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On the Use of Median-Joining Network...

Kong, Sungsik.

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On the Use of Median-Joining Networks: A Philosophical and Empirical Evaluation of Its Suitability in Evolutionary Biology.

Record Type:	Electronic resources : Monograph/item
Title/Author:	On the Use of Median-Joining Networks: A Philosophical and Empirical Evaluation of Its Suitability in Evolutionary Biology./
Author:	Kong, Sungsik.
Description:	81 p.
Notes:	Source: Masters Abstracts International, Volume: 55-02.
Contained By:	Masters Abstracts International55-02(E).
Subject:	Evolution & development. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=1604375
ISBN:	9781339269016

On the Use of Median-Joining Networks: A Philosophical and Empirical Evaluation of Its Suitability in Evolutionary Biology.
Kong, Sungsik.

On the Use of Median-Joining Networks: A Philosophical and Empirical Evaluation of Its Suitability in Evolutionary Biology. - 81 p.

Source: Masters Abstracts International, Volume: 55-02.

Thesis (M.Sc.)--University of Toronto (Canada), 2015.

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.

ISBN: 9781339269016Subjects--Topical Terms:

3172418
Evolution & development.

On the Use of Median-Joining Networks: A Philosophical and Empirical Evaluation of Its Suitability in Evolutionary Biology.
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100 1 $a Kong, Sungsik. $3 3194870
245 1 0 $a On the Use of Median-Joining Networks: A Philosophical and Empirical Evaluation of Its Suitability in Evolutionary Biology.
300 $a 81 p.
500 $a Source: Masters Abstracts International, Volume: 55-02.
500 $a Includes supplementary digital materials.
500 $a Adviser: Robert W. Murphy.
502 $a Thesis (M.Sc.)--University of Toronto (Canada), 2015.
520 $a 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.
590 $a School code: 0779.
650 4 $a Evolution & development. $3 3172418
650 4 $a Bioinformatics. $3 553671
650 4 $a Biology. $3 522710
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710 2 $a University of Toronto (Canada). $b Ecology and Evolutionary Biology. $3 3190014
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