Panicum spikelets from the Early Holocene Takarkori rockshelter (SW Libya): Archaeo-molecular and -botanical investigations

Abstract

This paper deals with the extraction, amplification and sequencing of ancient DNA (aDNA) from spikelets of wild cereals dated at ca. 9000 cal yr BP, representing the most ancient plants with preserved genetic material from the Sahara desert. The sub-fossil records were collected from the archaeological excavation carried out at Takarkori, an archaeological site located in south-western Libya. Morphological and genetic analyses were made on 100 well preserved dried spikelets. Ten DNA extraction protocols were performed to evaluate nucleic acid recovery in terms of DNA yield, purity and amplification success of the chloroplast barcode region matK. The extraction protocol that returned the most suitable DNA to be amplified is the Kistler and Shapiro (2011: J Archaeol Sci 38: 3549-3554) modified protocol. In our study, the results from matK amplification suggested that four specimens are the most appropriate number of spikelets for these analyses. DNA was then used for PCR amplifications of four chloroplast barcode genes: rbcL, matK, trnH-psbA and trnL. A phylogenetic analysis shows the strict relation between the archaeological specimens and modern Panicoideae, supporting the morphological identification. The results indicate that spikelets have a close relation to Panicum laetum Kunth, a wild cereal still collected in tropical Africa.

Keywords:

• aDNA
• archaeobotany
• DNA-barcode
• Panicum
• Sahara

Acknowledgements

The research has been carried out under the aegis of the Italian-Libyan Archaeological Mission in the Acacus and Messak, Sapienza University of Rome and Department of Archaeology, Tripoli, directed by Prof. S. di Lernia. All necessary permits were obtained for the field studies and laboratory analyses (including destructive processes) presented here. Many thanks to Dr. S. Cassanelli for his help in setting up the extraction protocols and PCR reactions, and to Dr. J. Košnar for his advices in the performing of the phylogenetic analysis. We would also like to thank Dr. L. Olmi for her help on the first steps of this research and Dr. S.E. Jones for her valuable assistance in revising English language. Many thanks also to the three anonymous referees that allowed the improving of this paper.