3.3 Perspectives on the phylogenetic tree  (Page 5/19)

The nucleus-first hypothesis proposes that the nucleus evolved in prokaryotes first ( [link] a ), followed by a later fusion of the new eukaryote with bacteria that became mitochondria. The mitochondria-first hypothesis proposes that mitochondria were first established in a prokaryotic host ( [link] b ), which subsequently acquired a nucleus, by fusion or other mechanisms, to become the first eukaryotic cell. Most interestingly, the eukaryote-first hypothesis proposes that prokaryotes actually evolved from eukaryotes by losing genes and complexity ( [link] c ). All of these hypotheses are testable. Only time and more experimentation will determine which hypothesis is best supported by data.

Web and network models

The recognition of the importance of HGT, especially in the evolution of prokaryotes, has caused some to propose abandoning the classic “tree of life” model. In 1999, W. Ford Doolittle proposed a phylogenetic model that resembles a web or a network more than a tree. The hypothesis is that eukaryotes evolved not from a single prokaryotic ancestor, but from a pool of many species that were sharing genes by HGT mechanisms. As shown in [link] a , some individual prokaryotes were responsible for transferring the bacteria that caused mitochondrial development to the new eukaryotes, whereas other species transferred the bacteria that gave rise to chloroplasts. This model is often called the “ web of life    .” In an effort to save the tree analogy, some have proposed using the Ficus tree ( [link] b ) with its multiple trunks as a phylogenetic to represent a diminished evolutionary role for HGT.

Ring of life models

Others have proposed abandoning any tree-like model of phylogeny in favor of a ring structure, the so-called “ ring of life    ” ( [link] ); a phylogenetic model where all three domains of life evolved from a pool of primitive prokaryotes. Lake, again using the conditioned reconstruction algorithm, proposes a ring-like model in which species of all three domains—Archaea, Bacteria, and Eukarya—evolved from a single pool of gene-swapping prokaryotes. His laboratory proposes that this structure is the best fit for data from extensive DNA analyses performed in his laboratory, and that the ring model is the only one that adequately takes HGT and genomic fusion into account. However, other phylogeneticists remain highly skeptical of this model.

In summary, the “tree of life” model proposed by Darwin must be modified to include HGT. Does this mean abandoning the tree model completely? Even Lake argues that all attempts should be made to discover some modification of the tree model to allow it to accurately fit his data, and only the inability to do so will sway people toward his ring proposal.

This doesn’t mean a tree, web, or a ring will correlate completely to an accurate description of phylogenetic relationships of life. A consequence of the new thinking about phylogenetic models is the idea that Darwin’s original conception of the phylogenetic tree is too simple, but made sense based on what was known at the time. However, the search for a more useful model moves on: each model serving as hypotheses to be tested with the possibility of developing new models. This is how science advances. These models are used as visualizations to help construct hypothetical evolutionary relationships and understand the massive amount of data being analyzed.

Section summary

The phylogenetic tree, first used by Darwin, is the classic “tree of life” model describing phylogenetic relationships among species, and the most common model used today. New ideas about HGT and genome fusion have caused some to suggest revising the model to resemble webs or rings.