The Philippines samples were made up of three haplotypes, H1 H3, with four missing haplotypes; H1 (n=13) was comprised of samples from 10 localities, H2 included one sample from the Barangay Bulo site, and H3 (n=24) included samples from 17 sites.
Therefore |D'| is rather an indicator of missing haplotypes than a reliable measure of LD [ 1].
However, haplotypes that show greater divergence from the common haplotypes, five or more missing haplotypes connecting two haplotypes, are more often from the spiny forest (5 occurrences) or from Ihazoara (2 occurrences), compared to the gallery forest (no occurrences).
In both cyt b and control region networks, New Zealand lineages were notably separated from the Peruvian clade by a mixture of haplotypes from South Africa, Argentina, New Zealand, and several missing haplotypes.
Most haplotypes were distributed in the outside nodes of the reticulate evolutionary diagram, and many missing haplotypes, specifically between Hap 1 and Hap 2, were evident in the reticulate evolutionary diagram of the nrDNA haplotypes.
This abundance of missing haplotypes, relative to other haplotype groups, could be the result of inadequate sampling, or it may suggest that disproportionately more haplotypes in that lineage have gone extinct.
A list of the genotypes for each sample was collated and PHASE [ 28] was used to infer missing haplotypes.
The last haplotype H8 (n=4) contained samples from Thailand with one missing haplotype.
Low MAF increases chances of a missing haplotype and if at least one haplotype is missing |D'| = 1.
SE and W populations showed private haplotypes, which are connected to the network through missing intermediate haplotypes.
