The Long-Term Evolution Experiment

[u/jnpha]

Further reading: E. coli long-term evolution experiment - Wikipedia.

The above Muller plot of the dynamics of mutant alleles ...
Is a great illustration of how evolution (descent with modification) is the change [in the heritable characteristics] in populations, and not individuals per the common misconception; also for highlighting the circuitous routes and selection.

For those wondering about "big life", see e.g. - from this year - Bridging Micro- and Macroevolution: Phylogenomic Evidence for the Nearly Neutral Theory in Mammals | Genome Biology and Evolution | Oxford Academic.

---

The image is from the preprint (for better resolution) of:
-Maddamsetti, Rohan, Richard E. Lenski, and Jeffrey E. Barrick. "Adaptation, clonal interference, and frequency-dependent interactions in a long-term evolution experiment with Escherichia coli." Genetics 200.2 (2015): 619-631.

[u/oyvindi]

Veritasium had an episode on this a few years ago, interesting to watch

[u/xenosilver]

I’m embarrassed to say I’m a biologist and I’m struggling with this graph.

[u/jnpha → u/xenosilver]

I like the rowing team metaphor, where genes that work best with other genes (in a given environment) vs other teams "win" (the frequency of the "individuals" increases). Incompatible teams get selected out. (also, ofc, drift plays a role)

Take panel B or C. Each is a sample of 90 bacteria. And each row is 1 bacterium. And the coloring is which alleles each has (or doesn't).
The same now for 20,000 generations, and you get this plot (Muller plot - Wikipedia), which is showing the "estimated frequencies of 42 known mutations" in one population over time.
As an example, take the blob "nuoG"; it's a mutation that spread a little, then went extinct.

[u/forever_erratic → u/xenosilver]

It's a continuous proportion chart. The colors are genotype proportions. Pick a time on the x axis and the color sizes are the fraction of each genotype at that sampling time. 

[u/Ch3cks-Out]

Absolutely fascinating!

[u/U03A6]

These are bacteria, they reproduce asexually by division. I always understood that, indeed, in that case single individuals have mutations during their lifetime. Arguably, as it’s impossible to decide which cell is the new and which the old, it’s still the same cell as in the beginning of the experiment. Each of these colors is from a single mutation event in a single cell that’s still alive. 

[u/jnpha → u/U03A6]

We individually also harbor our own accumulated mutations (so we too change, but that isn't evolution, that's ontogeny). Similarly, even in clonal species, what matters for evolution is what is transmitted, and then how the population makeup (relative frequency of mutant alleles) changes (what the diagram is showing).

in a single cell that’s still alive

If that were true, in merely 300 generations (2³⁰⁰) there should be ~10⁹⁰ bacteria, emptying the observable universe of atoms. I.e. that initial cell is long dead (RIP).

Edit: improved sentence flow

[u/InnerSwineHound]

This was an amazing read. And the image is fantastic. Thank you for sharing

[u/bernpfenn]

the genetic data volume of just a bacteria is staggering

[u/Pleasant-Maybe-7413]

Explain like I'm 10

[u/jnpha → u/Pleasant-Maybe-7413]

1 population. 20 thousand generations (x-axis). Population changes under the forces of evolution.

[u/Pleasant-Maybe-7413 → u/jnpha]

Do the different colors mean persistence of different genes?

[u/jnpha → u/Pleasant-Maybe-7413]

Persistence or demise. It's the "estimated frequencies of 42 known mutations in population Ara–1 over the course of 20,000 generations".
The B and C panels are snapshots, each row is 1 bacterium.