Perl scripts from: The genomes of ancient date palms germinated from 2,000-year-old seeds

Seven date palm seeds (Phoenix dactylifera L.), radiocarbon dated
from the fourth century BCE to the second century CE, were recovered from
archaeological sites in the Southern Levant and germinated to yield viable
plants. We conducted whole-genome sequencing of these germinated ancient
samples and used single-nucleotide polymorphism data to examine the
genetics of these previously extinct Judean date palms. We find that the
oldest seeds from the fourth to first century BCE are related to modern
West Asian date varieties, but later material from the second century BCE
to second century CE showed increasing genetic affinities to present-day
North African date palms. Population genomic analysis reveals that by
∼2,400 to 2,000 y ago, the P. dactylifera gene pool in
the Eastern Mediterranean already contained introgressed segments from the
Cretan palm Phoenix theophrasti, a crucial genetic feature of the
modern North African date palm populations. The P.
theophrasti introgression fraction content is generally higher in
the later samples, while introgression tracts are longer in these ancient
germinated date palms compared to modern North African varieties. These
results provide insights into crop evolution arising from an analysis of
plants originating from ancient germinated seeds and demonstrate what can
be accomplished with the application of a resurrection genomics approach.