Could the new genomics start a scientific revolution that traps Darwin in its web? His iconic “tree of life” is morphing into a network, thanks to a flood of new data showing that lateral gene transfer (LGT) is ubiquitous. If the opinions of some geneticists take root, phylogenetic studies may become relics of the last paradigm. The implications for evolutionary theory are enormous.

Ever since Darwin sketched a branching tree in his notes, the “tree of life” icon has become a fixture in the minds of biologists and students. It seems intuitively obvious: since individuals are descended from parents and grandparents, each species has a genetic lineage. According to Darwin’s thinking, these lineages connect back in time due to the repeated “origin of species” by natural selection. Each species would have originated at one of these branching points. If followed far back enough, all the bifurcating twigs and branches would connect in a tree-like pattern of universal common descent. Implicit in this picture is the assumption that branches do not re-connect; once bifurcated, they share the traits of the common ancestor but evolve thereon in their own direction. 

A Profound Rethink

Writing in Current Biology, Cédric Blais and John M. Archibald look back at the modern genomics revolution and the profound rethink it is causing about “biology’s unifying metaphor,” the tree of life. 

Some twenty years ago, the foundations of the tree of life were shaken by the realization that prokaryotic genomes are comprised of genes with different evolutionary histories…. [W]ith Charles Darwin’s On the Origin of Species and Ernst Haeckel’s vivid depictions of evolutionary trees, the tree of life took root as biology’s unifying metaphor. Molecular phylogenetics emerged in the 1960s and 1970s and followed Darwin’s template: the branches of life’s tree diverged and never merged (Box 1). Comparative genomics was expected to solidify this view of evolution, but the genomes of bacteria and archaea were found to be mosaic in nature, having acquired genes from both closely and distantly related taxa by lateral (or horizontal) gene transfer. This realization unsettled the primacy of vertical descent in the history of life and its use in the taxonomic classification of organisms. It ushered in a heated debate over how best to depict the relationships between organisms in nature. Should the tree of life be abandoned, and could it be suitably replaced by a network of life? Or was lateral gene transfer largely inconsequential, mere noise that could and should be filtered out, with the remaining signal thus revealing life’s true tree? [Emphasis added.]

Think of how profound a scientific revolution is at hand, when “biology’s unifying metaphor” is being questioned. Some geneticists are standing with an axe in hand at the base of the iconic tree. Blais and Archibald point out that the exponential rise in genome sequencing, particularly of microbes, has led to this major reconsideration. It wouldn’t be happening without big data forcing it. Look at the long-accepted concepts that are at risk:

• The existence of a single phylogenetic tree
• Carl Woese’s concept of three domains (bacteria, archaea, eukarya)
• Molecular phylogenetic practice
• Taxonomy
• Universal common ancestry

Taking Sides

As in any revolution, people take sides. Radicals on one end of the spectrum are happy to cut down the old tree and replace it with a modern network. Radicals on the other side want to save the tree, like conservationists sitting in the branches to stop the chainsaws. Then there is middle ground where peacemakers think both concepts can coexist, and everybody will be happy. Every scientist, though, must be united about the facts. Blais and Archibald describe the party politics without taking sides, but they point out that LGT is real and cannot be ignored:

The primacy of the tree of life must be qualified by the recognition that it represents only a fraction of evolutionary history and that networks capture bona fide evolutionary dynamics that are incompatible with it. Networks now encompass far more entities and processes than were first considered when discussing the tree and the network of life. Even though the tree of life survives, it is now clear that vertical and reticulate lineages co-exist within gene exchange communities of varied topologies.

And yet think of how the tree picture changes if twigs interconnect. The tree morphs into a network of interconnecting nodes. There’s no necessary vertical component to a network diagram; it can be rotated at will and the connections remain. If LGT is indeed rampant throughout life, as appears beyond doubt, the universal tree of life concept becomes a matter of philosophical preference, not empirical demonstration.

How do organisms share genetic information? For prokaryotes, it’s simple: they routinely share plasmids (this is how antibiotic resistance genes can travel from species to species). This phenomenon gave rise to the “quasispecies” concept, where individuals within a species may not have the entire repertoire of genes but can get them from other members when under stress. For higher organisms, other methods of information transfer include phages and mobile genetic elements (“jumping genes” or transposons), hybridization, and introgression. Microbiologists are studying nanoscopic channels that appear to connect cells, through which information can travel. If so, cells become less like individual buildings and more like commercial plazas with walkways between them.

A Hindrance to Scientific Advance

The old tree concept can hinder scientific progress, the authors say.

[L]ateral gene transfer does not respect species boundaries and is enabled by mobile genetic elements and their vehicles not included in the tree of life, such as viruses, gene transfer agents, plasmids and transposons… Moreover, even though it allows for lateral connections, the tree of life recognizes only one ‘right’ way of grouping existing taxa: vertical descent. It is thus ill-equipped to study species groupings reflective of the complex gene-transfer dynamics that exist in the microbial world. Networks, on the other hand, are not restricted by a tree structure and can be used to shine new light on evolutionary questions. Indeed, recent studies have found that networks can outperform trees when faced with complex or ambiguous phylogenetic scenarios,

“Evolutionary questions” in the new paradigm, if they are not vertical, can hardly be called evolutionary in the Darwinian sense. The question now becomes whether the boundaries of the nested hierarchies by which organisms have been classified are as impenetrable as previously believed. The implications of network thinking have yet to be fully explored, but the prospects are as exciting as they are revolutionary.

Implications for Intelligent Design

If the network concept continues to supplant or supplement the old tree concept, here are some research questions that design advocates might consider.

• The primacy of information over ancestry.
• The ability of LGT to prime a migrating organism for a new environment.
• Adaptation in light of LGT rather than ancestry.
• How networking provides resilience.
• New explanations for “convergent evolution” — sharing instead of ancestry.
• Expanded taxonomical principles that include LGT.
• Limits to information sharing that preserve species identity.
• Interpreting the fossil record in light of network genomics.
• Replacing phylogenetic trees with network diagrams.

The essay by Blais and Archibald, “The past, present and future of the tree of life,” is worth reading. We may be on the verge of a major scientific revolution in biology. It appears that the new genomics will be more compatible with design than Darwin’s model ever was. 

Discovery Institute is co-sponsoring an event this week in Texas, the “Conference on Engineering in Living Systems” (CELS). Participants will likely be discussing some of the concepts coming to light in the new genomics, and how they intersect with engineering principles evident in life. What’s more engineered than a network?