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| Challenges |
There have been tremendous advances in comparative evolution brought on by the new methods of phylogenetic analysis and burgeoning amounts of DNA sequence data; however, the field is not without challenges and limitations. Some of these challenges are due to features of the organism and some are due to limitations of the tools we currently possess.
One feature of the organism that presents a challenge is the horizontal transfer of genes across different species. In the standard mode of vertical transmission, genes are transmitted from parent to offspring (whether by sexual or asexual means). Genetic material can also be exchanged among different organisms, especially bacteria. This general type of transmission is called lateral (horizontal) gene transfer. One mode by which lateral gene transfer can occur is conjugation, whereby some bacteria exchange genes (plasmids or small parts of the bacterial chromosome) by physical contact. Bacteriophages can also mediate lateral gene transfer by cross-infection. Amazingly, these processes that result in lateral gene transfer can occur among bacteria that differ by as much as fifteen percent at the DNA sequence level. The implication of widespread and random lateral transfer of genes is that the genetic structure of bacteria can be mosaic - different genes or gene regions may have different histories. If lateral transfer is sufficiently pervasive, it could lead to the inability of constructing the true phylogeny for all bacteria. (See the Microbial Diversity unit.)
The most dramatic case of lateral gene transfer involving eukaryotes is the endosymbiotic origin of mitochondria. This view, championed by Lynn Margulis, speculates that these ATP-producing organelles were once free-living prokaryotes that were engulfed by a proto-eukaryote - an idea now strongly supported. The evidence includes similarities of ribosomal structure, sensitivity to antibiotics, and DNA sequences between mitochondria and prokaryotes. The major controversy is when and how this process occurred. Other eukaryotic organelles have been shown to probably have endosymbiotic origins. The conventional wisdom, however, is that lateral gene transfer involving eukaryotes was limited from these exceeding rare endosymbioic events.
Recent evidence strongly suggests that lateral gene transfer involving eukaryotes may be more prevalent than once thought. In some DNA sequences, bacterial or archaeal sequences cluster in clades that are otherwise strictly eukaryotic. The extent to which lateral gene transfer among the kingdoms and within the eukaryotes has occurred is still a matter of controversy and inquiry. The implications for our ability to construct accurate phylogenies for these "deep" relationships are also controversial. There appears to be a continuum of the degree to which different genes transfer across distantly related taxa. Some researchers have argued that we may be able to get around the problem of lateral gene transfer by choosing genes that display very little - if any - horizontal gene transfer.
Another major challenge to comparative evolution is that the methodology of phylogenetic systematics is computationally extensive. The number of potential trees increases extremely quickly - faster than exponentially - as the number of taxa increases. For three taxa, there are only three possible rooted trees. For a given data set, one can readily determine by inspection which tree is the most parsimonious. Given seven taxa, it would be exceedingly painstaking for a person to search for the most parsimonious tree through the 10,395 rooted possibilities; however, a desktop computer with the correct software could search among all of these possibilities in a tiny fraction of a second.
Increasing computing power alone will not solve this problem. At twenty taxa, the number of possible rooted trees exceeds 8 times 1021 - a number of similar magnitude to the total number of cells in all living human beings. Soon after this point, it becomes impractical for computers to search through all the possibilities to find the most parsimonious one. Given fifty taxa, it would take literally longer than the age of the universe to search through every single possible unrooted tree -- even if computers were a million times faster than they are now. Therefore, phylogenetic systematics must employ methods other than searching every single possible tree when evaluating data sets that involve a large number of taxa. One method is to collapse taxa that are known (by other information) to be close relatives into a single taxon to make the analysis more feasible. Researchers have also used various searching approaches, sometimes called heuristics. This approach uses algorithms to identify regions of "tree space" that are likely to contain very parsimonious trees. These heuristic methods may not always identify the best tree, but they will identify trees that are nearly as parsimonious as the best tree most of the time.