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

Multiporate Pollen of Poaceae as Bioindicator of Environmental Stress: First Archaeobotanical Evidence from the Early–Middle Holocene Site of Takarkori in the Central Sahara

“…The preservation of organic matter in this sheltered site is exceptional and allowed the preservation of molecular residues, lipids, and ancient DNA. They revealed, together with archaeology and archaeobotany, hitherto unknown details of plants consumption and uses [21,22]. The cp-DNA of some wild cereals preserved by dehydration was extracted, amplified, and sequenced, confirming the morphological identification of the African minor cereals Echinochloa colona (L.) Link., Panicum laetum Kunth., and Sorghum bicolor (L.) Moench [23].…”

Phylogenetic and population structural inference from genomic ancestry maintained in present‐day common wheat Chinese landraces

“…Considering the morphological changes resulting from ancient preservation, molecular methods have been widely adopted to ascertain the genomic identity of archeological plant samples of interest in population studies (Li et al ., ; Bilgic et al ., ; Fornaciari et al ., ; Mascher et al ., ; Wales et al ., ; Di et al ., ). Our Xiaohe ancient wheat seeds were previously determined to be hexaploid based on their longer amplified D‐subgenomic rDNA IGS (intergenic spacer region), which should be absent from the respective regions in the A and B subgenomes (Li et al ., ).…”

Brassica and Sinapis Seeds in Medieval Archaeological Sites: An Example of Multiproxy Analysis for Their Identification and Ethnobotanical Interpretation

“…DNA yields from ancient biological samples (aDNA) are typically low and highly degraded [58]. However, several groups have successfully used the DNA extracted from ancient plant material to confirm species identity using short amplicons of the core DNA barcodes [59,60] or else elected to target supplementary or non-coding barcode markers [61]. Such works typically use either large volumes of starting materials [62] or next-generation sequencing platforms [63].…”