Molecular phylogenetics has been perceived as the route to reconstructing the details of the Tree of Life (the icon of descent from one common ancestor). In their recent essay on the subject, Lane and Archibald explain that the existence of the Tree has the status of fact and the task for researchers is to fill-in the details.
"A well-resolved and accurate phylogenetic reconstruction of life on Earth is the ultimate goal of systematics."
Most research to clarify eukaryotic relationships assumes they will be resolved as a single tree.
One of the major findings of the past decade has been the identification of six eukaryotic 'supergroups' "erected on the basis of an eclectic mix of morphological and molecular sequence data". Whilst there is widespread agreement that the six groups exist, there has been much debate over the specifics and "the relationships between the supergroups are largely unknown".
The main stumbling block concerns the discovery that the genomes of representatives of these groups show a curious mosaic of genes which are interpreted to have come from quite different sources. The inference has been made that endosymbiosis occurred several times in the past: primary endosymbiosis involved the envelopment and integration of prokaryotic genes and secondary endosymbiosis is used to describe genetic interactions between two eukaryotic cells.
"In the case of secondary endosymbiosis, the plastid acts as a genetic Trojan horse, bringing with it the nucleus of an unrelated eukaryotic endosymbiont whose genes meld with - and can replace - their counterparts in the host nuclear genome. The mixing and matching of eukaryotic genes that occurs in the context of secondary endosymbiosis seriously challenges our ability to accurately infer the evolutionary history of these organisms."
Primary endosymbiosis is perceived as a rare and improbable event, whereas secondary endosymbiosis may have occurred many times. In addition to the Trojan horse analogy, the image of Russian dolls is employed to describe the conceptual model.
"Organisms harboring secondary plastids are thus the biological equivalent of nested Russian dolls - a cyanobacterium encased within a eukaryote, enveloped within a second eukaryote. To further complicate matters, some dinoflagellate algae have replaced their plastid with a 'tertiary' plastid, stolen from other chromalveolates including cryptophytes, diatoms and haptophytes, and even a green algal plastid in a case of serial secondary endosymbiosis. Therefore, although all plastids probably trace back to a single primary endosymbiotic event, they have been propagated throughout eukaryotic diversity multiple times by a similar process."
The methodology, then, is to identify these aberrant flows of genetic information and exclude them from the analysis. This leaves "only the genes that accurately reflect the history of the host cell lineage" for further consideration. The problem is that we do not yet know the magnitude of this task. It is certainly not a straightforward or trivial exercise.
"If the number of 'foreign' eukaryotic genes in the genomes of secondary plastid-containing (or formerly containing) organisms is significant, but difficult to detect, then the evolutionary history of the host organism would be very difficult to resolve, because of the presence of genes with two (or more) evolutionary histories."
Whilst endosymbiosis is widely regarded as the mechanism for introducing foreign genes to organisms, the evidence is primarily circumstantial. This is somewhat reminiscent of Darwinism: the overwhelming evidence for Darwinism is not empirical (for the examples of Darwinian mechanisms in action do not add up to explain the origins of complex specified information, body plans and the higher taxa).
"Despite an overwhelming amount of evidence demonstrating that endosymbiont-derived genes readily establish themselves in the nuclear genome of their host, to our knowledge only a handful of studies have thoroughly investigated bona fide transfers of a eukaryotic gene from a secondary endosymbiont nucleus to a host nucleus."
Where is this research going? Like prokaryotes, the two options envisaged by researchers are (1) with enough data, taxonomic resolution will be possible and (2) the formidable challenges cannot be overcome because some foreign genes cannot be identified as such. But there should be a third option on the table for analysis: (3) polyphyletic origins of the eukaryotes. This will not please the Darwinians, but science should be more concerned with truth than with fitting data into a preconceived model.
The eukaryotic tree of life: endosymbiosis takes its TOL
Christopher E. Lane and John M. Archibald
Trends in Ecology & Evolution, 23(5), May 2008, Pages 268-275
Abstract: Resolving the structure of the eukaryotic tree of life remains one of the most important and challenging tasks facing biologists. The notion of six eukaryotic 'supergroups' has recently gained some acceptance, and several papers in 2007 suggest that resolution of higher taxonomic levels is possible. However, in organisms that acquired photosynthesis via secondary (i.e. eukaryote-eukaryote) endosymbiosis, the host nuclear genome is a mosaic of genes derived from two (or more) nuclei, a fact that is often overlooked in studies attempting to reconstruct the deep evolutionary history of eukaryotes. Accurate identification of gene transfers and replacements involving eukaryotic donor and recipient genomes represents a potentially formidable challenge for the phylogenomics community as more protist genomes are sequenced and concatenated data sets grow.
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