Blog: A New Step In Evolution.

A New Step In Evolution
by Carl Zimmer
Thanks to Calilasseia for the link.

http://scienceblogs.com/loom/2008/06/02/a_new_step_in_evolution.php

A New Step In Evolution

One of the most important experiments in evolution is going on right
now in a laboratory in Michigan State University. A dozen flasks full
of E. coli are sloshing around on a gently rocking table. The bacteria
in those flasks has been evolving since 1988--for over 44,000
generations. And because they've been so carefully observed all that
time, they've revealed some important lessons about how evolution
works.

The experiment was launched by MSU biologist Richard Lenski. I wrote
about Lenski's work last year in the New York Times, and in more
detail my new book Microcosm. Lenski started off with a single
microbe. It divided a few times into identical clones, from which
Lenski started 12 colonies. He kept each of these 12 lines in its own
flask. Each day he and his colleagues provided the bacteria with a
little glucose, which was gobbled up by the afternoon. The next
morning, the scientists took a small sample from each flask and put it
in a new one with fresh glucose. And on and on and on, for 20 years
and running.

Based on what scientists already knew about evolution, Lenski expected
that the bacteria would experience natural selection in their new
environment. In each generation, some of the microbes would mutate.
Most of the mutations would be harmful, killing the bacteria or making
them grow more slowly. Others would be beneficial allowing them to
breed faster in their new environment. They would gradually dominate
the population, only to be replaced when a new mutation arose to
produce an even fitter sort of microbe.

Lenski used a simple but elegant method to find out if this would
happen. He froze some of the original bacteria in each line, and then
froze bacteria every 500 generations. Whenever he was so inclined, he
could go back into this fossil record and thaw out some bacteria,
bringing them back to life. By putting the newest bacteria in his
lines in a flask along with their ancestors, for example, he could
compare how well the bacteria had adapted to the environment he had
created.

Over the generations, in fits and starts, the bacteria did indeed
evolve into faster breeders. The bacteria in the flasks today breed
75% faster on average than their original ancestor. Lenski and his
colleagues have pinpointed some of the genes that have evolved along
the way; in some cases, for example, the same gene has changed in
almost every line, but it has mutated in a different spot in each
case. Lenski and his colleagues have also shown how natural selection
has demanded trade-offs from the bacteria; while they grow faster on a
meager diet of glucose, they've gotten worse at feeding on some other
kinds of sugars.

Last year Lenski was elected to the National Academy of Sciences. This
week he is publishing an inaugural paper in the Proceedings of the
National Academy of Sciences with his student Zachary Blount and
postdoc Christina Borland. Lenski told me about the discovery behind
the paper when I first met him a few years ago. He was clearly
excited, but he wasn't ready to go public. There were still a lot of
tests to run to understand exactly what had happened to the bacteria.

Now they're sure. Out of the blue, their bacteria had abandoned
Lenski's their glucose-only diet and had evolved a new way to eat.

After 33,127 generations Lenski and his students noticed something
strange in one of the colonies. The flask started to turn cloudy. This
happens sometimes when contaminating bacteria slip into a flask and
start feeding on a compound in the broth known as citrate. Citrate is
made up of carbon, hydrogen, and oxygen; it's essentially the same as
the citric acid that makes lemons tart. Our own cells produce citrate
in the long chain of chemical reactions that lets us draw energy from
food. Many species of bacteria can eat citrate, but in an oxygen-rich
environment like Lenski's lab, E. coli can't. The problem is that the
bacteria can't pull the molecule in through their membranes. In fact,
their failure has long been one of the defining hallmarks of E. coli
as a species.

If citrate-eating bacteria invade the flasks, however, they can feast
on the abundant citrate, and their exploding population turns the
flask cloudy. This has only happened rarely in Lenski's experiment,
and when it does, he and his colleagues throw out the flask and start
the line again from its most recently frozen ancestors.

But in one remarkable case, however, they discovered that a flask had
turned cloudy without any contamination. It was E. coli chowing down
on the citrate. The researchers found that when they put the bacteria
in pure citrate, the microbes could thrive on it as their sole source
of carbon.

In nature, there have been a few reports of E. coli that can feed on
citrate. But these oddballs all acquired a ring of DNA called a
plasmid from some other species of bacteria. Lenski selected a strain
of E. coli for his experiments that doesn't have any plasmids, there
were no other bacteria in the experiment, and the evolved bacteria
remain plasmid-free. So the only explanation was that this one line of
E. coli had evolved the ability to eat citrate on its own.

Blount took on the job of figuring out what happened. He first tried
to figure out when it happened. He went back through the ancestral
stocks to see if they included any citrate-eaters. For the first
31,000 generations, he could find none. Then, in generation 31,500,
they made up 0.5% of the population. Their population rose to 19% in
the next 1000 generations, but then they nearly vanished at generation
33,000. But in the next 120 generations or so, the citrate-eaters went
berserk, coming to dominate the population.

This rise and fall and rise suggests that the evolution of
citrate-eating was not a one-mutation affair. The first mutation (or
mutations) allowed the bacteria to eat citrate, but they were
outcompeted by some glucose-eating mutants that still had the upper
hand. Only after they mutated further did their citrate-eating become
a recipe for success.

The scientists wondered if other lines of E. coli carried some of
these invisible populations of weak citrate-eaters. They didn't. This
was quite remarkable. As I said earlier, Lenski's research has shown
that in many ways, evolution is repeatable. The 12 lines tend to
evolve in the same direction. (They even tend to get plump, for
reasons yet to be understood.) Often these parallel changes are the
result of changes to the same genes. And yet when it comes to
citrate-eating, evolution seems to have produced a fluke.

To gauge the flukiness of the citrate-eaters, Blount and Lenski
replayed evolution. They grew new populations from 12 time points in
the 33,000-generations of pre-citrate-eating bacteria. They let the
bacteria evolve for thousands of generations, monitoring them for any
signs of citrate-eating. They then transferred the bacteria to Petri
dishes with nothing but citrate to eat. All told, they tested 40
trillion cells. Here's a movie of what that looks like...
http://www.youtube.com/watch?v=UNaXlK_3Fik

Out of that staggering hoard of bacteria, only a handful of
citrate-eating mutants arose. None of the original ancestors or early
predecessors gave rise to citrate-eaters; only later stages in the
line could--mostly from 27,000 generations or beyond. Still, even
among these later E. coli, the odds of evolving into a citrate-eater
was staggeringly low, on the order of one-in-a-trillion.

Now the scientists must determine the precise genetic steps these
bacteria took to evolve from glucose-eaters to citrate-eaters. In
order to eat a particular molecule, E. coli needs a special channel in
its membranes through which to draw it. It's possible, for example,
that a channel dedicated to some other molecule mutated into a form
that could also take in citrate. Later mutations could have fine-tuned
it so that it could suck in citrate quickly.

If E. coli is defined as a species that can't eat citrate, does that
mean that Lenski's team has witnessed the origin of a new species? The
question is actually murkier than it seems, because the traditional
concept of species doesn't fit bacteria very comfortably. (For the
details, check out my new article on Scientific American, "What is a
Species?") In nature, E. coli swaps lots of genes with other species.
In just the past 15 years or so, for example, one disease-causing
strain of E. coli acquired hundreds of genes not found in closely
related E. coli strains. (See my recent article in Slate.) Another
hallmark of E. coli is its ability to break down lactose, the sugar in
milk. But several strains have lost the ability to break it down. (In
fact, these strains were originally given a different
name--Shigella--until scientists realized that they were just weird
strains of E. coli.)

Nevertheless, Lenski and his colleagues have witnessed a significant
change. And their new paper makes clear that just because the odds of
such a significant change are incredibly rare doesn't mean that it
can't happen. Natural selection, in fact, ensures that sometimes it
does. And, finally, it demonstrates that after twenty years, Lenski's
invisible dynasty still has some surprises in store.

Source: Z.D. Blount, C.Z. Borland, and R.E. Lenski, "HI istorical
Contigency and the Evolution of a Key Innovation in an Experimental
Population of Escherichia coli." PNAS in press
(http://www.pnas.org/cgi/doi/10.1073/pnas.0803151105) [Link will go
live at some point this week]

--
Bob.

.

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