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

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

Phylogeography of Rhinella spinulosa (Anura: Bufonidae) in northern Chile

The southern part of the Altiplano of the Andes Range is characterized by a complex hydrography, due to an intense geologic activity and the effects of the Pleistocene glaciations. This has produced a high degree of diversity at the species level in some aquatic taxa (e.g., fish and amphibians), which suggests that these same processes have produced divergence at the intraspecific level in co-distributed taxa. We investigated the genetic variation in populations of the anuran Rhinella spinulosa which represent its entire distribution in the extreme north of Chile (17°44′S-23°47′S). Haplotype networks of the mitochondrial control region recognized two main lineages, one of which is distributed from the northern boundary of Chile to the Salar de Alconcha and the other from the Salar de Carcote to the locality of Tilomonte. The northern lineage showed little phylogeographic structure; a few very frequent haplotypes are widely distributed. The southern lineage had greater structure, due principally to the high divergence of the populations from the eastern springs of the Salar de Atacama. Fu's Fs test and the mismatch distributions suggested that most of the populations of both lineages are in the process of demographic expansion. The spatial distribution of the genetic variability was correlated with the hydrography and the paleoclimatological data available for the region, which suggested that geographic expansions followed by periods of contraction of population ranges, together with sporadic floods may explain the observed phylogeographic patterns.