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.

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.

Rare crested rat subfossils unveil Afro-Eurasian ecological corridors synchronous with early human dispersals.

Biotic interactions between Africa and Eurasia across the Levant have invoked particular attention among scientists aiming to unravel early human dispersals. However, it remains unclear whether behavioral capacities enabled early modern humans to surpass the Saharo-Arabian deserts or if climatic changes triggered punctuated dispersals out of Africa. Here, we report an unusual subfossil assemblage discovered in a Judean Desert's cliff cave near the Dead Sea and dated to between ∼42,000 and at least 103,000 y ago. Paleogenomic and morphological comparisons indicate that the specimens belong to an extinct subspecies of the eastern African crested rat, Lophiomys imhausi maremortum subspecies nova, which diverged from the modern eastern African populations in the late Middle Pleistocene ∼226,000 to 165,000 y ago. The reported paleomitogenome is the oldest so far in the Levant, opening the door for future paleoDNA analyses in the region. Species distribution modeling points to the presence of continuous habitat corridors connecting eastern Africa with the Levant during the Last Interglacial ∼129,000 to 116,000 y ago, providing further evidence of the northern ingression of African biomes into Eurasia and reinforcing previous suggestions of the critical role of climate change in Late Pleistocene intercontinental biogeography. Furthermore, our study complements other paleoenvironmental proxies with local-instead of interregional-paleoenvironmental data, opening an unprecedented window into the Dead Sea rift paleolandscape.

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.

Eastern Mediterranean Mobility in the Bronze and Early Iron Ages: Inferences from Ancient DNA of Pigs and Cattle.

The Late Bronze of the Eastern Mediterranean (1550-1150 BCE) was a period of strong commercial relations and great prosperity, which ended in collapse and migration of groups to the Levant. Here we aim at studying the translocation of cattle and pigs during this period. We sequenced the first ancient mitochondrial and Y chromosome DNA of cattle from Greece and Israel and compared the results with morphometric analysis of the metacarpal in cattle. We also increased previous ancient pig DNA datasets from Israel and extracted the first mitochondrial DNA for samples from Greece. We found that pigs underwent a complex translocation history, with links between Anatolia with southeastern Europe in the Bronze Age, and movement from southeastern Europe to the Levant in the Iron I (ca. 1150-950 BCE). Our genetic data did not indicate movement of cattle between the Aegean region and the southern Levant. We detected the earliest evidence for crossbreeding between taurine and zebu cattle in the Iron IIA (ca. 900 BCE). In light of archaeological and historical evidence on Egyptian imperial domination in the region in the Late Bronze Age, we suggest that Egypt attempted to expand dry farming in the region in a period of severe droughts.

Faunal record identifies Bering isthmus conditions as constraint to end-Pleistocene migration to the New World.

Human colonization of the New World is generally believed to have entailed migrations from Siberia across the Bering isthmus. However, the limited archaeological record of these migrations means that details of the timing, cause and rate remain cryptic. Here, we have used a combination of ancient DNA, 14C dating, hydrogen and oxygen isotopes, and collagen sequencing to explore the colonization history of one of the few other large mammals to have successfully migrated into the Americas at this time: the North American elk (Cervus elaphus canadensis), also known as wapiti. We identify a long-term occupation of northeast Siberia, far beyond the species's current Old World distribution. Migration into North America occurred at the end of the last glaciation, while the northeast Siberian source population became extinct only within the last 500 years. This finding is congruent with a similar proposed delay in human colonization, inferred from modern human mitochondrial DNA, and suggestions that the Bering isthmus was not traversable during parts of the Late Pleistocene. Our data imply a fundamental constraint in crossing Beringia, placing limits on the age and mode of human settlement in the Americas, and further establish the utility of ancient DNA in palaeontological investigations of species histories.

Ancient DNA and population turnover in southern levantine pigs--signature of the sea peoples migration?

Near Eastern wild boars possess a characteristic DNA signature. Unexpectedly, wild boars from Israel have the DNA sequences of European wild boars and domestic pigs. To understand how this anomaly evolved, we sequenced DNA from ancient and modern pigs from Israel. Pigs from Late Bronze Age (until ca. 1150 BCE) in Israel shared haplotypes of modern and ancient Near Eastern pigs. European haplotypes became dominant only during the Iron Age (ca. 900 BCE). This raises the possibility that European pigs were brought to the region by the Sea Peoples who migrated to the Levant at that time. Then, a complete genetic turnover took place, most likely because of repeated admixture between local and introduced European domestic pigs that went feral. Severe population bottlenecks likely accelerated this process. Introductions by humans have strongly affected the phylogeography of wild animals, and interpretations of phylogeography based on modern DNA alone should be taken with caution.

Late-glacial recolonization and phylogeography of European red deer (Cervus elaphus L.).

The Pleistocene was an epoch of extreme climatic and environmental changes. How individual species responded to the repeated cycles of warm and cold stages is a major topic of debate. For the European fauna and flora, an expansion-contraction model has been suggested, whereby temperate species were restricted to southern refugia during glacial times and expanded northwards during interglacials, including the present interglacial (Holocene). Here, we test this model on the red deer (Cervus elaphus) a large and highly mobile herbivore, using both modern and ancient mitochondrial DNA from the entire European range of the species over the last c. 40,000 years. Our results indicate that this species was sensitive to the effects of climate change. Prior to the Last Glacial Maximum (LGM) haplogroups restricted today to South-East Europe and Western Asia reached as far west as the UK. During the LGM, red deer was mainly restricted to southern refugia, in Iberia, the Balkans and possibly in Italy and South-Western Asia. At the end of the LGM, red deer expanded from the Iberian refugium, to Central and Northern Europe, including the UK, Belgium, Scandinavia, Germany, Poland and Belarus. Ancient DNA data cannot rule out refugial survival of red deer in North-West Europe through the LGM. Had such deer survived, though, they were replaced by deer migrating from Iberia at the end of the glacial. The Balkans served as a separate LGM refugium and were probably connected to Western Asia with genetic exchange between the two areas.