguard biodiversity under climate change

Author(s): Damien A. Fordham, Stephen T. Jackson, Stuart C. Brown, Brian Huntley, Barry W. Brook, Dorthe Dahl-Jensen, M. Thomas P. Gilbert, Bette L. Otto-Bliesner, Anders Svensson, Spyros Theodoridis, Janet M. Wilmshurst, Jessie C. Buettel, Elisabetta Canteri, Matthew McDowell, Ludovic Orlando, Julia Pilowsky, Carsten Rahbek, David Nogues-Bravo
Published in: Science, Issue 369/6507, 2020, Page(s) -, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abc5654

Author Correction: Improved reference genome for the domestic horse increases assembly contiguity and composition

Author(s): Theodore S. Kalbfleisch, Edward S. Rice, Michael S. DePriest, Brian P. Walenz, Matthew S. Hestand, Joris R. Vermeesch, Brendan L. O’Connell, Ian T. Fiddes, Alisa O. Vershinina, Nedda F. Saremi, Jessica L. Petersen, Carrie J. Finno, Rebecca R. Bellone, Molly E. McCue, Samantha A. Brooks, Ernest Bailey, Ludovic Orlando, Richard E. Green, Donald C. Miller, Douglas F. Antczak, James N. MacLeod
Published in: Communications Biology, Issue 2/1, 2019, Page(s) -, ISSN 2399-3642
Publisher: Commun Biol
DOI: 10.1038/s42003-019-0591-3

High-Throughput DNA sequencing of ancient wood

Author(s): Stefanie Wagner, Frédéric Lagane, Andaine Seguin-Orlando, Mikkel Schubert, Thibault Leroy, Erwan Guichoux, Emilie Chancerel, Inger Bech-Hebelstrup, Vincent Bernard, Cyrille Billard, Yves Billaud, Matthias Bolliger, Christophe Croutsch, Katarina Čufar, Frédérique Eynaud, Karl Uwe Heussner, Joachim Köninger, Fabien Langenegger, Frédéric Leroy, Christine Lima, Nicoletta Martinelli, Garry Momb
Published in: Molecular Ecology, Issue 27/5, 2018, Page(s) 1138-1154, ISSN 0962-1083
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/mec.14514

mapDATAge: a ShinyR package to chart ancient DNA data through space and time

Author(s): Xuexue Liu; Ludovic Orlando
Published in: Bioinformatics, Issue 38, 2022, Page(s) 3992-3994, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btac425

Performance and automation of ancient DNA capture with RNA hyRAD probes

Author(s): Tomasz Suchan; Mariya A. Kusliy; Naveed Khan; Naveed Khan; Lorelei Chauvey; Laure Tonasso-Calvière; Stéphanie Schiavinato; John Southon; Marcel Keller; Keiko Kitagawa; Johannes Krause; Alexander Bessudnov; Alexander A. Bessudnov; Alexander S. Graphodatsky; Silvia Valenzuela-Lamas; Jarosław Wilczyński; Sylwia Pospuła; Krzysztof Tunia; Marek Nowak; Magdalena Moskal-del-Hoyo; Alexey A. Tishkin;
Published in: ISSN: 1755-098X, Issue 22, 2022, Page(s) 891-907, ISSN 1755-098X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1755-0998.13518

Authentication and Assessment of Contamination in Ancient DNA

Author(s): Gabriel Renaud, Mikkel Schubert, Susanna Sawyer, Ludovic Orlando
Published in: Ancient DNA - Methods and Protocols, Issue 1963, 2019, Page(s) 163-194, ISBN 978-1-4939-9175-4
Publisher: Springer New York
DOI: 10.1007/978-1-4939-9176-1_17

Ancient Epigenomics

Author(s): Kristian Hanghøj, Ludovic Orlando
Published in: Paleogenomics Genome-Scale Analysis of Ancient DNA, 2019, ISBN 978-3-030-04753-5
Publisher: Springer

L’ADN ancien comme nouvelle source historique

Author(s): Ludovic Orlando
Published in: Aux sources de l'histoire animale, 2019, ISSN 0292-6679
Publisher: Éditions de la Sorbonne

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