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pgHMA: Application of the Heteroduplex Mobility Assay Analysis in Phylogenetics and Population Genetics
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  • Teng Li,
  • Thomas Wong,
  • Louis Ranjard,
  • Allen Rodrigo
Teng Li
Australian National University
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Thomas Wong
Australian National University
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Louis Ranjard
Australian National University
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Allen Rodrigo
Australian National University
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Abstract

The Heteroduplex mobility assay (HMA) has proven to be a robust tool for the detection of genetic variation. Here, we describe a simple and rapid application of the HMA by microfluidic capillary electrophoresis, for phylogenetics and population genetic analyses (pgHMA). We show how commonly applied techniques in phylogenetics and population genetics have equivalents with pgHMA: phylogenetic reconstruction with bootstrapping, skyline plots, and mismatch distribution analysis. We assess the performance and accuracy of pgHMA by comparing the results obtained against those obtained using standard methods of analyses applied to sequencing data. The resulting comparisons demonstrate that: (1) there is a significant linear relationship (R = 0.992) between heteroduplex mobility and genetic distance; (2) phylogenetic trees obtained by HMA and nucleotide sequences present nearly identical topologies; (3) clades with high pgHMA parametric bootstrap support also have high bootstrap support on nucleotide phylogenies; (4) skyline plots estimated from the UPGMA trees of HMA and Bayesian trees of nucleotide data reveal similar trends, especially for the median trend estimate of effective population size; and (5) optimized mismatch distributions of HMA are closely fitted to the mismatch distributions of nucleotide sequences. In summary, pgHMA is an easily-applied method for approximating phylogenetic diversity and population trends. KEYWORDS: bootstrap, heteroduplex mobility assay, mismatch distribution, phylogenetics, skyline plot

Peer review status:ACCEPTED

16 Jul 2021Submitted to Molecular Ecology Resources
23 Jul 2021Submission Checks Completed
23 Jul 2021Assigned to Editor
26 Jul 2021Reviewer(s) Assigned
19 Aug 2021Review(s) Completed, Editorial Evaluation Pending
20 Aug 2021Editorial Decision: Revise Minor
01 Sep 2021Review(s) Completed, Editorial Evaluation Pending
01 Sep 20211st Revision Received
06 Sep 2021Editorial Decision: Accept