Multiplexing PCR allows the identification of within‐species genetic diversity in ancient eDNA

• Published in: Molecular Ecology Resources
• Main Authors: Lammers, Y., Taberlet, P., Coissac, E., Elliott, L. D., Merkel, M. F., Pitelkova, I., Alsos, I. G.
• Other Authors: Norges Forskningsråd, Norwegian Biodiversity Information Centre, H2020 European Research Council
• Format: Article in Journal/Newspaper
• Language: English
• Published: Wiley 2024
• Subjects: Norway; Northern Norway
• Online Access: http://dx.doi.org/10.1111/1755-0998.13926; https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13926

Abstract Sedimentary ancient DNA ( sed aDNA) has rarely been used to obtain population‐level data due to either a lack of taxonomic resolution for the molecular method used, limitations in the reference material or inefficient methods. Here, we present the potential of multiplexing different PCR primers to retrieve population‐level genetic data from sed aDNA samples. Vaccinium uliginosum (Ericaceae) is a widespread species with a circumpolar distribution and three lineages in present‐day populations. We searched 18 plastid genomes for intraspecific variable regions and developed 61 primer sets to target these. Initial multiplex PCR testing resulted in a final set of 38 primer sets. These primer sets were used to analyse 20 lake sed aDNA samples (11,200 cal. yr BP to present) from five different localities in northern Norway, the Alps and the Polar Urals. All known V. uliginosum lineages in these regions and all primer sets could be recovered from the sed aDNA data. For each sample on average 28.1 primer sets, representing 34.15 sequence variants, were recovered. All sediment samples were dominated by a single lineage, except three Alpine samples which had co‐occurrence of two different lineages. Furthermore, lineage turnover was observed in the Alps and northern Norway, suggesting that present‐day phylogeographical studies may overlook past genetic patterns. Multiplexing primer is a promising tool for generating population‐level genetic information from sed aDNA. The relatively simple method, combined with high sensitivity, provides a scalable method which will allow researchers to track populations through time and space using environmental DNA.