We don't normally discuss individual papers in this blog (except as example datasets), but today I am simply drawing your attention to what appears to be a little-known paper on phylogenetic networks.
Naruya Saitou has not contributed much to the theory of networks, being instead best known for the development of the neighbor-joining method for phylogenetic trees. (The 20th most cited paper ever; see Massive citations of bioinformatics in biology papers) However, this recent paper is of interest:
Naruya Saitou, Takashi Kitano (2013) The PNarec method for detection of ancient recombinations through phylogenetic network analysis. Molecular Phylogenetics and Evolution 66: 507-514.The paper presents a new method for detecting ancient recombinations through phylogenetic network analysis. Recent recombinations are easily detectable using alternative methods, although splits graphs can also be used, but older recombinations are more tricky.
Importantly, I particularly like the opening paragraph of the paper:
The good old days of constructing phylogenetic trees from relatively short sequences are over. Reticulated or "non-tree" structures are omnipresent in genome sequences, and the construction of phylogenetic networks is now the default for describing these complex realities. Recombinations, gene conversions, and gene fusions are biological mechanisms to produce non-tree structures to gene phylogenies, while gene flow is a well known factor for creating reticulations within population phylogenies.These are heart-warming words from the developer of the most commonly used tree-building method!