Sample size and haplotype richness in population samples of the lichen-forming ascomycete Xanthoria parietina

The fine-scale genetic variation and population structure of lichen-forming fungi is little known and sampling strategies are rarely recommended or discussed. I tested if the sample sizes of molecular data sets used in recent population studies of Xanthoria parietina revealed all haplotypes potentially present and, accordingly, quantified how many haplotypes were potentially missing in the samples. Data sets were concatenated from two geographical regions in Scandinavia and investigated if the sampling reached saturation at two levels: 1) individual-based using rarefaction curves and 2) population-based using species accumulation curves. At both levels, the matrices of two molecular markers (IGS and ITS) were analysed separately. The molecular markers show similar and parallel patterns in all analyses. Rarefaction analyses did not reveal different patterns for populations in different habitats, i.e., bark and rock. Species accumulation curves estimated with the Chao 1 richness estimator indicated that 23% of the IGS and 8% of the ITS haplotypes were not detected. Corresponding figures from an abundance-based coverage estimator (ACE) were 37% and 18%. Pilot studies are recommended to determine appropriate sample sizes for genetic-based population studies of lichen-forming fungi.