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Researchers Use Modern Genomes to Reconstruct Ancient Gene Expansion Event

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – In a study appearing online yesterday in Nature, a research duo from the Massachusetts Institute of Technology and the Broad Institute reported that they were able to discern the evolutionary history of many modern gene families using computational biology.

The team used a new phylogenomic approach to assess nearly 4,000 gene families found in the tree of life today. Their data suggest more than a quarter of these gene families arose around three billion years ago, during an event dubbed the Archaean Expansion. Based on the sorts of gene families that seem to have expanded most at that time, the researchers speculated that this expansion coincided with the development of electron transport, a process involved in photosynthesis and respiration.

"Our results can't say if the development of electron transport directly caused the Archaean Expansion," lead author Lawrence David, an MIT computational and systems biology researcher, said in a statement. "Nonetheless, we can speculate that having access to a much larger energy budget enabled the biosphere to host larger and more complex microbial ecosystems."

In an effort to better understand the interplay between the Earth's history and ancient organisms, David and co-author Eric Alm, a researcher affiliated with MIT and the Broad Institute, used a phylogenomic strategy called "analyzer of gene and species trees" or AnGST to assess genes from 3,983 of the major modern day gene families.

The AnGST method takes horizontal gene transfer events into consideration by looking at both individual gene phylogeny and a broader reference phylogeny representing the tree of life overall, the researchers explained. That, in turn, provides an opportunity to test various hypotheses about how evolutionary history corresponds to other events on the planet, including the Great Oxidation Event, when oxygen levels rose in the environment.

"If DNA sequences from extant organisms bear an imprint of this event, they can be used to make and test predictions; for example, genes that use molecular oxygen are more likely to appear in organisms that emerged after the Great Oxidation Event," the researchers noted.

Based on their analyses, the team estimates that some 27 percent of gene families tested — including many metabolic genes — sprung up relatively quickly during a gene diversification event that occurred between 2.8 billion and 3.3 billion years ago.

"A functional analysis of genes born during this Archaean expansion reveals that they are likely to be involved in electron-transport and respiratory pathways," the pair wrote. "Genes arising after this expansion show increasing use of molecular oxygen and redox-sensitive transition metals and compounds, which is consistent with an increasingly oxygenating biosphere."

Shortly after the expansion, they say, there was a short period of gene loss before gene loss and gene transfer events began to level off. Their findings also hint that the incidence of gene expansions has dropped since the Archaean expansion, while gene duplication has become more common.

"What is really remarkable about these findings is that they prove that the histories of very ancient events are recorded in the shared DNA of living organisms," Alm said in a statement. "And now that we are beginning to understand how to decode that history, I have hope that we can reconstruct some of the earliest events in the evolution of life in great detail."

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