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Computation 2015, 3(2), 177-196; doi:10.3390/computation3020177

A Guide to Phylogenetic Reconstruction Using Heterogeneous Models—A Case Study from the Root of the Placental Mammal Tree

1
Bioinformatics and Molecular Evolution Group, Dublin City University, Glasnevin, Dublin 9, Ireland
2
Centre for Scientific Computing & Complex Systems Modeling (SCI-SYM), Dublin City University, Glasnevin, Dublin 9, Ireland
3
National Heart and Lung Institute, Faculty of Medicine, Imperial College, London W12 0NN, UK
*
Author to whom correspondence should be addressed.
Academic Editors: Marnix Medema and Rainer Breitling
Received: 26 December 2014 / Revised: 30 March 2015 / Accepted: 31 March 2015 / Published: 15 April 2015
(This article belongs to the Special Issue Genomes and Evolution: Computational Approaches)
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Abstract

There are numerous phylogenetic reconstruction methods and models available—but which should you use and why? Important considerations in phylogenetic analyses include data quality, structure, signal, alignment length and sampling. If poorly modelled, variation in rates of change across proteins and across lineages can lead to incorrect phylogeny reconstruction which can then lead to downstream misinterpretation of the underlying data. The risk of choosing and applying an inappropriate model can be reduced with some critical yet straightforward steps outlined in this paper. We use the question of the position of the root of placental mammals as our working example to illustrate the topological impact of model misspecification. Using this case study we focus on using models in a Bayesian framework and we outline the steps involved in identifying and assessing better fitting models for specific datasets. View Full-Text
Keywords: mammal phylogeny; phylogeny reconstruction; molecular phylogenetics; heterogeneous modeling; placental mammals mammal phylogeny; phylogeny reconstruction; molecular phylogenetics; heterogeneous modeling; placental mammals
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Moran, R.J.; Morgan, C.C.; O'Connell, M.J. A Guide to Phylogenetic Reconstruction Using Heterogeneous Models—A Case Study from the Root of the Placental Mammal Tree. Computation 2015, 3, 177-196.

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