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
pgHMA: Application of the Heteroduplex Mobility Assay Analysis in Phylogenetics and Population Genetics