Computational protocol: Genetic Diversity and Evolution of Chinese Traditional Medicinal Fungus Polyporus umbellatus (Polyporales, Basidiomycota)

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[…] Sequences of ITS and LSU were aligned with Clustal X version 2.0 , and ambiguous regions in both sides of each region were excluded. For ITS sequences, the subsequences including partial 18S (7 bp), ITS1 (184–212 bp), 5.8S (161 bp), ITS2 (178–203 bp), and partial 28S (40 bp) were used. Pairwise distance matrices and minimum evolutionary (ME) phylogenetic analysis were conducted with Kimura 2-Parameter model using MEGA version 5 . Bootstrap analyses were performed for 1000 replicates. For Maximum Parsimony (MP) analyses, an initial heuristic search of 100 random taxon addition replicate searches was conducted with TBR branch-swapping, MAXTREES set to autoincrease, without constraints, all characters unordered and equally weighted, gaps treated as missing data, and with two trees held during each stepwise addition cycle. The shortest trees from this analysis were used as starting trees in a second heuristic search, with the same parameters described above, to find the most parsimonious trees. For the Maximum Likelihood (ML) analyses, jModelTest 2 was used to identify the model of DNA substitution that best fits. HKY+G was estimated as the best-fit likelihood model for the combined ITS and LSU datasets. The best-fit likelihood model for ITS and LSU was K80+I and HKY respectively. Maximum likelihood analysis was performed with PAUP 4.0b10 . Genetic parameters of nucleotide diversity were calculated by DnaSP software (version 5.10.01) . Genetic differentiation between populations and analysis of molecular variance (AMOVA) were assessed using the Program Arlequin 3.5 . For AMOVA, FSC estimates the variation among populations relative to a regional grouping of populations. FST estimates the proportions of genetic variation within populations relative to the genetic variation for the whole samples. FCT estimates the proportion of genetic variation among groups of populations relative to the whole species. Samples from the same province were regarded as one population. The one sample from Beijing (ZL-BJ-1) was put into the population of Hebei for the following analyses because location of Beijing is geographically located in the Hebei Province. […]

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