|
|
Post by Admin on Jul 21, 2020 20:22:45 GMT
The earliest archaeological evidence for cultivating plants and herding animals dates back 10,000 to 12,000 years ago in the Fertile Crescent, which arcs from the Persian Gulf to Turkey and south to Egypt (see map, above). Excavations at Jericho in Jordan, Jarmo in Iraq, and Çatalhöyük in Turkey, for example, have found evidence of early grain farming and sheep and goat domestication in different areas at roughly the same time. Geneticists have been trying to track whether one group of people—or just their ideas—spread farming early on. A single group did carry farming to Europe: DNA from ancient farmers in western Anatolia1 shows that they were the direct ancestors of Europe’s first farmers, known as the Linear Pottery culture; present-day Sardinians share the most DNA with these ancient Anatolians. But the trail of the first farmers went cold in the hot climate of the Middle East, which destroys DNA. Now, researchers are using new methods to prepare samples and extract them from the petrous bone of the ear, which is unusually rich in DNA. A team led by Joachim Burger of the Johannes Gutenberg University of Mainz in Germany and including Marjan Mashkour and
Fereidoun Biglari of the National Museum of Iran in Tehran sequenced the complete genomes of four goat herders who lived in the Zagros Mountains of Iran. They include a 9000-year-old male from Wezmeh Cave, and three 10,000-year-old skeletons from a site called Tepe Abdul Hosein that are among the oldest remains of farmers in the world. Tests of isotopes in the teeth of all four farmers confirm they had diets rich in grains, a signature of an agricultural diet. By using a new method that looks at patterns of inheritance of chunks of DNA,
Hellenthal found that the early Zagros Mountain farmers have left a genetic legacy in Pakistanis, Afghans, and others, particularly in Zoroastrians in Iran. But the ancient Iranian DNA was dramatically different from that of the western Anatolian farmers. The two groups of farmers, who lived about 2000 kilometers and 2000 years apart, must have descended from completely different groups of hunter-gatherers who separated 46,000 to 77,000 years ago, Burger says. A similar genetic disjunction appears in a study led by Harvard University’s David Reich2 and posted on bioRxiv. This study analyzed ancient DNA from 44 Middle Easterners who lived 14,000 to 3400 years ago, including Natufian hunter-gatherers in Israel, Zagros farmers, and Bronze Age pastoralists in the Eurasian steppe, and compared it with that of 2864 living and ancient people from around the world. By sequencing 1.2 million nucleotides from across each genome, the team found that early farmers of Israel and Jordan (known as the Levant) were genetically distinct from those in the Zagros Mountains, and that both populations were distinct from the western Anatolians who later spread their genes throughout Europe. The third study3, also published on bioRxiv, reported the same stark differences. That study analyzed the complete genome of a 10,000-year-old woman from Ganj Dareh, a site in the Zagros Mountains with the world’s oldest evidence of goat herding.  Burger and Reich also each used their data to peer even further back in time, to the ancestors of the Zagros Mountain farmers. They found that the Zagros people descend from a group of basal Eurasians who separated from the ancestors of all other people outside of Africa 50,000 to 60,000 years ago—before other non-Africans interbred with Neandertals. So the Zagros Mountain farmers had less Neandertal DNA than the western Anatolian farmers, whose ancestors must have branched off later. The descendants of these early farmers went separate ways. Whereas the western Anatolians later migrated to Europe, Reich’s team proposes that the ancient farmers of the Levant migrated to East Africa, where living people carry some of their distinct DNA, and the Zagros Mountain farmers spread north into the Eurasian steppe and east into South Asia.  Did these early people learn farming from each other, or was it invented more than once? Here, opinion differs. Archaeologists have noted that early farmers in different regions used different tools and grains, supporting the idea of multiple origins, says archaeologist Roger Matthews of the University of Reading in the United Kingdom. “The genetic and archaeological evidence suggest at least two separate pathways to agriculture, at distant ends of the Fertile Crescent, eventually merging into a unified package that then spreads outwards,” he says. But these groups traded obsidian, suggesting to Renfrew and Harvard archaeo
logist Ofer Bar-Yosef that seeds and farming knowledge could have been shared, too. Because new kinds of food preparation tools turn up first in the Levant, Bar-Yosef thinks farming sprouted here: “Zagros foothills people adopted agriculture from the Levant.” Burger suggests that farming was such an advantage that it spread both as an idea and by migration of people. “Initially, agri
culture was an idea that spread,” he proposes. “Then, when it reaches the borders of Europe, it becomes people spreading farming. We have an extremely complex agricultural revolution that was created by people who were extremely diverse.” 1. science.sciencemag.org/content/342/6155/181.full2. biorxiv.org/content/early/2016/06/16/0593113. biorxiv.org/content/early/2016/06/18/059568 |
|
|
|
Post by Admin on Jul 22, 2020 5:37:19 GMT
Early Neolithic genomes from the eastern Fertile Crescent
Farnaz Broushaki1, Mark G. Thomas2, Vivian Link3,4, Saioa López2, Lucy van Dorp2, Karola Kirsanow1, Zuzana Hofmanová1, Yoan Diekmann2, Lara M. Cassidy5, David Díez-del-Molino2,6, Athanasios Kousathanas3,4,7, Christian Sell1, Harry K. Robson8, Rui Martiniano5, Jens Blöcher1, Amelie Scheu1,5, Susanne Kreutzer1, Ruth Bollongino1, Dean Bobo9, Hossein Davoudi10, Olivia Munoz11, Mathias Currat12, Kamyar Abdi13, Fereidoun Biglari14, Oliver E. Craig8, Daniel G. Bradley5, Stephen Shennan15, Krishna R. Veeramah9, Marjan Mashkour16, Daniel Wegmann3,4,*,†, Garrett Hellenthal2,*,†, Joachim Burger1,*,†
Science 29 Jul 2016:
Vol. 353, Issue 6298, pp. 499-503
DOI: 10.1126/science.aaf7943
Near Eastern genomes from Iran
The genetic composition of populations in Europe changed during the Neolithic transition from hunting and gathering to farming. To better understand the origin of modern populations, Broushaki et al. sequenced ancient DNA from four individuals from the Zagros region of present-day Iran, representing the early Neolithic Fertile Crescent. These individuals unexpectedly were not ancestral to early European farmers, and their genetic structures did not contribute significantly to those of present-day Europeans. These data indicate that a parallel Neolithic transition probably resulted from structured farming populations across southwest Asia.
Science, this issue p. 499
Abstract
We sequenced Early Neolithic genomes from the Zagros region of Iran (eastern Fertile Crescent), where some of the earliest evidence for farming is found, and identify a previously uncharacterized population that is neither ancestral to the first European farmers nor has contributed substantially to the ancestry of modern Europeans. These people are estimated to have separated from Early Neolithic farmers in Anatolia some 46,000 to 77,000 years ago and show affinities to modern-day Pakistani and Afghan populations, but particularly to Iranian Zoroastrians. We conclude that multiple, genetically differentiated hunter-gatherer populations adopted farming in southwestern Asia, that components of pre-Neolithic population structure were preserved as farming spread into neighboring regions, and that the Zagros region was the cradle of eastward expansion.
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 eastern Anatolia and northern 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 North 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 ~6500 to 6000 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 10× mean coverage from a well-preserved male sample from the central Zagros site of Wezmeh Cave [WC1, 7455 to 7082 calibrated years (cal) BCE]. The three other individuals were from Tepe Abdul Hosein and were less well preserved (genome coverage between 0.6 and 1.2×) but are around 10,000 years old, and therefore are among the earliest Neolithic human remains in the world (tables S1 and S3).
Despite a lack of a clear Neolithic context, the radiocarbon-inferred chronological age and palaeodietary data support WC1 being an early farmer (tables S1 to S3 and fig. S7). WC1 bone collagen δ13C and δ15N values are indistinguishable from those of a securely assigned Neolithic individual from Abdul Hosein and consistent with a diet rich in cultivated C3 cereals rather than animal protein. Specifically, collagen from WC1 and Abdul Hosein is 13C depleted compared to those from contemporaneous wild and domestic fauna from this region (5), which consumed C4 plants. Crucially, WC1 and the Abdul Hosein farmers exhibit very similar genomic signatures.
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 Pakistanis and Afghans and are well separated from European hunter-gatherers (HG) and other Neolithic farmers. In an outgroup f3-test (6, 7) (figs. S17 to S20), all four Neolithic Iranian individuals are genetically more similar to each other than to any other prehistoric genome except a Chalcolithic genome from northwestern Anatolia (see below). Despite 14C dates spanning around 1200 years, these data are consistent with all four genomes being sampled from a single eastern Fertile Crescent EN population.
|
|
|
|
Post by Admin on Jul 22, 2020 22:54:59 GMT
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. 3, A and B). However, of all ancient samples considered, WC1 displays the lowest total length of short ROH, suggesting that 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 1-Mb windows that takes into account postmortem damage and is unbiased even at low coverage (9) (Fig. 3, C and D). The mean Embedded Image in WC1 was higher than in HG individuals (Bichon and Kotias), similar to that in Bronze Age individuals from Hungary and modern Europeans, and lower than in 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 are more similar to those of 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 to 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 southwestern 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 northwestern 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 northwestern Anatolia and the Zagros descended from distinct ancestral populations. Furthermore, although 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.
The significant differences between ancient Iranians, Anatolian/European farmers, and European HGs suggest a pre-Neolithic separation. Assuming a mutation rate of 5 × 10−10 per site per year (12), the inferred mean split time for Anatolian/European farmers (as represented by Bar8, 4) and European HGs (Loschbour) ranged from 33,000 to 39,000 years ago [combined 95% confidence interval (CI) 15,000 to 61,000 years ago], whereas the preceding divergence of the ancestors of Neolithic Iranians (WC1) occurred 46,000 to 77,000 years ago (combined 95% CI 38,000 to 104,000 years ago) (13) (fig. S48 and tables S34 and S35). Furthermore, the European HGs were inferred to have an effective population size (Ne) that was ~10 to 20% of either Neolithic farming group, consistent with the ROH and Embedded Image analyses.
Levels of inferred Neanderthal ancestry in WC1 are low (fig. S22 and table S21), but fall within the general trend described recently in Fu et al. (14). Fu et al. (14) also inferred a basal Eurasian ancestry component in the Caucasus HG sample Satsurblia when examined within the context of a “base model” for various ancient Eurasian genomes dated from ~45,000 to 7,000 years ago. We examined this base model using ADMIXTUREGRAPH (6) and inferred almost twice as much basal Eurasian ancestry for WC1 as for Satsurblia (62 versus 32%) (fig. S52), with the remaining ancestry derived from a population most similar to ancient north Eurasians such as Mal`ta1 (15). Thus, Neolithic Iranians appear to derive predominantly from the earliest known Eurasian population branching event (7).
“Chromosome painting” and an analysis of recent haplotype sharing using a Bayesian mixture model (7) revealed that, when compared to 160 to 220 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 northwestern Anatolia (Bar8; Barcın, Fig. 4), Germany (LBK; Stuttgart), and Hungary (NE1; Polgár-Ferenci-hát). Unlike WC1, these Anatolian and European Neolithics shared ~60 to 100% of recent ancestry with modern groups sampled from southern Europe (figs. S24, S30, and S32 to S37; table S22).
|
|
|
|
Post by Admin on Jul 23, 2020 4:39:37 GMT
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 4500-year-old genome from Ethiopia (Mota) and Ust’-Ishim, and a 45,000-year-old genome from Siberia. Modern groups from south, central, and northwestern Europe shared haplotypes predominantly with European Neolithic samples LBK and NE1, and European HGs, whereas modern Near and Middle Eastern, as well as southern Asian samples, had higher sharing with WC1 (figs. S28 and 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 and 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 (southeastern Iran, Pakistan, and Afghanistan), Brahui (Pakistan and Afghanistan), Kalash (Pakistan), and Georgians (figs. S12 to 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 to S33). Although there is a strong Neolithic component in these modern south 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). While Early Neolithic samples from eastern and western southwest Asia differ conspicuously, comparisons to genomes from Chalcolithic Anatolia and Iron Age Iran indicate a degree of subsequent homogenization. Kumtepe6, a ~6750-year-old genome from northwestern Anatolia (16), was more similar to Neolithic Iranians than to any other non-Iranian ancient genome (figs. S17 to S20 and table S18.1). Furthermore, our male Iron Age genome (F38; 971 to 832 BCE; sequenced to 1.9×) from Tepe Hasanlu in northwestern Iran shares greatest similarity with Kumtepe6 (fig. S21) even when compared to Neolithic Iranians (table S20). We inferred additional non-Iranian or non-Anatolian ancestry in F38 from sources such as European Neolithics and even post-Neolithic Steppe populations (table S20). Consistent with this, F38 carried a N1a subclade mitochondrial DNA (mtDNA), which is common in early European and northwestern Anatolian farmers (3). In contrast, his Y chromosome belongs to subhaplogroup R1b1a2a2, also found in five Yamnaya individuals (17) and in two individuals from the Poltavka culture (3). These patterns indicate that post-Neolithic homogenization in southwestern Asia involved substantial bidirectional gene flow between the east and west of the region, as well as possible gene flow from the Steppe. Migration of people associated with the Yamnaya culture has been implicated in the spread of Indo-European languages (17, 18), and some level of Near Eastern ancestry was previously inferred in southern Russian pre-Yamnaya populations (3). However, our analyses suggest that Neolithic Iranians were unlikely to be the main source of Near Eastern ancestry in the Steppe population (table S20) and that this ancestry in pre-Yamnaya populations originated primarily in the west of southwest Asia. We also inferred shared ancestry between Steppe and Hasanlu Iron Age genomes that was distinct from EN Iranians (table S20) (7). In addition, modern Middle Easterners and South Asians appear to possess mixed ancestry from ancient Iranian and Steppe populations (tables S19 and S20). However, Steppe-related ancestry may also have been acquired indirectly from other sources (7), and it is not clear if this is sufficient to explain the spread of Indo-European languages from a hypothesized Steppe homeland to the region where Indo-Iranian languages are spoken today. Yet, the affinities of Zagros Neolithic individuals to modern populations of Pakistan, Afghanistan, Iran, and India is consistent with a spread of Indo-Iranian languages, or of Dravidian languages (which includes Brahui), from the Zagros into southern Asia, in association with farming (19). The Neolithic transition in southwest 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 highlights the Zagros as a key region in the Neolithization process (1). Given the evidence of domestic species movement from east to west across southwest Asia (21), it is surprising that EN human genomes from the Zagros are not closely related to those from northwestern 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. Nevertheless, it seems probable that the Zagros region was the source of an eastern expansion of the southwestern Asian domestic plant and animal economy. Our inferred persistence of ancient Zagros genetic components in modern day south Asians lends weight to a strong demic component to this expansion. Supplementary Materials www.sciencemag.org/content/353/6298/499/suppl/DC1 |
|
|
|
Post by Admin on Jul 23, 2020 20:17:31 GMT
The genetics of an early Neolithic pastoralist from the Zagros, Iran M. Gallego-Llorente, S. Connell, E. R. Jones, D. C. Merrett, Y. Jeon, A. Eriksson, V. Siska, C. Gamba, C. Meiklejohn, R. Beyer, S. Jeon, Y. S. Cho, M. Hofreiter, J. Bhak, A. Manica & R. Pinhasi Scientific Reports volume 6, Article number: 31326 (2016) Abstract The agricultural transition profoundly changed human societies. We sequenced and analysed the first genome (1.39x) of an early Neolithic woman from Ganj Dareh, in the Zagros Mountains of Iran, a site with early evidence for an economy based on goat herding, ca. 10,000 BP. We show that Western Iran was inhabited by a population genetically most similar to hunter-gatherers from the Caucasus, but distinct from the Neolithic Anatolian people who later brought food production into Europe. The inhabitants of Ganj Dareh made little direct genetic contribution to modern European populations, suggesting those of the Central Zagros were somewhat isolated from other populations of the Fertile Crescent. Runs of homozygosity are of a similar length to those from Neolithic farmers, and shorter than those of Caucasus and Western Hunter-Gatherers, suggesting that the inhabitants of Ganj Dareh did not undergo the large population bottleneck suffered by their northern neighbours. While some degree of cultural diffusion between Anatolia, Western Iran and other neighbouring regions is possible, the genetic dissimilarity between early Anatolian farmers and the inhabitants of Ganj Dareh supports a model in which Neolithic societies in these areas were distinct.  Introduction The agricultural transition started in a region comprising the Ancient Near East and Anatolia ~12,000 years ago with the first Pre-Pottery Neolithic villages and the first domestication of cereals and legumes1,2. Archaeological evidence suggests a complex scenario of multiple domestications in a number of areas3, coupled with examples of trade4. Ancient DNA (aDNA) has revealed that this cultural package was later brought into Europe by dispersing farmers from Anatolia (so called ‘demic’ diffusion, as opposed to non-demic cultural diffusion5,6) ~8,400 years ago. However a lack of aDNA from early Neolithic individuals from the Near East leaves a key question unanswered: was the agricultural transition developed by one major population group spanning the Near East, including Anatolia and the Central Zagros Mountains; or was the region inhabited by genetically diverse populations, as is suggested by the heterogeneous mode and timing of the appearance of early domesticates at different localities? To answer this question, we sequenced the genome of an early Neolithic female from Ganj Dareh, GD13a, from the Central Zagros (Western Iran), dated to 10000-9700 cal BP7, a region located at the eastern edge of the Near East. Ganj Dareh is well known for providing the earliest evidence of herd management of goats beginning at 9,900 BP7,8,9. It is a classic mound site at an altitude of ~1400 m in the Gamas-Ab Valley of the High Zagros zone in Kermanshah Province, Western Iran. It was discovered in the 1960s during survey work and excavated over four seasons between 1967 and 1974. The mound, ~40 m in diameter, shows 7 to 8 m of early Neolithic cultural deposits. Five major levels were found, labelled A through E from top to bottom. Extended evidence showed a warren of rooms with evidence of under-floor inhumations within what may be burial chambers and/or disused houses10. The current Minimum Number of Individuals is 116, with 56 catalogued as skeletons that had four or more bones recovered11. The individual analysed here was part of burial 13, which contained three individuals, and was recovered in level C in 1971 from the floor of a brick-walled structure. The individual sampled, 13A (referred to as GD13a throughout the text), was a 30–50 year old female; the other individuals in the burial unit were a second adult (13B) and an adolescent (13). The site has been directly dated to 9650–9950 cal BP7, and shows intense occupation over two to three centuries. The economy of the population was that of pastoralists with an emphasis on goat herding7. Archaeobotanical evidence is limited12 but the evidence present is for two-row barley with no evidence for wheat, rye or other domesticates. This implies that the overall economy was at a much earlier stage in the development of cereal agriculture than that found in the Levant, Anatolia and Northern Mesopotamian basin.  |
|
