The earliest evidence for cultivation and stock-keeping is found in the Neolithic core zone of the Fertile Crescent (1, 2); a region stretching north from the southern Levant through E-Anatolia and N-Mesopotamia then east into the Zagros Mountains on the border of modern-day Iran and Iraq (Fig. 1). From there farming spread into surrounding regions, including Anatolia and later Europe, southern Asia, and parts of Arabia and N-Africa. Whether the transition to agriculture was a homogeneous process across the core zone, or a mosaic of localized domestications is unknown. Likewise, the extent to which core zone farming populations were genetically homogeneous, or exhibited structure that may have been preserved as agriculture spread into surrounding regions, is undetermined.
Ancient DNA (aDNA) studies indicate that early Aegean farmers dating to c. 6,500-6,000 BCE are the main ancestors of early European farmers (3, 4), although it is not known if they were predominantly descended from core zone farming populations. We sequenced four Early Neolithic (EN) genomes from Zagros, Iran, including one to 10x mean coverage from a well-preserved male sample from the central Zagros site of Wezmeh Cave (WC1, 7,455-7,082 cal BCE). The three other individuals were from Tepe Abdul Hosein and were less well-preserved (genome coverage between 0.6 and 1.2 x) but are around 10,000 years old, and therefore are among the earliest Neolithic human remains in the world (tables S1 and S3).
The four EN Zagros genomes form a distinct cluster in the first two dimensions of a principal components analysis (PCA; Fig. 2); they plot closest to modern-day Pakistani and Afghans and are well-separated from European hunter-gatherers (HG) and other Neolithic farmers. In an outgroup f3-test (6, 7) (figs. S17-S20) all four Neolithic Iranian individuals are genetically more similar to each other than to any other prehistoric genome except a Chalcolithic genome from NW-Anatolia (see below). Despite 14C dates spanning around 1,200 years, these data are consistent with all four genomes being sampled from a single eastern Fertile Crescent EN population.
Examination of runs of homozygosity (ROH) above 500 kb in length in WC1 demonstrated that he shared a similar ROH distribution with European and Aegean Neolithics, as well as modern day Europeans (Fig. 3A, B). However, of all ancient samples considered, WC1 displays the lowest total length of short ROH, suggesting he was descended from a relatively large HG population. In contrast, the ROH distributions of the HG Kotias from Georgia, and Loschbour from Luxembourg indicate prolonged periods of small ancestral population size (8).
We also developed a method to estimate heterozygosity Embedded Image in 1Mb windows that takes into account post-mortem damage and is unbiased even at low coverage (9) (Fig. 3C, D). The mean Embedded Image in WC1 was higher than in HG individuals (Bichon and Kotias), similar to Bronze Age individuals from Hungary and modern Europeans, and lower than ancient (10) and modern Africans. Multidimensional scaling on a matrix of centered Spearman correlations of local Embedded Image across the whole genome again puts WC1 closer to modern populations than to ancient foragers, indicating that both the mean and distribution of diversity over the genome is more similar to modern populations (Fig. 3E). However, WC1 does have an excess of long ROH segments (>1.6 Mb), relative to Aegean and European Neolithics (Fig. 3B). This includes several very long (7-16 Mb) ROH segments (Fig. 3A), confirmed by low Embedded Image estimates in those regions (Fig. 3C). These regions do not show reduced coverage in WC1 nor a reduction in diversity in other samples, with the exception of the longest such segment where we find reduced diversity in modern and HG individuals, although less extended than in WC1 (7) (Fig. 3B). This observed excess of long segments of reduced heterozygosity could be the result of cultural practices such as consanguinity and endogamy, or demographic constraints such as a recent or ongoing bottleneck (11).
The extent of population genetic structure in Neolithic SW-Asia has important implications for the origins of farming. High levels of structuring would be expected under a scenario of localized independent domestication processes by distinct populations, whereas low structure would be more consistent with a single population origin of farming or a diffuse homogeneous domestication process, perhaps involving high rates of gene flow across the entire Neolithic core zone. The ancient Zagros individuals show stronger affinities to Caucasus HGs (table S17.1) whereas Neolithic Aegeans showed closer affinities to other European HGs (tables S17.2 and S17.3). Formal tests of admixture of the form f3(Neo_Iranian, HG; Anatolia_Neolithic) were all positive with Z-scores above 15.78 (table S17.6), indicating that Neolithic NW-Anatolians did not descend from a population formed by the mixing of Zagros Neolithics and known HG groups. These results suggest that Neolithic populations from NW-Anatolia and the Zagros descended from distinct ancestral populations. Furthermore, while the Caucasus HGs are genetically closest to EN Zagros individuals, they also share unique ancestry with eastern, western, and Scandinavian European HGs (table S16.1), indicating that they are not the direct ancestors of Zagros Neolithics.
‘Chromosome painting’ and an analysis of recent haplotype sharing using a Bayesian mixture model (7) revealed that, when compared to 170-230 modern groups, WC1 shared a high proportion (>95%) of recent ancestry with individuals from the Middle East, Caucasus and India. We also compared WC1's haplotype sharing profile to that of three high coverage Neolithic genomes from NW-Anatolia (Bar8; Barcın, Fig. 4), Germany (LBK; Stuttgart) and Hungary (NE1; Polgár-Ferenci-hát). Unlike WC1, these Anatolian and European Neolithics shared ~60-100% of recent ancestry with modern groups sampled from South Europe (figs. S24, S30, S32-S37, table S22).
We also examined recent haplotype sharing between each modern group and ancient Neolithic genomes from Iran (WC1) and Europe (LBK, NE1), HG genomes sampled from Luxembourg (Loschbour) and the Caucasus (KK1; Kotias), a 4.5k-year old genome from Ethiopia (Mota) and Ust’-Ishim, a 45k-year old genome from Siberia. Modern groups from S-, C- and NW-Europe shared haplotypes predominantly with European Neolithic samples LBK and NE1, and European HGs, while modern Near and Middle Eastern, as well as S-Asian samples had higher sharing with WC1 (figs. S28-S29). Modern Pakistani, Iranian, Armenian, Tajikistani, Uzbekistani and Yemeni samples were inferred to share >10% of haplotypes with WC1. This was true even when modern groups from neighboring geographic regions were added as potential ancestry surrogates (figs. S26-S27 and table S23). Iranian Zoroastrians had the highest inferred sharing with WC1 out of all modern groups (table S23). Consistent with this, outgroup f3 statistics indicate that Iranian Zoroastrians are the most genetically similar to all four Neolithic Iranians, followed by other modern Iranians (Fars), Balochi (SE-Iran, Pakistan and Afghanistan), Brahui (Pakistan and Afghanistan), Kalash (Pakistan) and Georgians (figs. S12-S15). Interestingly, WC1 most likely had brown eyes, relatively dark skin, and black hair, although Neolithic Iranians carried reduced pigmentation-associated alleles in several genes and derived alleles at 7 of the 12 loci showing the strongest signatures of selection in ancient Eurasians (3) (tables S29-S33). While there is a strong Neolithic component in these modern S-Asian populations, simulation of allele sharing rejected full population continuity under plausible ancestral population sizes, indicating some population turnover in Iran since the Neolithic (7).
The Neolithic transition in SW-Asia involved the appearance of different domestic species, particularly crops, in different parts of the Neolithic core zone, with no single center (20). Early evidence of plant cultivation and goat management between the 10th and the 8th millennium BCE highlight the Zagros as a key region in the Neolithisation process (1). Given the evidence of domestic species movement from East to West across SW-Asia (21), it is surprising that EN human genomes from the Zagros are not closely related to those from NW-Anatolia and Europe. Instead they represent a previously undescribed Neolithic population. Our data show that the chain of Neolithic migration into Europe does not reach back to the eastern Fertile Crescent, also raising questions about whether intermediate populations in southeastern and Central Anatolia form part of this expansion. On the other hand, it seems probable that the Zagros region was the source of an eastern expansion of the SW-Asian domestic plant and animal economy. Our inferred persistence of ancient Zagros genetic components in modern day S-Asians lends weight to a strong demic component to this expansion.
Some answers are now emerging from a surprising source: DNA extracted from skeletons at Ain Ghazal and other early settlements in the Near East. These findings have already challenged long-held ideas about how agriculture and domestication arose.
What’s more, the new data are showing that early farmers would leave a tremendous mark. People from Ireland to India trace some of their ancestry to people who began growing barley and wheat in the Near East thousands of years ago.
“It’s a part of the story of civilization that we’re just beginning to understand,” said Iosif Lazaridis, a postdoctoral researcher at Harvard Medical School.
The agricultural revolution changed our species and our planet. As bands of hunter-gatherers began domesticating plants and animals, they quit the nomadic life, building villages and towns that endured for thousands of years.
A stable food supply enabled their populations to explode, and small egalitarian groups turned into kingdoms sprawling across hundreds of miles.
Agriculture originated in a few small hubs around the world, but probably first in the Fertile Crescent, a region of the Near East including parts of modern-day Iraq, Syria, Lebanon, Israel and Jordan. The evidence for full-blown agriculture there — crops, livestock, tools for food preparation, and villages — dates back about 11,000 years.
In the 1990s, archaeologists largely concluded that farming in the Fertile Crescent began in Jordan and Israel, a region known as the southern Levant. “The model was that everything started there, and then everything spread out from there, including maybe the people,” said Melinda A. Zeder, a senior research scientist at the Smithsonian National Museum of Natural History.
But in recent years, Dr. Zeder and other archaeologists have overturned that consensus. Their research suggests that people were inventing farming at several sites in the Fertile Crescent at roughly the same time. In the Zagros Mountains of Iran, for example, Dr. Zeder and her colleagues have found evidence of the gradual domestication of wild goats over many centuries around 10,000 years ago.
In two recent studies, geneticists including Dr. Reich used new methods to fish out enough DNA from the bones of the first farmers to figure out their relationship to other people. A team of researchers based at Johannes Gutenberg University in Mainz, Germany, reconstructed the genomes of four early farmers from the Zagros Mountains whose bones date back as much as 10,000 years.
Dr. Reich and his colleagues — including Ron Pinhasi, an archaeologist at University College Dublin, and Dr. Lazaridis of Harvard — recovered genetic material from 44 sets of remains around the Near East. Their haul included DNA from early farmers in Iran, as well as from bones from another site in the Southern Levant like Ain Ghazal. Dr. Reich’s group discovered even older genetic material from hunter-gatherers in the region, from as far back as 14,000 years ago.
The new results all point to the same overall conclusion: The first farmers in each region were the descendants of the earlier hunter-gatherers. What’s more, each population had its own distinct ancestry, going back tens of thousands of years.
About 8,000 years ago, the barriers between peoples in the Fertile Crescent fell away, and genes began to flow across the entire region. The Near East became one homogeneous mix of people.
Why? Dr. Reich speculated that growing populations of farmers began linking to one another via trade networks. People moved along those routes and began to intermarry and have children together. Genes did not just flow across the Fertile Crescent — they also rippled outward. The scientists have detected DNA from the first farmers in living people on three continents.
Early farmers in Turkey moved across the western part of the country, crossed the Bosporus and traveled into Europe about 8,000 years ago. They encountered no farmers there. Europe had been home to groups of hunter-gatherers for more than 30,000 years. The farmers seized much of their territory and converted it to farmland, without interbreeding with them.
The hunter-gatherers clung to existence for centuries, and were eventually absorbed by bigger farming communities. Europeans today can trace much of their ancestry to both groups. The early farmers in what is now Iran expanded eastward. Eventually, their descendants ended up in present-day India, and their DNA makes up a substantial portion of the genomes of Indians.
The eastern and western parts of the northern Mediterranean, including parts of modern-day Spain, France and Turkey, commonly practiced dairying, but northern Greece did not, they said. Rather, "lipids from pots and the animal bones tell the same story: Meat production [in northern Greece] was the main activity, not dairying," they said.
The new analysis supports the team's earlier work showing "that milk use was highly regionalized in the Near East in the seventh millennium B.C.," study researchers Mélanie Roffet-Salque and Richard Evershed, chemists at the University of Bristol in the United Kingdom, said in a statement. "This new multidisciplinary study further emphasizes the existence of diverse use of animal products in the northern Mediterranean Neolithic."
The varying landscape in the northern Mediterranean likely influenced what sort of animals the Neolithic people domesticated, the researchers added.
Dairying began with the onset of agriculture, and likely helped early farmers, said the study's lead researcher, Cynthianne Spiteri, a junior professor of archaeometry at the University of Tübingen in Germany, who conducted the residue analysis as part of her doctorate in archaeology at the University of York in the United Kingdom.
However, more research is needed to verify that Neolithic people consumed milk products. This could be accomplished by analyzing ancient human skeletons, said study researcher Oliver Craig, a professor of archaeology at the University of York.
Abstract
In the absence of any direct evidence, the relative importance of meat and dairy productions to Neolithic prehistoric Mediterranean communities has been extensively debated. Here, we combine lipid residue analysis of ceramic vessels with osteo-archaeological age-at-death analysis from 82 northern Mediterranean and Near Eastern sites dating from the seventh to fifth millennia BC to address this question. The findings show variable intensities in dairy and nondairy activities in the Mediterranean region with the slaughter profiles of domesticated ruminants mirroring the results of the organic residue analyses. The finding of milk residues in very early Neolithic pottery (seventh millennium BC) from both the east and west of the region contrasts with much lower intensities in sites of northern Greece, where pig bones are present in higher frequencies compared with other locations. In this region, the slaughter profiles of all domesticated ruminants suggest meat production predominated. Overall, it appears that milk or the by-products of milk was an important foodstuff, which may have contributed significantly to the spread of these cultural groups by providing a nourishing and sustainable product for early farming communities.
Cynthianne Debono Spiteri et al. Regional asynchronicity in dairy production and processing in early farming communities of the northern Mediterranean, Proceedings of the National Academy of Sciences (2016).
Archaeologists from the British museum have reconstructed an ancient man's face, allowing visitors to see what he looked like for the first time.
The man lived 9,500 years ago in the holy city of Jericho, now found in the Palestinian territories near the West Bank.
The 'Jericho skull' was found by British archaeologists in 1953, but until now nobody knew what the he had looked like.
The team hopes to gather DNA samples from the skull in future, laying out 10,000 year-old genes for investigation. But the process would be risky - it's likely to damage the skull and useful results aren't guaranteed.
'If we were able to extract DNA from the human remains beneath the plaster, there is currently a very slight chance that we would be able to find out this individual's hair and eye colour,' Fletcher said. 'I say a slight chance because the DNA preservation in such ancient human remains can be too poor to obtain any information.'
Figure 1 Geographical, Archaeological, and Genetic Information for the Ancient Spanish and Romanian Samples
We investigated the interactions between hunter-gatherers and Neolithic farmers in the Lower Danube basin in Romania by recovering the genomes of four prehistoric individuals: a Mesolithic hunter-gatherer from Ostrovul Corbului (OC1_Meso) dated at 8.7 thousand years ago (kya), two Mesolithic hunter-gatherers from Schela Cladovei (SC1_Meso and SC2_Meso) dated at around 8.8 kya, and an Eneolithic (the period between the Neolithic and the Bronze Age) individual dated at 5.3 kya from Gura Baciului (GB1_Eneo), located north-northeast of the Iron Gates on a terrace of the Suceag creek (Figure 1A and STAR Methods, Method Details). Contact between hunter-gatherers and farmers has been hypothesized for a number of archaeological sites across Europe. In 2012, Skoglund et al. [4] reported the first genomic data suggesting different origins for hunter-gatherers and early farmers in Scandinavia. Further work [1, 5, 6] provided additional paleogenomic evidence that Neolithization was driven by immigration of farming populations, supporting the demic diffusion model, at least for Scandinavia and Western and Central Europe. In Southeast Europe, the Lower Danube Basin has provided some of the best evidence for cultural exchange, and thus possible mixing, between hunter-gatherers and farmers [10, 11, 12]. Archaeological data put the arrival of the typical Neolithic package, including farming, pottery, and new burial practices, at around 8 kya. Isotopic analysis of very late Mesolithic burials from Lepenski Vir around that time revealed several individuals whose diets were relatively high in terrestrial proteins, a profile more typical of farming communities [11]; although the genetic origin of these individuals is unknown, their presence points to contact of this Mesolithic community with farmers (either through cultural exchange or immigration). The presence of personal ornaments of Neolithic type in some Late Mesolithic (8.3–8.0 kya) graves at Lepenski Vir and Vlasac [13] and the recovery of cereal starch granules from dental calculus on Mesolithic teeth from Vlasac [12] further support the hypothesized adoption of new practices by local hunter-gatherers in the Lower Danube basin [11].
Table 1 Origin, Age, Next-Generation Sequencing Data, Uniparental Haplogroups, and Stable Carbon and Nitrogen Isotope Values Related to Diet for the Samples Analyzed in This Study
Sample IDSiteCal BP Age Range (2σ) [OxCal 4.2] aGenome Coverage Biol. Sex mtDNA hg. Y hg. Isotope Values (‰) δ13C δ15N C:N Ratioc SC1_MesoSchela Cladovei (Romania) 8,814 ± 261 1.11× XY U5b2c R −18.5 15.0 3.2 SC2_MesoSchela Cladovei (Romania)− 2.83 ×XY U5a1c R1 −19.1 14.7 3.2 OC1_MesoOstrovul Corbului (Romania) 8,704 ± 269 1.86× XY K1 + 16362 R1b −18.7 15.5 3.1 GB1_EneoGura Baciului (Romania) 5,377 ± 774 .05× XX K1a4a NA −20.0 12.7 3.3 Chan_MesoChan do Lindeiro (Spain) 9,131 ± 124 5.28× XX U5b NA −20.5 8.4 3.1 Canes1_MesoCanes (Spain) 7,115 ± 130 1.73× XX U5a2a NA −20.0 7.9 −
Cal BP, calibrated age before present; hg., haplogroup. See also Figure S4 and Tables S1, S2, and S4.
aThe radiocarbon dates of samples from the Iron Gates (Schela Cladovei and Ostrovul Corbului) were corrected for the Danube Freshwater Reservoir Effect [14]. bIsotope values for SC1_Meso, Canes1_Meso, and Chan_Meso were published by [14], [15], and [16], respectively. Isotope values for OC1_Meso, SC2_Meso, and GB1_Eneo were obtained in this study. cThe C:N atomic ratio serves as an indicator of collagen preservation suitable for radiocarbon dating and paleodiet reconstruction.
Mitochondrial and Y Chromosome Haplogroups At the level of mitochondrial DNA sequences, SC1_Meso belongs to U5b (Table 1), the same subhaplogroup to which a number of Western hunter-gatherers (WHGs) belong [17, 18, 19, 20]. SC2_Meso was assigned to U5a, a subhaplogroup mainly found in Scandinavian [5, 21] and Latvian hunter-gatherers and also in some samples from later periods in Eastern and Central Europe [6, 7, 22]. The two other samples from Romania, the Mesolithic OC1_Meso and the Eneolithic GB1_Eneo, both belong to K1, a haplogroup commonly found among early European farmers [17, 18] (see Table S4 and Method Details in STAR Methods for description of haplogroup assignment). At the Y chromosome level, all of our three male samples, SC1_Meso, SC2_Meso, and OC1_Meso, were assigned to the R1 and R1b haplogroups, both common in modern Europeans (Table 1 and STAR Methods, Quantification and Statistical Analysis).
