Browsing by Author "Khan, Naveed"
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- The genomic history of Iberian horses since the last Ice AgePublication . Garrido, Jaime Lira; Tressières, Gaétan; Chauvey, Lorelei; Schiavinato, Stéphanie; Calvière-Tonasso, Laure; Seguin-Orlando, Andaine; Southon, John; Shapiro, Beth; Bataille, Clément; Birgel, Julie; Wagner, Stefanie; Khan, Naveed; Liu, Xuexue; Rodanés, José María; Millán, Jesús V. Picazo; Giralt, Josep; Alonso, Natàlia; Aguilera, Isidro; Orsingher, Adriano; Trentacoste, Angela; Payà, Xavier; Morán, Marta; Eres, María Pilar Iborra; Albizuri, Silvia; Lamas, Silvia Valenzuela; Santandreu, Imma Mestres; Caixal, Montserrat Duran; Principal, Jordi; Huguet, Jordi Farré; Esteve, Xavier; Pasqual, Mireia Pedro; Sala, Nohemi; Pablos, Adrián; Martín, Patricia; Vergès, Josep Maria; Portero, Rodrigo; Arias, Pablo; Peredo, Roberto Ontañón; Detry, Cleia; Luís, Cristina; Cardoso, João Luis; Maeir, Aren M.; Valente, Maria João; Grau, Elena; Poles, Vicent Estall i; Llorens, Joaquín Alfonso; González, Ana Miguélez; Gardeisen, Armelle; Cupitò, Michele; Tecchiati, Umberto; Bradley, Daniel G.; Horwitz, Liora Kolska; González, Esther Rodríguez; Espinet, Ariadna Nieto; Bover, Pere; Entrecanales, Rosa Ruiz; Estallo, Ignasi Garcés; Fragoso, Joaquín Jiménez; Celestino, Sebastián; Orlando, LudovicHorses have inhabited Iberia (present-day Spain and Portugal) since the Middle Pleistocene, shaping a complex history in the region. Iberia has been proposed as a potential domestication centre and is renowned for producing world-class bloodlines. Here, we generate genome-wide sequence data from 87 ancient horse specimens (median coverage = 0.97X) from Iberia and the broader Mediterranean to reconstruct their genetic history over the last ~26,000 years. Here, we report that wild horses of the divergent IBE lineage inhabited Iberia from the Late Pleistocene, while domesticated DOM2 horses, native from the Pontic-Caspian steppes, already arrived ~1850 BCE. Admixture dating suggests breeding practices involving continued wild restocking until at least ~350 BCE, with IBE disappearing shortly after. Patterns of genetic affinity highlight the far-reaching influence of Iberian bloodlines across Europe and north Africa during the Iron Age and Antiquity, with continued impact extending thereafter, particularly during the colonization of the Americas.
- The genomic history of Iberian horses since the last Ice Age.Publication . Garrido, Jaime Lira; Tressières, Gaétan; Chauvey, Lorelei; Schiavinato, Stéphanie; Calvière-Tonasso, Laure; Seguin-Orlando, Andaine; Southon, John; Shapiro, Beth; Bataille, Clément; Birgel, Julie; Wagner, Stefanie; Khan, Naveed; Liu, Xuexue; Rodanés, José María; Picazo Millán, Jesús V.; Giralt, Josep; Alonso, Natàlia; Aguilera, Isidro; Orsingher, Adriano; Trentacoste, Angela; Payà, Xavier; Morán, Marta; Iborra Eres, María Pilar; Albizuri, Silvia; Valenzuela Lamas, Silvia; Mestres Santandreu, Imma; Duran Caixal, Montserrat; Principal, Jordi; Farré Huguet, Jordi; Esteve, Xavier; Pedro Pasqual, Mireia; Sala, Nohemi; Pablos, Adrián; Martín, Patricia; Vergès, Josep Maria; Portero, Rodrigo; Arias, Pablo; Ontañón Peredo, Roberto; Detry, Cleia; Luís, Cristina; Cardoso, João Luis; Maeir, Aren M.; Valente, Maria João; Grau, Elena; Estall I Poles, Vicent; Alfonso Llorens, Joaquín; Miguélez González, Ana; Gardeisen, Armelle; Cupitò, Michele; Tecchiati, Umberto; Bradley, Daniel G.; Kolska Horwitz, Liora; Rodríguez González, Esther; Nieto Espinet, Ariadna; Bover, Pere; Ruiz Entrecanales, Rosa; Garcés Estallo, Ignasi; Jiménez Fragoso, Joaquín; Celestino, Sebastián; Orlando, LudovicHorses have inhabited Iberia (present-day Spain and Portugal) since the Middle Pleistocene, shaping a complex history in the region. Iberia has been proposed as a potential domestication centre and is renowned for producing world-class bloodlines. Here, we generate genome-wide sequence data from 87 ancient horse specimens (median coverage = 0.97X) from Iberia and the broader Mediterranean to reconstruct their genetic history over the last ~26,000 years. Here, we report that wild horses of the divergent IBE lineage inhabited Iberia from the Late Pleistocene, while domesticated DOM2 horses, native from the Pontic-Caspian steppes, already arrived ~1850 BCE. Admixture dating suggests breeding practices involving continued wild restocking until at least ~350 BCE, with IBE disappearing shortly after. Patterns of genetic affinity highlight the far-reaching influence of Iberian bloodlines across Europe and north Africa during the Iron Age and Antiquity, with continued impact extending thereafter, particularly during the colonization of the Americas.
- The genomic history and global expansion of domestic donkeysPublication . Todd, Evelyn T.; Tonasso-Calvière, Laure; Chauvey, Loreleï; Schiavinato, Stéphanie; Fages, Antoine; Seguin-Orlando, Andaine; Clavel, Pierre; Khan, Naveed; Pérez Pardal, Lucía; Patterson Rosa, Laura; Librado, Pablo; Ringbauer, Harald; Verdugo, Marta; Southon, John; Aury, Jean-Marc; Perdereau, Aude; Vila, Emmanuelle; Marzullo, Matilde; Prato, Ornella; Tecchiati, Umberto; Bagnasco Gianni, Giovanna; Tagliacozzo, Antonio; Tinè, Vincenzo; Alhaique, Francesca; Luis Cardoso, João; Valente, Maria João; Telles Antunes, Miguel; Frantz, Laurent; Shapiro, Beth; Bradley, Daniel G.; Boulbes, Nicolas; Gardeisen, Armelle; Horwitz, Liora Kolska; Öztan, Aliye; Arbuckle, Benjamin S.; Onar, Vedat; Clavel, Benoît; Lepetz, Sébastien; Vahdati, Ali Akbar; Davoudi, Hossein; Mohaseb, Azadeh; Mashkour, Marjan; Bouchez, Olivier; Donnadieu, Cécile; Wincker, Patrick; Brooks, Samantha A.; Beja-Pereira, Albano; Wu, Dong-Dong; Orlando, LudovicDonkeys transformed human history as essential beasts of burden for long-distance movement, especially across semi-arid and upland environments. They remain insufficiently studied despite globally expanding and providing key support to low- to middle-income communities. To elucidate their domestication history, we constructed a comprehensive genome panel of 207 modern and 31 ancient donkeys, as well as 15 wild equids. We found a strong phylogeographic structure in modern donkeys that supports a single domestication in Africa similar to 5000 BCE, followed by further expansions in this continent and Eurasia and ultimately returning to Africa. We uncover a previously unknown genetic lineage in the Levant similar to 200 BCE, which contributed increasing ancestry toward Asia. Donkey management involved inbreeding and the production of giant bloodlines at a time when mules were essential to the Roman economy and military.
- Widespread horse-based mobility arose around 2200 BCE in EurasiaPublication . Librado, Pablo; Tressières, Gaetan; Chauvey, Lorelei; Fages, Antoine; Khan, Naveed; Schiavinato, Stéphanie; Calvière-Tonasso, Laure; Kusliy, Mariya A; Gaunitz, Charleen; Liu, Xuexue; Wagner, Stefanie; Der Sarkissian, Clio; Seguin-Orlando, Andaine; Perdereau, Aude; Aury, Jean-Marc; Southon, John; Shapiro, Beth; Bouchez, Olivier; Donnadieu, Cécile; Collin, Yvette Running Horse; Gregersen, Kristian M; Jessen, Mads Dengsø; Christensen, Kirsten; Claudi-Hansen, Lone; Pruvost, Mélanie; Pucher, Erich; Vulic, Hrvoje; Novak, Mario; Rimpf, Andrea; Turk, Peter; Reiter, Simone; Brem, Gottfried; Schwall, Christoph; Barrey, Éric; Robert, Céline; Degueurce, Christophe; Horwitz, Liora Kolska; Klassen, Lutz; Rasmussen, Uffe; Kveiborg, Jacob; Johannsen, Niels Nørkjær; Makowiecki, Daniel; Makarowicz, Przemysław; Szeliga, Marcin; Ilchyshyn, Vasyl; Rud, Vitalii; Romaniszyn, Jan; Mullin, Victoria E; Verdugo, Marta; Bradley, Daniel G; Valente, Maria J; Telles Antunes, Miguel; Ameen, Carly; Thomas, Richard; Ludwig, Arne; Marzullo, Matilde; Prato, Ornella; Bagnasco Gianni, Giovanna; Tecchiati, Umberto; Granado, José; Schlumbaum, Angela; Deschler-Erb, Sabine; Mráz, Monika Schernig; Boulbes, Nicolas; Gardeisen, Armelle; Mayer, Christian; Döhle, Hans-Jürgen; Vicze, Magdolna; Kosintsev, Pavel A; Kyselý, René; Peške, Lubomír; O'Connor, Terry; Ananyevskaya, Elina; Shevnina, Irina; Logvin, Andrey; Kovalev, Alexey A; Iderkhangai, Tumur-Ochir; Sablin, Mikhail V; Dashkovskiy, Petr K; Graphodatsky, Alexander S; Merts, Ilia; Merts, Viktor; Kasparov, Aleksei K; Pitulko, Vladimir V; Onar, Vedat; Öztan, Aliye; Arbuckle, Benjamin S; McColl, Hugh; Renaud, Gabriel; Khaskhanov, Ruslan; Demidenko, Sergey; Kadieva, Anna; Atabiev, Biyaslan; Sundqvist, Marie; Lindgren, Gabriella; López-Cachero, F Javier; Albizuri, Silvia; Trbojević Vukičević, Tajana; Rapan Papeša, Anita; Burić, Marcel; Rajić Šikanjić, Petra; Weinstock, Jaco; Asensio Vilaró, David; Codina, Ferran; García Dalmau, Cristina; Morer de Llorens, Jordi; Pou, Josep; de Prado, Gabriel; Sanmartí, Joan; Kallala, Nabil; Torres, Joan Ramon; Maraoui-Telmini, Bouthéina; Belarte Franco, Maria-Carme; Valenzuela-Lamas, Silvia; Zazzo, Antoine; Lepetz, Sébastien; Duchesne, Sylvie; Alexeev, Anatoly; Bayarsaikhan, Jamsranjav; Houle, Jean-Luc; Bayarkhuu, Noost; Turbat, Tsagaan; Crubézy, Éric; Shingiray, Irina; Mashkour, Marjan; Berezina, Natalia Ya; Korobov, Dmitriy S; Belinskiy, Andrey; Kalmykov, Alexey; Demoule, Jean-Paul; Reinhold, Sabine; Hansen, Svend; Wallner, Barbara; Roslyakova, Natalia; Kuznetsov, Pavel F; Tishkin, Alexey A; Wincker, Patrick; Kanne, Katherine; Outram, Alan; Orlando, Ludovic; Cardoso, João LuisHorses revolutionized human history with fast mobility. However, the timeline between their domestication and their widespread integration as a means of transport remains contentious. Here we assemble a collection of 475 ancient horse genomes to assess the period when these animals were first reshaped by human agency in Eurasia. We find that reproductive control of the modern domestic lineage emerged around 2200 BCE, through close-kin mating and shortened generation times. Reproductive control emerged following a severe domestication bottleneck starting no earlier than approximately 2700 BCE, and coincided with a sudden expansion across Eurasia that ultimately resulted in the replacement of nearly every local horse lineage. This expansion marked the rise of widespread horse-based mobility in human history, which refutes the commonly held narrative of large horse herds accompanying the massive migration of steppe peoples across Europe around 3000 BCE and earlier. Finally, we detect significantly shortened generation times at Botai around 3500 BCE, a settlement from central Asia associated with corrals and a subsistence economy centred on horses. This supports local horse husbandry before the rise of modern domestic bloodlines.