Integrating Phylogenetic and Network Approaches to Study Gene Family Evolution: The Case of the AGAMOUS Family of Floral Genes

Authors

Daniel Santana de Carvalho, University of Nebraska-LincolnFollow
James C. Schnable, University of Nebraska-LincolnFollow
Ana Maria R. Almeida, California State University East Bay

Date of this Version

2018

Citation

Evolutionary Bioinformatics Volume 14: 1–11

Comments

© The Author(s) 2018

Open access

https://doi.org/10.1177/1176934318764

Abstract

The study of gene family evolution has benefited from the use of phylogenetic tools, which can greatly inform studies of both relationships within gene families and functional divergence. Here, we propose the use of a network-based approach that in combination with phylogenetic methods can provide additional support for models of gene family evolution. We dissect the contributions of each method to the improved understanding of relationships and functions within the well-characterized family of AGAMOUS floral development genes. The results obtained with the two methods largely agreed with one another. In particular, we show how network approaches can provide improved interpretations of branches with low support in a conventional gene tree. The network approach used here may also better reflect known and suspected patterns of functional divergence relative to phylogenetic methods. Overall, we believe that the combined use of phylogenetic and network tools provide a more robust assessment of gene family evolution.