@article{WutkeSandovalCastellanosBeneckeetal.2018, author = {Wutke, Saskia and Sandoval-Castellanos, Edson and Benecke, Norbert and D{\"o}hle, Hans-J{\"u}rgen and Friederich, Susanne and Gonzalez, Javier and Hofreiter, Michael and Lougas, Lembi and Magnell, Ola and Malaspinas, Anna-Sapfo and Morales-Muniz, Arturo and Orlando, Ludovic and Reissmann, Monika and Trinks, Alexandra and Ludwig, Arne}, title = {Decline of genetic diversity in ancient domestic stallions in Europe}, series = {Science Advances}, volume = {4}, journal = {Science Advances}, number = {4}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, issn = {2375-2548}, doi = {10.1126/sciadv.aap9691}, pages = {7}, year = {2018}, abstract = {Present-day domestic horses are immensely diverse in their maternally inherited mitochondrial DNA, yet they show very little variation on their paternally inherited Y chromosome. Although it has recently been shown that Y chromosomal diversity in domestic horses was higher at least until the Iron Age, when and why this diversity disappeared remain controversial questions. We genotyped 16 recently discovered Y chromosomal single-nucleotide polymorphisms in 96 ancient Eurasian stallions spanning the early domestication stages (Copper and Bronze Age) to the Middle Ages. Using this Y chromosomal time series, which covers nearly the entire history of horse domestication, we reveal how Y chromosomal diversity changed over time. Our results also show that the lack of multiple stallion lineages in the extant domestic population is caused by neither a founder effect nor random demographic effects but instead is the result of artificial selection-initially during the Iron Age by nomadic people from the Eurasian steppes and later during the Roman period. Moreover, the modern domestic haplotype probably derived from another, already advantageous, haplotype, most likely after the beginning of the domestication. In line with recent findings indicating that the Przewalski and domestic horse lineages remained connected by gene flow after they diverged about 45,000 years ago, we present evidence for Y chromosomal introgression of Przewalski horses into the gene pool of European domestic horses at least until medieval times.}, language = {en} } @article{FagesHanghojKhanetal.2019, author = {Fages, Antoine and Hanghoj, Kristian and Khan, Naveed and Gaunitz, Charleen and Seguin-Orlando, Andaine and Leonardi, Michela and Constantz, Christian McCrory and Gamba, Cristina and Al-Rasheid, Khaled A. S. and Albizuri, Silvia and Alfarhan, Ahmed H. and Allentoft, Morten and Alquraishi, Saleh and Anthony, David and Baimukhanov, Nurbol and Barrett, James H. and Bayarsaikhan, Jamsranjav and Benecke, Norbert and Bernaldez-Sanchez, Eloisa and Berrocal-Rangel, Luis and Biglari, Fereidoun and Boessenkool, Sanne and Boldgiv, Bazartseren and Brem, Gottfried and Brown, Dorcas and Burger, Joachim and Crubezy, Eric and Daugnora, Linas and Davoudi, Hossein and Damgaard, Peter de Barros and de Chorro y de Villa-Ceballos, Maria de los Angeles and Deschler-Erb, Sabine and Detry, Cleia and Dill, Nadine and Oom, Maria do Mar and Dohr, Anna and Ellingvag, Sturla and Erdenebaatar, Diimaajav and Fathi, Homa and Felkel, Sabine and Fernandez-Rodriguez, Carlos and Garcia-Vinas, Esteban and Germonpre, Mietje and Granado, Jose D. and Hallsson, Jon H. and Hemmer, Helmut and Hofreiter, Michael and Kasparov, Aleksei and Khasanov, Mutalib and Khazaeli, Roya and Kosintsev, Pavel and Kristiansen, Kristian and Kubatbek, Tabaldiev and Kuderna, Lukas and Kuznetsov, Pavel and Laleh, Haeedeh and Leonard, Jennifer A. and Lhuillier, Johanna and von Lettow-Vorbeck, Corina Liesau and Logvin, Andrey and Lougas, Lembi and Ludwig, Arne and Luis, Cristina and Arruda, Ana Margarida and Marques-Bonet, Tomas and Silva, Raquel Matoso and Merz, Victor and Mijiddorj, Enkhbayar and Miller, Bryan K. and Monchalov, Oleg and Mohaseb, Fatemeh A. and Morales, Arturo and Nieto-Espinet, Ariadna and Nistelberger, Heidi and Onar, Vedat and Palsdottir, Albina H. and Pitulko, Vladimir and Pitskhelauri, Konstantin and Pruvost, Melanie and Sikanjic, Petra Rajic and Papesa, Anita Rapan and Roslyakova, Natalia and Sardari, Alireza and Sauer, Eberhard and Schafberg, Renate and Scheu, Amelie and Schibler, Jorg and Schlumbaum, Angela and Serrand, Nathalie and Serres-Armero, Aitor and Shapiro, Beth and Seno, Shiva Sheikhi and Shevnina, Irina and Shidrang, Sonia and Southon, John and Star, Bastiaan and Sykes, Naomi and Taheri, Kamal and Taylor, William and Teegen, Wolf-Rudiger and Vukicevic, Tajana Trbojevic and Trixl, Simon and Tumen, Dashzeveg and Undrakhbold, Sainbileg and Usmanova, Emma and Vahdati, Ali and Valenzuela-Lamas, Silvia and Viegas, Catarina and Wallner, Barbara and Weinstock, Jaco and Zaibert, Victor and Clavel, Benoit and Lepetz, Sebastien and Mashkour, Marjan and Helgason, Agnar and Stefansson, Kari and Barrey, Eric and Willerslev, Eske and Outram, Alan K. and Librado, Pablo and Orlando, Ludovic}, title = {Tracking five millennia of horse management with extensive ancient genome time series}, series = {Cell}, volume = {177}, journal = {Cell}, number = {6}, publisher = {Cell Press}, address = {Cambridge}, issn = {0092-8674}, doi = {10.1016/j.cell.2019.03.049}, pages = {1419 -- 1435}, year = {2019}, abstract = {Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (>= 1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modem legacy of past equestrian civilisations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN "speed gene," only rose in popularity within the last millennium. Finally, the development of modem breeding impacted genetic diversity more dramatically than the previous millennia of human management.}, language = {en} } @article{SchubertJonssonChangetal.2014, author = {Schubert, Mikkel and Jonsson, Hakon and Chang, Dan and Sarkissian, Clio Der and Ermini, Luca and Ginolhac, Aurelien and Albrechtsen, Anders and Dupanloup, Isabelle and Foucal, Adrien and Petersen, Bent Larsen and Fumagalli, Matteo and Raghavan, Maanasa and Seguin-Orlando, Andaine and Korneliussen, Thorfinn S. and Velazquez, Amhed M. V. and Stenderup, Jesper and Hoover, Cindi A. and Rubin, Carl-Johan and Alfarhan, Ahmed H. and Alquraishi, Saleh A. and Al-Rasheid, Khaled A. S. and MacHugh, David E. and Kalbfleisch, Ted and MacLeod, James N. and Rubin, Edward M. and Sicheritz-Ponten, Thomas and Andersson, Leif and Hofreiter, Michael and Marques-Bonet, Tomas and Gilbert, M. Thomas P. and Nielsen, Rasmus and Excoffier, Laurent and Willerslev, Eske and Shapiro, Beth and Orlando, Ludovic}, title = {Prehistoric genomes reveal the genetic foundation and cost of horse domestication}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {52}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1416991111}, pages = {E5661 -- E5669}, year = {2014}, language = {en} } @article{WutkeBeneckeSandovalCastellanosetal.2016, author = {Wutke, Saskia and Benecke, Norbert and Sandoval-Castellanos, Edson and D{\"o}hle, Hans-J{\"u}rgen and Friederich, Susanne and Gonzalez Soto, Javier Esteban and Hallsson, Jon Hallsteinn and Hofreiter, Michael and Lougas, Lembi and Magnell, Ola and Morales-Muniz, Arturo and Orlando, Ludovic and Palsdottir, Albina Hulda and Reissmann, Monika and Ruttkay, Matej and Trinks, Alexandra and Ludwig, Arne}, title = {Spotted phenotypes in horses lost attractiveness in the Middle Ages}, series = {Scientific reports}, volume = {6}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep38548}, pages = {9}, year = {2016}, abstract = {Horses have been valued for their diversity of coat colour since prehistoric times; this is especially the case since their domestication in the Caspian steppe in similar to 3,500 BC. Although we can assume that human preferences were not constant, we have only anecdotal information about how domestic horses were influenced by humans. Our results from genotype analyses show a significant increase in spotted coats in early domestic horses (Copper Age to Iron Age). In contrast, medieval horses carried significantly fewer alleles for these phenotypes, whereas solid phenotypes (i.e., chestnut) became dominant. This shift may have been supported because of (i) pleiotropic disadvantages, (ii) a reduced need to separate domestic horses from their wild counterparts, (iii) a lower religious prestige, or (iv) novel developments in weaponry. These scenarios may have acted alone or in combination. However, the dominance of chestnut is a remarkable feature of the medieval horse population.}, language = {en} } @misc{WutkeAnderssonBeneckeetal.2016, author = {Wutke, Saskia and Andersson, Leif and Benecke, Norbert and Sandoval-Castellanos, Edson and Gonzalez, Javier and Hallsson, Jon Hallsteinn and Lougas, Lembi and Magnell, Ola and Morales-Muniz, Arturo and Orlando, Ludovic and Palsdottir, Albina Hulda and Reissmann, Monika and Munoz-Rodriguez, Mariana B. and Ruttkay, Matej and Trinks, Alexandra and Hofreiter, Michael and Ludwig, Arne}, title = {The origin of ambling horses}, series = {Current biology}, volume = {26}, journal = {Current biology}, publisher = {Cell Press}, address = {Cambridge}, issn = {0960-9822}, doi = {10.1016/j.cub.2016.07.001}, pages = {R697 -- R699}, year = {2016}, abstract = {Horseback riding is the most fundamental use of domestic horses and has had a huge influence on the development of human societies for millennia. Over time, riding techniques and the style of riding improved. Therefore, horses with the ability to perform comfortable gaits (e.g. ambling or pacing), so-called 'gaited' horses, have been highly valued by humans, especially for long distance travel. Recently, the causative mutation for gaitedness in horses has been linked to a substitution causing a premature stop codon in the DMRT3 gene (DMRT3_Ser301STOP) [1]. In mice, Dmrt3 is expressed in spinal cord interneurons and plays an important role in the development of limb movement coordination [1]. Genotyping the position in 4396 modern horses from 141 breeds revealed that nowadays the mutated allele is distributed worldwide with an especially high frequency in gaited horses and breeds used for harness racing [2]. Here, we examine historic horse remains for the DMRT3 SNP, tracking the origin of gaitedness to Medieval England between 850 and 900 AD. The presence of the corresponding allele in Icelandic horses (9th-11th century) strongly suggests that ambling horses were brought from the British Isles to Iceland by Norse people. Considering the high frequency of the ambling allele in early Icelandic horses, we believe that Norse settlers selected for this comfortable mode of horse riding soon after arrival. The absence of the allele in samples from continental Europe (including Scandinavia) at this time implies that ambling horses may have spread from Iceland and maybe also the British Isles across the continent at a later date.}, language = {en} } @article{LibradoGambaGaunitzetal.2017, author = {Librado, Pablo and Gamba, Cristina and Gaunitz, Charleen and Sarkissian, Clio Der and Pruvost, Melanie and Albrechtsen, Anders and Fages, Antoine and Khan, Naveed and Schubert, Mikkel and Jagannathan, Vidhya and Serres-Armero, Aitor and Kuderna, Lukas F. K. and Povolotskaya, Inna S. and Seguin-Orlando, Andaine and Lepetz, Sebastien and Neuditschko, Markus and Theves, Catherine and Alquraishi, Saleh A. and Alfarhan, Ahmed H. and Al-Rasheid, Khaled A. S. and Rieder, Stefan and Samashev, Zainolla and Francfort, Henri-Paul and Benecke, Norbert and Hofreiter, Michael and Ludwig, Arne and Keyser, Christine and Marques-Bonet, Tomas and Ludes, Bertrand and Crubezy, Eric and Leeb, Tosso and Willerslev, Eske and Orlando, Ludovic}, title = {Ancient genomic changes associated with domestication of the horse}, series = {Science}, volume = {356}, journal = {Science}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, issn = {0036-8075}, doi = {10.1126/science.aam5298}, pages = {442 -- 445}, year = {2017}, abstract = {The genomic changes underlying both early and late stages of horse domestication remain largely unknown. We examined the genomes of 14 early domestic horses from the Bronze and Iron Ages, dating to between similar to 4.1 and 2.3 thousand years before present. We find early domestication selection patterns supporting the neural crest hypothesis, which provides a unified developmental origin for common domestic traits. Within the past 2.3 thousand years, horses lost genetic diversity and archaic DNA tracts introgressed from a now-extinct lineage. They accumulated deleterious mutations later than expected under the cost-of-domestication hypothesis, probably because of breeding from limited numbers of stallions. We also reveal that Iron Age Scythian steppe nomads implemented breeding strategies involving no detectable inbreeding and selection for coat-color variation and robust forelimbs.}, language = {en} } @article{ZhangPaijmansChangetal.2013, author = {Zhang, Hucai and Paijmans, Johanna L. A. and Chang, Fengqin and Wu, Xiaohong and Chen, Guangjie and Lei, Chuzhao and Yang, Xiujuan and Wei, Zhenyi and Bradley, Daniel G. and Orlando, Ludovic and O'Connor, Terry and Hofreiter, Michael}, title = {Morphological and genetic evidence for early Holocene cattle management in northeastern China}, series = {Nature Communications}, volume = {4}, journal = {Nature Communications}, number = {6}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/ncomms3755}, pages = {7}, year = {2013}, abstract = {The domestication of cattle is generally accepted to have taken place in two independent centres: around 10,500 years ago in the Near East, giving rise to modern taurine cattle, and two millennia later in southern Asia, giving rise to zebu cattle. Here we provide firmly dated morphological and genetic evidence for early Holocene management of taurine cattle in northeastern China. We describe conjoining mandibles from this region that show evidence of oral stereotypy, dated to the early Holocene by two independent C-14 dates. Using Illumina high-throughput sequencing coupled with DNA hybridization capture, we characterize 15,406 bp of the mitogenome with on average 16.7-fold coverage. Phylogenetic analyses reveal a hitherto unknown mitochondrial haplogroup that falls outside the known taurine diversity. Our data suggest that the first attempts to manage cattle in northern China predate the introduction of domestic cattle that gave rise to the current stock by several thousand years.}, language = {en} }