The formation of human populations in South and Central Asia

Cost-effective straightforward method for captured whole mitogenome sequencing of ancient DNA

Working with mitochondrial DNA from highly degraded samples is challenging. We present a whole mitogenome Illumina-based sequencing method suitable for highly degraded samples. The method makes use of double-stranded library preparation with hybridization-based target enrichment. The aim of the study was to implement a new user-friendly method for analysing many ancient DNA samples at low cost. The method combines the Swift 2S™ Turbo library preparation kit and xGen® panel for mitogenome enrichment. Swift allows to use low input of aDNA and own adapters and primers, handles inhibitors well, and has only two purification steps. xGen is straightforward to use and is able to leverage already pooled libraries. Given the ancient DNA is more challenging to work with, the protocol was developed with several improvements, especially multiplying DNA input in case of low concentration DNA extractions followed by AMPure® beads size selection and real-time pre-capture PCR monitoring in order to avoid cycle-optimization step. Nine out of eleven analysed samples successfully retrieved mitogenomes. Hence, our method provides an effective analysis of whole mtDNA, and has proven to be fast, cost-effective, straightforward, with utilisation in population-wide research of burial sites.

Interspecific introgression and natural selection in the evolution of Japanese apricot (Prunus mume)

Domestication and population differentiation in crops involve considerable phenotypic changes. The logs of these evolutionary paths, including natural/artificial selection, can be found in the genomes of the current populations. However, these profiles have been little studied in tree crops, which have specific characters, such as long generation time and clonal propagation, maintaining high levels of heterozygosity. We conducted exon-targeted resequencing of 129 genomes in the genus Prunus, mainly Japanese apricot (Prunus mume), and apricot (Prunus armeniaca), plum (Prunus salicina), and peach (Prunus persica). Based on their genome-wide single-nucleotide polymorphisms merged with published resequencing data of 79 Chinese P. mume cultivars, we inferred complete and ongoing population differentiation in P. mume. Sliding window characterization of the indexes for genetic differentiation identified interspecific fragment introgressions between P. mume and related species (plum and apricot). These regions often exhibited strong selective sweeps formed in the paths of establishment or formation of substructures of P. mume, suggesting that P. mume has frequently imported advantageous genes from other species in the subgenus Prunus as adaptive evolution. These findings shed light on the complicated nature of adaptive evolution in a tree crop that has undergone interspecific exchange of genome fragments with natural/artificial selections.

The Evolutionary and Historical Foundation of the Modern Horse: Lessons from Ancient Genomics

The domestication of the horse some 5,500 years ago followed those of dogs, sheep, goats, cattle, and pigs by ∼2,500-10,000 years. By providing fast transportation and transforming warfare, the horse had an impact on human history with no equivalent in the animal kingdom. Even though the equine sport industry has considerable economic value today, the evolutionary history underlying the emergence of the modern domestic horse remains contentious. In the last decade, novel sequencing technologies have revolutionized our capacity to sequence the complete genome of organisms, including from archaeological remains. Applied to horses, these technologies have provided unprecedented levels of information and have considerably changed models of horse domestication. This review illustrates how ancient DNA, especially ancient genomes, has inspired researchers to rethink the process by which horses were first domesticated and then diversified into a variety of breeds showing a range of traits that are useful to humans.

A Dynamic 6,000-Year Genetic History of Eurasia's Eastern Steppe

The Eastern Eurasian Steppe was home to historic empires of nomadic pastoralists, including the Xiongnu and the Mongols. However, little is known about the region’s population history. Here, we reveal its dynamic genetic history by analyzing new genome-wide data for 214 ancient individuals spanning 6,000 years. We identify a pastoralist expansion into Mongolia ca. 3000 BCE, and by the Late Bronze Age, Mongolian populations were biogeographically structured into three distinct groups, all practicing dairy pastoralism regardless of ancestry. The Xiongnu emerged from the mixing of these populations and those from surrounding regions. By comparison, the Mongols exhibit much higher eastern Eurasian ancestry, resembling present-day Mongolic-speaking populations. Our results illuminate the complex interplay between genetic, sociopolitical, and cultural changes on the Eastern Steppe.

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Genome-wide analysis of 214 ancient individuals from Mongolia and the Baikal region

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Three genetically distinct dairy pastoralist groups in Late Bronze Age Mongolia

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Xiongnu nomadic empire formed through mixing of distinct local and distant groups

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No selection on the lactase persistence alleles despite 5,000 years of dairy culture

Recent Common Origin, Reduced Population Size, and Marked Admixture Have Shaped European Roma Genomes

The Roma Diaspora-traditionally known as Gypsies-remains among the least explored population migratory events in historical times. It involved the migration of Roma ancestors out-of-India through the plateaus of Western Asia ultimately reaching Europe. The demographic effects of the Diaspora-bottlenecks, endogamy, and gene flow-might have left marked molecular traces in the Roma genomes. Here, we analyze the whole-genome sequence of 46 Roma individuals pertaining to four migrant groups in six European countries. Our analyses revealed a strong, early founder effect followed by a drastic reduction of ∼44% in effective population size. The Roma common ancestors split from the Punjabi population, from Northwest India, some generations before the Diaspora started, <2,000 years ago. The initial bottleneck and subsequent endogamy are revealed by the occurrence of extensive runs of homozygosity and identity-by-descent segments in all Roma populations. Furthermore, we provide evidence of gene flow from Armenian and Anatolian groups in present-day Roma, although the primary contribution to Roma gene pool comes from non-Roma Europeans, which accounts for >50% of their genomes. The linguistic and historical differentiation of Roma in migrant groups is confirmed by the differential proportion, but not a differential source, of European admixture in the Roma groups, which shows a westward cline. In the present study, we found that despite the strong admixture Roma had in their diaspora, the signature of the initial bottleneck and the subsequent endogamy is still present in Roma genomes.

The Impact of Ancient Genome Studies in Archaeology

The study of ancient genomes has burgeoned at an incredible rate in the last decade. The result is a shift in archaeological narratives, bringing with it a fierce debate on the place of genetics in anthropological research. Archaeogenomics has challenged and scrutinized fundamental themes of anthropological research, including human origins, movement of ancient and modern populations, the role of social organization in shaping material culture, and the relationship between culture, language, and ancestry. Moreover, the discussion has inevitably invoked new debates on indigenous rights, ownership of ancient materials, inclusion in the scientific process, and even the meaning of what it is to be a human. We argue that the broad and seemingly daunting ethical, methodological, and theoretical challenges posed by archaeogenomics, in fact, represent the very cutting edge of social science research. Here, we provide a general review of the field by introducing the contemporary discussion points and summarizing methodological and ethical concerns, while highlighting the exciting possibilities of ancient genome studies in archaeology from an anthropological perspective.

Genetics of Obesity in East Asians

Obesity has become a public health problem worldwide. Compared with Europe, people in Asia tend to suffer from type 2 diabetes with a lower body mass index (BMI). Genome-wide association studies (GWASs) have identified over 750 loci associated with obesity. Although the majority of GWAS results were conducted in individuals of European ancestry, a recent GWAS in individuals of Asian ancestry has made a significant contribution to the identification of obesity susceptibility loci. Indeed, owing to the multifactorial character of obesity with a strong environmental component, the revealed loci may have distinct contributions in different ancestral genetic backgrounds and in different environments as presented through diet and exercise among other factors. Uncovering novel, yet unrevealed genes in non-European ancestries may further contribute to explaining the missing heritability for BMI. In this review, we aimed to summarize recent advances in obesity genetics in individuals of Asian ancestry. We therefore compared proposed mechanisms underlying susceptibility loci for obesity associated with individuals of European and Asian ancestries and discussed whether known genetic variants might explain ethnic differences in obesity risk. We further acknowledged that GWAS implemented in individuals of Asian ancestries have not only validated the potential role of previously specified obesity susceptibility loci but also exposed novel ones, which have been missed in the initial genetic studies in individuals of European ancestries. Thus, multi-ethnic studies have a great potential not only to contribute to a better understanding of the complex etiology of human obesity but also potentially of ethnic differences in the prevalence of obesity, which may ultimately pave new avenues in more targeted and personalized obesity treatments.

Y-DNA genetic evidence reveals several different ancient origins in the Brahmin population

The ancient geographical origins of Brahmins-a prominent ethnic group in the Indian subcontinent-have remained controversial for a long time. This study employed the AMOVA (analysis of molecular variance) test to evaluate genetic affinities of this group with thirty populations of Central Asia and Europe. A domestic comparison was performed with fifty non-Brahmin groups in India. The results showed that Brahmins had genetic affinities with several foreign populations and also shared their genetic heritage with several domestic non-Brahmin groups. The study identified the deep ancient origins of Brahmins by tracing their Y-chromosome haplogroups and genetic markers on the Y-DNA phylogenetic tree. It was confirmed that the progenitors of this group emerged from at least 12 different geographic regions of the world. The study concluded that about 83% of the Brahmins in the dataset belonged to four major haplogroups, of which two emerged from Central Asia, one from the Fertile Crescent, and one was of an indigenous Indian origin.

Skin colour and vitamin D: An update

Homo sapiens evolved in East Africa and had dark skin, hair, and eyes, in order to protect against deleterious consequences of intensive UV radiation at equatorial latitudes. Intensive skin pigmentation was thought to bear the risk of inefficient vitamin D3 synthesis in the skin. This initiated the hypothesis that within the past 75 000 years, in which humans migrated to higher latitudes in Asia and Europe, the need for vitamin D3 synthesis served as an evolutionary driver for skin lightening. In this review, we summarize the recent archeogenomic reconstruction of population admixture in Europe and demonstrate that skin lightening happened as late as 5000 years ago through immigration of lighter pigmented populations from western Anatolia and the Russian steppe but not primarily via evolutionary pressure for vitamin D3 synthesis. We show that variations in genes encoding for proteins being responsible for the transport, metabolism and signalling of vitamin D provide alternative mechanisms of adaptation to a life in northern latitudes without suffering from consequences of vitamin D deficiency. This includes hypotheses explaining differences in the vitamin D status and response index of European populations.

Ancient genomes in South Patagonia reveal population movements associated with technological shifts and geography

Archaeological research documents major technological shifts among people who have lived in the southern tip of South America (South Patagonia) during the last thirteen millennia, including the development of marine-based economies and changes in tools and raw materials. It has been proposed that movements of people spreading culture and technology propelled some of these shifts, but these hypotheses have not been tested with ancient DNA. Here we report genome-wide data from 20 ancient individuals, and co-analyze it with previously reported data. We reveal that immigration does not explain the appearance of marine adaptations in South Patagonia. We describe partial genetic continuity since ~6600 BP and two later gene flows correlated with technological changes: one between 4700-2000 BP that affected primarily marine-based groups, and a later one impacting all <2000 BP groups. From ~2200-1200 BP, mixture among neighbors resulted in a cline correlated to geographic ordering along the coast.

Human evolutionary history in Eastern Eurasia using insights from ancient DNA

Advances in ancient genomics are providing unprecedented insight into modern human history. Here, we review recent progress uncovering prehistoric populations in Eastern Eurasia based on ancient DNA studies from the Upper Pleistocene to the Holocene. Many ancient populations existed during the Upper Pleistocene of Eastern Eurasia-some with no substantial ancestry related to present-day populations, some with an affinity to East Asians, and some who contributed to Native Americans. By the Holocene, the genetic composition across East Asia greatly shifted, with several substantial migrations. Three are southward: an increase in northern East Asian-related ancestry in southern East Asia; movement of East Asian-related ancestry into Southeast Asia, mixing with Basal Asian ancestry; and movement of southern East Asian ancestry to islands of Southeast Asia and the Southwest Pacific through the expansion of Austronesians. We anticipate that additional ancient DNA will magnify our understanding of the genetic history in Eastern Eurasia.

A Genetic History of the Near East from an aDNA Time Course Sampling Eight Points in the Past 4,000 Years

The Iron and Classical Ages in the Near East were marked by population expansions carrying cultural transformations that shaped human history, but the genetic impact of these events on the people who lived through them is little-known. Here, we sequenced the whole genomes of 19 individuals who each lived during one of four time periods between 800 BCE and 200 CE in Beirut on the Eastern Mediterranean coast at the center of the ancient world's great civilizations. We combined these data with published data to traverse eight archaeological periods and observed any genetic changes as they arose. During the Iron Age (∼1000 BCE), people with Anatolian and South-East European ancestry admixed with people in the Near East. The region was then conquered by the Persians (539 BCE), who facilitated movement exemplified in Beirut by an ancient family with Egyptian-Lebanese admixed members. But the genetic impact at a population level does not appear until the time of Alexander the Great (beginning 330 BCE), when a fusion of Asian and Near Easterner ancestry can be seen, paralleling the cultural fusion that appears in the archaeological records from this period. The Romans then conquered the region (31 BCE) but had little genetic impact over their 600 years of rule. Finally, during the Ottoman rule (beginning 1516 CE), Caucasus-related ancestry penetrated the Near East. Thus, in the past 4,000 years, three limited admixture events detectably impacted the population, complementing the historical records of this culturally complex region dominated by the elite with genetic insights from the general population.

Inferring evolutionary dynamics of mutation rates through the lens of mutation spectrum variation

There are many possible failure points in the transmission of genetic information that can produce heritable germline mutations. Once a mutation has been passed from parents to offspring for several generations, it can be difficult or impossible to identify its root cause; however, sometimes the nature of the ancestral and derived DNA sequences can provide mechanistic clues about a genetic change that happened hundreds or thousands of generations ago. Here, we review evidence that the sequence context 'spectrum' of germline mutagenesis has been evolving surprisingly rapidly over the history of humans and other species. We go on to discuss possible causal factors that might underlie rapid mutation spectrum evolution.

Mitochondrial DNA diversity in the Khattak and Kheshgi of the Peshawar Valley, Pakistan

The strategic location of Pakistan and its presence at the crossroads of Asia has resulted in it playing a central role in both prehistoric and historic human migratory events, thereby linking and facilitating contacts between the inhabitants of the Middle East, Central Asia, China and South Asia. Despite the importance of this region and its inhabitants for our understanding of modern human origins and population dispersals, the nature of mitochondrial DNA (mtDNA) variation among members of the myriad populations of this area has largely been unexplored. Here, we report mtDNA control region sequences in 58 individuals from the Khattak and the Kheshgi, two major Pakhtun tribes residing within the Peshawar Valley of northwestern Pakistan. The results reveal that these ethnic groups are genetically heterogeneous, having 55.7% West Eurasian, 33.9% South Asian and 10.2% East Asian haplogroups. The genetic diversity observed for the Kheshgi was somewhat higher than that of the Khattak. A multidimensional scaling plot based on haplogroup frequencies for the Khattak, Kheshgi and neighboring populations indicates that the Khattak have close affinities with Baluch, Uzbek and Kazak populations but are only distantly related to the Kheshgi and other Pakistani populations. By contrast, the Kheshgi cluster closely with other Pakhtun or Pathan populations of Pakistan, suggesting a possible common maternal gene pool shared amongst them. These mtDNA data allow us to begin reconstructing the origins of the Khattak and Kheshgi and describe their complex interactions with populations from the surrounding regions.

Latest trends in archaeogenetic research of west Eurasians

During the past ten years, archaeogenetic research has exponentially grown to study the genetic history of human populations, using genome-wide data from large numbers of ancient individuals. Of the entire globe, Europe and the Near East are the regions where ancient DNA data is by far most abundant with over 2500 genomes published at present. In this review, we focus on archaeological contexts that have received less attention in the literature, specifically those associated with west Eurasian hunter-gatherers as well as populations from the Iron Age and later historical periods. In addition, we emphasize a recent shift from continent-wide to regional and even site-specific studies, which is starting to provide novel insights into sociocultural aspects of past societies.

Novel insights on demographic history of tribal and caste groups from West Maharashtra (India) using genome-wide data

The South Asian subcontinent is characterized by a complex history of human migrations and population interactions. In this study, we used genome-wide data to provide novel insights on the demographic history and population relationships of six Indo-European populations from the Indian State of West Maharashtra. The samples correspond to two castes (Deshastha Brahmins and Kunbi Marathas) and four tribal groups (Kokana, Warli, Bhil and Pawara). We show that tribal groups have had much smaller effective population sizes than castes, and that genetic drift has had a higher impact in tribal populations. We also show clear affinities between the Bhil and Pawara tribes, and to a lesser extent, between the Warli and Kokana tribes. Our comparisons with available modern and ancient DNA datasets from South Asia indicate that the Brahmin caste has higher Ancient Iranian and Steppe pastoralist contributions than the Kunbi Marathas caste. Additionally, in contrast to the two castes, tribal groups have very high Ancient Ancestral South Indian (AASI) contributions. Indo-European tribal groups tend to have higher Steppe contributions than Dravidian tribal groups, providing further support for the hypothesis that Steppe pastoralists were the source of Indo-European languages in South Asia, as well as Europe.

About millets and beans, words and genes

In this special collection, we address the origin and dispersal of the Transeurasian languages, i.e. Japonic, Koreanic, Tungusic, Mongolic and Turkic, from an interdisciplinary perspective. Our key objective is to effectively synthesize linguistic, archaeological and genetic evidence in a single approach, for which we use the term 'triangulation'. The 10 articles collected in this volume contribute to the question of whether and to what extent the early spread of Transeurasian languages was driven by agriculture in general, and by economic reliance on millet cultivation in particular.

Influence of Paleolithic range contraction, admixture and long-distance dispersal on genetic gradients of modern humans in Asia

Cavalli-Sforza and coauthors originally explored the genetic variation of modern humans throughout the world and observed an overall east-west genetic gradient in Asia. However, the specific environmental and population genetics processes causing this gradient were not formally investigated and promoted discussion in recent studies. Here we studied the influence of diverse environmental and population genetics processes on Asian genetic gradients and identified which could have produced the observed gradient. To do so, we performed extensive spatially-explicit computer simulations of genetic data under the following scenarios: (a) variable levels of admixture between Paleolithic and Neolithic populations, (b) migration through long-distance dispersal (LDD), (c) Paleolithic range contraction induced by the last glacial maximum (LGM), and (d) Neolithic range expansions from one or two geographic origins (the Fertile Crescent and the Yangzi and Yellow River Basins). Next, we estimated genetic gradients from the simulated data and we found that they were sensible to the analysed processes, especially to the range contraction induced by LGM and to the number of Neolithic expansions. Some scenarios were compatible with the observed east-west genetic gradient, such as the Paleolithic expansion with a range contraction induced by the LGM or two Neolithic range expansions from both the east and the west. In general, LDD increased the variance of genetic gradients among simulations. We interpreted the obtained gradients as a consequence of both allele surfing caused by range expansions and isolation by distance along the vast east-west geographic axis of this continent.

Why and when was lactase persistence selected for? Insights from Central Asian herders and ancient DNA

The genetic adaptation of humans to the consumption of milk from dairying animals is one of the most emblematic cases of recent human evolution. While the phenotypic change under selection, lactase persistence (LP), is known, the evolutionary advantage conferred to persistent individuals remains obscure. One informative but underappreciated observation is that not all populations whose ancestors had access to milk genetically adapted to become lactase persistent. Indeed, Central Asian herders are mostly lactase nonpersistent, despite their significant dietary reliance on dairy products. Investigating the temporal dynamic of the -13.910:C>T Eurasian mutation associated with LP, we found that, after its emergence in Ukraine 5,960 before present (BP), the T allele spread between 4,000 BP and 3,500 BP throughout Eurasia, from Spain to Kazakhstan. The timing and geographical progression of the mutation coincides well with the migration of steppe populations across and outside of Europe. After 3,000 BP, the mutation strongly increased in frequency in Europe, but not in Asia. We propose that Central Asian herders have adapted to milk consumption culturally, by fermentation, and/or by colonic adaptation, rather than genetically. Given the possibility of a nongenetic adaptation to avoid intestinal symptoms when consuming dairy products, the puzzle then becomes this: why has LP been selected for at all?

Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa

Africa hosts the greatest human genetic diversity globally, but legacies of ancient population interactions and dispersals across the continent remain understudied. Here, we report genome-wide data from 20 ancient sub-Saharan African individuals, including the first reported ancient DNA from the DRC, Uganda, and Botswana. These data demonstrate the contraction of diverse, once contiguous hunter-gatherer populations, and suggest the resistance to interaction with incoming pastoralists of delayed-return foragers in aquatic environments. We refine models for the spread of food producers into eastern and southern Africa, demonstrating more complex trajectories of admixture than previously suggested. In Botswana, we show that Bantu ancestry post-dates admixture between pastoralists and foragers, suggesting an earlier spread of pastoralism than farming to southern Africa. Our findings demonstrate how processes of migration and admixture have markedly reshaped the genetic map of sub-Saharan Africa in the past few millennia and highlight the utility of combined archaeological and archaeogenetic approaches.

A Paleogenomic Reconstruction of the Deep Population History of the Andes

There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today's genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000-500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. VIDEO ABSTRACT.

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.

Populations dynamics in Northern Eurasian forests: a long-term perspective from Northeast Asia

The 'Northern Eurasian Greenbelt' (NEG) is the northern forest zone stretching from the Japanese Archipelago to Northern Europe. The NEG has created highly productive biomes for humanity to exploit since the end of the Pleistocene. This research explores how the ecological conditions in northern Eurasia contributed to and affected human migrations and cultural trajectories by synthesizing the complimentary viewpoints of environmental archaeology, Geographic Information Science (GIS), genetics and linguistics. First, the environmental archaeology perspective raises the possibility that the NEG functioned as a vessel fostering people to develop diverse cultures and engage in extensive cross-cultural exchanges. Second, geographical analysis of genomic data on mitochondrial DNA using GIS reveals the high probability that population dynamics in the southeastern NEG promoted the peopling of the Americas at the end of the Pleistocene. Finally, a linguistic examination of environmental- and landscape-related vocabulary of the proto-Turkic language groups enables the outline of their original cultural landscape and natural conditions, demonstrating significant cultural spheres, i.e. from southern Siberia to eastern Inner Mongolia during Neolithization. All of these results combine to suggest that the ecological complex in the southern edge of the NEG in northeast Asia played a significant role in peopling across the continents during prehistory.

Early nomads of the Eastern Steppe and their tentative connections in the West

The origin of the Xiongnu and the Rourans, the nomadic groups that dominated the eastern Eurasian steppe in the late first millennium BC/early first millennium AD, is one of the most controversial topics in the early history of Inner Asia. As debatable is the evidence linking these two groups with the steppe nomads of early medieval Europe, i.e. the Huns and the Avars, respectively. In this paper, we address the problems of Xiongnu-Hun and Rouran-Avar connections from an interdisciplinary perspective, complementing current archaeological and historical research with a critical analysis of the available evidence from historical linguistics and population genetics. Both lines of research suggest a mixed origin of the Xiongnu population, consisting of eastern and western Eurasian substrata, and emphasize the lack of unambiguous evidence for a continuity between the Xiongnu and the European Huns. In parallel, both disciplines suggest that at least some of the European Avars were of Eastern Asian ancestry, but neither linguistic nor genetic evidence provides a sufficient support for a specific connection between the Avars and the Asian Rourans.

Ancient genome-wide DNA from France highlights the complexity of interactions between Mesolithic hunter-gatherers and Neolithic farmers

Starting from 12,000 years ago in the Middle East, the Neolithic lifestyle spread across Europe via separate continental and Mediterranean routes. Genomes from early European farmers have shown a clear Near Eastern/Anatolian genetic affinity with limited contribution from hunter-gatherers. However, no genomic data are available from modern-day France, where both routes converged, as evidenced by a mosaic cultural pattern. Here, we present genome-wide data from 101 individuals from 12 sites covering today's France and Germany from the Mesolithic (N = 3) to the Neolithic (N = 98) (7000-3000 BCE). Using the genetic substructure observed in European hunter-gatherers, we characterize diverse patterns of admixture in different regions, consistent with both routes of expansion. Early western European farmers show a higher proportion of distinctly western hunter-gatherer ancestry compared to central/southeastern farmers. Our data highlight the complexity of the biological interactions during the Neolithic expansion by revealing major regional variations.

Ancient genomes reveal social and genetic structure of Late Neolithic Switzerland

Genetic studies of Neolithic and Bronze Age skeletons from Europe have provided evidence for strong population genetic changes at the beginning and the end of the Neolithic period. To further understand the implications of these in Southern Central Europe, we analyze 96 ancient genomes from Switzerland, Southern Germany, and the Alsace region in France, covering the Middle/Late Neolithic to Early Bronze Age. Similar to previously described genetic changes in other parts of Europe from the early 3rd millennium BCE, we detect an arrival of ancestry related to Late Neolithic pastoralists from the Pontic-Caspian steppe in Switzerland as early as 2860–2460 calBCE. Our analyses suggest that this genetic turnover was a complex process lasting almost 1000 years and involved highly genetically structured populations in this region.

European populations underwent strong genetic changes during the Neolithic. Here, Furtwängler et al. provide ancient nuclear and mitochondrial genomic data from the region of Switzerland during the end of the Neolithic and the Early Bronze Age that reveal a complex genetic turnover during the arrival of steppe ancestry.

Molecular Mechanism of Functional Ingredients in Barley to Combat Human Chronic Diseases

Barley plays an important role in health and civilization of human migration from Africa to Asia, later to Eurasia. We demonstrated the systematic mechanism of functional ingredients in barley to combat chronic diseases, based on PubMed, CNKI, and ISI Web of Science databases from 2004 to 2020. Barley and its extracts are rich in 30 ingredients to combat more than 20 chronic diseases, which include the 14 similar and 9 different chronic diseases between grains and grass, due to the major molecular mechanism of six functional ingredients of barley grass (GABA, flavonoids, SOD, K-Ca, vitamins, and tryptophan) and grains (β-glucans, polyphenols, arabinoxylan, phytosterols, tocols, and resistant starch). The antioxidant activity of barley grass and grain has the same and different functional components. These results support findings that barley grain and its grass are the best functional food, promoting ancient Babylonian and Egyptian civilizations, and further show the depending functional ingredients for diet from Pliocene hominids in Africa and Neanderthals in Europe to modern humans in the world. This review paper not only reveals the formation and action mechanism of barley diet overcoming human chronic diseases, but also provides scientific basis for the development of health products and drugs for the prevention and treatment of human chronic diseases.

AN ANCIENT DNA PACIFIC JOURNEY: A CASE STUDY OF COLLABORATION BETWEEN ARCHAEOLOGISTS AND GENETICISTS

We present a case-study of a collaboration between archaeologists and geneticists that has helped settle a long-standing controversy and opened up new research questions for the Pacific region. The work provided insights into the history of human settlement and cultural changes in Vanuatu in the western Pacific, which in turn shed light on the origins of the cultural and linguistic diversity that characterizes the archipelago. Close interdisciplinary collaborations like this maximize the potential of ancient DNA to contribute to our understanding of the past and advance the scholarship of practitioners in both disciplines.

The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean

Steppe-pastoralist-related ancestry reached Central Europe by at least 2500 BC, whereas Iranian farmer-related ancestry was present in Aegean Europe by at least 1900 BC. However, the spread of these ancestries into the western Mediterranean, where they have contributed to many populations that live today, remains poorly understood. Here, we generated genome-wide ancient-DNA data from the Balearic Islands, Sicily and Sardinia, increasing the number of individuals with reported data from 5 to 66. The oldest individual from the Balearic Islands (~2400 BC) carried ancestry from steppe pastoralists that probably derived from west-to-east migration from Iberia, although two later Balearic individuals had less ancestry from steppe pastoralists. In Sicily, steppe pastoralist ancestry arrived by ~2200 BC, in part from Iberia; Iranian-related ancestry arrived by the mid-second millennium BC, contemporary to its previously documented spread to the Aegean; and there was large-scale population replacement after the Bronze Age. In Sardinia, nearly all ancestry derived from the island's early farmers until the first millennium BC, with the exception of an outlier from the third millennium BC, who had primarily North African ancestry and who-along with an approximately contemporary Iberian-documents widespread Africa-to-Europe gene flow in the Chalcolithic. Major immigration into Sardinia began in the first millennium BC and, at present, no more than 56-62% of Sardinian ancestry is from its first farmers. This value is lower than previous estimates, highlighting that Sardinia, similar to every other region in Europe, has been a stage for major movement and mixtures of people.

An Ancient Genome from the Indus Valley Civilization

Shinde et al. report the first genome-wide data from an ancient individual from the Indus Valley Civilization in South Asia. Their findings have implications for the origins and spread of farming and Indo-European languages in the region and the makings of the South Asian gene pool.

An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers

We report an ancient genome from the Indus Valley Civilization (IVC). The individual we sequenced fits as a mixture of people related to ancient Iranians (the largest component) and Southeast Asian hunter-gatherers, a unique profile that matches ancient DNA from 11 genetic outliers from sites in Iran and Turkmenistan in cultural communication with the IVC. These individuals had little if any Steppe pastoralist-derived ancestry, showing that it was not ubiquitous in northwest South Asia during the IVC as it is today. The Iranian-related ancestry in the IVC derives from a lineage leading to early Iranian farmers, herders, and hunter-gatherers before their ancestors separated, contradicting the hypothesis that the shared ancestry between early Iranians and South Asians reflects a large-scale spread of western Iranian farmers east. Instead, sampled ancient genomes from the Iranian plateau and IVC descend from different groups of hunter-gatherers who began farming without being connected by substantial movement of people.

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.

New middle chapter in the story of human evolution

Analyzing genomic data from ancient humans illuminates South Asian ancestry