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Accueil > Equipes > Archaeology, Genomics, Evolution and Societies (AGES)

Publications | Publications

par Ludovic Orlando - publié le , mis à jour le

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A list of all articles released prior to 2017 is available through each researchers’s individual webpage.

2018

- Orlando L. 2018.Late Bronze Age cultural origins of dairy pastoralism in Mongolia. PNAS published ahead of print November 12, 2018 https://doi.org/10.1073/pnas.1817559115
- Leonardi M, Boschin F, Giampoudakis K, Beyer RM, Krapp M, Bendrey R, Sommer R, Boscato P, Manica A, Nogues-Bravo D, Orlando L. 2018. Late Quaternary horses in Eurasia in the face of climate and vegetation change. Sci Adv, 4:eaar5589.
- Kalbfleisch TS, Rice ES, DePriest MS Jr, Walenz BP, Hestand MS, Vermeesch JR, O Connell BL, Fiddes IT, Vershinina AO, Saremi NF, Petersen JL, Finno CJ, Bellone RR, McCue ME, Brooks SA, Bailey E, Orlando L, Green RE, Miller DC, Antczak DF, MacLeod JN. 2018. Improved reference genome for the domestic horse increases assembly contiguity and composition. Commun Biol 1:197.
- Taylor W, Schnaider S, Abdykanova A, Fages A, Welker F, Irmer F, Seguin-Orlando A, Khan N, Douka K, Kolobova K, Orlando L, Krivoshapkin A, Boivin N. 2018. Early pastoral economies along the Ancient Silk Road : biomolecular evidence from the Alay Valley Kyrgyzstan. PLoS One 13:ee0205646.
- McColl H, Racimo F, Vinner L, Demeter F, Gakuhari T, Moreno-Mayar JV, van Driem G, Gram Wilken U, Seguin-Orlando A, de la Fuente Castro C, Wasef S, Shoocongdej R, Souksavatdy V, Sayavongkhamdy T, Saidin MM, Allentoft ME, Sato T, Malaspinas AS, Aghakhanian FA, Korneliussen T, Prohaska A, Margaryan A, de Barros Damgaard P, Kaewsutthi S, Lertrit P, Nguyen TMH, Hung HC, Minh Tran T, Nghia Truong H, Nguyen GH, Shahidan S, Wiradnyana K, Matsumae H, Shigehara N, Yoneda M, Ishida H, Masuyama T, Yamada Y, Tajima A, Shibata H, Toyoda A, Hanihara T, Nakagome S, Deviese T, Bacon AM, Duringer P, Ponche JL, Shackelford L, Patole-Edoumba E, Nguyen AT, Bellina-Pryce B, Galipaud JC, Kinaston R, Buckley H, Pottier C, Rasmussen S, Higham T, Foley RA, Lahr MM, Orlando L, Sikora M, Phipps ME, Oota H, Higham C, Lambert DM, Willerslev E. 2018. The prehistoric peopling of Southeast Asia. Science 361:88-92.
- Janečka J, Davis B, Ghosh S, Paria N, Das P, Orlando L, Schubert M, Nielsen M, Stout T, Brashear W, Li G, Johnson C, Metz R, Al Zadjali A-M, Love C, Varner D, Bellott D, Murphy W, Chowdhary B, Raudsepp T. 2018. Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes. Nat Commun, 9:2945.
- Willmann C, Mata X, Hanghoej K, Tonasso L, Tisseyre L, Jeziorski C, Cabot E, Chevet P, Crubézy E, Orlando L, Esclassan R, Thèves C. 2018. Oral health status in historic population : Macroscopic and metagenomic evidence. PLoS One 13:e0196482.
- Damgaard PB, Marchi N, Rasmussen S, Peyrot M, Renaud G, Korneliussen T, Moreno-Mayar JV, Pedersen MW, Goldberg A, Usmanova E, Baimukhanov N, Loman V, Hedeager L, Pedersen AG, Nielsen K, Afanasiev G, Akmatov K, Aldashev A, Alpaslan A, Baimbetov G, Bazaliiskii VI, Beisenov A, Boldbaatar B, Boldgiv B, Dorzhu C, Ellingvag S, Erdenebaatar D, Dajani R, Dmitriev E, Evdokimov V, Frei KM, Gromov A, Goryachev A, Hakonarson H, Hegay T, Khachatryan Z, Khaskhanov R, Kitov E, Kolbina A, Kubatbek T, Kukushkin A, Kukushkin I, Lau N, Margaryan A, Merkyte I, Mertz IV, Mertz VK, Mijiddorj E, Moiyesev V, Mukhtarova G, Nurmukhanbetov B, Orozbekova Z, Panyushkina I, Pieta K, Smrčka V, Shevnina I, Logvin A, Sjögren KG, Štolcová T, Tashbaeva K, Tkachev A, Tulegenov T, Voyakin D, Yepiskoposyan L, Undrakhbold S, Varfolomeev V, Weber A, Kradin N, Allentoft ME, Orlando L, Nielsen R, Sikora M, Heyer E, Kristiansen K, Willerslev E. 2018. 137 ancient human genomes from across the Eurasian steppes. Nature 557:369-374.
- Mühlemann B, Jones TC, Damgaard PB, Allentoft ME, Shevnina I, Logvin A, Usmanova E, Panyushkina IP, Boldgiv B, Bazartseren T, Tashbaeva K, Merz V, Lau N, Smrčka V, Voyakin D, Kitov E, Epimakhov A, Pokutta D, Vicze M, Price TD, Moiseyev V, Hansen AJ, Orlando L, Rasmussen S, Sikora M, Vinner L, Osterhaus ADME, Smith DJ, Glebe D, Fouchier RAM, Drosten C, Sjögren KG, Kristiansen K, Willerslev E. 2018. Ancient hepatitis B viruses from the Bronze Age to the Medieval period. Nature 557:418-423.
- de Barros Damgaard P, Martiniano R, Kamm J, Moreno-Mayar JV, Kroonen G, Peyrot M, Barjamovic G, Rasmussen S, Zacho C, Baimukhanov N, Zaibert V, Merz V, Biddanda A, Merz I, Loman V, Evdokimov V, Usmanova E, Hemphill B, Seguin-Orlando A, Yediay FE, Ullah I, Sjögren KG, Iversen KH, Choin J, de la Fuente C, Ilardo M, Schroeder H, Moiseyev V, Gromov A, Polyakov A, Omura S, Senyurt SY, Ahmad H, McKenzie C, Margaryan A, Hameed A, Samad A, Gul N, Khokhar MH, Goriunova OI, Bazaliiskii VI, Novembre J, Weber AW, Orlando L, Allentoft ME, Nielsen R, Kristiansen K, Sikora M, Outram AK, Durbin R, Willerslev E. 2018. The first horse herders and the impact of early Bronze Age steppe expansions into Asia. Science May 9. pii : eaar7711.
- Librado P, Orlando L. 2018. Detecting signatures of positive selection along defined branches of a population tree using LSD. Mol Biol Evol. 2018 Mar 29. doi : 10.1093/molbev/msy053.
- Dias GM, Bidault A, Le Chevalier P, Choquet G, Der Sarkissian C, Orlando L, Medigue C, Barbe V, Mangenot S, Thompson CC, Thompson FL, Jacq A, Pichereau V, Paillard C. 2018. Vibrio tapetis Displays an Original Type IV Secretion System in Strains Pathogenic for Bivalve Molluscs. Front Microbiol. 9:227.
- Alberto FJ, Boyer F, Orozco-terWengel P, Streeter I, Servin B, de Villemereuil P, Benjelloun B, Librado P, Biscarini F, Colli L, Barbato M, Zamani W, Alberti A, Engelen S, Stella A, Joost S, Ajmone-Marsan P, Negrini R, Orlando L, Rezaei HR, Naderi S, Clarke L, Flicek P, Wincker P, Coissac E, Kijas J, Tosser-Klopp G, Chikhi A, Bruford MW, Taberlet P, Pompanon F. 2018. Convergent genomic signatures of domestication in sheep and goats. Nat Commun. 9:813.
- Renaud G, Petersen B, Seguin-Orlando A, Bertelsen MF, Waller A, Newton R, Paillot R, Bryant N, Vaudin M, Librado P, Orlando L. 2018. Improved de novo genomic assembly for the domestic donkey. Science Advances 4:eaaq0392
- Gaunitz C, Fages A, Hanghøj K, Albrechtsen A, Khan N, Schubert M, Seguin-Orlando A, Owens IJ, Felkel S, Bignon-Lau O, de Barros Damgaard P, Mittnik A, Mohaseb AF, Davoudi H, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, Crubézy E, Benecke N, Olsen S, Brown D, Anthony D, Massy K, Pitulko V, Kasparov A, Brem G, Hofreiter M, Mukhtarova G, Baimukhanov N, Lõugas L, Onar V, Stockhammer PW, Krause J, Boldgiv B, Undrakhbold S, Erdenebaatar D, Lepetz S, Mashkour M, Ludwig A, Wallner B, Merz V, Merz I, Zaibert V, Willerslev E, Librado P, Outram AK, Orlando L. Ancient genomes revisit the ancestry of domestic and Przewalski’s horses. 2018. Science Feb 22. pii : eaao3297. doi : 10.1126/science.aao3297.
- Wagner S, Lagane F, Seguin-Orlando A, Schubert M, Leroy T, Guichoux E, Chancerel E, Bech-Hebelstrup I, Bernard V, Billard C, Billaud Y, Bolliger M, Croutsch C, Čufar K, Eynaud F, Heussner KU, Köninger J, Langenegger F, Leroy F, Lima C, Martinelli N, Momber G, Billamboz A, Nelle O, Palomo A, Piqué R, Ramstein M, Schweichel R, Stäuble H, Tegel W, Terradas X, Verdin F, Plomion C, Kremer A, Orlando L. 2018. High-Throughput DNA sequencing of ancient wood. Mol Ecol. 2018 Feb 7. doi : 10.1111/mec.14514.
- Pedersen CT, Albrechtsen A, Etter PD, Johnson EA, Orlando L, Chikhi L, Siegismund HR, Heller R. 2018. A southern African origin and cryptic structure in the highly mobile plains zebra. Nat Ecol Evol 2018 Jan 22. doi : 10.1038/s41559-017-0453-7.
- Moreno-Mayar JV, Potter BA, Vinner L, Steinrücken M, Rasmussen S, Terhorst J, Kamm JA, Albrechtsen A, Malaspinas AS, Sikora M, Reuther JD, Irish JD, Malhi RS, Orlando L, Song YS, Nielsen R, Meltzer DJ, Willerslev E. 2018. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. Nature 553:203-207. doi : 10.1038/nature25173

2017

- Heintzman PD, Zazula GD, MacPhee R, Scott E, `Cahill JA, McHorse BK, Kapp JD, Stiller M, Wooller MJ, Orlando L, Southon J, Froese DG, Shapiro B. 2017. A new genus of horse from Pleistocene North America. Elife 6 pii:e29944. doi : 10.7554/eLife.29944.
- Metcalf J, Song Se Jin, Morton JT, WeissS, Seguin-Orlando A, Joly F, Feh C, Taberlet P, Coissac E, Amir A, WillerslevE, Knight R, McKenzie V, Orlando L. 2017. Evaluating the impact of domestication and captivity on the horse gut microbiome. Sci Rep 7:15497. doi : 10.1038/s41598-017-15375-9.
- Fortes-Lima C, Gessain A, Ruiz-Linares A, Bortolini MC, Migot-Nabias F,Bellis G, Moreno-Mayar JV, Restrepo BN, Rojas W, Avendaño-Tamayo E, Bedoya G,Orlando L, Salas A, Helgason A, GilbertMTP, Sikora M, Schroeder H, Dugoujon JM. 2017. Genome-wide Ancestryand Demographic History of African-Descendant Maroon Communities from French Guiana and Suriname. Am J Hum Genet 101:725-736. doi : 10.1016/j.ajhg.2017.09.021.
- Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R ; Earth Microbiome Project Consortium. 2017. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551:457-463. doi : 10.1038/nature24621.
- Benazzo A, Trucchi E, Cahill JA, MaisanoDelser P, Mona S, Fumagalli M, Bunnefeld L, Cornetti L, Ghirotto S, Girardi M,Ometto L, Panziera A, Rota-Stabelli O, Zanetti E, Karamanlidis A, Groff C,Paule L, Gentile L, Vilà C, Vicario S, Boitani L,Orlando L, Fuselli S, Vernesi C, Shapiro B, Ciucci P, Bertorelle G.2017. Survival and divergence in a small group : the extraordinary genomic history of the endangered Apennine brown bear stragglers. Proc Natl Acad Sci U S A 114:E9589-E9597. doi:10.1073/pnas.1707279114.
- MacKenzie VJ, Song S, Delsuc F, Prest TL, Oliverio AM, Korpita TM, Alexiev A, Amato KR, Metcalf JL, Kowalewski M, Avenant NL, Link A, Di Fiore A, Seguin-Orlando A, Feh A, Orlando L, Mendelson JR, Sanders J, Knight R. 2017. The effects of captivity on the mammalian gut microbiome. Integr Comp Biol 57:690-704. doi : 10.1093/icb/icx090.
- Sikora M, Seguin-Orlando A, Sousa VC, Albrechtsen A, Korneliussen T, Ko A,Rasmussen S, Dupanloup I, Nigst PR, Bosch MD, Renaud G, Allentoft ME, MargaryanA, Vasilyev SV, Veselovskaya EV, Borutskaya SB, Deviese T, Comeskey D, HighamT, Manica A, Foley R, Meltzer DJ, Nielsen R, Excoffier L, Lahr MM, Orlando L, Willerslev E. 2017. Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers. Science 358:659-62. doi : 10.1126/science.aao1807.
- Schaefer RJ, Schubert M, Bailey E, Bannasch DL, Barrey E, Bar-Gal GK, Brem G, Brooks SA,Distl O, Fries R, Finno CJ, Gerber V, Haase B, Jagannathan V, Kalbfleisch T,Leeb T, Lindgren G, Lopes MS, Mach N, da Câmara Machado A, MacLeod JN, McCoy A,Metzger J, Penedo C, Polani S, Rieder S, Tammen I, Tetens J, Thaller G,Verini-Supplizi A, Wade CM, Wallner B,OrlandoL, Mickelson JR, McCue ME. 2017. Developing a 670k genotyping array to tag 2M SNPs across 24 horse breeds. BMC Genomics 18:565. doi : 10.1186/s12864-017-3943-8.
- Gopalakrishnan S, Castruita JS, Sinding MH, Kuderna L, Raikkonen J, Petersen B, Sicheritz-Ponten T, Larson G, Orlando L, Marques-Bonet T, Hansen A, Dalen L, Gilbert MTP. 2017. The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics. BMC Genomics 18:495. doi : 10.1186/s12864-017-3883-3.
- Warinner C, Herbig A, Mann A, Fellows Yates JA, Weiß CL, Burbano HA, Orlando L, Krause J. 2017. A robust framework for microbial archaeology. Ann Rev Genomics Hum Genet 18:321-356. doi : 10.1146/annurev-genom-091416-035526.
- 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 A, Lepetz S, Neuditschko M, Theves C, Alquaraishi S, Alfarhan AH, Al-Rasheid K, Rieder S, Samashev Z, Francfort HP, Benecke 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 356:442-5. doi : 10.1126/science.aam5298.
- 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 27:1016-1028. doi : 10.1101/gr.212589.116.
- Der Sarkissian C, Pichereau V, Dupont C, Ilsøe P, Perrigault M, Butler P, Chauvaud L, Eiriksson J, Scourse J, Paillard C, Orlando L. 2017. Ancient DNA analysis identifies marine mollusk shells as new metagenomic archives of the past. Mol Ecol Resour 17:835-53. doi : 10.1111/1755-0998.12679.
- 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. doi : 10.1098/rsos.160997.
- Leonardi M, Librado P, Der Sarkissian C, Schubert M, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Gamba C, Willerslev E, Orlando L. 2017. Evolutionary patterns and processes : lessons from ancient DNA. Syst Biol 66:e1-e29. doi : 10.1093/sysbio/syw059.
- Fabre PH, Upham NS, Emmons LH, Justy F,Leite YL, Loss AC, 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. doi : 10.1093/molbev/msw261.
- Llamas B, Willerslev E, Orlando L. 2017. Human evolution : a tale from ancient genomes. Phil Trans Roy Soc B 372(1713) pii : 20150484.
- Schubert M, Mashkour M, Gaunitz C, Fages A, Seguin-Orlando S, Sheikhi S, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Chuang R, Ermini L, Gamba C, Vila E, WeinstockJ, Vedat O, Orlando L. 2017. Zonkey : a fast, simple, accurate and sensitive method to genetically identify F1-equid hybrids in archaeological assemblages. J Arc Sci 78:147-157. doi : 10.1016/j.jas.2016.12.005.
- Renaud G, Hanghøj K, Willeslev E, Orlando L. 2017. gargammel : a sequence simulator for ancient DNA. Bioinformatics 33:577-579. doi : 10.1093/bioinformatics/btw670.
- Boessenkool S, Hanghøj K, Nistelberger HM, Der Sarkissian C, Gondek A, Orlando L, Barrett JH, Star B. 2017. Combining bleach and mild pre-digestion improves ancient DNA recovery from bones. Mol Ecol Resour 17:742-751. doi : 10.1111/1755-0998.12623.
- Cruz-Davalos DI, Llamas B, Gaunitz C,Fages A, Gamba C, Soubrier J, Librado P, Seguin-Orlando A, Pruvost M, AlfarhanAH, Al Quraishi SA, Al-Rasheid KAS, Scheu A, Benecke N, Ludwig A, Cooper A, Willerslev E, Orlando L. 2017. Experimental conditions improving in solution target enrichment for ancient DNA. Mol Ecol Resour 17:508-522. doi : 10.1111/1755-0998.12595.
- MacHugh D, Larson G, Orlando L. 2017. Taming the Past : Ancient DNA and the Study of Animal Domestication. Ann Rev Anim Biosci 5:329-51. doi : 10.1146/annurev-animal-022516-022747.