2.6 Population Genetics, Phylogeographic Analyses, and
Demographic History
All the DNA sequences were edited by SeqMan (DNAstar package; DNAStar
Inc., Madison, WI, United States) to obtain consensus sequences. The
program MAFFT v.7.369b(Katoh & Standley, 2013) was used to align for
subsequent manual adjustments. Haplotype diversity
(Hd)(Nei & Tajima, 1981) and nucleotide diversity
(π)(Nei & Li, 1979) for each population were calculated using DNAsp
v6.0(Rozas et al., 2017) to verify the degrees and patterns of
diversity. The haplotypes of the two gene fragment datasets and the
distribution of all haplotypes on the map were then plotted separately
in the software PopART using the Minimum spanning method(Bandelt,
Forster, & Röhl, 1999). PERMUT was used to access the total diversity
(HT), within-population diversity (HS)
and population differentiation indices (GST and
NST)(Pons & Petit, 1996). And a U-statistic was used to
test the phylogeographic structure by comparing GST and
NST. In addition, analyses of molecular variance (AMOVA)
was performed using ARLEQUIN v3.5(Excoffier & Lischer, 2010) to assess
the genetic differentiation within and between populations, and 1000
random permutations were conducted to test the significance of
partitioning. To detect whether the populations in Notholirionexperienced a recent population expansion, a mismatch distribution
analysis (MDA)(Schneider & Excoffier, 1999) was carried out using the
ARLEQUIN v3.5(Excoffier & Lischer, 2010). Additionally, Neutrality test
(Fu’s Fs; Tajima’s D)(Tajima, 1989) was also conducted to test whether
there was potential population expansion in Notholirion using
DnaSP v6.0 program. The smoothness of observed mismatch distribution was
detected by calculating the Harpending’s raggedness index
(Hrag)(Schneider & Excoffier, 1999) and the sum of squared deviations
(SSD) between observed and expected mismatch distributions.