Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series.

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 modern legacy of past equestrian civilizations. 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 modern breeding impacted genetic diversity more dramatically than the previous millennia of human management.

Genome-wide population affinities and signatures of adaptation in hydruntines, sussemiones and Asian wild asses.

The extremely rich palaeontological record of the horse family, also known as equids, has provided many examples of macroevolutionary change over the last ~55 Mya. This family is also one of the most documented at the palaeogenomic level, with hundreds of ancient genomes sequenced. While these data have advanced understanding of the domestication history of horses and donkeys, the palaeogenomic record of other equids remains limited. In this study, we have generated genome-wide data for 25 ancient equid specimens spanning over 44 Ky and spread across Anatolia, the Caucasus, Central Asia and Mongolia. Our dataset includes the genomes from two extinct species, the European wild ass, Equus hydruntinus, and the sussemione Equus ovodovi. We document, for the first time, the presence of sussemiones in Mongolia and their survival around ~3.9 Kya, a finding that should be considered when discussing the timing of the first arrival of the domestic horse in the region. We also identify strong spatial differentiation within the historical ecological range of Asian wild asses, Equus hemionus, and incomplete reproductive isolation in several groups yet considered as different species. Finally, we find common selection signatures at ANTXR2 gene in European, Asian and African wild asses. This locus, which encodes a receptor for bacterial toxins, shows no selection signal in E. ovodovi, but a 5.4-kb deletion within intron 7. Whether such genetic modifications played any role in the sussemione extinction remains unknown.

Human auditory ossicles as an alternative optimal source of ancient DNA.

DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of ancient DNA. We show that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be used when available to reduce damage to human remains. Our results identify another optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.

Origins of equine dentistry.

From the American West to the steppes of Eurasia, the domestic horse transformed human societies, providing rapid transport, communication, and military power, and serving as an important subsistence animal. Because of the importance of oral equipment for horse riding, dentistry is an essential component of modern horse care. In the open grasslands of northeast Asia, horses remain the primary form of transport for many herders. Although free-range grazing on gritty forage mitigates many equine dental issues, contemporary Mongolian horsemen nonetheless practice some forms of dentistry, including the removal of problematic deciduous teeth and the vestigial first premolar ("wolf tooth"). Here, we present archaezoological data from equine skeletal remains spanning the past 3,200 y, indicating that nomadic dental practices have great antiquity. Anthropogenic modifications to malerupted deciduous central incisors in young horses from the Late Bronze Age demonstrate their attempted removal, coinciding with the local innovation or adoption of horseback riding and the florescence of Mongolian pastoral society. Horse specimens from this period show no evidence of first premolar removal, which we first identify in specimens dating to ca. 750 BCE. The onset of premolar extraction parallels the archaeological appearance of jointed bronze and iron bits, suggesting that this technological shift prompted innovations in dentistry that improved horse health and horse control. These discoveries provide the earliest directly dated evidence for veterinary dentistry, and suggest that innovations in equine care by nomadic peoples ca. 1150 BCE enabled the use of horses for increasingly sophisticated mounted riding and warfare.

Cauldrons of Bronze Age nomads reveals 2700 year old yak milk and the deep antiquity of food preparation techniques.

Cauldrons, vessels that are simultaneously common and enigmatic, offer insights into past cultural and social traditions. While assumed to possess a special function, what these cauldrons contained is still largely mysterious. These vessels, such as those made from bronze or copper alloys, function as reservoirs for ancient organics through the antibacterial qualities provided by the metal surfaces. Here we show, through protein analysis, that cauldrons from the Final Bronze Age (ca. 2700 BP) were primarily used to collect blood from ruminants, primarily caprines, likely for the production of sausages in a manner similar to contemporary practices in Mongolia's rural countryside. Our findings present a different function from the recent findings of cooked meat in copper-alloy vessels from the northern Caucasus 2000 years earlier, exposing the diversity in food preparation techniques. Our secondary findings of bovine milk within the cauldron, including peptides specific to Bos mutus, pushes back their regional domestication into the Bronze Age.

Genetic population structure of the Xiongnu Empire at imperial and local scales.

The Xiongnu established the first nomadic imperial power, controlling the Eastern Eurasian steppe from ca. 200 BCE to 100 CE. Recent archaeogenetic studies identified extreme levels of genetic diversity across the empire, corroborating historical records of the Xiongnu Empire being multiethnic. However, it has remained unknown how this diversity was structured at the local community level or by sociopolitical status. To address this, we investigated aristocratic and local elite cemeteries at the western frontier of the empire. Analyzing genome-wide data from 18 individuals, we show that genetic diversity within these communities was comparable to the empire as a whole, and that high diversity was also observed within extended families. Genetic heterogeneity was highest among the lowest-status individuals, implying diverse origins, while higher-status individuals harbored less genetic diversity, suggesting that elite status and power was concentrated within specific subsets of the broader Xiongnu population.

Permafrost preservation reveals proteomic evidence for yak milk consumption in the 13th century.

Domesticated yaks endure as iconic symbols of high-altitude frozen landscapes, where herding communities depend on their high-fat milk, transport, dung, and natural fibers. While there is established proteomic evidence for ancient consumption of ruminant and horse milk in the mountains and steppes of northern Eurasia, yak dairy products have yet to be detected. Yak domestication and the species' dispersal from Tibet into the mountainous zones to the north are also poorly resolved due to a paucity of zooarchaeological data. To examine the potential of paleoproteomics to shed light on domesticated yak in Mongolia, we analyzed human dental calculus from Mongol era elite individuals recovered from permafrost burials in Khovsgol province, where people continue to herd yak to this day. We report the first evidence for yak dairy consumption, linked to local resource control. In addition, we confirm a large diversity of recovered whey, curd, tissue, and blood proteins, likely reflecting the excellent preservation conditions found at permafrost sites.

The spread of herds and horses into the Altai: How livestock and dairying drove social complexity in Mongolia.

The initial movement of herders and livestock into the eastern steppe is of great interest, as this region has long been home to pastoralist groups. Due to a paucity of faunal remains, however, it has been difficult to discern the timing of the adoption of domesticated ruminants and horses into the region, though recent research on ancient dairying has started to shed new light on this history. Here we present proteomic evidence for shifts in dairy consumption in the Altai Mountains, drawing on evidence from sites dating from the Early Bronze to the Late Iron Age. We compare these finds with evidence for the rise of social complexity in western Mongolia, as reflected in material remains signaling population growth, the establishment of structured cemeteries, and the erection of large monuments. Our results suggest that the subsistence basis for the development of complex societies began at the dawn of the Bronze Age, with the adoption of ruminant livestock. Investments in pastoralism intensified over time, enabling a food production system that sustained growing populations. While pronounced social changes and monumental constructions occurred in tandem with the first evidence for horse dairying, ~1350 cal BCE, these shifts were fueled by a long-term economic dependence on ruminant livestock. Therefore, the spread into the Mongolian Altai of herds, and then horses, resulted in immediate dietary changes, with subsequent social and demographic transformations occurring later.

Cranial shape diversification in horses: variation and covariation patterns under the impact of artificial selection.

The potential of artificial selection to dramatically impact phenotypic diversity is well known. Large-scale morphological changes in domestic species, emerging over short timescales, offer an accelerated perspective on evolutionary processes. The domestic horse (Equus caballus) provides a striking example of rapid evolution, with major changes in morphology and size likely stemming from artificial selection. However, the microevolutionary mechanisms allowing to generate this variation in a short time interval remain little known. Here, we use 3D geometric morphometrics to quantify skull morphological diversity in the horse, and investigate modularity and integration patterns to understand how morphological associations contribute to cranial evolvability in this taxon. We find that changes in the magnitude of cranial integration contribute to the diversification of the skull morphology in horse breeds. Our results demonstrate that a conserved pattern of modularity does not constrain large-scale morphological variations in horses and that artificial selection has impacted mechanisms underlying phenotypic diversity to facilitate rapid shape changes. More broadly, this study demonstrates that studying microevolutionary processes in domestic species produces important insights into extant phenotypic diversity.

High altitude hunting, climate change, and pastoral resilience in eastern Eurasia.

The transition from hunting to herding transformed the cold, arid steppes of Mongolia and Eastern Eurasia into a key social and economic center of the ancient world, but a fragmentary archaeological record limits our understanding of the subsistence base for early pastoral societies in this key region. Organic material preserved in high mountain ice provides rare snapshots into the use of alpine and high altitude zones, which played a central role in the emergence of East Asian pastoralism. Here, we present the results of the first archaeological survey of melting ice margins in the Altai Mountains of western Mongolia, revealing a near-continuous record of more than 3500 years of human activity. Osteology, radiocarbon dating, and collagen fingerprinting analysis of wooden projectiles, animal bone, and other artifacts indicate that big-game hunting and exploitation of alpine ice played a significant role during the emergence of mobile pastoralism in the Altai, and remained a core element of pastoral adaptation into the modern era. Extensive ice melting and loss of wildlife in the study area over recent decades, driven by a warming climate, poaching, and poorly regulated hunting, presents an urgent threat to the future viability of herding lifeways and the archaeological record of hunting in montane zones.

High mitochondrial diversity of domesticated goats persisted among Bronze and Iron Age pastoralists in the Inner Asian Mountain Corridor.

Goats were initially managed in the Near East approximately 10,000 years ago and spread across Eurasia as economically productive and environmentally resilient herd animals. While the geographic origins of domesticated goats (Capra hircus) in the Near East have been long-established in the zooarchaeological record and, more recently, further revealed in ancient genomes, the precise pathways by which goats spread across Asia during the early Bronze Age (ca. 3000 to 2500 cal BC) and later remain unclear. We analyzed sequences of hypervariable region 1 and cytochrome b gene in the mitochondrial genome (mtDNA) of goats from archaeological sites along two proposed transmission pathways as well as geographically intermediary sites. Unexpectedly high genetic diversity was present in the Inner Asian Mountain Corridor (IAMC), indicated by mtDNA haplotypes representing common A lineages and rarer C and D lineages. High mtDNA diversity was also present in central Kazakhstan, while only mtDNA haplotypes of lineage A were observed from sites in the Northern Eurasian Steppe (NES). These findings suggest that herding communities living in montane ecosystems were drawing from genetically diverse goat populations, likely sourced from communities in the Iranian Plateau, that were sustained by repeated interaction and exchange. Notably, the mitochondrial genetic diversity associated with goats of the IAMC also extended into the semi-arid region of central Kazakhstan, while NES communities had goats reflecting an isolated founder population, possibly sourced via eastern Europe or the Caucasus region.

Author Correction: Early Pastoral Economies and Herding Transitions in Eastern Eurasia.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Early Pastoral Economies and Herding Transitions in Eastern Eurasia.

While classic models for the emergence of pastoral groups in Inner Asia describe mounted, horse-borne herders sweeping across the Eurasian Steppes during the Early or Middle Bronze Age (ca. 3000-1500 BCE), the actual economic basis of many early pastoral societies in the region is poorly characterized. In this paper, we use collagen mass fingerprinting and ancient DNA analysis of some of the first stratified and directly dated archaeofaunal assemblages from Mongolia's early pastoral cultures to undertake species identifications of this rare and highly fragmented material. Our results provide evidence for livestock-based, herding subsistence in Mongolia during the late 3rd and early 2nd millennia BCE. We observe no evidence for dietary exploitation of horses prior to the late Bronze Age, ca. 1200 BCE - at which point horses come to dominate ritual assemblages, play a key role in pastoral diets, and greatly influence pastoral mobility. In combination with the broader archaeofaunal record of Inner Asia, our analysis supports models for widespread changes in herding ecology linked to the innovation of horseback riding in Central Asia in the final 2nd millennium BCE. Such a framework can explain key broad-scale patterns in the movement of people, ideas, and material culture in Eurasian prehistory.

Radiocarbon dating and cultural dynamics across Mongolia's early pastoral transition.

The emergence of mobile herding lifeways in Mongolia and eastern Eurasia was one of the most crucial economic and cultural transitions in human prehistory. Understanding the process by which this played out, however, has been impeded by the absence of a precise chronological framework for the prehistoric era in Mongolia. One rare source of empirically dateable material useful for understanding eastern Eurasia's pastoral tradition comes from the stone burial mounds and monumental constructions that began to appear across the landscape of Mongolia and adjacent regions during the Bronze Age (ca. 3000-700 BCE). Here, along with presenting 28 new radiocarbon dates from Mongolia's earliest pastoral monumental burials, we synthesise, critically analyse, and model existing dates to present the first precision Bayesian radiocarbon model for the emergence and geographic spread of Bronze Age monument and burial forms. Model results demonstrate a cultural succession between ambiguously dated Afanasievo, Chemurchek, and Munkhkhairkhan traditions. Geographic patterning reveals the existence of important cultural frontiers during the second millennium BCE. This work demonstrates the utility of a Bayesian approach for investigating prehistoric cultural dynamics during the emergence of pastoral economies.

Investigating reindeer pastoralism and exploitation of high mountain zones in northern Mongolia through ice patch archaeology.

In interior Eurasia, high mountain zones are crucial to pastoral subsistence, providing seasonally productive pastures and abundant wild resources. In some areas of northern Mongolia, mountainous tundra zones also support a low-latitude population of domestic reindeer herders-a lifestyle whose origins are poorly characterized in the archaeological record of early Mongolia. Traditionally, reindeer pastoralists make significant seasonal use of munkh mus (eternal ice) for their domestic herds, using these features to cool heat-stressed animals and provide respite from insect harassment. In recent years, many of these features have begun to melt entirely for the first time, producing urgent threats to traditional management techniques, the viability of summer pastures, and reindeer health. The melting ice is also exposing fragile organic archaeological materials that had previously been contained in the patch. We present the results of horseback survey of ice patches in Baruun Taiga special protected area, providing the first archaeological insights from the region. Results reveal new evidence of historic tool production and wild resource use for fishing or other activities, and indicate that ice patches are likely to contain one of the few material records of premodern domestic reindeer use in Mongolia and lower Central Asia. The area's ancient ice appears to be rapidly melting due to changing climate and warming summer temperatures, putting both cultural heritage and traditional reindeer herding at extreme risk in the years to come.