Genomic Analysis Provides New Clues on the Origins of Metabolic Pathways in Earth’s Biosphere

Researchers mapped the evolutionary history of 3,983 gene families.

The Science

For the first three billion years of life’s history on Earth, microbes were the original and predominant form of life, but evolution during this period remains a mystery due to the lack of significant fossil evidence. Analysis of microbial gene sequences across the tree of life has yielded clues on the development of fundamental biological processes; however, horizontal gene transfer (HGT), the exchange of genetic material across species, has confounded efforts to map out deep evolutionary processes operating over geological time periods. In new results published in the January issue of Nature, researchers at the Massachusetts Institute of Technology describe a new comparative genomics approach for analyzing molecular evolution while accounting for HGT. The authors identified a period of rapid gene innovation between 3.3 and 2.8 billion years ago that gave rise to 27% of modern gene families. This evolutionary burst coincided with a period when oxygen concentrations in the atmosphere rapidly increased. The genes originating during this period include many involved in expanded energy production and metabolic reactions associated with an oxidizing environment. These results shed new light on fundamental processes that have shaped the metabolic potential of life on Earth and that continue to govern adaptation of the biosphere to changing conditions. This research was funded as part of a DOE Science Focus Area at Lawrence Berkeley National Laboratory.

The Impact

Gene histories reveal marked changes in the rates of gene birth, gene duplication, gene loss and HGT over geological timescales. 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.

BER Program Manager

Dawn Adin

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


David, L. A., and E. J. Alm. 2011. “Rapid Evolutionary Innovation During an Archaean Genetic Expansion,” Nature 469, 93–96. DOI:10.1038/nature09649.