Ancient Plasmodium genomes shed light on the history of human malaria.

Malaria-causing protozoa of the genus Plasmodium have exerted one of the strongest selective pressures on the human genome, and resistance alleles provide biomolecular footprints that outline the historical reach of these species1. Nevertheless, debate persists over when and how malaria parasites emerged as human pathogens and spread around the globe1,2. To address these questions, we generated high-coverage ancient mitochondrial and nuclear genome-wide data from P. falciparum, P. vivax and P. malariae from 16 countries spanning around 5,500 years of human history. We identified P. vivax and P. falciparum across geographically disparate regions of Eurasia from as early as the fourth and first millennia BCE, respectively; for P. vivax, this evidence pre-dates textual references by several millennia3. Genomic analysis supports distinct disease histories for P. falciparum and P. vivax in the Americas: similarities between now-eliminated European and peri-contact South American strains indicate that European colonizers were the source of American P. vivax, whereas the trans-Atlantic slave trade probably introduced P. falciparum into the Americas. Our data underscore the role of cross-cultural contacts in the dissemination of malaria, laying the biomolecular foundation for future palaeo-epidemiological research into the impact of Plasmodium parasites on human history. Finally, our unexpected discovery of P. falciparum in the high-altitude Himalayas provides a rare case study in which individual mobility can be inferred from infection status, adding to our knowledge of cross-cultural connectivity in the region nearly three millennia ago.

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.

Early integration of pastoralism and millet cultivation in Bronze Age Eurasia.

Mobile pastoralists are thought to have facilitated the first trans-Eurasian dispersals of domesticated plants during the Early Bronze Age (ca 2500-2300 BC). Problematically, the earliest seeds of wheat, barley and millet in Inner Asia were recovered from human mortuary contexts and do not inform on local cultivation or subsistence use, while contemporaneous evidence for the use and management of domesticated livestock in the region remains ambiguous. We analysed mitochondrial DNA and multi-stable isotopic ratios (δ13C, δ15N and δ18O) of faunal remains from key pastoralist sites in the Dzhungar Mountains of southeastern Kazakhstan. At ca 2700 BC, Near Eastern domesticated sheep and goat were present at the settlement of Dali, which were also winter foddered with the region's earliest cultivated millet spreading from its centre of domestication in northern China. In the following centuries, millet cultivation and caprine management became increasingly intertwined at the nearby site of Begash. Cattle, on the other hand, received low levels of millet fodder at the sites for millennia. By primarily examining livestock dietary intake, this study reveals that the initial transmission of millet across the mountains of Inner Asia coincided with a substantial connection between pastoralism and plant cultivation, suggesting that pastoralist livestock herding was integral for the westward dispersal of millet from farming societies in China.

Biomolecular evidence for changing millet reliance in Late Bronze Age central Germany.

The Bronze Age of Central Europe was a period of major social, economic, political and ideological change. The arrival of millet is often seen as part of wider Bronze Age connectivity, yet understanding of the subsistence regimes underpinning this dynamic period remains poor for this region, in large part due to a dominance of cremation funerary rites, which hinder biomolecular studies. Here, we apply stable isotope analysis, radiocarbon dating and archaeobotanical analysis to two Late Bronze Age (LBA) sites, Esperstedt and Kuckenburg, in central Germany, where human remains were inhumed rather than cremated. We find that people buried at these sites did not consume millet before the Middle Bronze Age (MBA) (ca. 1600 BCE). However, by the early LBA (ca. 1300-1050 BCE) people consumed millet, often in substantial quantities. This consumption appears to have subsequently diminished or ceased around 1050-800 BCE, despite charred millet grains still being found in the archaeological deposits from this period. The arrival of millet in this region, followed by a surge in consumption spanning two centuries, indicates a complex interplay of cultural and economic factors, as well as a potential use of millet to buffer changes in aridity in a region increasingly prone to crop failure in the face of climate change today.

Archaeological and molecular evidence for ancient chickens in Central Asia.

The origins and dispersal of the chicken across the ancient world remains one of the most enigmatic questions regarding Eurasian domesticated animals. The lack of agreement concerning timing and centers of origin is due to issues with morphological identifications, a lack of direct dating, and poor preservation of thin, brittle bird bones. Here we show that chickens were widely raised across southern Central Asia from the fourth century BC through medieval periods, likely dispersing along the ancient Silk Road. We present archaeological and molecular evidence for the raising of chickens for egg production, based on material from 12 different archaeological sites spanning a millennium and a half. These eggshells were recovered in high abundance at all of these sites, suggesting that chickens may have been an important part of the overall diet and that chickens may have lost seasonal egg-laying.

Emergence and intensification of dairying in the Caucasus and Eurasian steppes.

Archaeological and archaeogenetic evidence points to the Pontic-Caspian steppe zone between the Caucasus and the Black Sea as the crucible from which the earliest steppe pastoralist societies arose and spread, ultimately influencing populations from Europe to Inner Asia. However, little is known about their economic foundations and the factors that may have contributed to their extensive mobility. Here, we investigate dietary proteins within the dental calculus proteomes of 45 individuals spanning the Neolithic to Greco-Roman periods in the Pontic-Caspian Steppe and neighbouring South Caucasus, Oka-Volga-Don and East Urals regions. We find that sheep dairying accompanies the earliest forms of Eneolithic pastoralism in the North Caucasus. During the fourth millennium BC, Maykop and early Yamnaya populations also focused dairying exclusively on sheep while reserving cattle for traction and other purposes. We observe a breakdown in livestock specialization and an economic diversification of dairy herds coinciding with aridification during the subsequent late Yamnaya and North Caucasus Culture phases, followed by severe climate deterioration during the Catacomb and Lola periods. The need for additional pastures to support these herds may have driven the heightened mobility of the Middle and Late Bronze Age periods. Following a hiatus of more than 500 years, the North Caucasian steppe was repopulated by Early Iron Age societies with a broad mobile dairy economy, including a new focus on horse milking.

Evidence for early dispersal of domestic sheep into Central Asia.

The development and dispersal of agropastoralism transformed the cultural and ecological landscapes of the Old World, but little is known about when or how this process first impacted Central Asia. Here, we present archaeological and biomolecular evidence from Obishir V in southern Kyrgyzstan, establishing the presence of domesticated sheep by ca. 6,000 BCE. Zooarchaeological and collagen peptide mass fingerprinting show exploitation of Ovis and Capra, while cementum analysis of intact teeth implicates possible pastoral slaughter during the fall season. Most significantly, ancient DNA reveals these directly dated specimens as the domestic O. aries, within the genetic diversity of domesticated sheep lineages. Together, these results provide the earliest evidence for the use of livestock in the mountains of the Ferghana Valley, predating previous evidence by 3,000 years and suggesting that domestic animal economies reached the mountains of interior Central Asia far earlier than previously recognized.

Southwest Asian cereal crops facilitated high-elevation agriculture in the central Tien Shan during the mid-third millennium BCE.

We report the earliest and the most abundant archaeobotanical assemblage of southwest Asian grain crops from Early Bronze Age Central Asia, recovered from the Chap II site in Kyrgyzstan. The archaeobotanical remains consist of thousands of cultivated grains dating to the mid-late third millennium BCE. The recovery of cereal chaff and weeds suggest local cultivation at 2000 m.a.s.l., as crops first spread to the mountains of Central Asia. The site's inhabitants possibly cultivated two types of free-threshing wheats, glume wheats, and hulled and naked barleys. Highly compact caryopses of wheat and barley grains represent distinct morphotypes of cereals adapted to highland environments. While additional macrobotanical evidence is needed to confirm the presence of glume wheats at Chap II, the possible identification of glume wheats at Chap II may represent their most eastern distribution in Central Asia. Based on the presence of weed species, we argue that the past environment of Chap II was characterized by an open mountain landscape, where animal grazing likely took place, which may have been further modified by people irrigating agricultural fields. This research suggests that early farmers in the mountains of Central Asia cultivated compact morphotypes of southwest Asian crops during the initial eastward dispersal of agricultural technologies, which likely played a critical role in shaping montane adaptations and dynamic interaction networks between farming societies across highland and lowland cultivation 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.

Arboreal crops on the medieval Silk Road: Archaeobotanical studies at Tashbulak.

During the first millennium A.D., Central Asia was marked by broad networks of exchange and interaction, what many historians collectively refer to as the "Silk Road". Much of this contact relied on high-elevation mountain valleys, often linking towns and caravanserais through alpine territories. This cultural exchange is thought to have reached a peak in the late first millennium A.D., and these exchange networks fostered the spread of domesticated plants and animals across Eurasia. However, few systematic studies have investigated the cultivated plants that spread along the trans-Eurasian exchange during this time. New archaeobotanical data from the archaeological site of Tashbulak (800-1100 A.D.) in the mountains of Uzbekistan is shedding some light on what crops were being grown and consumed in Central Asia during the medieval period. The archaeobotanical assemblage contains grains and legumes, as well as a wide variety of fruits and nuts, which were likely cultivated at lower elevations and transported to the site. In addition, a number of arboreal fruits may have been collected from the wild or represent cultivated version of species that once grew in the wild shrubby forests of the foothills of southern Central Asia in prehistory. This study examines the spread of crops, notably arboreal crops, across Eurasia and ties together several data sets in order to add to discussions of what plant cultivation looked like in the central region of the Silk Road.

Correction: Arboreal crops on the medieval Silk Road: Archaeobotanical studies at Tashbulak.

[This corrects the article DOI: 10.1371/journal.pone.0201409.].

Urban and nomadic isotopic niches reveal dietary connectivities along Central Asia's Silk Roads.

The ancient 'Silk Roads' formed a vast network of trade and exchange that facilitated the movement of commodities and agricultural products across medieval Central Asia via settled urban communities and mobile pastoralists. Considering food consumption patterns as an expression of socio-economic interaction, we analyse human remains for carbon and nitrogen isotopes in order to establish dietary intake, then model isotopic niches to characterize dietary diversity and infer connectivity among communities of urbanites and nomadic pastoralists. The combination of low isotopic variation visible within urban groups with isotopic distinction between urban communities irrespective of local environmental conditions strongly suggests localized food production systems provided primary subsistence rather than agricultural goods exchanged along trade routes. Nomadic communities, in contrast, experienced higher dietary diversity reflecting engagements with a wide assortment of foodstuffs typical for mobile communities. These data indicate tightly bound social connectivity in urban centres pointedly funnelled local food products and homogenized dietary intake within settled communities, whereas open and opportunistic systems of food production and circulation were possible through more mobile lifeways.