For the 'isochore' score, it's mutation'1' and selection '0'

Contact: Howard Ochman, 520-626-8355, hochman@u.arizona.edu


In biological evolution, mutations provide the raw material for
evolutionary change, by introducing slight genetic variation among
individuals. The standard thinking is that mutations occur at random
and are then acted upon by the process of natural selection, which will
weed out individuals with harmful mutations and favor individuals with
beneficial mutations.

But do all mutations actually occur at random? And will selection act
on all mutations?
To both questions, Howard Ochman says no.

Ochman's research suggests that at the molecular level, mutations may
sometimes occur non-randomly. And it's generally believed that the vast
majority of our DNA is non-functional and therefore not subject to
natural selection.

In a report in today's issue (July 1) of the journal Nature, Ochman and
his graduate student M. Pilar Francino aim to resolve a longstanding
debate by showing that non-random mutation, rather than selection, can
explain intriguing patterns among gene regions called "isochores" found
in the genomes of mammals. Francino is a doctoral student at the
University of Rochester, which Ochman recently left to join The
University of Arizona in Tucson, where he is an associate professor in
the ecology and evolutionary biology department.

An isochore (pronounced iso-core) is a region of the chromosome that
shows a markedly different base composition than surrounding regions.
Recall from your Biology 101 days that chromosomes consist of DNA, which
in turn is made up of strings of nucleotides, or "bases" -- small
molecules that come in four varieties (abbreviated as G, A, T, and C
after the first letters of their names). Pairs of these bases are
strung together like links in a chain, forming the long molecule we know
as DNA, which encodes heritable genetic information passed between
generations.

The rare events called mutations occur when one type of nucleotide is
replaced by another -- a C replaced by a T, say, or an A by a G. But
although any given gene may include hundreds or thousands of bases, the
Gs, As, Ts, and Cs aren't necessarily evenly distributed. Instead, some
stretches of DNA contain more than their fair share of Gs and Cs, while
others include an overabundance of As and Ts. When one observes such
differences between regions -- as between isochores -- is it because
natural selection favors such a pattern, or is it due to non-selective
causes such as a bias in mutation rates?

Questions such as these are central to the rapidly growing field of
molecular evolution. The flowering of techniques in molecular biology
in the past few decades has allowed biologists to take questions
traditionally asked at the level of the organism and pose them at the
level of the gene. Determining under what conditions natural selection
does and does not play a role in driving change at the molecular level
has been one of the most prominent issues in molecular evolution.

So are isochores the result of biased mutation or of random mutation
followed by selection? While many American and Japanese scientists have
favored the mutational bias explanation, Ochman says, some Europeans
have insistently pushed the selective argument.

To address the issue, Francino and Ochman worked with non-functional
copies of the globin genes of primates. Using these non-functional
genes -- called pseudogenes -- assures that natural selection is not
constraining which mutations are allowed to persist; all mutations are
accepted and may be able to accumulate in the population. Globin genes
code for molecules (like our blood's hemoglobin) that are able to
transport oxygen. In the history of mammals, the ancestral globin gene
has duplicated a number of times, leaving clusters of genes, including
the pseudogenes, some of which fall within different isochores.

Francino and Ochman selected two pseudogenes located on different
chromosomes and in different isochores. One isochore had a
preponderance of Gs and Cs, while the other was overstocked with As and
Ts. By analyzing the patterns of mutation in the two pseudogenes, they
attempted to determine whether mutations of different types were
occurring at different rates in the two isochores, or whether the four
nucleotides were appearing in both regions with equal probability but
natural selection was favoring Gs and Cs in one region and As and Ts in
the other.

But of course you can't just watch mutations happen, especially when
your average primate nucleotide only mutates once per 400 million years.

"Since it's tough to do this in real time," Ochman understates, "we take
a phylogenetic approach," meaning the history of nucleotide changes is
inferred by using a phylogeny, or evolutionary history, of primate
species and their ancestors.

First Francino and Ochman used gene sequences from humans and a variety
of apes and monkeys in combination with a genealogy of primate evolution
to reconstruct likely gene sequences of ancestral primates. They then
used this information to infer the changes that had occurred in the
nucleotide sequences throughout the evolutionary history of primates.
The data showed that a bias in mutations -- rather than the process of
selection -- was responsible for the difference between isochores.

"This helps tell us how mutations occur in the genome," Ochman says.
"It tells us about the factors that mold the human genome, and whether
they're due to differential mutations or selective pressures."

But why should there be differences in base composition in different
areas of the genome? Ochman doesn't know for sure, and neither does
anyone else as of yet. A number of reasons have been proposed, and
Francino and Ochman suggest several in their paper. But that question
awaits further research in the booming field of molecular evolution.