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 - Bellot, 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 - Bogarín, 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, Guillaume
AU - Renner, Susanne S.
AU - Baker, William J.
N1 - Publisher Copyright:
© 2021 The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
PY - 2021/10/1
Y1 - 2021/10/1
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 - archeobotany
KW - Arecaceae
KW - gene flow
KW - phylogenomics
KW - population genomics
KW - UKRI
KW - NERC
KW - NE/S014470/1
UR - http://www.scopus.com/inward/record.url?scp=85109398520&partnerID=8YFLogxK
U2 - 10.1093/molbev/msab188
DO - 10.1093/molbev/msab188
M3 - Article
C2 - 34191029
AN - SCOPUS:85109398520
SN - 0737-4038
VL - 38
SP - 4475
EP - 4492
JO - Molecular Biology and Evolution
JF - Molecular Biology and Evolution
IS - 10
ER -