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Therefore |D'| is rather an indicator of missing haplotypes than a reliable measure of LD [ 1].
As expected for an RNA pathogen with a high mutation rate and a low sample-to-population ratio, the resulting network also contained many more missing haplotypes than such networks typically represent.
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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.
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.
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.
H11 is separated from other haplotypes by two missing intermediate haplotypes (Fig. 2).
SE and W populations showed private haplotypes, which are connected to the network through missing intermediate haplotypes.
The dusky dolphin d-loop and cyt b haplotype networks recovered a Peru-specific lineage divergent from other geographic regions by several missing intermediate haplotypes.
Therefore, two potential methylation sites are missing from haplotype 2, and none or one methylation site from the haplotypes corresponding to response.
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