www.checkbiotech.org ; www.raupp.info ; www.czu.cz

Biologists seeking elusive proof of natural selection at the single-gene
level have a powerful new tool at their disposal, April 2006.

Chris Toomajian, postdoctoral researcher in molecular and computational
biology in the USC College of Letters, Arts and Sciences, led a group that
sought to replace the standard neutral model, a common but unrealistic test
for natural selection, with a statistical method based on hard genomic data.

The group's research will be published online April 25 by Public Library of
Science.

"Do we now have enough data to see the standard neutral model wasn't
appropriate?" Toomajian asked. "We know something more now about how the
population has been structured."

The standard neutral model makes improbable assumptions about population
structure, such as assigning each individual an equal chance of reproducing.

Co-author Magnus Nordborg, associate professor of molecular and
computational biology in USC College, predicted that earlier research would
need to be revisited because the model makes it too easy to infer selection
at any given gene.

"Once you start looking at enough cases then you realize that, oops, it's
all under selection. I think a lot of that research is going to end up in
the trash can," Nordborg said.

The group's method can be applied to any organism, including humans.

The PLoS paper focused on the weed Arabidopsis thaliana, and in particular
on the FRIGIDA (FRI) gene, known to influence flowering time.

A. thaliana was once a plant that bloomed annually. But two versions of FRI
that appeared thousands of years ago enabled the plant to flower year-round,
helping it out-compete other plants.

Toomajian and his group showed that these two versions, also called gene
variants, are too common to have spread solely by chance.

"We've shown that for one gene with an important role in that [flowering]
process, there's good evidence that there's natural selection changing the
behavior of the plants," Toomajian said.

Why the variants were selected remains unclear, though some have suggested
that the plant evolved under pressure from the spread of agriculture.

Toomajian's group identified the gene variants through a comparison of 96
plants over 1,102 short fragments of the genome.

Each variant was assigned a score based on the similarity of two plants
around the FRI gene relative to their similarity at other regions in the
genome.

The higher the score, the less likely it is that a variant could have arisen
and spread randomly.

The scoring formula accounts for the greater similarity expected in related
plants.

Nordborg said that while natural selection is well documented at the
whole-organism level, researchers consider biochemical proof of selection
"the Holy Grail" of population genetics.

"What has proven very difficult is to connect specific molecular changes to
selection," Nordborg said.

The PLoS paper, along with other recent studies based on intrinsic genomic
comparisons, brings biology closer to this goal.

[www.eurekalert.org]

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