Wednesday, May 28, 2014

Phylogenetic networks and "evolutionary networks"

Complex networks are found in all parts of biology, graphically representing biological patterns and, if they are directed networks, also their causal processes. Directed networks are currently used to model various aspects of biological systems, such as gene regulation, protein interactions, metabolic pathways, ecological interactions, and evolutionary histories.

Two types of networks can be distinguished, and this distinction seems to me to be very important. Most networks are what might be called observed networks, in the sense that the nodes and edges represent empirical observations. For example, a food web consists of nodes representing animals with connecting edges representing who eats whom. Similarly, in a gene regulation network the genes (nodes) are connected by edges showing which genes affect the functioning of which other genes. In all cases, the presence of the nodes and edges in the graph is based on experimental data. These are collectively called interaction networks or regulation networks.

However, when studying historical patterns and processes not all of the nodes and edges can be observed. So, instead, they are inferred as part of the data-analysis procedure. That is, we infer the patterns as well as the processes; and we can call these inferred networks. In this case, the empirical data may consist solely of the leaf nodes, and we infer the other nodes plus all of the edges. For example, every person has two parents, and even if we do not observe those parents we can infer their existence with confidence, as we also can for the grandparents, and so on back through time with a continuous series of ancestors. Alternatively, we may also observe some of the internal nodes of the network, such as when we do record the parents and grandparents because they are contemporaneous (ie. their generations overlap). This type of pattern can be represented as a genealogical network, when referring to individual organisms, or a phylogenetic network when referring to groups (populations, species, or larger taxonomic groups).

What, then, are the things often referred to as "evolutionary networks" but which are clearly not phylogenetic networks? They are of the first type, the interaction networks. In an evolutionary network the observed nodes are directly connected to each other to represent some aspect of evolution. This aspect may have some component of phylogeny to it, but there is more to the study of evolution than solely phylogenetic history.

For example, directed LGT (dLGT) networks connect nodes representing contemporary organisms with edges that represent inferred lateral gene transfer. That is, the evolutionary networks show gene sharing. This is obviously related to the phylogeny of the organisms, but the network does not display the phylogeny itself. This first example (from Ovidiu Popa, Einat Hazkani-Covo, Giddy Landan, William Martin, Tal Dagan. 2011. Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Research 21: 599-609) shows "32,028 polarized lateral recipient–donor protein-coding gene transfer events" inferred from "the completely sequenced genomes of 657 prokaryote species".

The concept of a gene-sharing network as an evolutionary network has also been applied to viruses and their relatives, for example, as shown by this next diagram (from Natalya Yutin, Didier Raoult, Eugene V Koonin. 2013. Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies. Virology Journal 10: 158).

The question, then, is what to make of diagrams that combine both a phylogenetic tree and this type of evolutionary network, such as is done in the Minimal Lateral Network. This next example is from linguistics rather than biology (from Johann-Mattis List, Shijulal Nelson-Sathi, Hans Geisler, William Martin. 2013. Networks of lexical borrowing and lateral gene transfer in language and genome evolution. Bioessays 36: 141-150), and it superimposes the sharing network and the phylogenetic tree. (For a discussion in the context of LGT, see also Tal Dagan. 2011. Phylogenomic networks. Trends in Microbiology 19: 483-491).

In this diagram, the tree explicitly represents the phylogenetic history of the languages while the evolutionary network represents possible borrowings of words, with thicker lines representing more borrowed words. Clearly, the network also contains phylogenetic information of some sort. For example, the connection of the root of the Romance languages to English reflects the conquest of Britain by the French-speaking Normans, which modified the Old-German heritage of Old English. However, the diagram as a whole is a hybrid, rather than being a coherent phylogenetic network in the simplest sense (ie. a reticulation network).

To see this clearly, note that the phylogenetic tree is not fully resolved and that the evolutionary network does suggest possible resolutions for several of polychotomies, such as the relationship of Armenian and Greek, the relationship of Albanian to the Romance languages, and the relationship of the Gaelic languages to the Romance languages. So, in some cases the evolutionary network helps resolve the phylogenetic tree rather than forming a reticulating network.

It would be possible to derive a phylogenetic network from this minimal lateral network, but as it stands it is a combination of a phylogenetic tree and a so-called evolutionary network.

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