Periodic Reporting for period 5 - PEGASUS (The makeup of the modern horse: a history of the biological changes introduced by human management)
Période du rapport: 2021-12-01 au 2022-11-30
The domestication of the horse revolutionized human history. While most breeds have been engendered in the last few centuries, horses have been managed for 5+ky. As recent breeding management has tremendously impacted the horse population structure, patterns of modern diversity can only partly help reconstruct the domestication history prior to the modern era. Archaeological sciences coupled with ancient DNA offer the opportunity to bypass this limitation and follow past herders' practice as they modified horse biology. We endeavored to sequence the most extensive collection of ancient horse genomes from across their whole domestication range to identify how the many past equestrian cultures transformed the animal. By developing innovative solutions for sequencing ancient genomes, we have characterized the horse genome, prior to, during, and following domestication. We have leveraged DNA methylation patterns to assess how gene expression has been modified in response to changing breeding management strategies. Our work was not restricted to genetic information and gene expression only, but also integrated the broad range of morphological, cultural, and microbial changes accompanying domestication, including pathogen exposure. Our activities were divided into 3 main work packages (WP). The 1st WP targeted early domestication stages and identified the domestication homeland in the western Eurasian steppes around 4.2 kya. It revealed selection at 2 key genetic loci driving the horseback anatomy and their social behavior facilitated the transformation of wild animals into domesticated animals. The 2nd WP focused on the impact of emerging equestrian technologies in the Bronze and Iron Ages, a time when horsepower became instrumental for migration and warfare. It revealed that spoke-wheeled chariots played a major role in the spread of domestic horses and the Indo-Iranian language family throughout Asia. The 3rd WP focused on retracing the changes in breeding management from Antiquity to modern times, especially the modern legacy of close stud breeding.
We have published a total of 60 scientific publications, including articles (2 of which in Science, 1 in Nature, and 1 in Cell, with 3 featuring on the cover page of these journals), reviews, and book(s) (chapters). We have focused on: (1) acquiring archaeological material; (2) assessing their DNA preservation levels, taxonomic status (including hybrids) and sex; (3) developing an extensive collection of radiocarbon dates and 3D-models of the archaeological remains, prior to destructive sampling; (4) sequencing and analyzing the genomes of an extensive collection of ancient horses; (5) interacting with researchers in (field) archaeology, history, and linguistics, to contextualize spatial, cultural and temporal patterns of genetic changes in horse populations, and; (6) disseminating our research findings through XXX invited seminars and XXX conferences, and communicating research results to the widest possible audience through XXX press and radio interviews, and participation to 2 TV shows and 3 scientific documentaries. Collectively, our working team has obtained exceptional data, which led to the following major achievements, each addressing our 3 work packages. First, we have revolutionized our understanding of the horse domestication process, revealing 2 independent domestication centres, the 2nd and most recent of which giving rise to the diversity of domestic breeds known to the present time. Second, we have characterized major changes in equine breeding management during the last 4 ky, revealing: (1) protohistoric selection for increasing size in Asia, (2) fluctuating preferences for various coat colorations, (3) the increasing influence of Oriental bloodlines during the last millennium, paired with the intensified selection for specific male lineages; (4) the origins of Indigenous horses in the Americas, and; (5) arising inbreeding practice in the last 200 years. We have also identified the rise of important epidemics soon after the onset of domestication. Finally, we have developed community tools and resources for equine genomics and ancient DNA research, including: (1) new reference genomes, with improved annotations; (2) the 1st Y chromosome assembly; (3) a new high-density genotyping array; (4) a genome-wide panel for in-solution target-enrichment; (5) statistical packages facilitating the analysis of (ancient) sequence data for data management, inbreeding inference, population structure, epigenetic analysis and more ; (7) developed new techniques based on DNA methylation patterns and aimed at predicting the age-at-death and castration status of ancient horses.
Our work has resulted in the production of the most extensive ancient genome collection for a non-human organism. It totals up to 500+ published horse genomes and includes ~500 pending publications, as well as a complement of 1,200 additional ones characterized through a novel target-enrichment method characterizing ~200k SNP markers for ancestry and phenotype inference. Together with ~400 radiocarbon dates, this provides an invaluable legacy for the research community focused on horse genomics, domestication, and evolutionary biology. Our work has revealed an especially complex domestication process, involving 2 domestication stages from different sources, first during the 4th millennium BCE and likely involving a diversity of management techniques. Controlled reproduction only became systematic ~4.2 kya, a time when the 2nd domestication process was fully achieved in the western Eurasian steppes of the lower Don-Volga. These domestic horses, nicknamed DOM2, rapidly spread outside their original homeland, with the rise of spoke-wheeled chariotry, to replace the multitude of genetic lineages of wild horses that existed across the Old World. Two major genetic loci have been critical in the success of DOM2 horses and were selected during the 2nd half of the 3rd millennium for driving a more docile social behavior and stronger horseback anatomy. Our work has also revealed important changes in the DOM2 genomic makeup during the 4+ky following their initial domestication. These resulted from: (1) the selection for specific characteristics such as size from the second half of the Iron Age, as well as changing phenotypes through space, time and cultures; (2) the increasing breeding influence of Oriental lineages from the middle ages; (3) the management of horses together with other equine resources, and the spatial separation of stallions and mares between urban and rural environments, respectively; (4) dramatic recent changes in breeding management, leading to increased inbreeding and deleterious loads. Our work also clarified how the colonization of the Americas transformed the horse genetic makeup. Finally, while mainly focused on horses, genetic screening has revealed a significant number of donkey remains that were in fact confused for horses. Genome sequencing illuminated the domestication process of the donkey, revealing origins in eastern Africa ~3 ky before DOM2 domestication, and the further spread to western Africa and Eurasia following 5 kya.