9/20/12 Researchers track evolution through snapshots of 40,000 generations | Ars Technica 1/3 arstechnica.com/science/…/researchers-track-evolution-through-snapshots-of-40000-generations/ Researchers track evolution through snapshots of 40,000 generations The experiment, bane of Conservapedians, traces evolution to the DNA level. DNA extraction from a maize leaf sample. CIMMYT In 1988, Richard Lenski's lab began an experiment. A set of 12 bacterial cultures were started, but only given enough sugar to keep them growing for a few hours. The next day, the bacteria were again given another burst of sugar. And the process has been repeated every day since. The goal? To be able to follow major evolutionary innovations as bacteria try to outcompete their peers under nearstarvation. Back in 2008, one of the 12 cultures had its big breakthrough, a sudden burst of growth powered by citrate, a chemical that was present in the mix, but not normally used by bacteria (a result that was hilariously contested by the founders of Conservapedia). Now, Lenski is benefitting from a technology that didn't exist when he started the work—whole genome sequencing—and reconstructing exactly how the bacteria evolved the new ability. The team behind the latest work took advantage of the fact that the experiment has involved taking snapshots of the bacteria every few thousand generations, simply by siphoning a few off and sticking them in the freezer. These bacteria can be used to figure out what the status of the genomes were at a given generation, or even grown again, to see whether the same evolutionary history can take place. In the new paper, the authors sequence the genomes of 29 different clones of bacteria, obtained from various points in the culture's history. One distinct genetic lineage appeared in the culture a bit before 10,000 generations but had apparently died off before 20,000 generations, never to be seen again (the authors called this UC, for "unsuccessful clade"). Three large groups of related strains still persist in the cultures, but only one of them has citrateeating bacteria, which evolved sometime around 31,000 generations in. The first citrateeating bacteria appear to have left a lot of descendants, since that group has diversified rapidly (although it hasn't completely killed off its competition). In fact, one branch of the TOP FEATURE STORY STAY IN THE KNOW WITH LATEST NEWS Endeavour makes its final rounds: a photoessay Hands-off hands-on: the HTC Windows Phone 8X and 8S ECCE PECUNIA! Internet-famous octogenerian Ecce Homo "restorer" seeks royalties VOTE FOR ME! California launches online voter registration iCloud for Windows 2.0: An improvement, but not much has changed LOOKING FOR SOFTWARE UPDATES OS X Lion, Mountain Lion updated with security and battery life fixes ARS JOBS Manager of Information Technology NYNew York, Located in New York, NY, the IT Manager supervises the information technology needs (ha… Senior Software Engineer (C++, Networking) MAFramingham, Our client is a growing communications company developing innovative speech recogniti… MS.NET C# / ASP.NET Developer NYChestnut Ridge, Kforce is looking for a smart MS.NET Programmer to join our client's Chestnut SCIENTIFIC METHOD / SCIENCE & EXPLORATION by John Timmer Sept 19 2012, 1:00pm EDT LIFE SCIENCES 106 FEATURE STORY (5 PAGES) Review: iOS 6 gets the spit and polish treatment The name of the game: refinement. 168 Main Menu ▼ My Stories: 24 ▼ Forums Subscribe Now Log In Search
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9/20/12 Researchers track evolution through snapshots of 40,000 generations | Ars Technica
Researchers track evolution throughsnapshots of 40,000 generationsThe experiment, bane of Conservapedians, traces evolution to the DNA level.
DNA extraction from a maize leaf sample.CIMMYT
In 1988, Richard Lenski's lab began an experiment. A set of 12 bacterial cultures were started, butonly given enough sugar to keep them growing for a few hours. The next day, the bacteria wereagain given another burst of sugar. And the process has been repeated every day since. The goal?To be able to follow major evolutionary innovations as bacteria try to outcompete their peers undernearstarvation.
Back in 2008, one of the 12 cultures had its big breakthrough, a sudden burst of growth powered bycitrate, a chemical that was present in the mix, but not normally used by bacteria (a result that washilariously contested by the founders of Conservapedia). Now, Lenski is benefitting from a technologythat didn't exist when he started the work—whole genome sequencing—and reconstructing exactlyhow the bacteria evolved the new ability.
The team behind the latest work took advantage of the fact that the experiment has involved takingsnapshots of the bacteria every few thousand generations, simply by siphoning a few off and stickingthem in the freezer. These bacteria can be used to figure out what the status of the genomes were ata given generation, or even grown again, to see whether the same evolutionary history can takeplace.
In the new paper, the authors sequence the genomes of 29 different clones of bacteria, obtainedfrom various points in the culture's history. One distinct genetic lineage appeared in the culture a bitbefore 10,000 generations but had apparently died off before 20,000 generations, never to be seenagain (the authors called this UC, for "unsuccessful clade"). Three large groups of related strains stillpersist in the cultures, but only one of them has citrateeating bacteria, which evolved sometimearound 31,000 generations in.
The first citrateeating bacteria appear to have left a lot of descendants, since that group hasdiversified rapidly (although it hasn't completely killed off its competition). In fact, one branch of the
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citrate eaters has picked up a mutation that wipes out a gene involved in DNA repair, which causesan increased rate of mutation and an even faster diversification.
The genomes also let the researchers figure out exactly how citrate eating evolved. The E. coli usedin the experiment actually have a gene that brings citrate inside the cell, but it's normally shut downwhen oxygen is present. In the first citrate eaters, a bad duplication of this gene made an extra copy,but put it under the control of regulatory DNA for a neighboring gene. This worked, in that the newcontrol sequence expressed the gene even when oxygen was around, but it didn't work well. Theresulting bacteria only had a one percent advantage in reproductive success relative to their peers.
Things accelerated afterwards, as further duplications put more and more copies of the newlygenerated gene into the genomes. By the time there were three copies of this gene present, thebacteria had a large competitive advantage. Presumably, somewhere in Michigan, their descendantsare finetuning that ability even as you read this.
On its own, this would be a great story, as the researchers have traced the evolution of a complextrait that's so rare that it took tens of thousands of generations of bacteria to produce it. But theauthors also show there's still a bit of mystery to their system. They had previously showed that somespecific change had occurred somewhere near 20,000 generations that made evolving citrateeatingmore probable.
So, the authors took a copy of the newly evolved citrate transporter gene, and inserted it into bacteriafrom earlier in the history. Although it worked, in that they could eat citrate, it worked very poorly. Thesame problem occurred when the gene was placed in lineages that had split off prior to 20,000generations. So, what happened at 20,000 generations that makes citrate easier to deal with?
They don't know. Sequencing the genomes reveal a variety of changes, but none of them wouldobviously make digesting citrate easier. So, even as this experiment goes on, it's got some of theresearchers scratching their heads about its past.