Phylogenetic Networks: A Review of Methods to Display Evolutionary History

Abstract

The author DAM conceived the idea and wrote, read and approved the manuscript.

Phylogenomics of the green ash eucalypts (Myrtaceae): a tale of reticulate evolution and misidentification

“…Previous studies have discussed the possibility that evolution in many eucalypts may not necessarily have been divergent (Chappill and Ladiges 1996;McKinnon et al 2008) and that speciation in both plants and animals can occur during partial reproductive isolation (Wu 2001;Lexer and Widmer 2008;Mallet 2005). Although more traditional evolutionary models assume a tree, it is well known that more complex evolutionary scenarios (such as rapid radiation and reticulate evolution) are poorly described by these models (Huson and Bryant 2006;Morrison 2014). Phylogenetic networks, which allow horizontal reticulation events as well as vertical processes to be visualised, are increasingly being recognised as providing a more comprehensive picture of evolutionary history (Francis and Steel 2015).…”

Evolutionary change and phylogenetic relationships in light of horizontal gene transfer

“…In addition, an increasing number of bioinformatics tools are being developed to cope with this new scope of evolution such as a network (Dagan 2011;Bapteste et al 2013;Morrison 2014) that complements the plethora of phylogenetic tools developed in the past to study evolution in the framework of the Tree of Life.…”

Delimitation of a novel member of genus Metarhizium (Clavicipitaceae) by phylogenetic and network analysis

“…However, on the other hand, conflicting phenomena from multi-gene trees has frequently been found (Zou & Ge 2008, Kepler et al 2013, Short et al 2014, Simmons et al 2015. There has been increased interest in using networks in order to avoid the conflicting phenomenon with multi-gene trees (Morrison 2014, Liang et al 2016. Phylogenetic networks could not only reveal multi-gene data conflict and ambiguous information, but also differentiate between allied species which were uncertain and concealed and could not be differentiated by bifurcating trees (Huson & Bryant 2006, Morrison 2014.…”

“…There has been increased interest in using networks in order to avoid the conflicting phenomenon with multi-gene trees (Morrison 2014, Liang et al 2016. Phylogenetic networks could not only reveal multi-gene data conflict and ambiguous information, but also differentiate between allied species which were uncertain and concealed and could not be differentiated by bifurcating trees (Huson & Bryant 2006, Morrison 2014. In the present study, the split network and Min Spanning Network were applied to show the relationship among a new species and its allies.…”