Decoding cryptic diversity of moss populations in a forest-tundra ecotone

Cryptic lineages are widespread in bryophytes, particularly in Subarctic ecosystems, yet they are rarely considered in biodiversity assessment. Ignoring cryptic lineages may bias estimates of genetic diversity, especially in plants with dominant clonal growth. We evaluated the effect of accounting for molecular lineages on genetic diversity, clonal structure and host-associated microbial communities in the subarctic moss Racomitrium lanuginosum from a forest-tundra ecotone in eastern Canada. We performed genotyping-by-sequencing to infer genetic diversity and structure in forest tundra and shrub tundra populations. Genetic groups were identified using haplotype-based coancestry matrices and phylogenetics. Clonal structure was determined through multilocus genotypes at population and fine spatial scale (225 cm 2 ). Total bacterial and diazotrophic bacterial communities associated with the genetic groups were characterized using metabarcoding. Two sympatric genetic groups were identified within and among habitats.Accounting for these groups revealed habitat-related differences that remained undetected when treating R. lanuginosum as a single species. Clonal growth predominated and affected the local genetic structure. Neither bacterial nor diazotrophic communities differed significantly between genetic groups, suggesting a limited genetic influence on moss microbial associations. Our findings demonstrate that incorporating cryptic molecular lineages into genetic analyses provides a more accurate assessment of biodiversity in northern ecosystems.