TY - JOUR A1 - Wutke, Saskia A1 - Sandoval-Castellanos, Edson A1 - Benecke, Norbert A1 - Döhle, Hans-Jürgen A1 - Friederich, Susanne A1 - Gonzalez, Javier A1 - Hofreiter, Michael A1 - Lougas, Lembi A1 - Magnell, Ola A1 - Malaspinas, Anna-Sapfo A1 - Morales-Muniz, Arturo A1 - Orlando, Ludovic A1 - Reissmann, Monika A1 - Trinks, Alexandra A1 - Ludwig, Arne T1 - Decline of genetic diversity in ancient domestic stallions in Europe JF - Science Advances N2 - 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. Y1 - 2018 U6 - https://doi.org/10.1126/sciadv.aap9691 SN - 2375-2548 VL - 4 IS - 4 PB - American Assoc. for the Advancement of Science CY - Washington ER - TY - JOUR A1 - Alberti, Federica A1 - Gonzalez, Javier A1 - Paijmans, Johanna L. A. A1 - Basler, Nikolas A1 - Preick, Michaela A1 - Henneberger, Kirstin A1 - Trinks, Alexandra A1 - Rabeder, Gernot A1 - Conard, Nicholas J. A1 - Muenzel, Susanne C. A1 - Joger, Ulrich A1 - Fritsch, Guido A1 - Hildebrandt, Thomas A1 - Hofreiter, Michael A1 - Barlow, Axel T1 - Optimized DNA sampling of ancient bones using Computed Tomography scans JF - Molecular ecology resources N2 - The prevalence of contaminant microbial DNA in ancient bone samples represents the principal limiting factor for palaeogenomic studies, as it may comprise more than 99% of DNA molecules obtained. Efforts to exclude or reduce this contaminant fraction have been numerous but also variable in their success. Here, we present a simple but highly effective method to increase the relative proportion of endogenous molecules obtained from ancient bones. Using computed tomography (CT) scanning, we identify the densest region of a bone as optimal for sampling. This approach accurately identifies the densest internal regions of petrous bones, which are known to be a source of high-purity ancient DNA. For ancient long bones, CT scans reveal a high-density outermost layer, which has been routinely removed and discarded prior to DNA extraction. For almost all long bones investigated, we find that targeted sampling of this outermost layer provides an increase in endogenous DNA content over that obtained from softer, trabecular bone. This targeted sampling can produce as much as 50-fold increase in the proportion of endogenous DNA, providing a directly proportional reduction in sequencing costs for shotgun sequencing experiments. The observed increases in endogenous DNA proportion are not associated with any reduction in absolute endogenous molecule recovery. Although sampling the outermost layer can result in higher levels of human contamination, some bones were found to have more contamination associated with the internal bone structures. Our method is highly consistent, reproducible and applicable across a wide range of bone types, ages and species. We predict that this discovery will greatly extend the potential to study ancient populations and species in the genomics era. KW - ancient DNA KW - computer tomography KW - palaeogenomics KW - paleogenetics KW - petrous bone Y1 - 2018 U6 - https://doi.org/10.1111/1755-0998.12911 SN - 1755-098X SN - 1755-0998 VL - 18 IS - 6 SP - 1196 EP - 1208 PB - Wiley CY - Hoboken ER - TY - GEN A1 - Wutke, Saskia A1 - Andersson, Leif A1 - Benecke, Norbert A1 - Sandoval-Castellanos, Edson A1 - Gonzalez, Javier A1 - Hallsson, Jon Hallsteinn A1 - Lougas, Lembi A1 - Magnell, Ola A1 - Morales-Muniz, Arturo A1 - Orlando, Ludovic A1 - Palsdottir, Albina Hulda A1 - Reissmann, Monika A1 - Munoz-Rodriguez, Mariana B. A1 - Ruttkay, Matej A1 - Trinks, Alexandra A1 - Hofreiter, Michael A1 - Ludwig, Arne T1 - The origin of ambling horses T2 - Current biology N2 - 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. Y1 - 2016 U6 - https://doi.org/10.1016/j.cub.2016.07.001 SN - 0960-9822 SN - 1879-0445 VL - 26 SP - R697 EP - R699 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Wutke, Saskia A1 - Benecke, Norbert A1 - Sandoval-Castellanos, Edson A1 - Döhle, Hans-Jürgen A1 - Friederich, Susanne A1 - Gonzalez Soto, Javier Esteban A1 - Hallsson, Jon Hallsteinn A1 - Hofreiter, Michael A1 - Lougas, Lembi A1 - Magnell, Ola A1 - Morales-Muniz, Arturo A1 - Orlando, Ludovic A1 - Palsdottir, Albina Hulda A1 - Reissmann, Monika A1 - Ruttkay, Matej A1 - Trinks, Alexandra A1 - Ludwig, Arne T1 - Spotted phenotypes in horses lost attractiveness in the Middle Ages JF - Scientific reports N2 - 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. Y1 - 2016 U6 - https://doi.org/10.1038/srep38548 SN - 2045-2322 VL - 6 PB - Nature Publ. Group CY - London ER -