23 June 2022
Dating date evolution with resurrection genomics
Published online 12 May 2021
Germinating ancient date palm seeds allows genetic analysis to reveal secrets of evolution.
Researchers have germinated seeds from previously extinct varieties of date palm that were formed in the southern Levant region, around the Dead Sea, approximately 2,000 years ago, resurrecting viable plants for gene sequencing analysis.
The work, by a team based at New York University Abu Dhabi (NYUAD), demonstrates the value of a technique called resurrection genomics. Bringing ancient seeds back to life for modern genetic analysis offers insights into crop evolution. It may also yield information about the agricultural practices of ancient times by tracing plant hybridizations.
“In a sense, these date palms are time travellers, and our genomic analysis provides us a window to look back in time,” says NYUAD plant biologist, Michael D. Purugganan.
Thirty five well-preserved seeds of the date palm species Phoenix dactylifera were retrieved during archeological excavations in three regions of the historical southern Levant Judean region, now part of Israel. Radiocarbon dating indicated the seeds were around 2,000 years old. Seven specimens were successfully germinated into plant tissue for whole genome sequencing.
The results indicated that hybridization between Phoenix dactylifera and other species had occurred by at least the second century BCE. They also suggest that genes from the Cretan date palm, Phoenix theophrasti, increasingly spread into the southern Levant date palm populations between the fourth century BCE and mid-second century CE. Overall, the work reveals a mixing of genetic material among date palm populations from the Eastern Mediterranean, West Asia and North Africa.
The researchers were also able to examine genes associated with fruit colour and sugar composition, providing information on genetic characteristics of previously extinct, but now resurrected Judean dates.
“Our study provides a glimpse into the role that hybridization plays in the evolution of date palms, and shows us the early stages of the process,” says Purugganan. He coined the term resurrection genomics for this type of work, while pioneering it in parallel with somewhat similar work by plant biologist, Steve Franks, at Fordham University in New York. Franks called his work resurrection ecology. Purugganan and Franks now work as close collaborators.
The research team hopes to extend their investigations to archaeological date palm samples from other areas of the Middle East and North Africa. They also hope it can be widened to include other plant and microbe species. Further insights into the interactions between geopolitics, human population changes, emerging agricultural practices and crop plant evolution can be expected.
Gross-Balthazard, K. et al. The genomes of ancient date palms germinated from 2,000 y old seeds. PNAS 118(19), e2025337118 https://doi.org/10.1073/pnas.2025337118 (2021).