Time Travel in Experimental Evolution – Dr. Richard Lenski

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Dr. Richard Lenski, Michigan State University (blog)

Fascinating long-term research experiment, has been culturing E. coli over several decades

Historical context of evolution experiments: Darwin thought evolution too slow to observe, “no wonder evolutionary biologists are interested in time travel”…fossils, comparative methods – looking at unique morphology strategies used to occupy niches…

Others who watch evolution? Peter and Rosemary Grant in Galapagos islands, looking at changes in response to environmental changes, Herculean efforts.

Motivating question: How repeatable is evolution?

Core tension between chance and necessity, between mutation and natural selection.
Convergent evolution, similar environmental pressures, organisms as diverse as mollucs and people with eyes have light-sensitive organs (adaptive convergent evolution)

Want to study what directional pressure natural selection can produce, and have repeatability!

1:100 transfer in liquid medium with limiting glucose, citrate also for chelating agent for iron (E. coli cannot grow on citrate), logbase2(100)=6.6cell generations per day
started in 1988 Feb, now 63,000+ generations

Size of populations, size of genomics, every lineage has had billions of mutations, majority are lost during dilution – random genetic drift, deleterious also – frozen fossil record, each population frozen – can bring out of freezer and directly compare – then repeat!

Rapid generations allow us to watch evolution proceed.

When something interesting happens, then go back and repeat

Directly measure competitive performance of one line relative to ancestor

fitness = ratio of growth of one / growth of the other

Cannot do this with humans. Suggests, “wouldn’t it be cool to compete neaderthals against humans?”

Adapting to environment, climbing in fitness in similar trajectories

Strikingly similar in improvement

Measuring fitness in environment, different environments from where they evolved

Tech improvement, reduction in cost made it possible to start sequencing ancestral strain, 2k, 5K, 10K, 15K, 20K

20K clone has 29 point mutations, 15 indels, 1 inversion

45 total mutations out of genome has ~4,000 protein-coding, == 1% of genes have mutation

Yet, many of these 45 genes have mutations in some for all of the other 11 populations, rarely the exact same mutation

Parallel or convergent evolution implies selection favored those mutations, isogenic constructs identical

What are same tumors in different patients?

What mutations are in common between different species?

Experiment has yielded a lot of parallel evolution. Until a striking exception. One of 12 populations was growing on citrate. But, know E. coli cannot transport citrate into cell under oxic conditions

An extremely rare mutation? or historical contingency dependent on particular evolutionary parth? maybe this could be rare mutation?

20151007_164829

tested over40 trillion cells
zero gave Cit+ mutation!!!!!!!! Did not get mad!

clones from generation onwards produced 19 additional Cit_ mutatnts

citrate positive population has mutation in DNA repair

actualization step was a tandem duplication of citT that encodes anaerobic citrate transporter. only works under anaerobic conditions,

regulatory elements upstream, might work under original, second copy might have regulatory elements might be upstream of second copy – cell has been required by putting different regulatory element next o the second citT copy, generating a new module and function

evolution doesn’t built whole new things, tinkering existing parts

generating new module and physiological capacity

“mount glucose” 3D graph of ancestor living in trough, climbing up to glucose, citrate is in distance – need to get there

New species?

cladogenesis: divergence, followed by stable coexistence of Cit+ and Cit- lineages

discrete novelty: citrate usage new function, not merely quantitative change
meangingful novelty: citrate usage contradict historical definition of well-studied species

too loose definition, everything that has antibiotic resistance would be new species then if that were to be true

concept: Ernst Mayr – what are species groups, reproductively isolated from other such groups

However, bacteria are asexual and there’s no horizontal gene transfer in the long-term experiment

if hybrids are ecologically inferior, neither fish nor fowl- that would imply a maladaptive valley between the Cit+ and Cit- lineages

And that would present a barrier to gene flow

Are they getting better, competing later generations against earliest Cit+ and in fact they are getting better and better

Experimental evolution studies are fun!

Lab management is important. 🙂

Q: Differences in point mutations or indels?

A: lot of parallelism, mixed: different synonymous some cases of deleted operon in 12/12, one end point is different in every case, some insertions, move around and make second copy,

Question: hybrids?

A: at least a couple of genes are responsible, hitchhikers – responsible for loss

Q: nature of species in bacteria, arising often? missing diversity surrounding? problem to study with millions of species, operational definition – happening constantly and rarely see it

So grateful to be present for Dr. Lenski’s evolutionary discussion and analysis of this very cool experiment, fascinating research program.

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About Lisa Cohen

PhD student at UC Davis.
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