2.3 Genetic diversity
The chromatograms from both directions of the ITS1/2 and cpDNA sequences
were edited with the software BioEdit (Hall, 1999) for base confirmation
and contiguous sequences editing. The sequences were manually aligned
where necessary using MEGA v.6.5 (Kumar et al. , 2008). All
sequences have been deposited in Genbank. The two non-coding cpDNA
sequences were assembled as a single locus by SequenceMatrix v.1.7.8
(Vaidya et al., 2011), and a Partition Homogeneity Test (PHT) vs the ITS
sequences was carried out with PAUP* v. 4.0a164 (Swofford, 2002). Since
the test resulted in the non-homogeneity of both matrices, we analysed
the geographic distribution of ribotypes/chlorotypes for nrITS and cpDNA
sequences separately.
DNASP v. 6.12.01 (Rozas et al. , 2017) was used to compute the
number of ribotype/chlorotype (h ), haplotype diversity (Hd)
within populations, polymorphic sites (S), nucleotide diversity (π),
average number of nucleotide difference (K).