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Aside from these 2,000 y old date palms, we have already noted studies of germination of 1,300 y old lotus seeds (20) and even ∼30,000 y old Silene sp. from the Siberian permafrost (19). Investigators have also reported germinating 151 y old acacia seeds (65) and 680 y old peatland Sphagnum spores (66) as well as obtaining live callus tissue from 1,600 y old Anagyris foetida seeds (67). Reviving organisms need not be limited to plants, as there have been sediments with reported revivals of 100 y old diatoms (68), 150 y old dinoflagellates (69), and 700 y old Daphnia pulicaria (70). As in ancient DNA studies, it will be important to ensure that the samples have good provenance and are properly dated to ensure authenticity. Moreover, there is a possibility that a bias in which samples can be revived may lead to a skew in the resulting data, and this should be considered when drawing conclusions from these studies. Nevertheless, the prospect of investigating the genomes of individuals that have lived 10 2 to 10 4 y ago provides unprecedented opportunities to directly examine the biology of life from the past.
Oasis agriculture and the cultivation of the date palm is first apparent in southern Mesopotamia during the fifth millennium BCE and was developed across the Gulf region from around 3,000 BCE (23). Phoenix dactylifera was presumably domesticated in this region, supported by the discovery of wild date populations in Oman (31, 35). In North Africa, date palm cultivation may not have begun in Egypt until ∼3,500 y ago (26, 27) and further west in the Maghreb, by the first millennium BCE (25, 36). Modern North African date palms are both strongly differentiated from and have higher levels of nucleotide diversity than West Asian P. dactylifera (29 ⇓ –31). It was shown recently that this pattern can be explained in part by interspecific hybridization of wild P. theophrasti or a theophrasti-like population into West Asian P. dactylifera (30). Phoenix theophrasti is found on the island of Crete and in isolated populations on other Aegean islands and southwest Turkey (45) but may have had a broader geographic range in the Eastern Mediterranean in the past (46). The timing and localization of the introgression event(s) remain largely unknown (30, 35), and genome analysis of the germinated Judean date palms provides an opportunity to characterize this introgression in ∼2,000 y old samples originating from a region at the geographic juncture of North Africa and West Asia.
We previously showed that the cultivated date palms of North Africa evolved as a hybrid between the domesticated palms of West Asia and the wild P. theophrasti, although when and where this hybridization took place remains unclear (30, 35). From our analyses of the Judean date palms, it is apparent that by ∼2,400 to 2,000 y ago, the hybridization event(s) that introduced P. theophrasti genomic segments into the P. dactylifera cultivated gene pool had already occurred. This is also consistent with sequencing of an ancient date palm leaf from an archaeological excavation of a temple complex of the animal necropolis in Saqqara, Egypt, that dates to ∼2,100 y ago and which likewise shows P. theophrasti introgression (60).
Individual and Population Statistics.
We calculated the heterozygosity of each date palm accession (Fig. 3B and SI Appendix, Table S3) and confirmed that, on average, North African date palms (mean heterozygosity = 0.245 ± 0.00635%) are more diverse than the West Asian date palms (0.196 ± 0.00341%) (one-sided Wilcoxon rank sum test, W = 1,097, P = 7.66 × 10 −11 ) as previously reported (29 ⇓ –31). The Judean date palms have a mean heterozygosity similar to North African P. dactylifera (0.238 ± 0.00781%; Wilcoxon rank sum test, W = 68, P = 0.40). This can be attributed to the five samples previously shown to cluster with North African date palms and that show an elevated proportion of heterozygous sites compared to West Asian date palms (one-sided Wilcoxon rank sum test, W = 240, P = 3.49 × 10 −7 ). In contrast, the heterozygosity of Methuselah and Hannah, which cluster with West Asian date palms in previous analyses, is comparable to other samples in this cluster (Wilcoxon rank sum test, W = 75, P = 0.22). Furthermore, we find that only 0.7% of the total date palm polymorphisms is unique to the ancient germinated samples (SI Appendix, Fig. S7), indicating that most of the diversity found in the ancient Judean date palms is shared with modern P. dactylifera.
We do not know if these early examples of date palm cultivation in Africa were already impacted by genetic contributions from P. theophrasti, and determining when this interspecific hybridization occurred could tell us whether this took place during antiquity or much later in the evolution of this domesticated fruit species. An analysis of the full genome sequences of the Judean date palms germinated from ∼2,000 y old seeds could also advance our understanding of the role that interspecies hybridization has played in the evolution of this fruit crop species. Here, we report whole-genome sequencing of the seven germinated ancient Judean date palm samples, which provides an opportunity to study the change in genomic composition of date palms in the Southern Levant two millennia ago. We demonstrate that hybridization between P. dactylifera and P. theophrasti took place at least by the second century BCE, and we show increasing levels of Cretan palm introgression in the Southern Levant date palm populations across a period that spanned the fourth century BCE to mid-second century CE. We also use genome data to examine genes associated with fruit color and sugar composition, providing information on genetic characteristics of previously extinct (but now resurrected) Judean dates from ∼2,000 y ago.
To examine population structuring and the genetic relationships of the seven Judean date palms with present-day Phoenix spp., we performed model-based genetic clustering using ADMIXTURE (44). Analyses with all Phoenix spp. accessions (SI Appendix, Figs. S2 and S3A) or including only date palms (P. dactylifera) and P. theophrasti (Fig. 2 and SI Appendix, Figs. S3B and S4) showed that the germinated ancient seedlings have a genetic makeup resembling that of modern date palms.
Our ancient date palm samples were recovered in the Levant, an area between Asia, Africa, and Europe that played a critical role throughout history, from early human dispersal (55) to the origins of agriculture (56). It notably served as a waystation for the dispersal of crops such as emmer wheat (57) and barley (12) as they moved south and west from the Fertile Crescent. In this region, the oldest archaeobotanical records of date palms stretch to the fifth millennium BCE, but it is unclear whether they derive from wild or cultivated stands and if they are of local origin (25, 30, 58, 59). The availability of whole-genome sequences of date palm plants from ∼2,000 y ago allowed us to examine the dynamics of date palm evolution in the Southern Levant at a crucial time, when this area was influenced or even controlled by several great empires from both east and west, including Babylon, Persia, Egypt, and Rome.