Plant macrofossils from lake sediment as the material to assess ancient genetic diversity: Did deforestation influence Norway spruce (Picea abies) in the South Carpathians?

How genetic diversity of populations reacts to neutral or adaptive processes such as population bottlenecks, immigration or local adaptation are central questions of population genetics. They may be directly answered through ancient DNA analysis, however such studies in plants are remarkably scarce, owing to the difficulty of gaining population-scale samples with good DNA preservation. Plant macrofossils are abundant in lake sediments, and here we assessed if they can be valuable material for population genetic studies. We extracted ancient DNA from early to late Holocene seed and needle remains of Norway spruce (Picea abies L. Karst) recovered from the sediment of a lake in the Retezat Mts. (South Carpathians). We aimed to reveal whether deforestations starting in the late Holocene and reaching maximum in the 19th and early 20th centuries have caused decreased genetic diversity in the modern Norway spruce population of the Retezat Mts. In a combined approach, we sequenced two plastid regions and generated detailed paleobotanical data to reconstruct the population history of Norway spruce. Our results show that genotyping success of the ancient material was high in samples younger than c. 2000-year-old, but was very low in early Holocene samples, and needles allowed genotyping with higher success compared to seeds. We discovered macrofossil samples that contained DNA from more than a single Norway spruce individual. This phenomenon, together with the possible multiple sampling of the same individual needs to be kept in mind when interpreting the genetic data obtained from macrofossils. Our results overall indicate a genetic diversity decrease during the late Holocene. We demonstrate that macrofossils preserved in sediments are invaluable material for population genetic studies.