A New Tree of Life

By Shanti Menon|Saturday, June 01, 1996
All life, says Russell Doolittle, had a common ancestor 2 billion years ago. That’s a billion years too late for most biologists.

By a billion years or so after Earth formed, life had already taken hold. Microfossils found in 3.5-billion-year-old rocks in Australia show that the first living things were prokaryotes, like today’s bacteria, with DNA floating freely in their cells. For the next 3 billion years-- until larger life-forms evolved--the fossil record is sparse.

Many biologists, however, believe that life split into two branches more than 3 billion years ago. That split was between bacteria and archaea--bacteria-like organisms that still exist today. Eukaryotes, with DNA packed in a nucleus, branched off from the archaea later and gave rise to all other life, from amoebas to people. Or so the conventional view holds. Russell Doolittle, a molecular evolutionist at the University of California at San Diego, believes that view is flawed. He has found evidence that the split between bacteria and all other life occurred much later, probably as recently as 2 billion years ago.

The standard evolutionary family tree is based on studies of mutation rates in RNA. The more similar the RNA sequences between any two creatures, the reasoning goes, the more closely related are the creatures. The problem with using RNA as an evolutionary clock, though, is that RNA sequences work within only relatively small groups of closely related organisms. Doolittle wanted a clock that he could apply on a broader scale.

He and his colleagues decided to use 57 proteins--enzymes, to be precise--found in almost every living thing. By comparing how much the amino acid sequences of these enzymes differed among assorted forms of life, the researchers could tell how closely related certain groups were, using a similar logic to the one applied in RNA studies. The researchers sampled 15 groups of organisms.

To calibrate the enzyme clock--to convert the amino acid changes, or evolutionary distance, into units of time--Doolittle and his colleagues relied on well-known species-divergence dates from the fossil record. This enabled them to plot a straight line of the evolutionary distances they detected in enzymes versus time that extended back some 550 million years. Finally they extrapolated that line backward through time to find out when earlier lineages diverged.

All plants, animals, and fungi, according to this enzyme clock, had a common ancestor around a billion years ago. Fungi and animals shared an ancestor a little more recently than that. None of this was terribly surprising. But toward the base of the tree, things got interesting. Even after Doolittle tried to account for the slower or faster evolution characteristic of particular groups, his results still said the same thing: all living things last shared an ancestor only 2 billion years ago, instead of more than 3 billion, and the first split was between bacteria and the ancestor of eukaryotes and archaea. The archaea did not appear until 1.8 billion years ago.

Doolittle’s result has attracted criticism. It’s ridiculous, says Norman Pace, a microbiologist at Indiana University. The 3.5-billion- year-old Australian fossils, he says, look like cyanobacteria, a type of photosynthesizing bacteria, and the RNA family tree indicates that cyanobacteria were not the first organisms. The archaea, the eukaryotes, and most of the bacterial lineages had already been generated by the time cyanobacteria were invented, says Pace. Moreover, Doolittle’s extrapolation of a mutation rate back 2 billion years, about three times the original length supported by the fossil record, strikes Pace as untenable. The evolutionary clock is not linear, he says. Evolution rates differ among different organisms, and at different times during the course of their evolution. There is simply no way you can extrapolate it. I don’t know why Russ did that.

Doolittle claims that with a large data set covering a long time, all the fits and starts of evolution even out. Molecular clocks do tend to be erratic, he admits. They slow down and speed up, no doubt about it. But they never run backward. This is a challenge to people to figure out what was going on 2 billion years ago.
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