The biological model behind most phylogenetic networks is the same as the one behind most phylogenetic trees, in which there is a series of branches ramifying from a single base, with the additional feature that branches can fuse with each other.
In this model, attention has focussed on the osculations ("kissing") between branches. However, I wish to draw your attention to the base of the tree, where in some biological models multiple stems appear. These stems represent multiple origins for the organisms being modelled.
The idea is, simply, that life is not monophyletic, and nor are some of the commonly recognized taxonomic groups. This model appears most famously in the paper by Doolittle (1999), but it's basic premise has been repeated a number of times (eg. Doolittle 2000a, from which the above figures are taken; Wells 2002).
Doolittle (2000b) credits the biological idea to Woese & Fox (1977), as further developed by Woese (1987, 1998), so the idea is not a particularly recent one. The premise is that "... the three contemporary domains of life arose not from a single cell, but from a population of very different cellular entities ('progenotes') ... such a population [could] give rise to two (and then three) discrete cellular domains without passing through a bottleneck represented by a single cellular universal ancestor" (Doolittle 2000b).
There is, of course, a biological precedent for this multiple tree model: the "Husband and Wife tree" or "Marriage tree", which is formed from two trees that have branches conjoined by the process known as self-grafting (or osculation). Here, there literally are two trunks and roots, since the conjoined structure starts as two separate trees.
|Inosculated (self-grafted) crab apple trees, Lynncraigs farm, Scotland|
My question, though, is this: Can the mathematics of phylogenetic networks handle multiple roots? All current definitions that I have seen of phylogenetic networks specify a single root node with indegree 0. However, I have seen no discussion of this point in the literature, as to the necessity of this imposed mathematical constraint.
Doolittle W.F. (1999) Phylogenetic classification and the universal tree. Science 284: 2124-2128.
Doolittle W.F. (2000a) Uprooting the tree of life. Scientific American 282(2): 90–95.
Doolittle W.F. (2000b) The nature of the universal ancestor and the evolution of the proteome. Current Opinion in Structural Biology 10: 355-358.
Wells J. (2002) Icons of Evolution: Science or Myth? Regenery Publishing, Washington DC.
Woese C.R. (1987) Bacterial evolution. Microbiological Reviews 51: 221-271.
Woese C.R., Fox G.E. (1977) The concept of cellular evolution. Journal of Molecular Evolution 10: 1-6.