Five thousand years of tropical lake sediment DNA records from Benin

Abstract

37Until now, sedimentary DNA (sedDNA) studies have only focused on cold and temperate 38 regions were DNA is relatively well preserved. Consequently, the tropics, where 39 vegetation is hyperdiverse and natural archives are rare, have been neglected and 40 deserve attention. In this study, we used next-generation sequencing to barcode sedDNA 41 from Lake Sele, localized in the tropical lowlands of Benin (Africa), and compared the 42 taxonomic diversity detected by DNA analyses with pollen assemblages. Plant sedDNA 43 was successfully amplified from 33 of the 34 successfully extracted samples. In total, 43 44 taxa were identified along the 5,000 years spanned by the sediment: 22 taxa were 45 identified at the family level and 21 at the genus level. The plant diversity recovered 46 through sedDNA from Lake Sele showed a specific local signal and limited overlapping 47 with pollen. Introduced plants, grown and cultivated close to the water, such as sweet 48 potato, were also well recorded by sedDNA. It appears, therefore, to be a promising 49 approach to studying past diversity in tropical regions, and could help in tracking the 50 introduction and history of agriculture. This is the first time this method has been used 51

Vegetation state changes in the course of shrub encroachment in an African savanna since about 1850 CE and their potential drivers

“…Recently, sedimentary ancient DNA (sedaDNA) using the g-h universal primers (Taberlet et al, 2007) was established as a further proxy. This technique enables the reconstruction of tropical plant diversity at high taxonomic resolution (Boessenkool et al, 2014;Bremond et al, 2017). Further, fire dynamics and its impact on savanna vegetation can be reconstructed from sedimentary charcoal (Colombaroli, van der Plas, Rucina, & Verschuren, 2018;Gillson & Ekblom, 2009), while carbon (δ 13 C) and deuterium (δD) isotope compositions of plant-wax n-alkanes can be used to reconstruct vegetation structure and hydrological variability (Garcin et al, 2018;Miller et al, 2019;Walther & Neumann, 2011).…”

New insights on lake sediment DNA from the catchment: importance of taphonomic and analytical issues on the record quality

“…This is due to the absence of a well-developed hydrographic network and low erosion, both a consequence of flat topography. The role of catchment relief on catchment flora reconstructions has also been proposed in two recent studies, in Arctic and African environments 40,75 .…”

Genome Sequencing of Ancient Plant Remains: Findings, Uses and Potential Applications for the Study and Improvement of Modern Crops

“…Another important source of aDNA consists in lake and cave sediments, where several kinds of ancient plant remains can be found. The geological context of lakes provides a robust archive for the retrieval of ancient plant DNA through time and reflects the effect of all environments worldwide (Willerslev, 2003 ; Bremond et al, 2017 ; Parducci et al, 2017 ). Plant residues can also be found in ancient animal and human remains such as palaeofaeces, hair, dental calculus, and gastrointestinal contents (Poinar et al, 2001 ; Rawlence et al, 2014 ; Van Geel et al, 2014 ; Weyrich et al, 2015 ).…”

“…For instance, through meta-barcoding studies on lake sediments it was possible to trace the introduction and history of agriculture in Benin, detecting when the sweet potato ( Ipomoea sp.) was introduced into the region (Bremond et al, 2017 ).…”