Haggerty, Leanne S. and Jachiet, Pierre-Alain and Hanage, William P. and Fitzpatrick, David A. and Lopez, Philippe and O'Connell, Mary J. and Pisani, Davide and Wilkinson, Mark and Bapteste, Eric and McInerney, James O. (2014) A Pluralistic Account of Homology: Adapting the Models to the Data. Molecular Biology and Evolution, 31 (3). pp. 501-506. ISSN 0737-4038

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Abstract

Defining homologous genes is important in many evolutionary studies but raises obvious issues. Some of these issues are conceptual, and stem from our assumptions of how a gene evolves, others are practical, and depend on the algorithmic decisions implemented in existing software. Therefore, in order to make progress in the study of homology, both ontological and epistemological questions must be considered. In particular, defining homologous genes cannot solely be addressed under the classic assumptions of strong tree-thinking, according to which genes evolve in a strictly tree-like fashion of vertical descent and divergence and the problems of homology detection are primarily methodological. Gene homology could also be considered under a different perspective where genes evolve as ‘public goods’, subjected to various introgressive processes. In this latter case, defining homologous genes becomes a matter of designing models suited to the actual complexity of the data and how such complexity arises, rather than trying to fit genetic data to some a priori tree-like evolutionary model, a practice that inevitably results in the loss of much information. Here we show how important aspects of the problems raised by homology detection methods can be overcome when even more fundamental roots of these problems are addressed by analysing ‘public goods thinking’ evolutionary processes through which genes have frequently originated. This kind of thinking acknowledges distinct types of homologs, characterised by distinct patterns, in phylogenetic and non phylogenetic unrooted or multi-rooted networks. In addition, we define “family resemblances” to include genes that are related through intermediate relatives, thereby placing notions of homology in the broader context of evolutionary relationships. We conclude by presenting some pay-offs of adopting such a pluralistic account of homology and family relationship, that expands the scope of evolutionary analyses beyond the traditional, yet relatively narrow focus allowed by a strong tree-thinking view on gene evolution.

Item Type:	Article
Additional Information:	This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
Keywords:	homology; network; comparative genomics; epaktolog; ortholog; paralog;
Academic Unit:	Faculty of Science and Engineering > Biology
Item ID:	7443
Identification Number:	https://doi.org/10.1093/molbev/mst228
Depositing User:	David Fitzpatrick
Date Deposited:	14 Sep 2016 15:58
Journal or Publication Title:	Molecular Biology and Evolution
Publisher:	Oxford University Press
Refereed:	Yes
URI:	http://mbe.oxfordjournals.org
Use Licence:	This item is available under a Creative Commons Attribution Non Commercial Share Alike Licence (CC BY-NC-SA). Details of this licence are available here

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