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Act now, this opportunity only comes around once every 10,000-60,000 (E. coli) generations!

Of course, the LTEE E. coli were going about their normal business and replicating during the event, a few hours after their daily transfer. We noted the eclipse in the lab notebook, but just to note the passing of time on human and astronomical scales rather than because it would affect their evolution.

The next total solar eclipse over Austin won’t be for hundreds of years… which is hundreds of thousands of E. coli generations, and also many human ones.

The work was performed by two outstanding teams:

• Anurag Limdi, Siân Owen, Cristina Herren, and Michael Baym
• Alejandro Couce, Melanie Magnan, and Olivier Tenaillon

Both studies generated high-coverage transposon-insertion libraries in the LTEE ancestor and various evolved isolates. Importantly, the approach allows the identification of the insertion sites of each mutant. They then propagated the mutant libraries in the LTEE environment and tracked the frequencies of all the mutants over time—in essence, bulk fitness assays involving hundreds of thousands of mutations. The figure below, from the paper by Limdi et al., outlines the approach.

Limdi et al. first show that the overall structure of the DFE has hardly changed after 50,000 generations, contrary to some predictions from evolutionary theory.

Limdi et al. also discover that the identity of essential genes has changed substantially, and often in parallel across multiple LTEE lineages.

Couce et al., by contrast, focus their attention on the small tail of the beneficial mutations that drive adaptive evolution. They show that the beneficial tail becomes much smaller over time and approaches an exponential distribution.

Couce et al. also demonstrate rapid turnover in the identity of the genes that harbor potential beneficial mutations.

Together these papers provide an unprecedented description of how the fitness effects of the same mutations can change over time, even under the constant conditions of the LTEE. These changes radically alter the fate of specific mutations, even as the overall genomic and fitness dynamics of the evolving populations follow more predictable trajectories.

Here are links to the two preprints:

• Limdi et al:  https://www.biorxiv.org/content/10.1101/2022.05.17.492023
• Couce et al: https://www.biorxiv.org/content/10.1101/2022.05.17.492360

With the invasion of Ukraine, however, it’s not a day to celebrate. 

The LTEE will move to the capable lab and hands of Jeff Barrick this Spring, after all 12 lines have reached 75,000 generations.

Over the decades, several lines fell behind others due to cross-contamination (or concerns about the possibility), which we detected by examining the alternating Arabinose marker and seeing the resulting colony colors on TA plates. Those lines were then restarted from whole-population samples, but they would be 500 generations behind the others (or a multiple of 500 generations behind in some cases).

The picture above shows red and white colonies growing on TA agar in a Petri dish. The red colonies cannot grow on the sugar arabinose that is part of the TA medium, while the white ones can use arabinose. Half of the LTEE lines started from red colonies (Ara–1 to Ara–6), and half started from white colonies (Ara+1 to Ara+6). We alternate the red and white lines each day during their propagation. That way, if cross-contamination occurs, we can detect it by the presence of bacteria that make colonies that are the wrong color. We check colonies before every periodic freeze of the LTEE. These days, with DNA sequencing, we can also use derived mutations that are unique to each lineage to check whether a putative contamination event is real or not. (Indeed, in some populations, especially those that evolved hypermutability, the colony markers don’t work like they did when the LTEE started.) If we confirm that a cross-contamination event has occurred, we restart the affected population from the last frozen sample of that population.

So today, Devin Lake will propagate the last two lagging populations. Our lab will continue to propagate them until they, too, reach 75,000 generations. The last one should reach that goal in late May.

Zack always adds something about what makes the date special.  He’s an amazing scientist and scholar!

Every day, the E. coli populations in the long-term evolution experiment experience a cycle of renewed resources and growth followed by depletion of their food and then waiting for the next transfer event. 

On a much longer timescale, the LTEE also experiences cycles as it is passed from one scientific generation to the next. This website reflects the beginning of the second scientific generation of the LTEE, as the populations and responsibility for their sustenance will soon pass from my lab to that of the new director, Jeff Barrick.

On this website, you can get an introduction and quick overview of the LTEE including how it works, its goals, some of the key findings, and plans for its future.  You can see a timeline of the experiment with some of the milestones and key events in its history.  You can read, watch, and listen to a few of the news stories about the LTEE.  You can find resources including protocols and links to important datasets.  You can search and find links to the publications that report findings from the LTEE itself as well as descendant experiments that have used the LTEE lines. And last, but not least, you can see the talented people who’ve done and are doing the work behind the LTEE, including propagating the populations, performing analyses, analyzing data, and reporting the findings.

We’ve probably missed some papers, and we know that we’re still missing photos for some participants. We’ve also only scratched the surface of reporting past news.  So please let us know if you find someone or something LTEE-related that you’d like to see included on this website.  For now, enjoy the new beginnings as seasons and generations continue onward!

While these insights have helped open up new avenues of interrogation, they are still limited to a regime where natural selection is dominant. This is because most whole-genome sequencing studies are limited to detecting mutations at frequencies higher than 1-10%. At this ratio, given the large population size of the LTEE, the mutation has already escaped the drift barrier and is fully under the influence of selection. Sequencing costs make it prohibitive to delve into the dynamics of mutations much below 1%.

Deathrage and Barrick circumvent this problem using an innovative solution: multiplex adaptome capture sequencing (mAdCap-seq). All 12 LTEE populations show high parallelism in the mutations they fix early in evolution; a handful genes are highly targeted. Deathrage and Barrick call these portions of genome that are particularly important to adapting to a certain environment as the organism’s ‘adaptome’. By hybridizing probes to select genes in the adaptome and sequencing those genes over a dense timecourse at very high depth, Deathrage and Barrick inferred and visualized mutational dynamics in the initial phase of the LTEE at frequencies as low as 0.01%. This allows them to study the full spectrum of beneficial mutations that arise in important genes, but are ultimately lost in the zero sum game of clonal evolution (where sex cannot recombine multiple beneficial mutations on to the same background). Indeed, in the first 500 generations, they see beneficial mutations arise that didn’t fix in the LTEE until hundreds or even thousands of generations had passed. Moreover, in 3 of the most important adaptome genes — nadR, pykF, and topA — they see unique signatures of selection on protein structure, helping understand better and perhaps even predict the spectrum of mutations that dominate early during evolution.

Many past and present LTEE researchers gathered at Michigan State University to celebrate Richard Lenski’s 60th birthday in conjunction with the annual Congress of the BEACON Center for the Study of Evolution in Action! Highlights included scientific talks by many lab alumni and a performance by Baba Brinkman, “peer-reviewed” rap artist who created the The Rap Guide to Evolution.