experimental evolution

Cooperation and Experimental Evolution

cagapakis — Sun, 24 Jan 2010 11:41:54 +0000

Cooperation and Experimental Evolution

Cooperation and altruism are widespread in biology, from molecules and genes working together in a cell, to bacterial communities that require coordinated behavior to survive in a tough environment, to human relationships and societies. Our human cultural perspective (perhaps even more specifically our American cultural perspective, focused as it is on individuality, free markets, and the American Dream), however, treats cooperation as an outright anomaly that has to be explained away by science (or often, religion). If natural selection is about the "survival of the fittest" how can a selfless gene be rewarded evolutionarily, surviving to the next generation? If evolution is about individuals locked in a battle for resources, why would anyone share with a friend?

Many experiments have shown that cooperation may actually not be so anomalous, and in fact may be a driving force for evolutionary change and diversity. Using experimental evolution, a synthetic approach to evolutionary theory where researchers try to observe evolutionary changes in controlled populations in the lab, several groups have shown that symbiotic, cooperative, and altruistic behaviors can rapidly evolve in many different situations. A recent paper from PLoS Biology, "Experimental Evolution of a Plant Pathogen into a Legume Symbiont" (ht Coturnix!) applied this kind of synthetic approach to plant/bacteria cooperation (in depth paper synopsis here). Many plants and bacteria have evolved a complex mutualistic relationship, where the plants will protect the bacteria from the harsh soil environment and the bacteria will provide crucial nutrients to the plant. Rhizobia are species of bacteria that invade the root tissue of legume plants and form small nodules where the bacteria grow and provide nitrogen that the host plant needs to grow. These species have coevolved to this complex mutualistic relationship over millions of years, but the authors found that after only a few generations pathogenic bacteria developed many of the behaviors required for the root nodule symbiosis, with many implications for evolutionary theory. From the paper's conclusion:

Our results show that adaptive genomic changes indeed allow effective dissemination of symbiotic traits over large phylogenetic and ecological distances. The fact that a single gene played a major role in the shift from extracellular pathogenesis to endosymbiosis reinforces previous reports that global regulators are preferred targets for evolution and supports fluid boundaries between parasitism and mutualism.

Other researchers have found similar results in very different model systems. Myxobacteria are single-celled organisms that live in large populations. When food is scarce, the bacteria activate a complex cascade of events where the population transforms itself from slime to a complicated fruiting body, with individuals performing highly specialized behaviors, including a huge number of individuals sacrificing themselves to provide food for the remaining cells, the ultimate altruistic behavior. Genetic mutations in a population of myxobacteria will lead to "cheater" cells that won't go through the same changes when they are on their own and starve, but will free-ride on altruistic neighbors in a mixed population with the wild type strain. A 2006 paper in Nature, "Evolution of an Obligate Social Cheater to a Superior Cooperator", started with this "obligate cheater strain" and allowed it to compete against the wild type in a laboratory evolution setup. They found that a single mutation in a gene that had previously not been identified as important for this process was able to turn the cheater strain not only into a cooperator, but into a cooperator that was able to outcompete all the ancestral strains. Scientists don't fully understand the processes that underly many of these cooperative interactions, but what is clear is that the evolution of these behaviors seems to be faster and more likely to spontaneously emerge than many people think.

There is a huge diversity of cooperative relationships in nature that expand the ability of living things to inhabit all ecological niches, but symbiosis has an even more central role in the evolution of life on earth. It is now widely accepted that complex eukaryotic cells (cells with a nucleus, like our own) evolved as the result of symbiosis between different prokaryotic (no nucleus, like bacteria). Organelles inside eukaryotic cells that provide energy, like chloroplasts in photosynthetic organisms and mitochondria in almost every eukaryotic cell, often have their own genetic material, left over from the time when they were free-living organisms. When Lynn Margulis proposed this serial endosymbiotic theory of eukaryotic evolution in the 1960's (based on theories of Russian botanists in the late 1800's and early 1900's) she was ridiculed by the biological establishment. The dogma at the time held not only that evolution must proceed through the accumulation of only small incremental changes, but also that symbiosis was a weird thing that only a few species of fungi did, not important stuff to molecular biologists. To the scientists, the notion that nature was cruel, that cooperation shouldn't exist was the norm, and the idea that evolution could be driven by cooperation at such a large scale was unthinkable. Margulis persevered, and eventually everyone realized that she was right all along. Decades later however, the marginal, "weird" status of cooperation in the biological literature remains, and Margulis warns that we should be careful with the words we use when discussing it, that we shouldn't color our understanding of reciprocal biological relationships with how we think about economics, politics, and other human constructions. Other synthetic biology experiments will perhaps further show that cooperation may be more "natural" than science currently allows it to be.

cagapakis Sun, 01/24/2010 - 06:41

The arc of evolutionary genetics is long

razib — Tue, 20 Oct 2009 08:09:10 +0000

The arc of evolutionary genetics is long

Evolutionary ideas have been around a long time, at least since the Greeks, and likely longer. I accept the arguments of researchers who suggest that humans are predisposed to Creationist thinking; after all, cross-cultural data shows the dominance of this model before the rise of modern evolutionary biology. But this does not mean that the possibility of evolution would be totally mystifying to the human race before Charles Darwin's time. After all, it may be that humans as a species have a predisposition toward theism as well, and yet all complex societies produce atheistic movements as counter-cultures, the Epicureans* among the Greeks, Carvaka among the Indians and the Dahrites among the Muslims.

Rather, what made Charles Darwin so important was the theoretical heft he brought to the idea of evolution, which was in the air at the time. In the early 20th century Darwin's verbal insights were given more formal structure by theoreticians such as R. A. Fisher and Sewall Wright. These population geneticists aimed to turn the helter skelter and descriptive clarity of evolutionary biology into a more predictive science through their mathematical frameworks. But despite the heroic efforts of biologists such as E. B. Ford testing these theoretical predictions before the molecular genetic era was often not feasible. In the age of genomics this is changing, as large data sets can now be viewed with an aim toward extracting out theoretical generality, or violations from expected generality.

But another advance, aided by molecular techniques, is experimental evolution. The most prominent practitioner today of this field is Richard Lenski, and he is co-author on a new paper which looks at the rate of evolution over time in E. coli. Genome evolution and adaptation in a long-term experiment with Escherichia coli:

The relationship between rates of genomic evolution and organismal adaptation remains uncertain, despite considerable interest. The feasibility of obtaining genome sequences from experimentally evolving populations offers the opportunity to investigate this relationship with new precision. Here we sequence genomes sampled through 40,000 generations from a laboratory population of Escherichia coli. Although adaptation decelerated sharply, genomic evolution was nearly constant for 20,000 generations. Such clock-like regularity is usually viewed as the signature of neutral evolution, but several lines of evidence indicate that almost all of these mutations were beneficial. This same population later evolved an elevated mutation rate and accumulated hundreds of additional mutations dominated by a neutral signature. Thus, the coupling between genomic and adaptive evolution is complex and can be counterintuitive even in a constant environment. In particular, beneficial substitutions were surprisingly uniform over time, whereas neutral substitutions were highly variable

The experiment involved a line from the ancestral colony which was maintained for approximately 15 years. The use of the term "counterintuitive" in some ways is a bit deceptive; would the person off the street find the results counterintuitive? I doubt it. Rather, intuitions here are actually framed by deductions one makes from theoretical assumptions about the nature of molecular evolution and the genomic impact of natural selection. For example, we expect that adaptation should converge upon an optimum and exhibit deceleration. Or that the rate of substitution should equal the rate of mutation.

Figure 2 illustrates the gist of the results:

The "fitness" lines up with our expectations. When you have a population which is switched to a new environment you expect that it will adapt as best as it can quickly, and over time "fine-tune" those adaptations and reach some sort of equilibrium. On the other hand, it looks as if two "neutral" equilibriums were at work (see inset), one before the emergence of a hypermutant strain, and one after. Remember that to a great extent evolutionary change should be proportional to mutation rate on the molecular level if most molecular change is not subject to selection pressure. A simple explanation for what's going on above is that only a small fraction of genetic changes are beneficial, and so neutral evolution was predominant. The relative strength of adaptive evolution in the early stages would have been of marginal significance when set next to dominance of neutral effects, so its removal would not have been noticeable.

The authors reject this simple model for four reasons:

- All 26 point mutations they found in coding regions were non-synonymous before the emergence of hypermutability. That means that they actually effect changes in amino acid and so function. This is very unlikely, so the inference must be that functional changes are driving this evolution.

- There were 12 total lines, though they only focused on one in this paper. But, neutral evolution would have distributed mutations randomly across genes, and so there shouldn't be much concordance across the lineages. In fact, there was a great deal of concordance, as the same genes were targets of mutation repeatedly across experimental populations. This parallelism is a strong indication that selection was targeting specific functional regions for specific traits.

- In a situation where neutrality is dominant there should be many lines where the frequencies of the mutants are intermediate as they "random-walk" up and down the range of potential frequencies. But this was not so. Rather, there was a trend toward fixation. Once a selectively favored mutant avoids extinction its probability of sweeping to fixation is rather high. In contrast, a neutral allele which is extant at frequency ~0.25 in a particular generation still has a 75% chance of going extinct.

- The new mutations do seem to confer fitness advantages vis-a-vis the ancestral strain. Obviously if a mutation is neutral it shouldn't confer fitness advantages.

One explanation they have for the relatively constant rate of the emergence of mutational variants is that the initial mutants are of large effect, and have negative pleiotropic effects. In other words, in a new environmental circumstance populations look for "good enough solutions," or kluges, which introduce deleterious trade-offs. There's still plenty of room for adaptive improvement and later mutations are driven to fixation in large part as solutions to the problems introduced by the earlier mutation. Additionally:

Clonal interference occurs in asexual organisms when sub-lineages with beneficial mutations are driven extinct by competition with other sub-lineages bearing mutations that are even more beneficial and this process might contribute to the relatively constant rate of genomic change. In particular, the most beneficial mutations should dominate the early phase of evolution for large populations in a new environment26, but there are more potential mutations that confer small advantages than large ones. Thus, the supply of contending beneficial mutations may increase enough to sustain a uniform rate of overall genomic change.

At some point the dynamics shift in a discontinuous manner, as a hypermutable lineage emerges at 40,000 generations. Whereas before all 26 of the mutations in coding regions were synonymous before hypermutability, only 83 of 599 were after. This suggests that the basal mutation rate has increased and neutral dynamics have become more powerful; in other words, the background noise has been cranked up considerably. They estimate that the point mutation rate increased about 70-fold after the emergence of the mutator phenotype, almost two orders of magnitude!

Here's their conclusion:

Genome re-sequencing in the context of experimental evolution provides new opportunities for quantifying evolutionary dynamics. We observed discordance between the rates of genomic change and fitness improvement during a 20-year experiment with E. coli in two respects. First, mutations accumulated at a near-constant rate even as fitness gains decelerated over the first 20,000 generations. Second, the rate of genomic evolution accelerated markedly when a mutator lineage became established later. The fluid and complex coupling observed between the rates of genomic evolution and adaptation even in this simple system cautions against categorical interpretations about rates of genomic evolution in nature without specific knowledge of molecular and population-genetic processes. Our results also call attention to new opportunities for population-genetic models to explore the longterm dynamic coupling between genome evolution and adaptation, including the effects of clonal interference, compensatory adaptation, and changing mutation rates.

Citation: Nature, Genome evolution and adaptation in a long-term experiment with Escherichia coli, 18 October 2009, doi:10.1038/nature08480.

* I am aware that Epicureans accepted gods as Buddhists accepted gods, but on a philosophical level these were not supernatural gods, but rather reducible down to atomic units just as man was.

razib Tue, 10/20/2009 - 04:09

Evolution: Random or Directed?

grrlscientist — Fri, 13 Jun 2008 12:06:59 +0000

Evolution: Random or Directed?

tags: researchblogging.org, evolution, experimental evolution, adaptation, mutation, natural selection, Richard E. Lenski

The common gut bacteria, Escherichia coli, typically known as E. coli.

Image: Dennis Kunkel.

Evolution is a random process -- or is it? I ask this because we all can name examples of convergent evolution where very different organisms arrived at similar solutions to the challenges they are faced with. One such example is the striking morphological similarities between sharks (marine fishes) and dolphins (marine mammals). Thus, based on observations of convergent evolution, one is tempted to hypothesize that, even if the mutations that underly evolution itself are random, the "end result" of evolution is not. In fact, this is the central premise of an interesting book by Simon Conway Morris, Life's Solution (Cambridge University Press, 2004), where he postulates that ''the evolutionary routes are many, but the destinations are limited''. This is in direct conflict with the late Stephen Jay Gould's hypothesis that a far different evolutionary outcome would occur if we could only replay the "tape of life". So which is it?

Of course, replaying this tape of life is impossible, except when the organisms being studied have a fast enough generation time that we can watch their evolution during our own lifetimes. One scientist, Richard E. Lenski, a professor in the department of Microbiology and Molecular Genetics at Michigan State University, has been conducting this very experiment for the past 20 years. His organism of choice is our own humble gut bacteria, Escherichia coli, which has a generation time of approximately 20 minutes under optimum conditions.

To investigate the repeatability of evolutionary trajectories and outcomes within a population, Lenski set up a long term evolution experiment in 1988 where he obtained twelve founding bacterial lineages from the same clone of E. coli. According to his experimental design, all twlve populations were grown separately from each other under identical conditions for more than 44,000 generations, so far (the experiment is ongoing). At time intervals of 500 generations, samples were collected from each of the twelve lineages and frozen. These samples can later be thawed, revived and grown in culture, providing a glimpse into the evolutionary past for each lineage, revealing a detailed living fossil record of evolutionary changes that occurred in each population, providing researchers with the opportunity to study the contributions from genetic mutation and drift, and of natural selection to evolutionary change.

Part of Lenski's experimental design was to grow the twelve E coli lineages under poor conditions, where their preferred energy source, glucose, was severely limited. Thus, one of the first characteristics that these bacterial populations evolved was the ability to rapidly metabolize all the available glucose in the culture and then wait patiently for their next daily meal. The culture broth also included a second energy source; citrate. But unlike glucose, which was limited, citrate was present in abundance. At first, the abundance of citrate was unimportant because E coli cannot metabolize this molecule when oxygen is present, and in fact, citrate metabolism (Cit+) is a characteristic that has long been used to differentiate this species from other similar, bacterial species.

Surprisingly, after 31,500 generations had passed, one of the twelve E coli lineages did the impossible: it evolved the capacity to metabolize citrate in the presence of oxygen.

But when exactly, did the citrate metabolic ability first appear? Referring to frozen bacterial stocks for this particular lineage, Lenski's team discovered that Cit+ variants first appeared after 31,000 generations had passed, but were unable to expand to dominance until a further 2000 generations had passed. This suggests that the Cit+ variants needed to accumulate several more mutations that enhanced their metabolic efficiency so they could out-compete their Cit- relatives.

The long period of time that elapsed before Cit+ appeared within one -- and only one -- population suggested one of two evolutionary possibilities; either the Cit+ mutational event was especially unusual or the evolution of this particular character is contingent upon a complex series of earlier mutations, at least some of which were not uniquely advantageous to the organisms possessing them. This second, more complex form of evolution is known as contingent adaptation.

To clarify the evolutionary events that underlie the appearance of citrate metabolism, the researchers asked if Cit+ would always arise among descendants from the evolutionary ancestors wihtin this one lineage. In short, would the Cit+ variant always appear in this lineage if the "tape of life" could be replayed? When the researchers replayed the "tape of life" for this lineage by reviving older bacterial stocks and growing them again, they found that Cit+ never appeared in populations grown from samples that were frozen before 20,000 generations had passed, that citrate metabolizers were "extremely rare" in populations grown from samples frozen afterwards up until 27,000 generations had passed, and after that point, citrate metabolizers then were only "rare". Based on all these data, Lenski's team concluded that evolution is a process of historical contingencies so that, if one can replay the "tape of life," the evolutionary trajectory would yield different outcomes.

But what traits had to change before Cit+ arose? To identify the specific mutations that gave rise to Cit+ variants, the team is currently sequencing the entire genome of this bacterial lineage, using samples that were frozen before and after Cit+ appeared. Conveniently, an ecological balance formed in this lineage; even though a large majority of the community consisted of Cit+ specialists, a minority of the bacteria in the population remained Cit- generalists. This fortuitous development allows Lenski's team to identify specific mutations that contribute to Cit+ by comparing genomic sequence data from Cit- clones to Cit+ after citrate metabolism appeared in the population.

Further, because there are now two subpopulations in this lineage, this experiment presents the unique opportunity for scientists to study population dynamics that govern the emergence of a new character and to understand how one phenotype affects the other under a variety of environmental conditions.

As a result of this experiment, Lenski's team hypothesizes that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.

Source

Blount, Z.D., Borland, C.Z., Lenski, R.E. (2008). Inaugural Article: Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proceedings of the National Academy of Sciences, 105(23), 7899-7906. DOI: 10.1073/pnas.0803151105

grrlscientist Fri, 06/13/2008 - 08:06