On the Use of Median-Joining Networks: A Philosophical and Empirical Evaluation of Its Suitability in Evolutionary Biology
Year: 2015
Type: dissertation
Abstract: A phylogenetic tree is a branching diagram illustrating the inferred evolutionary history of taxa. It only represents the vertical transmission of DNA due to its structure. Phylogenetic networks have been proposed to overcome this limitation and to show complex scenarios such as hybridization in a cyclic structure known as reticulation. Median-Joining Networks (MJNs) are one of the most popular approaches to discovering reticulations, but it has been used hastily in evolutionary studies without critical examination of its assumptions, performance and suitability. The MJ algorithm is based on phenetics, and the networks lack evolutionary direction. I evaluate the extent of congruence between MJNs and Bayesian inference phylogenies through likelihood-based tests and detect a significant difference in branching order between the two methods in more than one-third of unambiguous cases. Analyses document that MJNs are inappropriate for evolutionary inference, and I encourage the biologists to take a pause and reassess its usage.
Source: TSpace (University of Toronto)
Author: Sungsik Kong
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Funder: University of Toronto
OpenAlex ID: W2611911788