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June 11, 2012

Multicellular Yeast Defeats Rotifer

I really like this movie Will Ratcliff made, showing one of the benefits of being multicellular.

RatcliffEtalMulticellularYeastVsRotifer.mov

The rotifer at the right easily consumes single-cell yeast, but our lab-evolved multicellular yeast was more than it could handle. See our open-access paper in Proceedings of the National Academy of Sciences for scientific details and the Travisano/Dean/Denison Microbial Population Biology website for more videos.

Mike Travisano and Will Ratcliff, principal investigator and super-postdoc, respectively, on the multicellularity project, will have a poster and talk at the upcoming Evolution Meetings in Ottawa.

January 23, 2012

Does our recent work "prove evolution"?

Many aspects of evolution are already well understood. We have more data on recent events (the last 100 million years or so) than on ancient ones. For example, when was the last time anyone offered a detailed arguement that molecular data on humans and chimps are more consistent with independent creation than with evolution from a common ancestor? But we have much less information about the origin of life and (a billion or so years later), the evolution of multicellular life from unicellular ancestors.

There are thousands of papers on how natural selection and other processes change species over generations, and thousands more on how species split into more species, but far fewer on major transitions: genes uniting into chromosomes, the origin of eukaryotes, multicellularity, and so on. There are even fewer attempts to study such transitions under controlled, repeatable conditions. That's why our recent paper has generated so much interest -- not because it sheds any light on how life arose in the first place.

But some creationist is criticizing our recent paper, on You-Tube. He points out that we used centrifugation -- the lowest setting, but still much stronger than gravity -- to select for multicellularity. If such strong gravitational forces were the only way multicellularity could evolve by natural selection, then we would indeed have to look for other explanations. But regular gravity works, too; it just takes longer. (Longer settling time per selection cycle, not necessarily more cycles.) So does predation, as shown by Boraas et al. in 1998. Certain economies of scale might work, as suggested recently by Koschwanez et al. And resistance to stresses like UV might work, too, as I suggested in an earlier post.

We aren't so much asking what natural forces could select for multicellularity (protection from predators versus UV, say), but focusing on questions like:
* Given strong selection, how fast can multicellularity evolve? (fast! so why did it take billions of years?)
* What genetic changes are key to the initial transition -- are there multiple genetic routes to multicellularity? -- and what further changes occur early in multicellular evolution? (in progress)

To answer the latter sorts of questions, it helps to be able to apply exactly the same selection pressure to multiple replicate populations -- we've used ten -- and that's easier with centrifugation than with finicky predators.

Unlike us, Jesus isn't around to object that "that wasn't what I said." So I do want to point out an apparent misattribution in the You-Tube video:

"Jesus was right about creation, 2000 years ago. I wonder what else he was right about." -- creationist on U-tube

If Jesus said anything much about creation, I missed it, but there's this:
And when thou prayest, thou shalt not be as the hypocrites are: for they love to pray standing in the synagogues and in the corners of the streets, that they may be seen of men. Verily I say unto you, They have their reward. But thou, when thou prayest, enter into thy closet, and when thou hast shut thy door, pray to thy Father which is in secret; and thy Father which seeth in secret shall reward thee openly. -- Matthew 6:5-6

And God supposedly said something about not bearing false witness. Surely attributing things to Jesus that he never said would qualify.

January 17, 2012

Experimental evolution of multicellularity: the movies

In case you missed the news coverage by Carl Zimmer in the New York Times, Jeff Akst in The Scientist, and Ed Yong on Nature's news site, among others, our paper on experimental evolution of multicellularity has just been published in Proceedings of the National Academy of Sciences. It's open access, so you can read all the details yourself.

In nature, multicellularity has only evolved a few about 25 times, and it took billions of years. But Mike Travisano (a fellow faculty member in Ecology Evolution and Behavior) and postdoc Will Ratcliff (who earned a PhD with me recently) came up with a simple and repeatable way to speed the process enough to study under lab conditions: selection for rapid settling in liquid media, starting with unicellular yeast. They kindly invited Mark Borrello and me to participate in this exciting project, which also depended on hard work by undergrads Kristin Jacobsen, Mitch Hoverman, and Amanda Muehlbauer and funding from the National Science Foundation. We have also had some support for preliminary genetic analysis (in progress) from the College of Biological Sciences at the University of Minnesota.

The best collection of links related to this work is at the Microbial Population Biology (Micropop) website, which brings together people and projects from the laboratories of Mike Travisano, Tony Dean, and me. I particularly recommend the videos showing reproduction of snowflake-like multicellular yeast via smaller multicellular propagules -- think of plants reproducing from fragments, rather than seeds -- and genetic stability of the multicellular trait, shown by regrowth of multicellular clusters from enzymatically isolated single cells.

I gave some background for this work in an earlier post, when Elizabeth Pennisi wrote about it for Science.

Update: two scientists criticize some of our claims, and Will Ratcliff responds, on Carl Zimmer's blog, here.

November 28, 2011

Experimental evolution of metabolism, sex, and multicellularity

Update: links to our open-access Proceedings of the National Academy of Sciences paper on experimental evolution of multicellularity, including PDF and great videos, can be found at the Microbial Population Biology (Micropop) website.

The Nov. 18 issue of Science has a news feature by Elizabeth Pennisi on recent research using experimental evolution, including some work on the evolution of multicellularity, led by Mike Travisano and Will Ratcliff, in which I've been involved.

Two interesting experimental evolution projects are underway in Canada. In Montreal, Graham Bell has been evolving algae that get their energy from a simple organic molecule, acetate, instead of from light. At first, the algae could barely survive without light, but after five years (still a fraction of the time that Richard Lenski has been evolving E. coli) he has hundreds of independent lines that have evolved a variety of ways to grow on acetate in the dark.

In Toronto, Aneil Agrawal is subjecting the sex life of rotifers to experimental evolution. Like aphids, Daphnia, and some other species, rotifers normally reproduce asexually, resorting to sex only under stress. Populations consisting of females, producing other females asexually, grow twice as fast as populations that are half male. (In my forthcoming book, Darwinian Agriculture, I discuss how reindeer herders increase production by harvesting mostly male calves for meat, so that most adults are females producing more calves, rather than males fighting over females.) But sexual reproduction shuffles genomes in ways that may be beneficial under different conditions. Agrawal and his postdoc Lutz Becks found that the balance between sexual and asexual reproduction evolved in response to environmental conditions. In stable environments, sex eventually disappeared. Once you've evolved the perfect genotype for some particular stable environment, why scramble that genotype through sex?

Meanwhile, we've been exploring the transition to multicellularity.
ClusterShowingDifferentiation.jpg
Cellular differentiation in multicellular clusters evolved from unicellular yeast (photo by Will Ratcliff).

Unicellular life apparently had the earth to itself for over a billion years before even simple multicellular life evolved. So you might think that this major evolutionary transition requires some complicated series of genetic changes that would only happen rarely. Alternatively, maybe the first simple multicellular organisms weren't that different, genetically, from their unicellular ancestors -- they just couldn't out-compete their unicellular parents until conditions were right.

Individual cells would have greater access to nutrients in their environment than cells in the middle of a cluster, but what advantages might clusters have, under what conditions?

Continue reading "Experimental evolution of metabolism, sex, and multicellularity" »

September 9, 2011

This week's picks

A Gene for an Extended Phenotype "The viral gene that manipulates climbing behavior of the [Gypsy moth] host was identified"

The Foot and Ankle of Australopithecus sediba [hominin fossil from 1.78 and 1.95 million years ago] "may have practiced a unique form of bipedalism and some degree of arboreality"

Assured fitness returns in a social wasp with no worker caste "experimentally orphaned brood... continue to be provisioned by surviving adults... no evidence that naturally orphaned offspring received less food than those that still had mothers in the nest."

The sudden emergence of pathogenicity in insect-fungus symbioses threatens naive forest ecosystems "symbioses between wood-boring insects and fungi... are shifting from non-pathogenic saprotrophy in native ranges to a prolific tree-killing in invaded ranges... when several factors coincide"

Ultra-fast underwater suction traps "this unique trapping mechanism conducts suction in less than a millisecond and therefore ranks among the fastest plant movements known"

The taming of an impossible child - a standardized all-in approach to the phylogeny of Hymenoptera using public database sequences "combines some well-established programs with numerous newly developed software tools"

June 22, 2011

This is not a press release

Major journals often ask scientists to limit interactions with the press before their work is published. I agree with this policy, which prevents the public disillusionment with science that can happen when a scientist makes claims (like cold fusion) that don't stand up to subsequent peer review. But presentations at scientific meetings (where the audience can critique exaggerated claims) are allowed. Members of the press can attend those meetings, report on what they hear, and ask other scientists for their reactions.

That's what happened this week, when Will Ratcliff (my recent PhD student, now doing a postdoc with Mike Travisano, Mark Borrello and me) talked about experimental evolution of multicellularity in yeast, at the Evolution meetings. His PhD was recent enough that he was eligible for and won the (William) Hamilton Prize for "Best Student Presentation." Our interactions with the press are constrained, for now, by the journal that's considering our paper on this work, but I look forward to blogging about it once it's published.

Meanwhile, see my earlier posts on Will's theoretical work on the evolution of aging, commentary on multiple roles for antibiotics in interactions among bacteria, and the discovery of a new form of bet-hedging in bacteria. This work was made possible by support from the US National Science Foundation.

February 24, 2011

This week's picks

Responses to the Assurance game in monkeys, apes, and humans using equivalent procedures "...only a subset of humans achieved these efficient outcomes, and pairs of both other species did so as well"

The origin and dynamic evolution of chemical information transfer
"chemicals are emitted, which can unintentionally provide information (cues) and... act as direct precursors for the evolution of intentional communication (signals)."
"In most cases, the excrements are cues, but the behavioural modulations... constitute signals helping to draw receivers' attention to the cues "
"males prefer flower bouquets to the sexual pheromone of local females, presumably because [the orchid] exploits pre-existing sensory biases of their pollinators"

Classic Selective Sweeps Were Rare in Recent Human Evolution
"amino acid and putative regulatory sites are not significantly enriched in alleles that are highly differentiated between populations"

Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes
"the Thaumarchaea (including Nitrosopumilis maritimus in our analysis) forms an independent group distinct from the Crenarchaea or Euryarchaea"

Footprints pull origin and diversification of dinosaur stem lineage deep into Early Triassic "...a few million years after the Permian/Triassic mass extinction (252.3 Ma)"

Optimal antiviral treatment strategies and the effects of resistance
"contrary to previous results, it is always optimal to treat at the maximum rate provided that this treatment occurs at the right time. "

Resolving the infection process reveals striking differences in the contribution of environment, genetics and phylogeny to host-parasite interactions
"transparent Daphnia hosts and fluorescently-labelled spores of the bacterium"

January 3, 2011

How inevitable was the origin of life on Earth?

MAJIKTHISE: Seven-and-a-half million years? What are you talking about?

DEEP THOUGHT:
I said I'd have to think about it didn't I? And it occurs to me, that running a program like this is bound to cause sensational public interest.

Evolutionary biologists mainly study how life has diversified and changed or how it is diversifying and changing, rather than how it originated. But I thought this article was really interesting. "Chance or necessity? Bioenergetics and the probability of life", published in the Journal of Cosmology by Nick Lane (University College, London), doesn't have any original data, but cites lots of other papers that do.

This journal publishes some strange stuff, but journal review processes are never more than an somewhat-useful filter. If you can't get your hypothesis or data published in any peer-reviewed journal, you're probably a crackpot. On the other hand, there's no guarantee that a paper published in a top journal will stand up to subsequent criticism. Anyway...

Continue reading "How inevitable was the origin of life on Earth?" »

July 1, 2010

Earliest multicellular life? Maybe not.

This week's paper is "Large colonial organisms with coordinated growth in oxygenated environments 2.1 Gyr ago", published in Nature by Abderrazak El Albani and colleagues. These two-billion-year-old fossils are clearly the remains of something living, based on appearance, different carbon isotope composition from the surrounding rock. But are they colonies of unicellular organisms, or something more organized?

The authors note the resemblance to "bacterial colonies growing on surfaces" which they say are known to "coordinate their behavior" often via "repulsive chemotaxis." In other words, cells detect the presence of neighbors and tend to disperse in ways that can generate patterns similar to those seen in these fossils. Sometimes, bacteria may coordinate their activities in more sophisticated ways, which wouldn't leave fossil traces.

A commentary on the article is titled "Origins of multicellularity", but most people would expect more from a multicellular organism than a little coordination among cells. We expect differentiation, for example, where different cells specialize for different functions. Trichoplax is thought to have four different cell types, including cells with flagella that move these simple multicellular animals along, and cells that excrete digestive enzymes. In larger animals, a few cells specialize in reproduction, a potential source of conflict, especially if there are genetic differences among cells. I don't think we can tell from these fossils whether there was any such specialization.

A consistent size and shape is another criterion for true multicellularity, met by Volvox, for example. The fossils don't look any more consistent in size and shape than one would expect from bacterial colonies. On the other hand, Trichoplax individuals seems to vary somewhat, but I wouldn't argue against calling them multicellular organisms.

Interestingly, the authors found traces of the chemical sterane, which is typically found in eukaryotes. But apparently there's some possibility that it could have diffuses into the fossil rock from younger materials.

I've been reading about multicellularity recently and was particularly impressed by a 1998 paper by Boraas et al., in Evolutionary Ecology, and titled "Phagotrophy by a flagellate selects for colonial prey: a possible origin of multicellularity". (I would link to the paper, but the publisher Springer has this stupid system that sends you to their main web page.) Boraas et al. exposed unicellular algae to predators and evolved multicellular clumps in only 10-20 generations. The first clumps contained hundreds of cells, but eventually they evolved an 8-cell phenotype, too big for the predators to eat, but with better access to nutrients for each cell than if they were in a larger clump. Surprisingly, nobody seems to have done further evolution experiments with this system.

June 4, 2010

Cancer's deep evolutionary roots

This week's paper, "Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa" was published in BMC Biology by Tomislav Domazet-Lošo and Diethard Tautz. Each of our cells is descended from an unbroken lineage going back to the first living cell. Most cells in an adult, however, are at the end of the line and will have no descendants. Exceptions include sex cells, stem cells, and cancer cells.

We consider cancer an aberration, but think back to the first multicellular life, which may have resembled Trichoplax. A Trichoplax has an upper and a lower layer of cells, and not much in between. They can reproduce by dividing in half, producing two offspring with hundreds of cells each (video). Or they can bud off propagules containing a small number of cells. They also seem to be able to reproduce sexually, from a fertilized single-cell egg, although complete development from an egg hasn't been documented. A Trichoplax can reform from separated cells, sometimes combining cells from two individuals. In such a chimeric organism, cells with different genotypes could compete for resources and reproductive opportunities, undermining collective success. Similar problems can occur when social amoebae get together to form a stalk for their spores. Even in a genetically uniform organism, a mutant cell could start reproducing (perhaps generating many propagules) at the expense of the whole. Today, we call cells that reproduce at the expense of the whole cancers, but something similar would presumably have been a problem for the earliest multicellular organisms.

Presumably? The authors of this week's paper used "phylostratigraphic tracking" to see when the ancestors of our cancer-suppressing genes evolved. Sure enough, there was an evolutionary burst of such genes right around the time when multicellular animals first evolved.

March 14, 2009

Experimental evolution of an RNA world

How did the first life on Earth arise? We may never know for sure, but can we at least demonstrate one or more mechanisms that could have led to life as we know it? Not yet, but this week’s paper seems like a significant step towards that goal. “Self-sustained replication of an RNA enzyme” was published in Science by Tracey Lincoln and Gerald Joyce.

Most species have protein-based enzymes (running the biochemical reactions needed for growth and reproduction) and DNA-based heredity (passing genetic information to the next generation), with RNA serving various other functions. Under the “RNA-world” hypothesis, however, RNA molecules once served both as enzymes and for heredity. Some viruses use RNA as their hereditary material and some RNA molecules still act as enzymes, with a key role in protein synthesis, for example.

Can we recreate the early RNA world in a laboratory? What is the simplest system that could evolve by natural selection, eventually leading to something that would be universally recognized as alive?

Continue reading "Experimental evolution of an RNA world" »

March 1, 2008

Knowing when not to cheat

This week’s paper is Facultative cheater mutants reveal the genetic complexity of cooperation in social amoebae published in Nature by Lorenzo Santorelli and colleagues at Rice University and Baylor College of Medicine, both in Texas.

The evolution of cooperation is a central problem in the history of life. Darwin explained how sophisticated adaptations -- “the structure of the beetle which dives through the water… the plumed seed which is wafted by the gentlest breeze? -- can evolve in a series of small improvements over generations. But some of the major transitions in evolution are harder to explain, because It seems that they should have been opposed, rather than supported, by natural selection. The origin of multicellular life is a good example. It’s not that hard to imagine independent cells working together in loose groups for mutual benefit – huddling together for defense, say – but why would a cell give up the ability to reproduce, as most of the cells in our bodies have done?

Continue reading "Knowing when not to cheat" »

August 3, 2007

Left behind: social amoebae

This week's paper, published in Science (317:679) is "Immune-like phagocyte activity in the social amoeba" by Guokai Chen, Olga Zhuchenko, and Adam Kuspa of the Baylor College of Medicine.

Cells of the social amoeba, Dictyostyleium discoideum forage individually, but eventually group together into a "slug", which crawls through the soil for days before eventually forming a spore-tipped stalk. Previous work with this species has looked at conflicts of interest over which cells have to sacrifice future reproduction (as spores) and become part of the stalk. This week's paper uncovers another example of apparent altruism in Dictyostelium, which may shed light on the evolution of a key part of our immune system.

As a Dictyostelium slug crawls through the soil, some cells are left behind. Are these just random sluggards? Or do they function like human phagocytes, the immune system cells that gobble up bacteria?

Continue reading "Left behind: social amoebae" »

June 27, 2007

Individual and kin selection in legume-rhizobium mutualism

OK, I've been critiquing other people's work for a while. Your mission, should you choose to accept it, is to critique something I've written. It's the summary for a grant proposal I'm about to submit. It will be reviewed by ecologists and/or evolutionary biologists, but they're not likely to be specialists in legume-rhizobium symbiosis. So if something isn't clear to an intelligent but nonspecialist audience, you'll let me know, right? If you're not all too busy reading the many interesting evolution articles in today's New York Times, that is. By the way, the great Myxococcus xanthus photo in Carl Zimmer's article is from Supriya Kadam, who did her PhD with Greg Velicer and just finished a year as a postdoc in my lab.

Continue reading "Individual and kin selection in legume-rhizobium mutualism" »

May 18, 2007

Helpful cheaters?

Paul Rainey has a very interesting essay in the April 5 issue of Nature. Much of what we know about "cheating" in bacteria that form floating mats comes from his research, including collaboration with Michael Travisano, recently hired here at University of Minnesota. See my earlier post, "how disturbed are cheaters", for background on this system. Although cheaters that don't invest in the goop that holds floating mats together can result in mats breaking up and sinking, Rainey's new essay suggests that a similar form of cheating may have contributed to the evolution of multicellular life.

Continue reading "Helpful cheaters?" »

May 14, 2007

Evolution of babysitting in bluebirds

Major transitions in evolution have often involved loss of independence, as discussed last week. Most female bees work to increase their mother’s reproduction, rather than laying eggs themselves. Less extreme examples of helping others reproduce are known in some animals. “Kin selection? favors helping relatives, if the cost of helping is less than the benefit to the one helped, times their relatedness to the helper. This is known as Hamilton’s Rule. As Haldane put it, “I would jump into a river to save two brothers or eight cousins.? “Cost? and “benefit? are measured in number of offspring and “relatedness? is relative to one’s usual competitors. If surrounded by cousins, Hamilton’s Rule would lead to helping only siblings.

For helping behavior to have evolved, there must have been genetic variation in helpfulness. This week’s paper shows that this is still true for western bluebirds in Oregon.

Continue reading "Evolution of babysitting in bluebirds" »

May 6, 2007

How disturbed are most cheaters, really?

Yesterday, my wife asked, "why are there so many theoretical papers in evolutionary biology?" I suggested one reason may be that evolutionary theory is better developed, in the sense of making accurate predictions, than theory in much of biology. This week's paper, comparing results from an evolution experiment to predictions of a mathematical model, is a good example.

The paper is about the evolution of cooperation. This is a hot topic and also my own area of research. Humans enforce cooperation, to varying extents. For example, we often punish cheaters, those who try to benefit from cooperative activities of others without contributing anything themselves. Human cheaters are mostly pretty stupid -- don't even think about plagiarizing this blog for a term paper! -- but what about cheaters with no brains at all?

Continue reading "How disturbed are most cheaters, really?" »