To recognize everyone’s efforts, we’ve created the LTEE Leaderboard! (Follow the link for the interactive version.)

If we zoom out, the most overwhelming signal is that Lenski lab manager Neerja Hajela is the all-time LTEE champion with 4349 transfers. That’s more than 1/3 of all LTEE transfers to date, a feat than is unlikely to ever be equaled! As we can see from the plot over time, Neerja did the transfers on most weekdays from 1996 to 2018.

There were other historical epochs marked by other Lenski lab managers: Lynette Ekunwe (1427 transfers), Sue Simpson (950 transfers), and Devin Lake (838 transfers). So far, only one member of the Barrick lab, Jack Dwenger (407 transfers), cracks the top ten at 7th. The plot also shows some gaps (when the experiment was paused for a move or pandemic) and a plateau (when we allowed populations that were behind to catch up).

We can also use the LTEE Leaderboard to slice and dice the data. For example, what does the leaderboard look like when we restrict it to transfers that were done on the weekend (Saturday or Sunday)?

Longtime LTEE researcher Zack Blount wins this category and we see some new graduate students and postdocs appear in this top 10 list.

You can even use the LTEE Leaderboard to figure out who did a transfer on a specific day in history. Darwin Day (February 12th) in 1993? Ryszard Korona.The Ides of March (March 15th) in 2009? Zack Blount.

Our plan is to continue to periodically update the LTEE Leaderboard, at least once a year when it is time to determine bragging rights for our annual Barrick lab Year in Review group meeting.

P.S. Your humbled-by-his-small-contribution author only clocks in at 26th on the all-time list with 78 transfers.

Data Acknowledgements and Availability

Thanks especially to Zack Blount and Devin Lake for digging through many years of LTEE notebooks and compiling the spreadsheet that made creating the LTEE Leaderboard possible. Code for the LTEE Shiny app and a CSV file of the underlying data are available on GitHub (https://github.com/barricklab/LTEE-leaderboard).

There is a quote by Theodosius Dobzhansky that goes: “Nothing in biology makes sense except in the light of evolution.” In response, I wish to offer up a corollary: “Nothing in evolution makes sense except in the light of molecular biology and genetics.”* Building a comprehensive model of evolution requires a thorough understanding of the molecular events involved. Here is where experimental evolution coupled with modern molecular biology and next-generation sequencing can create new ways for us to answer fundamental questions about the nature of evolution.

This summer, I had the pleasure of working at the Barrick Lab to understand some of the changes in the genomes of the 12 populations of the LTEE. Chromosomal rearrangements include insertions, deletions, duplications and inversions. While point mutations affect a single base, chromosomal rearrangements affect multiple genetic loci at once. These rearrangements can change chromosomal organization, alter gene copy number and expression, produce chimeric gene products, and affect mutation rates. In both wild microbial populations and other experimental evolution studies, chromosomal rearrangements have been shown to play a pivotal role in evolution.

Previously, the genomes of the LTEE populations were generally sequenced with short-read sequencing methods, which are good at looking for small mutations, but have trouble with resolving larger genomic structural variants. This problem is worsened by the fact that most rearrangements are mediated by repeat or transposable elements. This is where long-read sequencing methods, like Oxford Nanopore, come in handy. We sequenced clones from the 12 populations of the LTEE at 75,000 generations, and at additional time points for Ara+1 and Ara-3. Using a combination of computational tools, we generated genome assemblies and compared them to the ancestor REL606 to see what changes have occurred since the start of the experiment more than 3 decades ago.

Turns out, there are a lot of interesting things going on inside these humble 4,600,000-base-pair E. coli genomes. Almost all populations have deletions, while inversions and duplications were observed only in some populations. For example, Ara+4 has no inversions, while Ara+1 has the most extensive changes, with complex rearrangements that appear to be produced by successive inversions. Most of these rearrangements appear to be mediated by recombination among insertion sequence (IS) elements in the genome.

The obvious question to ask is are these rearrangements adaptive? Their continued existence in the LTEE would indicate that at the very least they are not deleterious. Some of these rearrangements are seen in two or more populations, and this parallelism can indicate adaptive benefit, or merely reflect a high rate of certain recombination events occurring.

Few experiments have captured my imagination like the LTEE has; it introduced me to an entirely new way to think about evolution. It exemplifies the kind of science I want to do: conceptually simple yet ambitious in its desire to answer open-ended questions about how life on earth evolves. On some days when I sit at my desk in the lab, I think about how just a few feet away, in 12 flasks kept warm in an incubator, endless forms most beautiful and most wonderful are evolving.

Ira Zibbu is pursuing her Master’s in Biology at the Indian Institute of Science Education and Research, Thiruvananthapuram. She can be reached at ira.zibbu@gmail.com. This work was support by the Khorana Scholars Program, which is funded by the Department of Biotechnology (DBT), Government of India, the Indo-U.S. Science and Technology Forum (IUSSTF) and WINStep Forward. It was also made possible with the support of the Department of Molecular Biosciences at the University of Texas at Austin

*The author wishes to declare a conflict of interest given that she works in molecular biology and genetics

Our lab manager Emmanuel Chavarria has done most of the weekday transfers so far. He also set up the infrastructure, supplies, and protocols we follow for the LTEE. Three great undergraduates—Olivia Soto, Giselle Ramirez, and Logan Iruegas–have helped with cleaning glassware, pepping supplies, and making media.

Transfers on weekends and holidays have been covered by postdoc Isaac Gifford and graduate students Cameron Roots, Victor Li, and Zuberi Ashraf.

Emmanuel froze down the 75,500 generation samples on September 9th and the 76,000 generation samples the day before Thanksgiving. Two more strata in the “fossil” record of the LTEE are safely deposited in our freezers.

A few days after 76,000 generations, Emmanuel headed off for a new position in Virginia, after training our new lab manager Jack Dwenger in the ways of the LTEE. We are extremely grateful for the last year Emmanuel spent supporting and improving so much of the research in our lab!

Barrick lab LTEE leaderboard

Link: https://doi.org/10.1126/science.342.6160.790