PT  - JOURNAL ARTICLE
AU  - Daniel S. Carvalho
AU  - James C. Schnable
AU  - Ana Maria R. Almeida
TI  - Integrating phylogenetic and network approaches to study gene family evolution: the case of the AGAMOUS family of floral genes
AID  - 10.1101/195669
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 195669
4099  - http://biorxiv.org/content/early/2017/09/28/195669.short
4100  - http://biorxiv.org/content/early/2017/09/28/195669.full
AB  - 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 more robust assessments of gene family evolution.