Germination of 2000-year-old seeds of Phoenix dactylifera from Judean desert archaeological sites provides a unique opportunity to study the Judean date palm, described in antiquity for the quality, size, and medicinal properties of its fruit, but lost for centuries. Microsatellite genotyping of germinated seeds indicates that exchanges of genetic material occurred between the Middle East (eastern) and North Africa (western) date palm gene pools, with older seeds exhibiting a more eastern nuclear genome on a gradient from east to west of genetic contributions. Ancient seeds were significantly longer and wider than modern varieties, supporting historical records of the large size of the Judean date. These findings, in accord with the region’s location between east and west date palm gene pools, suggest that sophisticated agricultural practices may have contributed to the Judean date’s historical reputation. Given its exceptional storage potentialities, the date palm is a remarkable model for seed longevity research.

This study, which confirms the long-term survival of date palm seeds, provides a unique opportunity to rediscover the origins of a historic date palm population that existed in Judea 2000 years ago. The characteristics of the Judean date palm may shed light on aspects of ancient cultivation that contributed to the quality of its fruit and is thus of potential relevance to the agronomic improvement of modern dates.

In 2008, we reported the germination of a 1900-year-old date seed ( 6 ) recovered from the historical site of Masada overlooking the Dead Sea. In the current study, six additional ancient date seeds from archaeological sites in the Judean desert were germinated, bringing to seven the number of ancient genotypes genetically analyzed using molecular markers. In addition, morphometric analysis was used to compare the size and shape of ungerminated ancient date seeds with modern varieties and wild dates.

Date palms in the southern Levant (modern-day Israel, Palestine, and Jordan), situated between eastern and western domestication areas, have historically played an important economic role in the region and were also of symbolic and religious significance ( 5 ). The Kingdom of Judah (Judea) that arose in the southern part of the historic Land of Israel in the 11th century BCE was particularly renowned for the quality and quantity of its dates. These so-called “Judean dates” grown in plantations around Jericho and the Dead Sea were recognized by classical writers for their large size, sweet taste, extended storage, and medicinal properties ( 5 ). While evidence suggests that Judean date culture continued during the Byzantine and Arab periods (4th to 11th century CE), further waves of conquest proved so destructive that by the 19th century, no traces of these historic plantations remained ( 5 ).

The current date palm germplasm is constituted by two highly differentiated gene pools: an eastern population, consisting of cultivars extending from the Middle East and Arabian Peninsula to northwest India and Pakistan and a western population covering North Africa and sub-Saharan Africa ( 3 , 4 ). Introgressive hybridization by a wild relative in North African date palms has been proposed as a source of this differentiation ( 2 ).

The date palm (Phoenix dactylifera), a dioecious species in the Arecaceae (formerly Palmae) family has a historical distribution stretching from Mauritania in the west to the Indus Valley in the east ( 1 ). A major fruit crop in hot and arid regions of North Africa and the Middle East and one of the earliest domesticated tree crops, archaeobotanical records suggest that the earliest exploitation and consumption of dates is from the Arabian Neolithic some 7000 years before the present (yr B.P.) ( 1 ). Evidence of cultivation in Mesopotamia and Upper Arabian Gulf approximately 6700 to 6000 yr B.P. support these centers as the ancient origin of date palm domestication in this region, with a later establishment of oasis agriculture in North Africa ( 1 , 2 ).

To shed light on genetic diversity of the ancient dates, basic population genetic parameters were estimated and compared to modern reference collections (tables S5 and S6). The ancient genotypes showed an allelic richness value ( A r ) (i.e., the number of alleles) of 3.59, a relatively high diversity for such a small sample size (seven genotypes) compared to values of other countries sampled (table S6). Genetic relationships between the ancient date and current varieties ( Fig. 6 and table S7) show Methuselah and Adam close to eastern modern varieties Fardh4 and Khalass, respectively, assigned to current Arabian Gulf varieties; Hannah and Judith related to modern Iraqi varieties Khastawi and Khyara, respectively; and Uriel, Boaz, and Jonah, the most western genotypes, related to modern Moroccan varieties, Mahalbit, Jihel, and Medjool, respectively.

Structure analysis revealed that distribution of the germinated ancient date seeds was within previously described eastern and western date palm gene pools ( Fig. 5A ). Methuselah, Hannah, and Adam are the most eastern genotypes, although they also show ancient western contributions requiring numerous generations and highlighting ancient crosses. Boaz and Judith are the most admixed, with almost equal eastern and western contributions reflecting more recent crossings. Jonah and Uriel are the most western genotypes with the most western parental lineages ( Fig. 5B ).

The sex of the six germinated ancient date seedlings in the current study identified using three sex-linked simple sequence repeats (SSR) ( 11 ) were as follows: Judith and Hannah are female genotypes and Uriel, Jonah, Boaz, Adam, and Methuselah (seed 3) from the previous study ( 6 ) are male genotypes. Through microsatellite genotyping, three levels of genetic inheritance were investigated to highlight geographic origins ( Fig. 5, A and B ): (i) inheritance transmitted by both parents to progeny, obtained by microsatellite markers showing western and eastern patterns of the ancient seed’s genomes ( 4 ), as presented in structure analysis and pie charts ( Fig. 5A ); (ii) inheritance transmitted from mother to progeny through the chloroplast genome, reflecting maternal lineage origin by reporting chloroplastic minisatellite eastern or western alleles ( Fig. 5B , arrow) ( 12 ); and (iii) inheritance transmitted from father to son through the Y chromosome, reflecting paternal lineage origin by reporting male specific sex-linked eastern or western alleles ( Fig. 5B , arrow) ( 11 ).

Analysis of seed shape diversity in current and ancient date seeds using principal components analysis (PCA) (dudi.pca function) performed on seed outlines confirmed visual observation that modern cultivated seeds were more diverse in size than ancient ones but did not differentiate between the two groups [multivariate analysis of variance (MANOVA), P > 0.05]. Ancient seeds displayed an elongated shape similar to current cultivated samples (fig. S2).

When only compared to the cultivars, the ancient date seeds were still larger: 24.55% wider (t = −11.923, df = 18.391, P = 2.157 × 10 −10 ) and 34.06% longer (t = −7.422, df = 17.952, P = 3.564 × 10 −7 ). However, the contrast in seed size is even more marked when comparing ancient seeds and current wild date palms: The Judean date palm seeds were, on average, 39.55% wider (t = −19.185, df = 18.471, P = 5.943 × 10 −14 ) and 65.48% longer than current wild samples (t = −11.311, df = 19.574, P = 2.472 × 10 −10 ) (tables S3 and S4).

Length (millimeters) (left) and width (millimeters) (right) of ancient date seeds that failed to germinate (n = 18), 9 current wild individuals (n = 180), and 48 cultivated P. dactylifera varieties (n = 928). Letters a, b, and c above boxes indicate Tukey’s groups derived from HSD.test function and R package agricolae.

Eighteen ancient date seeds that failed to germinate were recovered from the potting soil and compared with modern seeds derived from 57 current date palms of which 48 are cultivated varieties and 9 are wild individuals ( 9 , 10 ). Ancient seeds were significantly larger in terms of both length and width (length, 27.62 ± 3.96 mm; width, 10.38 ± 0.71 mm) than both current cultivar (length, 20.60 ± 4.70 mm; width, 8.33 ± 1.02 mm) and wild date palm seeds (length, 16.69 ± 3.39 mm; width, 7.08 ± 0.46 mm) ( Fig. 4 ). Ancient seeds were, on average, 27.69% wider (t = −11.923, df = 18.391, P = 2.157 × 10 −10 ) and 38.37% longer than the combined current samples (wild and cultivated) (t = −7.422, df = 17.952, P = 3.564 × 10 −7 ).

Radiocarbon ages are shown ( Fig. 3 and table S2) for ancient date seeds germinated in the current study and also for the date seed (“seed 3”/“Methuselah”) germinated in our previous work ( 6 ). These ages were obtained from seed shell fragments found clinging to the rootlets of germinated seedlings during their transfer into larger pots (3 to 17 months of age). The values were recalculated to take into account contamination by modern carbon incorporated during seedling growth previously shown to reduce measured radiocarbon age by approximately 250 to 300 years, equivalent to 2 to 3% modern carbon (table S2) ( 6 ). On the basis of these calculations, Methuselah germinated in our previous study ( 6 ) and Hannah and Adam in the current study are the oldest samples (first to fourth centuries BCE), Uriel and Jonah are the youngest (first to second centuries CE), and Judith and Boaz are intermediate (mid-second century BCE to mid-first century CE) ( Fig. 3 ).

On visual inspection, no specific observation linked the ability of these seeds to germinate compared with those that failed to germinate. Before planting, the ancient date seeds had been weighted, and their length was measured, with the exception of those seeds from Masada, (including Adam, the germinated seed), which unfortunately were not measured (table S1). No statistically significant differences were found between germinated and ungerminated seeds in either weight {1.67 ± 0.55 and 1.61 ± 0.29 g, respectively [Student’s t test (t) = 0.348, degree of freedom (df) = 24, P = 0.731]} or length [27.60 ± 3.7 and 26.8 ± 3.7 mm, respectively (t = 0.455, df = 24, P = 0.653)].

Of the hundreds of ancient date seeds and other botanical material recovered from excavations carried out in the Judean desert between 1963 and 1991 ( 7 , 8 ) (fig. S1), 32 well-preserved date seeds from the archaeological sites of Masada, Qumran, Wadi Makukh, and Wadi Kelt were planted in a quarantine site at Kibbutz Ketura (table S1). Of these, six ancient seeds germinated and were further identified by the following monikers: Masada: “Adam”; Qumran: “Jonah,” “Uriel,” “Boaz,” and “Judith”; and Wadi Makukh: “Hannah” ( Figs. 1 and 2 ).

DISCUSSION

In the current study, six ancient date seeds, in addition to the seedling obtained in our previous study (6), were germinated. All the seeds were approximately 2000 years old and had been previously recovered from archaeological sites in the Judean desert, a rain shadow desert of ca. 1500 km2 located between the maquis-covered Judean Hills and the Dead Sea (fig. S1).

Little is known about the mechanisms determining seed longevity; however, it has been related to the ability to remain in a dry quiescent state (13). In the current study, low precipitation and very low humidity around the Dead Sea could have contributed to the longevity of the ancient date seeds, which may be an adaptation of date palms to extreme desert conditions fostering seed dispersion. Their remarkable durability, however, may also be connected to other extreme environmental conditions in this area; at 415 m below mean sea level, the Dead Sea and its surroundings have the thickest atmosphere on Earth, leading to a unique radiation regime and a complex haze layer associated with the chemical composition of the Dead Sea water (14). However, since no visible evidence in the current study was linked to seed germination and, accordingly, to their long term survival, further investigations are needed to understand the basis of date palm seed longevity.

Among the world’s oldest cultivated fruit trees, P. dactylifera is the emblematic of oasis agriculture and highly symbolic in Muslim, Christian, and Jewish religions (5). Closely connected to the history of human migrations, the first cultivated varieties of P. dactylifera are thought to have originated around Mesopotamia and the Upper Arabian Gulf some 6700 to 6000 yr B.P. (1, 2, 10). In Judea, an ancient geopolitical region that arose during the 11th century BCE in the southern part of the historic Land of Israel, and situated at the cross roads of Africa, Asia, and Europe, the origins of date palm cultivation are unknown. However, from historical records, a thriving Judean date culture was present around Jericho, the Dead Sea, and Jordan Valley from the fifth century BCE onward, benefitting from an optimal oasis agriculture environment of freshwater sources and subtropical climate (5).

Described by classical writers including Theophrastus, Herodotus, Galen, Strabo, Pliny the Elder, and Josephus, these valuable plantations produced dates attributed with various qualities including large size, nutritional and medicinal benefits, sweetness, and a long storage life, enabling them to be exported throughout the Roman Empire (5, 15, 16). Several types of Judean dates are also described in antiquity including the exceptionally large “Nicolai” variety measuring up to 11 cm (5, 15, 16).

In the current study, ancient seeds were significantly longer and wider than both modern date varieties and wild date palms. Previous research has established that both fruits and seeds are larger in domesticated fruit crops compared with their wild ancestors (17), suggesting that the ancient seeds were of cultivated origin (9, 18), most likely originating from the region’s date plantations. Furthermore, an increase in seed size has been linked allometrically to an increase in fruit size (19), corroborating the historical descriptions of the large fruits grown in this region.

Genotypes of the germinated ancient date seedlings cover a large part of present-day date palm distribution area, findings that reflect the variety, richness, and probable influences of the historic Judean date groves. Microsatellite genotyping shows a relatively high diversity, with eastern and western gene pool contributions, allelic richness, and genetic proximity to current varieties cultivated in the Arabian Peninsula, Iraq, and North Africa. Although the sample size is small, a predominance of eastern female lineages (six of seven) indicates that eastern female varieties grown from local germplasm were probably clonally propagated from offshoots to maintain desirable fruit qualities. Male lineages, mainly western (four of five), suggest that genetically different or “foreign” males were used for pollination. This assumption is supported by first century texts, indicating that substantial knowledge existed in ancient Judea 2000 years ago regarding the most suitable males for pollination of female date palms (20).

Our results reinforce the historical narrative that a highly sophisticated domestication culture existed in ancient Judea. Local farmers with an interest in maintaining genetic diversity in their date plantations and anthropogenic pressures leading to selection on fruit dimension and other desirable traits used cross-breeding with foreign (genetically different) males to develop a rich collection of varieties.

These findings suggest that Judean date culture was influenced by a variety of migratory, economic, and cultural exchanges that took place in this area over several millennia.

In Israel, the oldest remains of P. dactylifera are wood specimens 19,000 yr B.P. from Ohalo II site on the Sea of Galilee (21). Recovery of carbonized date seeds from Chalcolithic and Early Bronze Age sites (4500 to 2900 BCE) in the Judean desert, Jordan Valley, and Jericho (22, 23) and early Iron Age sites in Israel (12th to 11th century BCE) (24) suggest that human exploitation and consumption of dates occurred at this time. However, it is unclear whether these samples, which are relatively few in number and of very small size (22, 25, 26), are derived from ancient wild populations, as suggested by morphometric studies of modern wild date populations (18) or represent an early stage of the domestication process.

In the current study, although the sample size is too small to claim a trend, on a gradient from east to west genetic contributions, the older the germinated seeds are on radiocarbon dating (Fig. 3), the more eastern is the nuclear genome (Fig. 5, A and B ). In this respect, Methuselah, Adam, and Hannah (first to fourth centuries BCE) have a predominantly eastern nuclear genome and eastern maternal lineage, their relationship to modern varieties from the Arabian Gulf and Iraq suggesting that they belong to the same eastern genetic background.

The P. dactylifera cultivated by the inhabitants of Judea at that time therefore appears to be from the eastern gene pool, possibly growing locally and related to oasis populations, of which relict populations were recently found in Oman (9).

Elite female cultivars may also have been introduced to ancient Israel from these regions, consistent with a pattern of human intervention and possibly active acquisition of date palm varieties. Established trade links are documented with Arabia and the Persian Gulf from at least the 12th century BCE (27). Babylonian date palm cultivation in southern Mesopotamia (most of modern Iraq), originating some 6000 yr B.P. (1, 2), used deportees from ancient Judea following its conquest in the sixth century BCE (28). After the collapse of the Neo-Babylonian Empire, returning exiles may have brought this specialized knowledge and selected cultivars back to Judea; a date variety “Taali” cultivated in both Judea and Babylon is mentioned in the Talmud (29).

Western genetic admixtures in the germinated seedlings and their proximity to current cultivated date varieties from Morocco also suggest that ancient Judean date palms were the result of germplasm exchanges with this area and of multiple crosses. Introgression of eastern genomes into western ones are common, detected in varieties from Algeria, Morocco, Mauritania, and particularly east-west junction areas like Egypt (1, 2, 4, 30). In the latter, eastern contributions from the Persian Gulf, detected in ancient Egypt date seeds from 1400 BCE to 800 CE, reveal a chronological pattern of change in agrobiodiversity and the possible emergence of a western form in the Roman period (10).

Introgression of date palm western genomes into eastern ones, however, is far lower (1, 2, 4, 12), their presence in the current study reflecting west to east exchanges.

The origins of these exchanges are unclear; however, archaeological evidence indicates that North Africa, Near East, and Mediterranean cultures were clearly linked during the Neolithic in the southern Levant (approximately 11,700 to 7300 B.P.) and were associated in Jericho with the earliest origins of food production and fundamental changes in human subsistence strategies (31).

Phoenicia, a maritime trading nation occupying the coastal areas of modern northern Israel, Lebanon, and Syria (1500 to 300 BCE), was also historically associated with cultivation and trade of date palms (32). We can speculate that later west to east germplasm exchanges to this region may have been associated with domesticated varieties originating in Phoenician City States in North African (e.g., Carthage in present-day Tunisia) (32), where oasis agriculture appeared relatively late in the archaeological record (3).

The most western genotypes in the current study (Uriel and Jonah) are also the youngest seeds (mid-first to mid-second CE), coinciding with established trade routes linking this region to North Africa and supporting evidence for date consumption in the latter 2000 years ago (2, 3). This period coincides with Judea’s well-documented wars against Rome (66 to 73 CE and 132 to 136 CE) and deportation and displacement of its population (16). The ancient seeds in the current study were found in the Judean desert, historically a place of refuge due to its steep cliffs and inaccessible caves (16, 23). The loss of political autonomy and the final collapse of Judea have been postulated as causing major disruption to labor intensive practices associated with date cultivation (33). Elite cultivars no longer conserved by vegetative propagation (offshoots) were gradually replaced by seedling date palms producing fruits displaying considerable variation within the progeny. Although P. dactylifera can live for more than 100 years (33) and date groves in this region are thought to have persisted for several more centuries, they were already rare by the 11th century and had been entirely replaced by seedling populations or feral, wild trees producing only low-quality fruit (5, 33), by the 19th century.

The current study sheds light on the origins of the Judean date palm, suggesting that its cultivation, benefitting from genetically distinct eastern and western populations, arose from local or introduced eastern varieties, which only later were crossed with western varieties. These findings are consistent with Judea’s location between east-west date palm diversification areas, ancient centers of date palm cultivation, and the impact of human dispersal routes at this crossroads of continents.

Given its exceptional storage potentialities, the date palm is a remarkable model for seed longevity research. Investigations on the molecular mechanisms involved in long-term protection in the dried state have important implications on plant adaptation to changing environments and for biodiversity conservation and seed banking. As new information on specific gene-associated traits (e.g., fruit color and texture) (3) is found, we hope to reconstruct the phenotypes of this historic date palm, identify genomic regions associated with selection pressures over recent evolutionary history, and study the properties of dates produced by using ancient male seedlings to pollinate ancient females. In doing so, we will more fully understand the genetics and physiology of the ancient Judean date palm once cultivated in this region.