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Evolutionary Theory Horizontal Gene Transfer - A New Paradigm for Biology
The Old Metaphor: The Tree of Life Gogarten began by describing the emergence of the prevailing biological metaphor that is taught in most high school biology classes: the tree of life. Ever since the publication of Charles Darwin's "Origin of Species" biologists envisioned evolution as a steadily bifurcating tree-like process. About thirty years ago, two biologists, Carl Woese and George Fox, initiated a major breakthrough in biology by mapping life forms not by their appearance and physiological capabilities but by their molecular characteristics. Their work lead to the inclusion of small single celled organisms into a rational taxonomic system based on shared ancestry. The results of this pioneering work gave rise to a tree of life that describes the evolutionary hierarchy of all life forms on earth and that includes all living organisms. Present day organisms are located on the tips of the branches. At the bottom of the tree are the most ancient life forms on Earth. Prokaryotes (organisms whose cells do not have a nucleus) populate the deeper portions of the tree and also most of the present day branch tips, eukaryotes (organisms with a cell nucleus) followed later, and within the eukaryotes plants, fungi, animals, and humans emerged. Ever since, the compelling image of an all-encompassing tree has stood out in most people’s minds as the most accurate representation of the evolutionary process. Furthermore, Woese and Fox also contributed a new terminology. They recognized three Ur-kingdoms (today often called the 3 domains of life). They realized that all of life could be categorized into 3 large domains created based on molecular phylogenies:
1) Bacteria (sometimes known as Eubacteria). In prokaryotes the genetic information is not separated by a membrane from the rest of the cell. Although the first 2 domains are both prokaryotes, Woese and Fox separated them because their ribosomal RNAs (which are a part of the machinery that synthesizes proteins) are as dissimilar between these two groups as each of them is to the ribosomal RNAs of the Eukaryotes. The division of the prokaryotes into two groups is also supported by many other characteristics, including the composition of the cell wall (a finding that first prompted Otto Kandler, a German botanist, to suggest two very distinct groups of prokaryotes in the early 70's), types of lipids used in the cell membrane, and the way DNA is packaged and transcribed. In many respects the Archaea are more similar to the Eukaryotes than to the Bacteria. Gogarten pointed out that if the Archaea are indeed the sister group to the Eukaryotes, then the Bacteria would be the oldest of the three domains. Gogarten pointed out that the underlying assumption of the tree of life is that genetic changes are passed on by "vertical inheritance," meaning that the only way that genes are spread is by passing them on to one’s descendents. Today most biologists have accepted Woese and Fox’s work as foundational to their field, and they operate from the premise that all of life can be organized on a tree.
What is HGT (horizontal gene transfer)? In the late 1980s while conducting research on some newly sequenced bacterial and archaeal gene families, Gogarten began to notice that some genetic information that was common among the three separate domains did not reflect their fundamental division. The domains did not appear separate; rather, some bacteria possessed the archaeal type of an enzyme, whereas some of the archaea contained the bacterial versions. As biologists further analyzed microbial genes and completely sequenced genomes, they started to realize that the genomes were much more intermixed than previously thought. During the decade of the 1990s microbial biologists continued to see the same trend of intermixed genomic information. This information was like a windstorm shaking the original metaphor of "the tree of life." According to Gogarten, Horizontal Gene Transfer or HGT leads to a radical new organizing principle. Gogarten's and his colleagues work shows that genetic information is not only handed down from ancestor to descendent, but also is exchanged horizontally among and between contemporaries; even among different species and sometimes even between species belonging to different domains. Because evolution was first discovered and studied in animals and plants, the standard belief in biology has been that genes would mainly be transferred vertically, but in the microbial world, this paradigm does not appear to be the best way to explain what occurs. The frequent exchange of genetic information among organisms requires a reassessment of traditional ideas. Gogarten believes that HGT is more frequent and pervasive than most biologists could even imagine a decade ago. He suggested that a microbial species might look similar to one another not because of a relationship through vertical inheritance but rather because the frequency of HGT between them. In fact, Gogarten stated that if the full data of complete genome sequences is taken into account, the genomic history of all bacterial life could be explained exclusively through HGT without any reference to vertical inheritance at all. A well-known paleontologist, Stephen J. Gould, had proposed that a better metaphor for the evolutionary history of earth’s life forms is a fuzzy bush not a tall bifurcating tree. Even so, Gogarten maintains that Gould’s metaphor does not sufficiently describe the pattern of microbial genomic exchange that has been emerging from his own research on HGT. According to Gogarten evolution corresponds neither to a tree nor a bush, but rather to a net in which lines of descent not only diverge but also communicate and even merge with one another.
A New Paradigm for Biology? Gogarten invoked the name of Richard Dawkins, originator of the selfish gene theory, which asserts that genes have an autonomous rogue quality and will compete with other genes to survive at all costs. According to Dawkins' gene-centered view plants, animals, and humans are merely vessels designed by the genes to carry the genetic information from generation to generation. Genes can be transmitted between members of a population, and between different species present in the same microbial community. Once thought to be a static, unchanging record of the history of life, the genome is actually plastic and ever evolving. Selection occurs not at one level but at least at three levels (and maybe more):
1) the level of the gene The horizontal transfer of genes between members of a community ties together selection at the different levels. In the community-centered view, one can regard the microbial community as a super organisms in which the different members have access to a common shared genetic resource through horizontal gene transfer. Evolution is not a steadily bifurcating stream of organismal lineages, but a rich network of gene histories that interconnects the different organismal histories into a tangled web of life.
Other Problems Encountered in Molecular Evolution Besides the mosaic nature of genomes, Gogarten discussed other problems encountered in the study of molecular evolution. If one uses the fossil record of animal, plant and algal evolution to calibrate molecular phylogenies with respect to time, and extrapolates back to the early evolution, then many gene families seem to indicate that the most recent common ancestor to all of life would be about 8 billion years old, which is almost twice the age of our earth! Clearly, this seems to be impossible. In fact, this is what led Francis Crick (the co-discoverer with James Watson of DNA in 1953) to suggest directed panspermia for the origin of life on earth (meaning that the seeds of life were delivered to earth intentionally from space by another civilization). While panspermia is one possible explanation, another is that evolution of molecular sequences occurred at a much faster pace during the early evolution. Gogarten also described evidence that suggests that mutations, which were once thought to occur only randomly, may in fact happen in a directed fashion. For example, in response to stress some bacteria display an ability to mutate at a much faster rate in order to alter their ability to consume a food source that they were unable to digest before the mutations. However, not all mutations occur at the same rate. Gogarten cited reports that find beneficial mutations occurring more frequently than neutral mutations, hence the name "directed mutation" was used to describe this finding.
Implications, Questions, and Discussion While responding to questions from the other participants, Gogarten highlighted a number of the implications of the emerging new paradigm. One interesting theme he pointed to is "stability through diversity." It seems that one strategy that communities of organisms employ is to increase their genetic diversity to create a greater repertoire of responses to environmental changes and thereby increase their chance of survival. For example, Gogarten described a microbial community that lives inside sandstone rocks in the dry valleys of Antarctica. These communities live amongst an abundance of heavy metals, and the bacterial community shares genes that confer resistance to these metals. These genes are also available to newcomers that thus find an opportunity to integrate themselves into the community, thereby increasing the genomic resources, which might be useful in coping with changing living conditions. In effect, the bacteria stabilize themselves by welcoming diverse bacteria into their community, which are capable of doing different tasks and functions. Increased stability in a changing environment is achieved through increased diversity. Another interesting point came in response to a question about organisms that don’t participate in HGT. Gogarten noted that organisms that don’t exchange genes appear more primitive from a comparative standpoint. They fall out of the rich ongoing genetic exchange that is occurring among the other organisms, and thus they do not incorporate the latest inventions shared among the others. Thus, one hypothesis about the deep branching lineages in the tree of life is that these organisms stopped participating in HGT and therefore started to appear older on the evolutionary scale, when in fact they just had stopped sharing genes. Responding to a question about telos, Gogarten discussed some of the further implications of his work. First, he noted that in the new paradigm natural selection takes place on at least 3 levels (gene, population, community). Not just individual genes are evolving but larger populations and communities are being selected by the environment to succeed into the future. From this perspective, evolution is a multi-tiered process, in which "organisms" are being selected for at different levels. Not only are individual genes being selected to survive, but microbial communities that act in a unified fashion as "superorganisms" are as well. Gogarten raised the question how evolution by natural selection might function at the highest level of this multi-tiered system? In other words, if the earth’s biosphere is a considered a superorganism, then what selection principles act on it? When we think from the perspective of the whole biosphere, Gogarten noted that distinct taxonomic units have in fact evolved and persisted over the past 3.8 billion years of the earth’s life history. Therefore, one might reflect on whether the genetic diversity of life forms is of selective advantage to the biosphere as a whole organism. In other words, the partitioning of genetic diversity into distinct units might be a prerequisite for evolution of the biosphere.
Conclusion Concluding his presentation, Gogarten brought attention to the metaphors biologists use to describe their work to the general public. Because the original metaphor of a tree no longer fits the data from recent genome research, Gogarten suggested that biologists use the metaphor of a mosaic to describe the different histories of combined in individual genomes and use a the metaphor of a net to visualize the rich exchange and cooperative effects of HGT among microbes. Lastly, fellow biologist, David Deamer pointed out that Gogarten’s HGT hypothesis is based on only the first few genome sequences. As more research is conducted, biologists will be able to assess if HGT is as pervasive as Gogarten’s early indications seem to show.
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