According to Aliscore no sites had to be excluded from the alignment.
DAMBE showed no substantial substitution saturation and partition finder suggested analyzing stem and loop structures as well as codon positions of COI separately.
The best fitting substitution models are listed in Table 1. P-distances as a measure of genetic variation reached up to 11.03% in 16S rRNA, 20.43% in COI, and 32.20% in ITS2 considering only the New Caledonian taxa