Team Hopeful in Its Effort to Recreate Primal Life
September 9, 2004
By NICHOLAS WADE
Scientists analyzing the genomes of microbes believe that
they have reconstructed the pivotal event that created the
one-celled organism from which all animals and plants are
descended, including people.
The event was the merger of two primitive bacterial-type
cells into a eukaryote, the type of cell in all
Dr. James A. Lake, a biologist at the University of
California, Los Angeles, said he had spent four years
constructing the computer program that led to the analysis,
which is being published today in Nature.
William Martin, an expert on early life at the University
of Due¸sseldorf in Germany, describes the work of Dr. Lake's
team as a major contribution to the study of early
"They have opened up a whole new field of endeavor for
mathematicians and biologists to make more realistic graphs
of the history of life," Mr. Martin said.
Because all living creatures are part of the single tree of
life, it should in principle be possible to trace their
lineages from the tree's very root, the first cell from
which all life is presumably derived.
In 1977, shortly after the first DNA sequences of genes
became widely available, Dr. Carl R. Woese of the
University of Illinois showed that all life originated from
three basic types of cell, eukaryotes, bacteria and
archaea, the last a kind of bacteria found in boiling
geysers and around volcanic fissures in the ocean floor.
Dr. Woese's three cell kingdoms have become the accepted
account, even though it was not entirely clear how the
three might have evolved from the first cell.
"There's still a cloud down there at the root," Dr. Woese
said in an interview.
Since Dr. Woese's work, many more DNA sequences have become
available, including whole genomes. The genomes should let
biologists draw much more precise trees than those based on
a single gene, as Dr. Woese's was.
But the tree-constructing computer programs have been
confounded by an awkward fact. Early in the history of
life, genomes seem to have merged with one another. For
instance, mitochondria, the tiny energy-producing organs of
cells, were once free-living bacteria that were engulfed by
the first eukaryotic cell. The programs are good at
reconstructing standard evolutionary trees with a trunk and
branch points, but cannot handle unusual events like
merging two tree branches.
Dr. Lake's new program can apparently deconstruct the
merger of two genomes. Applying it to the genomes of
microbes from the three Woesian kingdoms, Dr. Lake and a
colleague, Dr. Maria Rivera, found that eukaryotes were
formed from a merger of an ancient photosynthetic bacterium
with an archaeal cell.
That is presumably the same as the event in which
mitochondria were captured, so Dr. Lake's conclusion is not
surprising. But this is apparently the first time that the
epochal merger has been reconstructed by genomic
computation, a result that should make it much more
amenable to further analysis.
Dr. Lake's finding also shows the three kingdoms of the
Woesian view are not all of equal standing, as often
supposed. By Dr. Lake's analysis, the bacteria and the
archaea must have existed first, both presumably being
descendants of the first cell, and the eukaryotes evolved
The findings fit with the fossil evidence, because the
earliest bacterial-type cells are 3.8 billion years old and
the earliest known eukaryotic cells occur much later, in
rocks that are just 1.4 billion years old.
Just as life seems to have evolved on earth just once, the
creation of the eukaryotic cell with its mitochondria seems
also to have been a one-time event. Many experts theorize
that all mitochondria in the far-flung kingdom of
eukaryotic creatures trace from a single ancestor.
Dr. Lake said his analysis so far pointed to one merger but
did not exclude the possibility of others. Because he has
identified some of the genes in the merger, he hopes to
calculate the date at which it occurred.
The field of early evolution has become extremely active,
spurred by new computational tools and the torrent of data
from machines that sequence DNA. It is also quite
controversial, and fierce arguments swirl around almost
every feature of the complex architecture of eukaryotic
cells like from where they got their nucleus, the
DNA-holding compartment that distinguishes them from
bacteria, and it was the eukaryotic cell that captured
mitochondria or mitochondria that invaded and took charge
of their eukaryotic host.
Dr. Woese said he believed that the three cell types
evolved independently and at different times from a
"universal ancestor state" that may have been a loose pool
of genes and not necessarily a cell. The universal ancestor
is unlikely to have survived until 1.4 billion years ago,
the date of the earliest known eukaryotes. But Dr. Woese
said he believed that eukaryotes existed much earlier.