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The most variable markers were SA0536.1, SA1691 and SA0591, which revealed importantly up-regulated in the vast majority of unrelated GISA strains.
The 12S and ND5 regions are the two most variable markers reported here, but they have not previously been used for intra-specific phylogeographic studies in elasmobranchs.
If the most variable markers are excluded from analyses however, then few or no isolates are distinguishable since variation is exclusively within the most polymorphic loci.
Lastly, the plasticity of DNA methylation was also evident when we compared fetal DNA methylation profiles to embryonic stem cells [ 31], with the most variable markers being linked to domains with bivalent histone modifications.
We used our two most variable markers, COI and ANT, to calculate the following statistics in A RLEQUIN v3.5 [ 55]: h (haplotype or gene diversity), π (nucleotide diversity), and pairwise fixation indices as a measure of population differentiation (ΦST for COI and FST for ANT).
Similar(54)
Here, we tested this idea for the first time, using a two-tiered approach: we first clustered the individuals into MOTUs using the most variable marker psbA-trnH.
In all species COI was the most variable marker.
Furthermore, the ITS region has a high mutation rate and is the most variable marker commonly used in Parmeliaceae [ 7, 8, 28, 36, 37].
All other loci examined had average genetic distances greater than 1%; trnH- psbA was the most variable chloroplast locus and nrITS was the most variable marker of those tested.
Comparison of allele distribution at the most variable marker (Ft-M3) showed an overall similarity between isolates causing the outbreaks, although the most common copy number was 4 during the first outbreak and 5 during the second outbreak, which might indicate a stepwise increase in copy number over time.
ANT was the most variable nuclear marker.
Related(20)
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