Enhanced reconstruction of Holocene bryophytes from sedimentary ancient DNA using bryophyte-specific primers

Abstract

The Arctic is warming rapidly, yet long-term data on how this affects bryophytes, key components of Arctic vegetation, remain limited. Sedimentary ancient DNA (sedaDNA) provides high-resolution taxonomic insights that can reveal vegetational responses to past environmental change, including functional responses via trait associations, but effective genomic tools for bryophyte sedaDNA are lacking. We applied bryophyte-specific primers targeting p6 loop in plastid DNA and compared their performance with bryophyte bycatch from vascular plant-specific primers. Using data from bryophyte-specific primers, we analyzed richness patterns across environmental gradients and assessed their potential for environmental reconstruction. The primers resolved nearly 60% of taxa to species level and over 80% to genus level, recovering 2.63 times more taxa with 1.48 times higher species-level resolution than vascular plant-specific primers. Taxonomic richness increased nonlinearly over time and along precipitation gradients, while exhibiting unimodal relationship with temperature and glacial activity. High-resolution data also enabled trait assignments for most bryophyte taxa, allowing temporal analyses of community development and functional dynamics. Overall, our results demonstrate that bryophyte-specific primers substantially improve bryophyte recovery from sedaDNA and, when combined with trait information, provide a powerful approach for reconstructing past bryophyte ecosystems and investigating functional ecological dynamics under long-term environmental change.