Technological Perspectives in Phylogeny Research: Revisiting Comparative Analysis of Complete Mitochondrial Genomes for Time-Extended Lineages
Comparative methods involving DNA-DNA hybridization are thought to be reliable in terms of phylogeny reconstruction, but also weigh heavy on computational resources. Processing large-scale genomic datasets can have potentially unfavorable drawbacks in computing, which can result in poor analysis leading to erroneous conclusions. Slim genomic datasets, such as those found in entire sets of complete mitochondrial DNA (mtDNA), are lucrative options for researchers seeking complete genomic datasets that fit the criteria of a computationally light model. Yet, a handful of incorrect conclusions in molecular phylogenetics have also raised questions about its reliability. This article seeks to emphasize a simplified approach to phylogeny research using complete mitochondrial genomes alone, while touching upon a number of technological perspectives, such as algorithmic selection, which can help improve accuracy and performance in comparative analysis. Moreover, my results will show that reliable estimations can be obtained by using mitochondrial markers, even among time-extended taxonomical rankings; although, admittedly, precise taxonomical boundaries for accurate resolution using complete sequences of mtDNA remain unclear, and it should be explored further. Six distinct mammalian groups of taxa were selected for comparison. In all cases, mtDNA models generated reliable phylogeny approximations when compared against other independent data, while rendering exceptional computational performance.