TY - JOUR

T1 - Molecular Clocks and Archeogenomics of a Late Period Egyptian Date Palm Leaf Reveal Introgression from Wild Relatives and Add Timestamps on the Domestication

AU - Pérez-Escobar, Oscar A

AU - Bellott, Sidonie

AU - Przelomska, Natalia A.S.

AU - Flowers, Jonathan M.

AU - Nesbitt, Mark

AU - Ryan, Philippa

AU - Gutaker, Rafal M.

AU - Gros-Balthazard, Muriel

AU - Wells, Tom

AU - Kuhnhäuser, Benedikt G.

AU - Schley, Rowan

AU - Bogarin, Diego

AU - Dodsworth, Steven

AU - Diaz, Rudy

AU - Lehmann, Manuela

AU - Petoe, Peter

AU - Eiserhardt, Wolf L.

AU - Preick, Michaela

AU - Hofreiter, Michael

AU - Hajdas, Irka

AU - Purugganan, Michael

AU - Antonelli, Alexandre

AU - Gravendeel, Barbara

AU - Leitch, Ilia J.

AU - Jimenez, Maria Fernanda Torres

AU - Papadopulos, Alexander S. T.

AU - Chomicki, Guillame

AU - Renner, Susanne S.

AU - Baker, William J.

N1 - © The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

PY - 2021/10

Y1 - 2021/10

N2 - The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in 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. Genomes of ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by ∼2,200 years ago, but traces of P. sylvestris could not be detected. We here integrate archeogenomics of a ∼2,100-year-old P. dactylifera leaf from Saqqara (Egypt), molecular-clock dating, and coalescence approaches with population genomic tests, to probe the hybridization between the date palm and its two closest relatives and provide minimum and maximum timestamps for its reticulated evolution. The Saqqara date palm shares a close genetic affinity with North African date palm populations, and we find clear 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 P. sylvestris and P. dactylifera. Our work highlights the ancient hybrid origin of the date palms, and prompts the investigation of the functional significance of genetic material introgressed from both close relatives, which in turn could prove useful for modern date palm breeding.

AB - The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in 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. Genomes of ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by ∼2,200 years ago, but traces of P. sylvestris could not be detected. We here integrate archeogenomics of a ∼2,100-year-old P. dactylifera leaf from Saqqara (Egypt), molecular-clock dating, and coalescence approaches with population genomic tests, to probe the hybridization between the date palm and its two closest relatives and provide minimum and maximum timestamps for its reticulated evolution. The Saqqara date palm shares a close genetic affinity with North African date palm populations, and we find clear 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 P. sylvestris and P. dactylifera. Our work highlights the ancient hybrid origin of the date palms, and prompts the investigation of the functional significance of genetic material introgressed from both close relatives, which in turn could prove useful for modern date palm breeding.

KW - Ancient DNA

KW - gene flow

KW - population genomics

KW - |Arecaceae

KW - archeobotany

KW - phylogenomics

U2 - 10.1093/molbev/msab188

DO - 10.1093/molbev/msab188

M3 - Article

C2 - 34191029

VL - 38

SP - 4475

EP - 4492

JO - Molecular Biology and Evolution

JF - Molecular Biology and Evolution

SN - 0737-4038

IS - 10

M1 - msab188

ER -