Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments

• Published in: Proceedings of the National Academy of Sciences
• Main Authors: Librado, Pablo, Der Sarkissian, Clio, Ermini, Luca, Schubert, Mikkel, Jónsson, Hákon, Albrechtsen, Anders, Fumagalli, Matteo, Yang, Melinda, A., Gamba, Cristina, Seguin-Orlando, Andaine, Mortensen, Cecilie, E., Petersen, Bent, Hoover, Cindi, A., Lorente-Galdos, Belen, Nedoluzhko, Artem, Boulygina, Eugenia, Tsygankova, Svetlana, Neuditschko, Markus, Jagannathan, Vidhya, Thèves, Catherine, Alfarhan, Ahmed, H, Alquraishin, Saleh, A., Al-Rasheidn, Khaled, A. S., Sicheritz-Ponten, Thomas, Popov, Ruslan, Grigoriev, Semyon, Alekseev, Anatoly N, Rubin, Edward, M., Mccue, Molly, Rieder, Stefan, Leeb, Tosso, Tikhonov, Alexei, Crubézy, Eric, Slatkin, Montgomery, Marques-Bonet, Tomas, Nielsen, Rasmus, Willerslev, Eske, Kantanen, Juha, Prokhortchouk, Egor, Orlando, Ludovic
• Other Authors: Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Bioinformatics Centre, Department of Biology Copenhagen, Faculty of Science Copenhagen, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science Copenhagen, Dept of Genetics, Evolution and Environment London (UCL-GEE), University College of London London (UCL), Department of Integrative Biology, National High-Throughput DNA Sequencing Centre, University of Copenhagen = Københavns Universitet (UCPH), Center for Biological Sequence Analysis, Department of Systems Biology, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Universitat Pompeu Fabra Barcelona (UPF), Centro Nacional de Análisis Genómico, National Research Centre Kurchatov Institute, Agroscope, Swiss National Stud Farm, Institute of Genetics, Universität Bern / University of Bern (UNIBE), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), King Saud University Riyadh (KSU), Yakutian Research Institute of Agriculture, North-Eastern Federal University, College of Veterinary Medicine, University of Minnesota Twin Cities (UMN), University of Minnesota System (UMN)-University of Minnesota System (UMN), Zoological Institute of Russian Academy of Sciences, Russian Academy of Sciences Moscow (RAS), Center for Theoretical Evolutionary Genomics Berkeley (CTEG), Department of Integrative Biology Berkeley (IB), University of California Berkeley (UC Berkeley), University of California (UC)-University of California (UC)-University of California Berkeley (UC Berkeley), University of California (UC)-University of California (UC), Agrifood Research Finland, University of Eastern Finland
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2015
• Subjects: ancient genomics; adaptation; population discontinuity; regulatory changes; horse; [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology; Arctic; Sakha Republic; Subarctic; Yakutia
• Online Access: https://hal.science/hal-01256914; https://hal.science/hal-01256914/document; https://hal.science/hal-01256914/file/2015-Librado-PNAS_tracking%20origins%20of%20Yakutian%20horses.pdf; https://doi.org/10.1073/pnas.1513696112

International audience Yakutia, Sakha Republic, in the Siberian Far East, represents one of the coldest places on Earth, with winter record temperatures dropping below −70 °C. Nevertheless, Yakutian horses survive all year round in the open air due to striking phenotypic adaptations, including compact body conformations, extremely hairy winter coats, and acute seasonal differences in metabolic activities. The evolutionary origins of Yakutian horses and the genetic basis of their adaptations remain, however, contentious. Here, we present the complete genomes of nine present-day Yakutian horses and two ancient specimens dating from the early 19th century and ∼5,200 y ago. By comparing these genomes with the genomes of two Late Pleistocene, 27 domesticated, and three wild Przewalski's horses, we find that contemporary Yakutian horses do not descend from the native horses that populated the region until the mid-Holocene, but were most likely introduced following the migration of the Yakut people a few centuries ago. Thus, they represent one of the fastest cases of adaptation to the extreme temperatures of the Arctic. We find cis-regulatory mutations to have contributed more than nonsynonymous changes to their adaptation, likely due to the comparatively limited standing variation within gene bodies at the time the population was founded. Genes involved in hair development, body size, and metabolic and hormone signaling pathways represent an essential part of the Yakutian horse adaptive genetic toolkit. Finally, we find evidence for convergent evolution with native human populations and woolly mammoths, suggesting that only a few evolutionary strategies are compatible with survival in extremely cold environments. ancient genomics | adaptation | population discontinuity | regulatory changes | horse