Vitis vinifera

To explore the research potential of high-throughput sequencing of ancient DNA (aDNA) from archaeological Vitis specimens, we performed targeted capture experiments on a collection of archeological grape pip and vine specimens from sites across Eurasia dating from 5800–500 BP. The chloroplast genome (plastome) represented an initial target of potential due to its high copy number in living plant cells and the availability of an existing body of knowledge on genetic diversity within modern Vitis populations. However, it was discovered the target was far from ideal for aDNA research due to unprecedented numbers of plastome insertions into the nuclear and mitochondrial genomes, yielding limited phylogenetically informative data. Nonetheless, analysis of non-targeted nuclear loci in the dataset demonstrates huge potential for understanding ancient vinicultural practices, including the genetic introgression from local wild populations and the use of particular varieties.