103 Perspectives on the Phylogenetic Tree

Limitations to the Classic Model

Classical thinking about prokaryotic evolution, included in the classic tree model, is that species evolve clonally. That is, they produce offspring themselves with only random mutations causing the descent into the variety of modern-day and extinct species known to science. This view is somewhat complicated in eukaryotes that reproduce sexually, but the laws of Mendelian genetics explain the variation in offspring, again, to be a result of a mutation within the species. Scientists did not consider the concept of genes transferring between unrelated species as a possibility until relatively recently. Horizontal gene transfer (HGT), or lateral gene transfer, is the transfer of genes between unrelated species. HGT is an ever-present phenomenon, with many evolutionists postulating a major role for this process in evolution, thus complicating the simple tree model. Genes pass between species which are only distantly related using standard phylogeny, thus adding a layer of complexity to understanding phylogenetic relationships.

The various ways that HGT occurs in prokaryotes is important to understanding phylogenies. Although at present some do not view HGT as important to eukaryotic evolution, HGT does occur in this domain as well. Finally, as an example of the ultimate gene transfer, some scientists have proposed genome fusion theories between symbiotic or endosymbiotic organisms to explain an event of great importance—the evolution of the first eukaryotic cell, without which humans could not have come into existence.

Horizontal Gene Transfer

Horizontal gene transfer (HGT) is the introduction of genetic material from one species to another species by mechanisms other than the vertical transmission from parent(s) to offspring. These transfers allow even distantly related species to share genes, influencing their phenotypes. Scientists believe that HGT is more prevalent in prokaryotes, but that this process transfers only about 2% of the prokaryotic genome. Some researchers believe such estimates are premature: we must view the actual importance of HGT to evolutionary processes as a work in progress. As scientists investigate this phenomenon more thoroughly, they may reveal more HGT transfer. Many scientists believe that HGT and mutation are (especially in prokaryotes) a significant source of genetic variation, which is the raw material in the natural selection process. These transfers may occur between any two species that share an intimate relationship ((Figure)).

Genome Fusion and Eukaryote Evolution

Scientists believe the ultimate in HGT occurs through genome fusion between different prokaryote species when two symbiotic organisms become endosymbiotic. This occurs when one species is taken inside another species’ cytoplasm, which ultimately results in a genome consisting of genes from both the endosymbiont and the host. This mechanism is an aspect of the Endosymbiont Theory, which most biologists accept as the mechanism whereby eukaryotic cells obtained their mitochondria and chloroplasts. However, the role of endosymbiosis in developing the nucleus is more controversial. Scientists believe that nuclear and mitochondrial DNA have different (separate) evolutionary origins, with the mitochondrial DNA derived from the bacteria’s circular genomes ancient prokaryotic cells engulfed. We can regard mitochondrial DNA as the smallest chromosome. Interestingly enough, mitochondrial DNA is inherited only from the mother. The mitochondrial DNA degrades in sperm when the sperm degrades in the fertilized egg or in other instances when the mitochondria located in the sperm’s flagellum fails to enter the egg.

Within the past decade, James Lake of the UCLA/NASA Astrobiology Institute proposed that the genome fusion process is responsible for the evolution of the first eukaryotic cells ((Figure)a). Using DNA analysis and a new mathematical algorithm, conditioned reconstruction (CR), his laboratory proposed that eukaryotic cells developed from an endosymbiotic gene fusion between two species, one an Archaea and the other a Bacteria. As mentioned, some eukaryotic genes resemble those of Archaea; whereas, others resemble those from Bacteria. An endosymbiotic fusion event, such as Lake has proposed, would clearly explain this observation. Alternatively, this work is new and the CR algorithm is relatively unsubstantiated, which causes many scientists to resist this hypothesis.

Lake’s more recent work ((Figure)b) proposes that gram-negative bacteria, which are unique within their domain in that they contain two lipid bilayer membranes, resulted from an endosymbiotic fusion of archaeal and bacterial species. The double membrane would be a direct result of the endosymbiosis, with the endosymbiont picking up the second membrane from the host as it was internalized. Scientists have also used this mechanism to explain the double membranes in mitochondria and chloroplasts. Lake’s work is not without skepticism, and the biological science community still debates his ideas. In addition to Lake’s hypothesis, there are several other competing theories as to the origin of eukaryotes. How did the eukaryotic nucleus evolve? One theory is that the prokaryotic cells produced an additional membrane that surrounded the bacterial chromosome. Some bacteria have the DNA enclosed by two membranes; however, there is no evidence of a nucleolus or nuclear pores. Other proteobacteria also have membrane-bound chromosomes. If the eukaryotic nucleus evolved this way, we would expect one of the two types of prokaryotes to be more closely related to eukaryotes.

The nucleus-first hypothesis proposes that the nucleus evolved in prokaryotes first ((Figure)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 ((Figure)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 ((Figure)c). All of these hypotheses are testable. Only time and more experimentation will determine which hypothesis data best supports.

Web and Network Models

Recognizing the importance of HGT, especially in prokaryote evolution, 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 (Figure)a shows, 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. Scientists often call this model the “web of life.” In an effort to save the tree analogy, some have proposed using the Ficus tree ((Figure)b) with its multiple trunks as a phylogenetic way 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” ((Figure)). This is 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, we must modify Darwin’s “tree of life” model to include HGT. Does this mean abandoning the tree model completely? Even Lake argues that scientists should attempt to modify 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 phylogenetic tree concept is too simple, but made sense based on what scientists knew at the time. However, the search for a more useful model moves on: each model serves as hypotheses to test with the possibility of developing new models. This is how science advances. Researchers use these models as visualizations to help construct hypothetical evolutionary relationships and understand the massive amount of data that requires analysis.