Researchers Sequence Genomes of Revived 2,000-Year-Old Date Palms

An international team of scientists from Israel, the United States, France, and the United Arab Emirates has successfully sequenced and analyzed the genomes of seven Judean date palms (Phoenix dactylifera) that were germinated from 2,000-year-old seeds recovered from archaeological sites in the Southern Levant. The results provide insights into the nature and timing of the spread of domesticated dates across the region.

A Judean date palm (Phoenix dactylifera) that was germinated from a 2,200-year-old seed, now growing in Israel. Image credit: Sarah Sallon.

Date palms are the iconic perennial plant of the arid lands of West Asia and North Africa. They are believed to have been domesticated around 7,000 years ago in the region around the Arabian Gulf. From there, dates presumably spread westward and were widely cultivated in Egypt from at least the mid-2nd millennium BCE and further west to the Maghreb at least by the 1st millennium BCE.

Date palms grown in antiquity around Jericho and along the Dead Sea in Judea were referred to as Judean date palms, although it was unclear whether this referred to a distinct genetic population. These date palms were discussed by classical writers such as Josephus and Pliny, who described them as producing superior fruit.

Studying the genomes of Judean date palms became possible several years ago when seven ancient seeds were germinated to yield viable plants. The seeds, radiocarbon dated from the 4th century BCE to the 2nd century CE, were recovered from archaeological sites of Masada, Qumran and Wadi Makukh in the Judean Desert.

We are fortunate that date palm seeds can live a long time — in this case, more than 2,000 years — and germinate with minimal DNA damage, in the dry environment of the region,” said Professor Michael Purugganan, a researcher in the Center for Genomics and Systems Biology and the Institute for the Study of the Ancient World at New York University. This resurrection genomics approach is a remarkably effective way to study the genetics and evolution of past and possibly extinct species like Judean date palms.”

In the research, Professor Purugganan and colleagues conducted whole-genome sequencing of the germinated ancient samples and used single-nucleotide polymorphism data to examine the genetics of the previously extinct Judean date palms. We found that the oldest seeds from the 4th to 1st century BCE are related to modern West Asian date varieties, but later material from the 2nd century BCE to 2nd century CE showed increasing genetic affinities to present-day North African date palms.

Population genomic analysis revealed that by 2,400 to 2,000 years ago, the gene pool of the Judean date palms in the Eastern Mediterranean already contained introgressed segments from the Cretan date palm(Phoenix dactylifera), a crucial genetic feature of the modern North African date palm populations. The 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.

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