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MIT Researchers Reconstruct Evolution of 3 Billion-Year-Old Microbes

Computational biologists at the Massachusetts Institute of Technology (MIT) have developed a mathematical model that is capable of using modern genomes to mimic the evolution of ancient microbes. Lawrence David and Eric Alm have traced the evolution of microbes back billions of years using modern genomes in an effort to identify points of change through history.

The Cambrian Explosion, which occurred approximately 580 million years ago, was a period of rapid change on Earth where new life forms came about and contributed to the modern diversity of animals. Paleontologists are able to understand and archive the evolution of life from the Cambrian Explosion until now because of fossils, but recording the evolution of life before the Cambrian Explosion has been difficult due to the fact that soft Precambrian cells hardly left "fossil imprints" behind.

But now, Alm and David have created a mathematical model that paints the picture of life more clearly over the 3 billion year period before the Cambrian Explosion. To do this, they used 100 modern genomes because all living organisms "inherit their genomes from ancestral genomes." All of the possible ways that genes evolve was combined with the mathematical model, such as the fact that new gene families can be born and inherited, duplicated in the same genome, lost, or swapped or horizontally transferred between organisms.

With the 100 modern genomes, researchers were able to trace thousands of genes back to their very first moment on Earth and were able to tell which ancient microbes carried these genes. According to the results, the genome of all life experienced an expansion between 3.3 and 2.8 billion years ago where 27 percent of all existing gene families were born. Alm and David are calling this period of time the Archean Expansion.

"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," said Alm. "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."

At first, Alm and David believed that the emergence of oxygen was the cause of the Archean Expansion since the new genes they've found are related to oxygen, and oxygen was not available on Earth until around 2.5 billion years ago when it started accumulating and killing off anaerobic life forms during the Great Oxidation Event. But when investigating further, they found that oxygen-utilizing genes didn't exist until the end of the Archean Expansion, which is when geochemists dated the Great Oxidation Event.

After eliminating that possibility, Alm and David now believe they've identified the beginnings of modern electron transport, which is the biochemical process that moves electrons around within cell membranes. The process is necessary for breathing, and is used by plants and some microbes during photosynthesis. It is believed that during the Great Oxide Event, a type of photosynthesis called oxygenic photosynthesis generated the oxygen we breathe today. Ultimately, electron transport's evolution through the Archean Expansion would be responsible for photosynthesis and respiration.

"Our results can't say if the development of electron transport directly caused the Archean Expansion," said David. "Nonetheless, we can speculate that having access to a much larger energy budget enabled the biosphere to host larger and more complex microbial ecosystems."

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