Haplotype networks
DnaSP was also used to prepare the sequence data for input into Network
v5.0.0.0 in order to construct
haplotype networks. The 16S data was exported in Rdf format with
gaps/missing data not considered, whereas the coding regions (CO1 and
EF-1ɣ) were exported with gaps considered. In order to accurately
estimate the relationship between closely related Stasimopusindividuals of the same species (which have not yet undergone
speciation), a haplotype network was constructed in Network. The Network
software uses the method of Maximum Parsimony to select the shortest and
least complex tree. The haplotype network was constructed using the
median-joining (MJ) network algorithm. This allows for multistate data
(A, T, G, C or N at any nucleotide position) . All settings for network
calculation were left on default. The post-processing option of Maximum
parsimony was used in order to remove all unnecessary median vectors.
Pie charts of haplotypes were plotted onto a map of the Karoo region
using the coordinates of each locality. This allowed for the
visualisation of the different haplotypes in geographic space.