Ancient DNA from a lost Negev Highlands desert grape reveals a Late Antiquity wine lineage.

Recent excavations of Late Antiquity settlements in the Negev Highlands of southern Israel uncovered a society that established commercial-scale viticulture in an arid environment [D. Fuks et al., Proc. Natl. Acad. Sci. U.S.A. 117, 19780-19791 (2020)]. We applied target-enriched genome-wide sequencing and radiocarbon dating to examine grapevine pips that were excavated at three of these sites. Our analyses revealed centuries long and continuous grape cultivation in the Southern Levant. The genetically diverse pips also provided clues to ancient cultivation strategies aimed at improving agricultural productivity and ensuring food security. Applying genomic prediction analysis, a pip dated to the eighth century CE was determined to likely be from a white grape, to date the oldest to be identified. In a kinship analysis, another pip was found to be descendant from a modern Greek cultivar and was thus linked with several popular historic wines that were once traded across the Byzantine Empire. These findings shed light on historical Byzantine trading networks and on the genetic contribution of Levantine varieties to the classic Aegean landscape.

Six-rowed wild-growing barleys are hybrids of diverse origins.

Crop-wild gene flow is common when domesticated plants and their wild relatives grow close to each other. The resultant hybrid forms appear as semi-domesticates and were sometimes considered as missing links between crops and their wild progenitors. Wild-growing barleys in Central and Eastern Asia, named Hordeum agriocrithon, show hallmark characters of both wild and domesticated forms. Their spikes disintegrate at maturity to disperse without human intervention, but bear lateral grains, which were favored by early farmers and are absent from other wild barleys. As an intermediate form, H. agriocrithon has been proposed several times as a progenitor of domesticated barley. Here, we used genome-wide marker data and whole-genome resequencing to show that all H. agriocrithon accessions of a major germplasm collection are hybrid forms that arose multiple times by admixture of diverse domesticated and wild populations. Although H. agriocrithon barleys have not played a special role in barley domestication, future analysis of the adaptative potential of bi-directional crop-wild gene flow in extant barleys may prove a fertile research field.

The rise and fall of viticulture in the Late Antique Negev Highlands reconstructed from archaeobotanical and ceramic data.

The international scope of the Mediterranean wine trade in Late Antiquity raises important questions concerning sustainability in an ancient international economy and offers a valuable historical precedent to modern globalization. Such questions involve the role of intercontinental commerce in maintaining sustainable production within important supply regions and the vulnerability of peripheral regions believed to have been especially sensitive to environmental and political disturbances. We provide archaeobotanical evidence from trash mounds at three sites in the central Negev Desert, Israel, unraveling the rise and fall of viticulture over the second to eighth centuries of the common era (CE). Using quantitative ceramic data obtained in the same archaeological contexts, we further investigate connections between Negev viticulture and circum-Mediterranean trade. Our findings demonstrate interrelated growth in viticulture and involvement in Mediterranean trade reaching what appears to be a commercial scale in the fourth to mid-sixth centuries. Following a mid-sixth century peak, decline of this system is evident in the mid- to late sixth century, nearly a century before the Islamic conquest. These findings closely correspond with other archaeological evidence for social, economic, and urban growth in the fourth century and decline centered on the mid-sixth century. Contracting markets were a likely proximate cause for the decline; possible triggers include climate change, plague, and wider sociopolitical developments. In long-term historical perspective, the unprecedented commercial florescence of the Late Antique Negev appears to have been unsustainable, reverting to an age-old pattern of smaller-scale settlement and survival-subsistence strategies within a time frame of about two centuries.

Ancient trash mounds unravel urban collapse a century before the end of Byzantine hegemony in the southern Levant.

The historic event of the Late Antique Little Ice Age (LALIA) was recently identified in dozens of natural and geological climate proxies of the northern hemisphere. Although this climatic downturn was proposed as a major cause for pandemic and extensive societal upheavals in the sixth-seventh centuries CE, archaeological evidence for the magnitude of societal response to this event is sparse. This study uses ancient trash mounds as a type of proxy for identifying societal crisis in the urban domain, and employs multidisciplinary investigations to establish the terminal date of organized trash collection and high-level municipal functioning on a city-wide scale. Survey, excavation, sediment analysis, and geographic information system assessment of mound volume were conducted on a series of mounds surrounding the Byzantine urban settlement of Elusa in the Negev Desert. These reveal the massive collection and dumping of domestic and construction waste over time on the city edges. Carbon dating of charred seeds and charcoal fragments combined with ceramic analysis establish the end date of orchestrated trash removal near the mid-sixth century, coinciding closely with the beginning of the LALIA event and outbreak of the Justinian Plague in the year 541. This evidence for societal decline during the sixth century ties with other arguments for urban dysfunction across the Byzantine Levant at this time. We demonstrate the utility of trash mounds as sensitive proxies of social response and unravel the time-space dynamics of urban collapse, suggesting diminished resilience to rapid climate change in the frontier Negev region of the empire.

Plant-related Philistine ritual practices at biblical Gath.

The Philistine culture (Iron Age, ca. 1200-604 BCE) profoundly impacted the southern Levant's cultural history, agronomy, and dietary customs. Nevertheless, our knowledge of the Philistines' cultic praxis and deities, is limited and uncertain. Here, we combine archaeological data with a meticulous study of plant use at two successive temples at Tell es-Sâfi/Gath. We provide a list of the plants used, their time of harvest, mode of offering, and possible symbolism. Analysis of the temples' macrobotanical (seed and fruits) plant assemblage reveals the offerings; that the inception date for rites was early spring; and sheds light on the date of the final utilization of the temples (late summer/early fall). Besides food crops, we note the earliest cultic use of chaste tree (Vitex agnus-castus), crown daisy (Glebionis coronaria), and scabious (Lomelosia argentea). These wide-spread Mediterranean plants were known so far only in later cults-of early Greek deities, such as Hera, Artemis, Demeter, and Asclepios. We discuss the data as reflecting that the Philistine religion relied on the magic and power of nature, such as fresh water and seasonality, which influence human life, health, and activity. In sum, our results offer novel insights into the culture of the Philistines.

Setting the morphologic quality limits enabling accurate classification of charred archaeological grape seeds.

This study investigates the morphological changes in grape pips resulting from various charring conditions. Employing high-resolution scanning combined with morphometric measurements for morphological analysis, we aimed to understand the effects of charring on grape pips. Our morphometric analysis demonstrated significant alterations in seed shape above 250 °C. The length-width ratio and the occurrence of cracks notably changed, providing a basis for assessing charring conditions. In addition, applying a machine learning classification method, we determined that accurate classification of grape varieties by the morphometric analysis method is feasible for seeds charred at up to 250 °C and 8 h. Integrating the morphometric changes and temperature ranges suitable for classification, we developed a sorting model for archaeological seeds. By projecting length-width ratios onto a curve calculated from controlled conditions, we estimated charring temperatures. Approximately 50% of archaeological seeds deviated from the model, indicating drastic charring conditions. This sorting model facilitates a stringent selection of seeds fit for classification, enhancing the accuracy of our machine learning-based methodology. In conclusion, combining machine learning with morphometric sorting enables the identification of charred grape seeds suitable for identification by the morphometric method. This comprehensive approach provides a valuable tool for future research for the identification of charred grape seeds found in archaeological contexts, enhancing our understanding of ancient viticulture practices and grape cultivation.

Unprecedented yet gradual nature of first millennium CE intercontinental crop plant dispersal revealed in ancient Negev desert refuse.

Global agro-biodiversity has resulted from processes of plant migration and agricultural adoption. Although critically affecting current diversity, crop diffusion from Classical antiquity to the Middle Ages is poorly researched, overshadowed by studies on that of prehistoric periods. A new archaeobotanical dataset from three Negev Highland desert sites demonstrates the first millennium CE's significance for long-term agricultural change in Southwest Asia. This enables evaluation of the 'Islamic Green Revolution (IGR)' thesis compared to 'Roman Agricultural Diffusion (RAD)', and both versus crop diffusion during and since the Neolithic. Among the findings, some of the earliest aubergine (Solanum melongena) seeds in the Levant represent the proposed IGR. Several other identified economic plants, including two unprecedented in Levantine archaeobotany-jujube (Ziziphus jujuba/mauritiana) and white lupine (Lupinus albus)-implicate RAD as the greater force for crop migrations. Altogether the evidence supports a gradualist model for Holocene-wide crop diffusion, within which the first millennium CE contributed more to global agricultural diversity than any earlier period.

Extinction of water plants in the Hula Valley: Evidence for climate change.

We describe two events of water plant extinction in the Hula Valley, northern Israel: the ancient, natural extinction of 3 out of 14 extinct species at Gesher Benot Ya'aqov, which occurred some 800-700 k.yr., and an anthropogenic, near contemporary extinction of seven species in the artificial drainage of the Hula Lake in the 1950s. We conclude that the considerable fraction of water plants that disappeared from the Hula Valley in the Early-Middle Pleistocene was the result of habitat desiccation and not global warming. Thus, there is evidence that the hominins who lived in the Hula Valley inhabited a comparatively dry place. The disappearance of water plant species was partially the result of reduced seed dispersal by birds (ornitochory) as a result of the shrinkage of water bodies and their number along the Rift Valley. We suggest that the disappearance of a group of rare, local water plants can be used as an indicator of climate drying and impacts on the local vegetation.

Accurate classification of fresh and charred grape seeds to the varietal level, using machine learning based classification method.

Grapevine (Vitis vinifera L.) currently includes thousands of cultivars. Discrimination between these varieties, historically done by ampelography, is done in recent decades mostly by genetic analysis. However, when aiming to identify archaeobotanical remains, which are mostly charred with extremely low genomic preservation, the application of the genomic approach is rarely successful. As a result, variety-level identification of most grape remains is currently prevented. Because grape pips are highly polymorphic, several attempts were made to utilize their morphological diversity as a classification tool, mostly using 2D image analysis technics. Here, we present a highly accurate varietal classification tool using an innovative and accessible 3D seed scanning approach. The suggested classification methodology is machine-learning-based, applied with the Iterative Closest Point (ICP) registration algorithm and the Linear Discriminant Analysis (LDA) technique. This methodology achieved classification results of 91% to 93% accuracy in average when trained by fresh or charred seeds to test fresh or charred seeds, respectively. We show that when classifying 8 groups, enhanced accuracy levels can be achieved using a "tournament" approach. Future development of this new methodology can lead to an effective seed classification tool, significantly improving the fields of archaeobotany, as well as general taxonomy.

Processing of wild cereal grains in the Upper Palaeolithic revealed by starch grain analysis.

Barley (Hordeum vulgare L.) and wheat (Triticum monococcum L. and Triticum turgidum L.) were among the principal 'founder crops' of southwest Asian agriculture. Two issues that were central to the cultural transition from foraging to food production are poorly understood. They are the dates at which human groups began to routinely exploit wild varieties of wheat and barley, and when foragers first utilized technologies to pound and grind the hard, fibrous seeds of these and other plants to turn them into easily digestible foodstuffs. Here we report the earliest direct evidence for human processing of grass seeds, including barley and possibly wheat, in the form of starch grains recovered from a ground stone artefact from the Upper Palaeolithic site of Ohalo II in Israel. Associated evidence for an oven-like hearth was also found at this site, suggesting that dough made from grain flour was baked. Our data indicate that routine processing of a selected group of wild cereals, combined with effective methods of cooking ground seeds, were practiced at least 12,000 years before their domestication in southwest Asia.

Development of a 3D seed morphological tool for grapevine variety identification, and its comparison with SSR analysis.

Grapevine (Vitis vinifera L.) is one of the classical fruits of the Old World. Among the thousands of domesticated grapevine varieties and variable wild sylvestris populations, the range of variation in pip morphology is very wide. In this study we scanned representative samples of grape pip populations, in an attempt to probe the possibility of using the 3D tool for grape variety identification. The scanning was followed by mathematical and statistical analysis using innovative algorithms from the field of computer sciences. Using selected Fourier coefficients, a very clear separation was obtained between most of the varieties, with only very few overlaps. These results show that this method enables the separation between different Vitis vinifera varieties. Interestingly, when using the 3D approach to analyze couples of varieties, considered synonyms by the standard 22 SSR analysis approach, we found that the varieties in two of the considered synonym couples were clearly separated by the morphological analysis. This work, therefore, suggests a new systematic tool for high resolution variety discrimination.

Collection and characterization of grapevine genetic resources (Vitis vinifera) in the Holy Land, towards the renewal of ancient winemaking practices.

The importance and extent of wine consumption in all life aspects at the Holy Land is well documented. The Muslim influence in this region led to the abandonment of winemaking practices, and possible loss of indigenous wine varieties. Here we present a country wide collection of the local grapevine population including wild and cultivated forms, and its characterization by genetic, ampelographic and enological methods. The ampelographic analysis shows clear differences between Sativa and Sylvestris groups in flower, leaf and cluster parameters, and that most Sativa belong to proles orientalis. Genetic population analysis was conducted by analyzing 22 common SSR markers, determining first the unique genotypes, and internally assessing the population's structure, showing the existence of two distinct Sativa and Sylvestris populations, and a third mixed one. Likewise, the relationship between the Israeli grapevine population and grapevine populations in Europe and parts of Asia was investigated, showing that the Israeli Sativa and Sylvestris populations cluster closely together, suggesting a common genetic source. Lastly, the enological characteristics of selected Sativa and Sylvestris genotypes are presented, demonstrating their potential for quality wine production. This research significantly contributes toward the re-establishment of indigenous and traditional local grapevine varieties into the modern international wine industry.

Composite Sickles and Cereal Harvesting Methods at 23,000-Years-Old Ohalo II, Israel.

Use-wear analysis of five glossed flint blades found at Ohalo II, a 23,000-years-old fisher-hunter-gatherers' camp on the shore of the Sea of Galilee, Northern Israel, provides the earliest evidence for the use of composite cereal harvesting tools. The wear traces indicate that tools were used for harvesting near-ripe semi-green wild cereals, shortly before grains are ripe and disperse naturally. The studied tools were not used intensively, and they reflect two harvesting modes: flint knives held by hand and inserts hafted in a handle. The finds shed new light on cereal harvesting techniques some 8,000 years before the Natufian and 12,000 years before the establishment of sedentary farming communities in the Near East. Furthermore, the new finds accord well with evidence for the earliest ever cereal cultivation at the site and the use of stone-made grinding implements.

Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley.

The cereal grass barley was domesticated about 10,000 years before the present in the Fertile Crescent and became a founder crop of Neolithic agriculture. Here we report the genome sequences of five 6,000-year-old barley grains excavated at a cave in the Judean Desert close to the Dead Sea. Comparison to whole-exome sequence data from a diversity panel of present-day barley accessions showed the close affinity of ancient samples to extant landraces from the Southern Levant and Egypt, consistent with a proposed origin of domesticated barley in the Upper Jordan Valley. Our findings suggest that barley landraces grown in present-day Israel have not experienced major lineage turnover over the past six millennia, although there is evidence for gene flow between cultivated and sympatric wild populations. We demonstrate the usefulness of ancient genomes from desiccated archaeobotanical remains in informing research into the origin, early domestication and subsequent migration of crop species.

Studying Ancient Anthropogenic Impacts on Current Floral Biodiversity in the Southern Levant as reflected by the Philistine Migration.

Human migrations across geographic boundaries can facilitate the introduction of new husbandry practices and dispersal of plants and animals, resulting in changes in biodiversity. As previously demonstrated, the 12th century BCE Philistine migration-to the southern Levantine littoral, involved the transportation of pigs from Europe, engendering long term genetic displacement of local Near Eastern haplotypes. Building on this, and combining biogeographical methods of Floral List comparisons with archaeological data, we have elucidated the Philistine impact on Southern Levantine floral ecosystems. We demonstrate that previously unexploited local plants were incorporated into the Philistine milieu, and new species were introduced-from Europe, the Aegean, Egypt and Mesopotamia -resulting in the earliest locally cultivated sycamore, cumin, coriander, bay tree and opium poppy. This research has highlighted the impact of past cultures on the formation of floral ecosystems and their long-term effects on contemporary local biological diversity.

The Origin of Cultivation and Proto-Weeds, Long Before Neolithic Farming.

Weeds are currently present in a wide range of ecosystems worldwide. Although the beginning of their evolution is largely unknown, researchers assumed that they developed in tandem with cultivation since the appearance of agricultural habitats some 12,000 years ago. These rapidly-evolving plants invaded the human disturbed areas and thrived in the new habitat. Here we present unprecedented new findings of the presence of "proto-weeds" and small-scale trial cultivation in Ohalo II, a 23,000-year-old hunter-gatherers' sedentary camp on the shore of the Sea of Galilee, Israel. We examined the plant remains retrieved from the site (ca. 150,000 specimens), placing particular emphasis on the search for evidence of plant cultivation by Ohalo II people and the presence of weed species. The archaeobotanically-rich plant assemblage demonstrates extensive human gathering of over 140 plant species and food preparation by grinding wild wheat and barley. Among these, we identified 13 well-known current weeds mixed with numerous seeds of wild emmer, barley, and oat. This collection provides the earliest evidence of a human-disturbed environment-at least 11 millennia before the onset of agriculture-that provided the conditions for the development of "proto-weeds", a prerequisite for weed evolution. Finally, we suggest that their presence indicates the earliest, small-scale attempt to cultivate wild cereals seen in the archaeological record.

The broad spectrum revisited: evidence from plant remains.

The beginning of agriculture is one of the most important developments in human history, with enormous consequences that paved the way for settled life and complex society. Much of the research on the origins of agriculture over the last 40 years has been guided by Flannery's [Flannery, K. V. (1969) in The Domestication and Exploitation of Plants and Animals, eds. Ucko, P. J. & Dimbleby, G. W. (Duckworth, London), pp. 73-100] "broad spectrum revolution" (BSR) hypothesis, which posits that the transition to farming in southwest Asia entailed a period during which foragers broadened their resource base to encompass a wide array of foods that were previously ignored in an attempt to overcome food shortages. Although these resources undoubtedly included plants, nearly all BSR hypothesis-inspired research has focused on animals because of a dearth of Upper Paleolithic archaeobotanical assemblages. Now, however, a collection of >90,000 plant remains, recently recovered from the Stone Age site Ohalo II (23,000 B.P.), Israel, offers insights into the plant foods of the late Upper Paleolithic. The staple foods of this assemblage were wild grasses, pushing back the dietary shift to grains some 10,000 years earlier than previously recognized. Besides the cereals (wild wheat and barley), small-grained grasses made up a large component of the assemblage, indicating that the BSR in the Levant was even broader than originally conceived, encompassing what would have been low-ranked plant foods. Over the next 15,000 years small-grained grasses were gradually replaced by the cereals and ultimately disappeared from the Levantine diet.

Impetus for sowing and the beginning of agriculture: ground collecting of wild cereals.

The Agricultural Revolution in Western Asia, which took place some 11,000 years ago, was a turning point in human history [Childe, V. G. (1952) New Light on the Most Ancient East (Routledge & Kegan Paul, London)]. In investigating the cultural processes that could have led from gathering to intentional cultivation, various authors have discussed and tested wild cereal harvesting techniques. Some argue that Near Eastern foragers gathered grains by means of sickle harvesting, uprooting, plucking (hand stripping), or beating into baskets [Hillman, G. C. & Davies, M. S. (1999) in Prehistory of Agriculture: New Experimental and Ethnographic Approaches, ed. Anderson, P. (The Institute of Archaeology, University of California, Los Angeles), pp. 70-102]. During systematic experiments, we found that archaeobotanical data from regional Neolithic sites support ground collection of grains by early hunter-gatherers. Ground collecting suits the natural shattering of wild species that ripen and drop grains at the beginning of summer. We show that continual collection off the ground from May to October would have provided surplus grains for deliberate sowing in more desirable fields, and facilitate the transition to intentional cultivation. Because ground gathering enabled collectors to observe that fallen seeds are responsible for the growth of new plants in late fall, they became aware of the profitability of sowing their surplus seeds for next year's food. Ground collecting of wild barley and wild wheat may comprise the missing link between seed collecting by hunter-gatherers and cereal harvesting by early farmers.

Stone Age hut in Israel yields world's oldest evidence of bedding.

The earliest archaeological remains of dwelling huts built by Homo sapiens were found in various European Upper Paleolithic open-air camps. Although floors of huts were found in a small number of cases, modern organization of the home space that includes defined resting areas and bedding remains was not discovered. We report here the earliest in situ bedding exposed on a brush hut floor. It has recently been found at the previously submerged, excellently preserved 23,000-year-old fisher-hunter-gatherers' camp of Ohalo II, situated in Israel on the shore of the Sea of Galilee. The grass bedding consists of bunches of partially charred Puccinellia confer convoluta stems and leaves, covered by a thin compact layer of clay. It is arranged in a repeated pattern, on the floor, around a central hearth. This study describes the bedding in its original context on a well preserved intentionally constructed floor. It also reconstructs on the basis of direct evidence (combined with ethnographic analogies) the Upper Paleolithic hut as a house with three major components: a hearth, specific working locales, and a comfortable sleeping area near the walls.