Unraveling the diversity and cultural heritage of fruit crops through paleogenomics.

Abundant and plentiful fruit crops are threatened by the loss of diverse legacy cultivars which are being replaced by a limited set of high-yielding ones. This article delves into the potential of paleogenomics that utilizes ancient DNA analysis to revive lost diversity. By focusing on grapevines, date palms, and tomatoes, recent studies showcase the effectiveness of paleogenomic techniques in identifying and understanding genetic traits crucial for crop resilience, disease resistance, and nutritional value. The approach not only tracks landrace dispersal and introgression but also sheds light on domestication events. In the face of major future environmental challenges, integrating paleogenomics with modern breeding strategies emerges as a promising avenue to significantly bolster fruit crop sustainability.

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.

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.

New insights into the Upper Palaeolithic of the Caucasus through the study of personal ornaments. Teeth and bones pendants from Satsurblia and Dzudzuana caves (Imereti, Georgia).

The region of western Georgia (Imereti) in the Southern Caucasus has been a major geographic corridor for human migrations during the Middle and Upper Paleolithic. Data of recent research and excavations in this region display its importance as a possible route for the dispersal of anatomically modern humans (AMH) into northern Eurasia. Nevertheless, within the local research context, bone-working and personal ornaments have yet contributed but little to the Upper Palaeolithic (UP) regional sequence's characterization. Here we present an archaeozoological, technological and use-wear study of pendants from two local UP assemblages, originating in the Dzudzuana Cave and Satsurblia Cave. The ornaments were made mostly of perforated teeth, though some specimens were made on bone. Both the manufacturing marks made during preparation and use-wear traces indicate that they were personal ornaments, used as pendants or attached to garments. Detailed comparison between ornament assemblages from northern and southern Caucasus reveal that they are quite similar, supporting the observation of cultural bonds between the two regions, demonstrated previously through lithic techno-typological affinities. Furthermore, our study highlights the importance attributed to red deer (Cervus elaphus) by the UP societies of the Caucasus in sharing aesthetic values and/or a symbolic sphere.

Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment.

Cave sediments have been shown to preserve ancient DNA but so far have not yielded the genome-scale information of skeletal remains. We retrieved and analyzed human and mammalian nuclear and mitochondrial environmental "shotgun" genomes from a single 25,000-year-old Upper Paleolithic sediment sample from Satsurblia cave, western Georgia:first, a human environmental genome with substantial basal Eurasian ancestry, which was an ancestral component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe; second, a wolf environmental genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage; and third, a European bison environmental genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the Late Pleistocene genetic histories of these three species and demonstrate that direct shotgun sequencing of sediment DNA, without target enrichment methods, can yield genome-wide data informative of ancestry and phylogenetic relationships.

Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears.

Palaeogenomes provide the potential to study evolutionary processes in real time, but this potential is limited by our ability to recover genetic data over extended timescales.1 As a consequence, most studies so far have focused on samples of Late Pleistocene or Holocene age, which covers only a small part of the history of many clades and species. Here, we report the recovery of a low coverage palaeogenome from the petrous bone of a ∼360,000 year old cave bear from Kudaro 1 cave in the Caucasus Mountains. Analysis of this genome alongside those of several Late Pleistocene cave bears reveals widespread mito-nuclear discordance in this group. Using the time interval between Middle and Late Pleistocene cave bear genomes, we directly estimate ursid nuclear and mitochondrial substitution rates to calibrate their respective phylogenies. This reveals post-divergence mitochondrial transfer as the dominant factor explaining their mito-nuclear discordance. Interestingly, these transfer events were not accompanied by large-scale nuclear introgression. However, we do detect additional instances of nuclear admixture among other cave bear lineages, and between cave bears and brown bears, which are not associated with mitochondrial exchange. Genomic data obtained from the Middle Pleistocene cave bear petrous bone has thus facilitated a revised evolutionary history of this extinct megafaunal group. Moreover, it suggests that petrous bones may provide a means of extending both the magnitude and time depth of palaeogenome retrieval over substantial portions of the evolutionary histories of many mammalian clades.

Origins and genetic legacy of prehistoric dogs.

Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry.

Byzantine-Early Islamic resource management detected through micro-geoarchaeological investigations of trash mounds (Negev, Israel).

Sustainable resource management is of central importance among agrarian societies in marginal drylands. In the Negev Desert, Israel, research on agropastoral resource management during Late Antiquity emphasizes intramural settlement contexts and landscape features. The importance of hinterland trash deposits as diachronic archives of resource use and disposal has been overlooked until recently. Without these data, assessments of community-scale responses to societal, economic, and environmental disruption and reconfiguration remain incomplete. In this study, micro-geoarchaeological investigations were conducted on trash mound features at the Byzantine-Early Islamic sites of Shivta, Elusa, and Nesanna to track spatiotemporal trends in the use and disposal of critical agropastoral resources. Refuse derived sediment deposits were characterized using stratigraphy, micro-remains (i.e., livestock dung spherulites, wood ash pseudomorphs, and plant phytoliths), and mineralogy by Fourier transform infrared spectroscopy. Our investigations detected a turning point in the management of herbivore livestock dung, a vital resource in the Negev. We propose that the scarcity of raw dung proxies in the studied deposits relates to the use of this resource as fuel and agricultural fertilizer. Refuse deposits contained dung ash, indicating the widespread use of dung as a sustainable fuel. Sharply contrasting this, raw dung was dumped and incinerated outside the village of Nessana. We discuss how this local shift in dung management corresponds with a growing emphasis on sedentised herding spurred by newly pressed taxation and declining market-oriented agriculture. Our work is among the first to deal with the role of waste management and its significance to economic strategies and urban development during the late Roman Imperial Period and Late Antiquity. The findings contribute to highlighting top-down societal and economic pressures, rather than environmental degradation, as key factors involved in the ruralisation of the Negev agricultural heartland toward the close of Late Antiquity.

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.

Climate stability and societal decline on the margins of the Byzantine empire in the Negev Desert.

Understanding past human settlement of inhospitable regions is one of the most intriguing puzzles in archaeological research, with implications for more sustainable use of marginal regions today. During the Byzantine period in the 4th century CE, large settlements were established in the arid region of the Negev Desert, Israel, but it remains unclear why it did so, and why the settlements were abandoned three centuries later. Previous theories proposed that the Negev was a "green desert" in the early 1st millennium CE, and that the Byzantine Empire withdrew from this region due to a dramatic climatic downturn. In the absence of a local climate archive correlated to the Byzantine/Early Islamic transition, testing this theory has proven challenging. We use stable isotopic indicators of animal dietary and mobility patterns to assess the extent of the vegetative cover in the desert. By doing so, we aim to detect possible climatic fluctuations that may have led to the abandonment of the Byzantine settlements. The findings show that the Negev Desert was not greener during the time period under investigation than it is today and that the composition of the animals' diets, as well as their grazing mobility patterns, remained unchanged through the Byzantine/Early Islamic transition. Favoring a non-climatic explanation, we propose instead that the abandonment of the Negev Byzantine settlements was motivated by restructuring of the Empire's territorial priorities.

Polyplax brachyrrhyncha (Anoplura: Polyplacidae) and Rhipicephalus turanicus (Ixodidae: Rhipicephalinae) in an Ancient Louse Comb.

A fine-toothed comb found in the Judean Desert and resembling an ancient louse comb was examined. Based on radiocarbon dating, it ranged between 1660 AD and 1950 AD. From the material accumulated between the teeth, an oribatid mite, a pseudoscorpion, exuviae of beetle larvae, a sucking louse (Polyplax brachyrrhyncha Cummings, 1915), as well as a fully engorged larva and a nymph of the ixodid tick Rhipicephalus turanicus Pomerantzev, 1936 were recorded. Additionally, the comb included numerous hairs of a spiny mouse (Acomys sp.). Although finding mites, beetle larvae, and a pseudoscorpion on a louse comb could be regarded as contamination, the findings of P. brachyrrhyncha, as well as of a larva and nymph of R. turanicus, are noteworthy. We hypothesize that the presence of animal lice and ticks could indicate some sort of pet grooming.

Zooarchaeology of the social and economic upheavals in the Late Antique-Early Islamic sequence of the Negev Desert.

The Byzantine - Islamic transition (7th-8th centuries CE) in the desert-edge Palaestina Tertia is examined using faunal remains recovered from archaeological sites in the Negev. Archaeozoological analyses suggest sharp differences between Late Byzantine and Early Islamic animal economies, especially in herding patterns and the exploitation of wildlife resources. These differences are suggested to reflect both cultural and land ownership changes following the Arab conquest, against the backdrop of climatic change. The archaeozoological record thereby provides independent evidence to the rise and fall of societal complexity in this marginal region.

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.

Partial genomic survival of cave bears in living brown bears.

Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species.

Ancient goat genomes reveal mosaic domestication in the Fertile Crescent.

Current genetic data are equivocal as to whether goat domestication occurred multiple times or was a singular process. We generated genomic data from 83 ancient goats (51 with genome-wide coverage) from Paleolithic to Medieval contexts throughout the Near East. Our findings demonstrate that multiple divergent ancient wild goat sources were domesticated in a dispersed process that resulted in genetically and geographically distinct Neolithic goat populations, echoing contemporaneous human divergence across the region. These early goat populations contributed differently to modern goats in Asia, Africa, and Europe. We also detect early selection for pigmentation, stature, reproduction, milking, and response to dietary change, providing 8000-year-old evidence for human agency in molding genome variation within a partner species.

The Emergence of Animal Management in the Southern Levant.

Our compilation of zooarchaeological data from a series of important archaeological sites spanning the Epipaleolithic through Pre-Pottery Neolithic B periods in the Mediterranean Hills of the southern Levant contributes to major debates about the beginnings of ungulate management in Southwest Asia. The data support an onset of ungulate management practices by the Early PPNB (10,500-10,000 cal. BP), more than 500 years earlier than previously thought for this region. There is a clear developmental connection between reduced hunting intensity and the uptake of ungulate management, confirming that this process began in response to local, density-dependent demographic factors. The early process of goat domestication in the southern Levant appears to have been overwhelmingly local. This may have been true for cattle and pigs as well. Nevertheless, the loose synchrony of animal management trends across Southwest Asia was undoubtedly enabled by large-scale social networks that transmitted knowledge. The results add to growing evidence that animal management processes followed multiple regional evolutionary pathways within the Fertile Crescent.

Pigeons at the edge of the empire: Bioarchaeological evidences for extensive management of pigeons in a Byzantine desert settlement in the southern Levant.

Metric data of 6th century CE pigeons from the Negev Desert, Israel, are employed to test competing hypotheses on flock management strategies: that directed selection for size or shape took place under intensive management; or, alternatively, that stabilizing selection was a stronger determinant of size and shape under extensive management conditions. The results of the analysis support the second hypothesis by demonstrating that the Byzantine Negev pigeons were like wild pigeon (Columba livia) in shape, albeit small-sized. The inferred extensive management system is then discussed in the context of pigeon domestication and human micro-ecologies in marginal regions.

A glimpse of an ancient agricultural ecosystem based on remains of micromammals in the Byzantine Negev Desert.

It is widely believed that Byzantine agriculture in the Negev Desert (fourth to seventh century Common Era; CE), with widespread construction of terraces and dams, altered local landscapes. However, no direct evidence in archaeological sites yet exists to test this assumption. We uncovered large amounts of small mammalian remains (rodents and insectivores) within agricultural installations built near fields, providing a new line of evidence for reconstructing anthropogenic impact on local habitats. Abandonment layers furnished high abundances of remains, whereas much smaller numbers were retrieved from the period of human use of the structures. Digestion marks are present in low frequencies (20% of long bones and teeth), with a light degree of impact, which indicate the role of owls (e.g. Tyto alba) as the principal means of accumulation. The most common taxa-gerbils (Gerbillus spp.) and jirds (Meriones spp.)-occur in nearly equal frequencies, which do not correspond with any modern Negev communities, where gerbils predominate in sandy low-precipitation environments and jirds in loessial, higher-precipitation ones. Although low-level climate change cannot be ruled out, the results suggest that Byzantine agriculture allowed jirds to colonize sandy anthropogenic habitats with other gerbilids and commensal mice and rats.