Comparison of ancient date seeds that failed to germinate with modern date seeds. This was performed on the following groups:

1) Modern date seed (P. dactylifera) samples (n = 56): Being either from cultivated varieties (n = 47) or uncultivated and possibly wild individuals (n = 9) (9). Seeds from these sources (total n = 1108) were used as a current referential for seed morphometric analysis. The cultivated modern samples originated from 11 countries spanning date palm distribution from Spain to North Africa to the Middle-East. The candidate wild date palms originated from Oman and have been hypothesized as wild date palms based on seed shape, seed size (18), and genetic studies based on microsatellite and whole-genome resequencing data (9).

2) Ancient date seeds (n = 18): Of 26 ancient date seeds obtained from Qumran, Wadi Makukh, and Wadi Kelt archaeological sites (described above) that had been planted in the quarantine site, 21 failed to germinate and were retrieved from the potting soil. Of these, three were discarded as they had fragmented and were in poor condition. The remaining 18 retrieved ancient date seeds together with modern reference seeds (described above) were rephotographed on dorsal and lateral sides, and measurements of length and width were remade (table S3) [Neither current or previous (6) ancient date seeds from Masada that failed to germinate were used in the morphometric study as these seeds were not retrieved from the potting soil].

The following statistical analyses were performed using R software (36).

1) Size analysis of modern seeds: The length and width of a total of 1108 seeds obtained from 47 current cultivated varieties (928 seeds) and 9 current wild individuals (180 seeds) were measured using ImageJ (37) following the protocol previously established by Gros-Balthazard et al. (18). The thickness was not measured since it is highly correlated with width (18).

2) Comparison of seed size between current and ancient samples: Measurements for current varieties were compared with those measured for the ancient date seeds using boxplots and Student’s and Tukey’s tests (table S4).

3) Analysis of seed shape diversity in current and ancient date seeds: PCA (dudi.pca function) was performed on seed outlines assessed by Fourier coefficients, a morphometric method applied to outline analysis.

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