W. Ford. Uprooting the Tree of
Life. Scientific American, February
About 10 years ago, scientists finally worked out the basic outline of
how modern life forms evolved. Now,
parts of their tidy scheme are unraveling.
Charles Darwin contended more than a century ago that all modern species
diverged from a more limited set of ancestral groups, which themselves evolved
from still fewer progenitors and so on back to the beginning of life. In
principle, the relationships among all living and extinct organisms could be
represented as a single genealogical tree.
Discoveries made in the past few years have begun to cast serious doubt
on some aspects of the tree, especially on the depiction of the relationships
near the root.
Scientists could not even begin to contemplate constructing a universal
tree until about 35 years ago. From
the time of Aristotle to the 1960’s, research deduced the relatedness of
organisms by comparing their anatomy or physiology or both.
For complex organisms, scientists were frequently able to draw reasonable
genealogical inferences in this manner. Microscopic
single-celled organisms, however, often provided too little information for
defining relationships. In the
mid-1960’s, Emile Zuckerland and Linus Pauling of the California Institute of
Technology came up with a different strategy other than just comparing anatomy
and physiology. They proposed
basing family trees on differences in the building block sequences for genes and
proteins. Their approach is known
as molecular phylogeny, and it states that individual genes are composed of
unique sequences of nucleotides that typically serve as the blueprint for making
specific proteins. These proteins
are in turn composed of particular strings of amino acids.
Consensus holds, that in the universal tree of life, the early
descendant’s last common universal ancestor was a small cell without a
nucleus. This ancestor was a
At this same time, Carl R. Woeses of the University of Illinois was turning his attention to a powerful new yardstick for evolutionary distances --- a small molecular subunit known as ribosomal RNA. Higher sections of the universal tree of life have based many of their branching patterns on sequence analysis of rRNA genes. By the 1960’s, microscopists had determined that the world of living things could be divided into two separate groups ---eukaryotes and prokaryotes, depending on the structure of the cells that composed them. The endosymbiont hypothesis proposes that mitochondria formed after a prokaryote that had evolved into an early eukaryote engulfed and then kept one or more alpha-proteobacteria cell. Eventually the bacterium gave up its ability to live on its own and transferred some of its genes to the nucleus of the host becoming a mitochondrion. Later, some mitochondrion bearing eukaryote ingested a cyanobacterium that became a chloroplast. Eventually most scientists accepted this hypothesis because the overall structures of certain molecules in archaeal species of bacteria. Similarly, the archaeal proteins responsible for several crucial cellular processes have a distinct structure from the proteins that do the same tasks in more modern bacteria.
scientists accepted the idea of 3 domains of life instead of two, they naturally
wanted to know which of the 2 structurally primitive groups --- true bacteria or
archaic--- gave rise to the first eukaryotic cell. In 1989, research groups led
by J. Peter Gogarten of the University of Connecticut and Takashi Miyata of the
Kyushu University in Japan used sequence information from genes for other
cellular components to establish the “root” for the universal tree of life.
Comparisons of rRNA can indicate which organisms are closely related, but
for technical reasons, cannot be themselves indicate which groups are the oldest
and therefore closest to the root of the tree. DNA sequences encoding 2
essential cellular proteins agreed that the last common ancestor spawned both
the true bacteria and archaic bacteria and then the eukaryotes (with a nucleus)
branched from the archaic.
Still, as the DNA sequences of complete genomes have become increasingly
available, research groups have noticed patterns that are disturbingly at odds
with the prevailing beliefs. If the
consensus tree were correct, transferred genes would be ones involved in
cellular respiration or photosynthesis and not in other cellular processes. A
good number of those bacterial genes though serve nonrespiratory and
nonphotosynthetic processes critical to the cell’s survival. This classic tree
also indicates that bacterial genes migrated only to a eukaryote, not to any
archaic. However, archaic have been found to contain a substantial store of
bacterial genes. Quite possibly, the pattern of evolution is not as linear and
treelike as Darwin imagined it. Although genes are passed vertically from
generation to generation, this vertical inheritance is not the only process that
has affected the evolution of the cells. Lateral
or horizontal gene transfer of genes has also profoundly affected evolution.
Such lateral transfer involves the delivery of genes, not from a parent
cell to its offspring, but across species barriers. Lateral gene transfer would
explain how eukaryotes that supposedly evolved from an archaeal cell obtained to
many bacterial genes important to metabolism. The eukaryotes picked up genes
from bacteria and kept those that proved most useful.
The “revised” tree of life retains a treelike structure at the top of
the eukaryotic domain and acknowledges that eukaryotes obtained mitochondria and
chloroplasts from bacteria. But it
also includes an extensive network of untreelike links between branches.
These links have been inserted somewhat randomly to symbolize the lateral
gene transfers that occur between unicellular organisms.
This “tree” also lacks a single cell at the root; the three major
domains of life probably arose from a population of primitive cells that
differed in their genes.