Molecular clocks and archaeogenomics of a Late Period Egyptian date palm leaf reveal introgression from wild relatives and highlight the role of Economic Botany Collections

The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. The earliest evidence for its domestication traces to the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives: P. theophrasti, currently restricted to Crete and Turkey, and P. sylvestris, widespread from Bangladesh to the West Himalayas. Genomic data from ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by ∼2,200 years ago. Here, we generate DNA sequence data from a ∼2,100-year-old P. dactylifera leaf from Saqqara (Egypt), an object currently held at the Royal Botanic Gardens, Kew. Integrating archaeogenomic analysis, molecular-clock dating, coalescence
approaches and population genomics, we investigate hybridization between the date palm and its two closest relatives and provide timestamps for its reticulated evolution. The Saqqara date palm shows a close genetic affinity with North African date palm populations, and we find genomic admixture from both P. theophrasti, and P. sylvestris, indicating that both had contributed to the date palm genome by 2,100  years ago. Molecular clocks placed the divergence of P. theophrasti from P. dactylifera/P. sylvestris and that of P. dactylifera from P. sylvestris in the Upper Miocene, but strongly supported, conflicting topologies point to older gene flow between P. theophrasti and P. dactylifera, and between P. sylvestris and P. dactylifera. Our research, the findings of which which could have implications for modern date palm breeding, was only possible thanks to support from RBG Kew’s Economic Botany Collections. We highlight recent work concerning these collections, involving Kew’s Interdisciplinary Research group.