Carl Zimmer: Tangling the tree

Carl Zimmer on “The Loom” describes recent work on the phylogenetic tree. Researchers have looked at vertical and horizontal transmission of genetic information in various bacteria.

I would like to focus on a particular aspect of the findings, namely the scale free nature of the horizontal gene transfer networks. People may remember the scale free networks in RNA for instance and how such networks have some very important properties. Scale free networks can be explained through the simple process of duplication and preferential attachment. In this case, the researchers showed that the horizontal ‘vines’ of the tree form scale free networks.

So what?

One property of scale-free networks is their “small-world” nature: travelling from one node to any other is very fast. (Other small-world networks include social networks, the internet and air-travel connections.) These characteristics allow the hubs to serve as bacterial “gene banks”, providing a medium to acquire and redistribute genes in microbial communities. “This has important implications for our understanding of horizontal gene transfer because, in small-world networks, the shortest path between any two network nodes is relatively small: in other words, a gene can rapidly be disseminated from organism to organism through very few horizontal gene transfer events,” explains Christos Ouzounis. A few species, including beneficial nitrogen-fixing soil bacteria, appear to be “champions” of horizontal gene transfer; “it’s entirely possible that apparently harmless organisms are quietly spreading antibiotic resistance under our feet,” concludes Christos Ouzounis.

Source: Press release

ID proponents have often described the horizontal transfer as being problematic for the tree of life concept or Darwinian evolution. First of all the researchers showed that “vertical inheritance constitutes the bulk of gene transfer on the tree of life”. Secondly, the press release observes that “Thus, although the distribution of most of the gene families present today can be explained by the classical theory of evolution by descent, anomalies of these patterns are revealed by the �minority report� of horizontal exchange.”

The net of life: Reconstructing the microbial phylogenetic network Victor Kunin1, Leon Goldovsky, Nikos Darzentas and Christos A. Ouzounis2

AbstractIt has previously been suggested that the phylogeny of microbial species might be better described as a network containing vertical and horizontal gene transfer (HGT) events. Yet, all phylogenetic reconstructions so far have presented microbial trees rather than networks. Here, we present a first attempt to reconstruct such an evolutionary network, which we term the “net of life.” We use available tree reconstruction methods to infer vertical inheritance, and use an ancestral state inference algorithm to map HGT events on the tree. We also describe a weighting scheme used to estimate the number of genes exchanged between pairs of organisms. We demonstrate that vertical inheritance constitutes the bulk of gene transfer on the tree of life. We term the bulk of horizontal gene flow between tree nodes as “vines,” and demonstrate that multiple but mostly tiny vines interconnect the tree. Our results strongly suggest that the HGT network is a scale-free graph, a finding with important implications for genome evolution. We propose that genes might propagate extremely rapidly across microbial species through the HGT network, using certain organisms as hubs.

A very readable Senior Thesis on scale free networks can be found here

Elizabeth Rach wrote:

In this paper, I will present three possible models that offer potential insights into the mechanisms underlying power law distributions for gene family sizes: the Preferential Attachment Model, the Branching Process With Immigration Model, and the Birth Death and Innovation Model.