Variability in the IGS1 region of Rhodocollybia laulaha: is it allelic, genomic, or artificial?

We tested the nuclear ribosomal intergenic spacer 1 (IGS1) to evaluate: 1) the utility of this gene region in the study of intra-lineage variation in the Hawaiian mushroom Rhodocollybia laulaha (Basidiomycota, Marasmiaceae); 2) the possibility of PCR-mediated artifacts from multiple cloned IGS1 inserts for five of the nine specimens included; and 3) the assignment of individual specimens to specific haplotype group genotypes. The IGS1 was sequenced for nine specimens of R. laulaha and multiple cloned copies of the IGS1 were sequenced for five of those nine to compare intra-specimen variation (i.e. among paralogous copies in a single genome) and inter-specimen variation (i.e. among different specimens). Three haplotype groups were identified with 25 of 510 aligned base pairs being variable (17 substitutions and eight indels). The observed variation could be due to the presence of various alleles of the IGS1 locus and/or variation among paralogous copies within a single genome. Issues associated with PCR error including artificial recombination and/or Taq error and the potential inefficiency of concerted evolution are considered as possible agents of variation.