BEACON Researchers at Work: The effect of landscapes and ecology on gene flow and speciation in amphibians

Posted on April 10, 2012 by Danielle Whittaker

This week’s BEACON Researchers at Work blog post is by University of Idaho graduate student Tyler Hether.

Photo of Tyler HetherThe amount of biological diversity at all levels of biological organization—from genes to ecosystems—fascinates me. This interest is the reason I study evolutionary biology, which attempts to understand the origins and patterns of such diversity. A major theme of my research is merging concepts from ecology, physiology, mathematics, computer science, and molecular biology in an attempt to elucidate how diversity arises and, hopefully, identify generalities in the diversification process found within and among species.

From Genes to Gene Flow, Landscapes to Landscape Genetics

Individuals of a species mate with one another non-randomly: individuals closer in space tend to mate more frequently than individuals who live further apart. This phenomenon, known as genetic “isolation-by-distance,” is nearly ubiquitous in natural populations and relies on a balance of two factors: population size and migration. Though isolation by distance is a common pattern in nature, its effect size can vary widely from one species to another. One possible explanation for this variation is physiological constraints of a particular taxon. Another (non-mutually exclusive) explanation is that the environment or landscape modulates migration and population size. In one research project, I asked if populations of a widespread and abundant southeastern USA frog, the squirrel tree frog (Hyla squirella), exhibited a pattern of isolation-by-distance and, if so, could environment or landscape data contribute in explaining variation in genetic divergence. Amphibians are well studied in population genetics because their life-history and physiological need for aquatic habitat during breeding shapes the pattern of genetic structure observed across the landscape. The squirrel tree frog is interesting to me because in addition to breeding in natural aquatic habitats they breed in anthropogenic structures (such as road-side ditches). Since much of the landscape across the southeast has been recently modified from natural habitat to pastures, tree plantations, and urban habitat, I was curious if any of the aforementioned habitats could potentially contribute to among-population genetic divergence. Comparing variation present at putatively neutral evolving molecular markers (microsatellites), I found that much of this variation could be explained by proximity to nearby populations (in other words, these populations have isolation-by-distance). In addition, I found that considering not only spatial distance between populations but also the percentage of upland oak habitat and the percentage of urbanized habitat that exist between two populations nearly doubles the amount of variation explained in genetic divergence estimates. It’s quite possible that these associations in landscape data and genetic data are simply correlations; however, these associations could spark future manipulative experiments that can directly assess cause and effect.

From Populations to Population Genomics; Ecology to Ecological Speciation

Not only can the intervening landscape affect patterns of neutral genetic variation seen among populations, but it can also change frequencies of genes that are under selection. Whenever there is an ecological source of divergent selection as well as a genetic mechanism linking this source to reproductive isolation, speciation may result. If the process of speciation under this regime is completed then we say that these once interbreeding populations have become reproductively isolated by ecological-mediated divergence leading to “ecological speciation.”

It is noteworthy to make an analogy between ecological speciation and landscape genetics (mentioned above) that may characterize my research interests. That is, landscape genetics is to isolation-by-distance as ecological speciation is to the more familiar allopatric speciation. In both cases there exists a spatial component to genetic divergence that has been studied extensively. In addition, there exists an ecological component to genetic divergence that, until recently, has received less attention.  This is not to say that “the ecology” of a system was deemed irrelevant until recently. Rather, only until recently has it been computationally easier to collect and analyze ecological data at the scale that population genetics studies take place.

Niko Balkenhol, professor at the University of Goettingen, once wrote, “Ecosystems are the stage on which the play of evolution unfolds.” It’s certainly true that ecosystems set the stage where evolutionary processes interact. It’s also worthwhile, I argue, to identify the mechanisms that start a completely interbreeding set of individuals to evolve into independent lineages and ask whether general mechanisms exist. Therefore, the core of my dissertation work at the University of Idaho takes a comparative approach to identify patterns of genomic divergence during ecological speciation.

One example of ecological speciation-in-action occurs in the Chihuahuan desert of the southwestern USA.  Over the last decade, my co-advisor Erica Bree Rosenblum has studied the local adaptation of lizards at White Sands National Monument, New Mexico, which consist of brilliantly white gypsum sand deposits responsible for forming a stark ecological boundary with the surrounding Adobe soils that typify the southwest.  Absolutely fascinating to me is that three lizard species occupy these gypsum sand dunes and appear light in color while their conspecifics in the surrounding desert are dark. Further, we know that variation at a single gene, melanocortin 1 receptor (mc1r), has a large effect on color. It is unknown, however, how variation at mc1r shapes divergence at other regions of the genome. Currently, I’m using next-generation technology to sequence the region of the genome that surrounds mc1r and comparing differences observed between dark and light individuals in this region and with other regions of the genome. Theory predicts that if natural selection is important in keeping White Sands individuals light and dark soils individuals dark then genes in close proximity to mc1r will effectively be linked together. I’m curious to see the influence of such selection on the rest of the genome. In other words, how much of the region flanking mc1r is diverged between White Sands and dark soils? Also, we know that other traits differ between White Sands and dark soils populations. Is natural selection acting on each trait independently or does it effectively act in a single “color” dimension with other traits merely in linkage to mc1r?

For more information about Tyler’s work, you can contact him at tyler dot hether at gmail dot com.

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BEACON Researchers at Work: Bringing evolution-in-action to high school students

Posted on April 2, 2012 by Danielle Whittaker

This week’s BEACON Researchers at Work post is by MSU graduate student Anne Royer.

Anne RoyerAlong with doing great science, learning how to communicate what we discover is one of the joys and challenges of graduate study. BEACON offers exciting opportunities to explore this dimension of academic life – I joined the education team last year with the assignment of helping design the first weeklong summer BEACON experience for high school students. What better venue could there be for sharing the excitement of evolution-in-action than a full-immersion summer camp?

With all the resources of BEACON and the MSU campus at our fingertips, fellow course designer Mike Wiser and I set about constructing a program to introduce the breadth of what BEACON does. Spending half of the week at MSU’s Kellogg Biological Station (KBS) in southwest Michigan and half on MSU’s main campus, we gave our students a crash course in what evolution is, how we study it, and what some of the applications are. This whirlwind tour included experiencing field biology, lab work with model biological systems, tinkering with digital systems, and learning about the breadth of the field of engineering and how evolution interfaces with it. 

Students examining milkweedFor me, getting students outside to observe organisms in the context in which they evolved is one of the most thrilling parts of education. The students recruited for the summer program had interests as diverse as BEACON itself, so many of them were attracted by the engineering and had little or no experience with field biology. We wasted no time loading them on a bus and plunging them into local field sites. KBS graduate student Raffica LaRosa guided the group through a project measuring natural selection on the flowers of one of her study organisms, the common milkweed (Asclepias syriaca). This first field experience was punctuated with encounters with insect pollinators and a thunderstorm. For more bugs and water, we set out the following morning for Augusta Creek, where BEACON postdoc Idelle Cooper and faculty member Tom Getty let our intrepid band into hip-high water. They chased damselflies with insect nets and explored how mating behavior influences the evolution of color in these flying jewels. In addition to the fun of handling charismatic organisms and exploring their environments, the students had the chance to form their own hypotheses and predictions, see the results of the data they collected, and talk through interpreting the new information.  

Students wading in waterMy colleague Mike Wiser brought expertise with the model organism Escherichia coli and a familiarity with the incomparable long-term experiments in the Lenski lab. Almost as soon as their parents dropped them off, the students donned gloves and wielded pipettes, setting up their own rapid-evolution experiment to explore how bacteria in settled and agitated environments evolve differently. On the final morning of the week-long program, each student had a petri dish in hand to count colonies and evaluate differences in appearances. Mike was also able to show them cultures from the Lenski lab and talk them through some of the exciting results of 50,000+ generations of experimental evolution.

Students at computersOnce we had introduced the basics of how evolution by natural selection operates, the students were primed to plunge into the world of digital evolution. We chose two systems to explore how computer science interfaces with the study of evolution: the internet-based BoxCar2D and BEACON’s Avida-Ed. With clear parallels to engineering applications and video-game-like graphic user interface – evolving colorful vehicles to run on different digital “tracks” – BoxCar2D was a perfect fit for our program and a lot of fun for the students to explore. We were fortunate to have Wendy Johnson, a Michigan high school teacher who spent last summer working on integrating Avida-Ed into the classroom, to introduce our group to this instance of evolution within a computation system, and an opportunity to test evolutionary hypotheses. 

Afternoons on campus were filled with visits from Engineering faculty to learn about the diversity of fields encompassed by this department. But like any proper camp, fun was liberally sprinkled in – from laser tag to salsa dancing to a greased watermelon in a lake, we made sure the students found plenty of ways to relax together long days of engaging their minds. Our first BEACON summer high school program turned out to be a great success. Working across different BEACON fields, we taught promising young students about the exciting opportunities evolution-in-action offers to problem solvers with curious minds. We’re invested in keeping this program running, and making it better each year. We’re reaching out to additional BEACON researchers to integrate more cutting-edge work into the curriculum, and increasing the independent inquiry component of the course. Stay tuned for more developments! 

For more information, you can contact Anne at royerann at msu dot edu.

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The Black Queen Hypothesis

Posted on March 30, 2012 by Danielle Whittaker

"Black Queen" image via io9.com

A new evolutionary theory proposes that microorganisms may be selected to lose costly functions if another organism can perform them instead.

BEACON postdoc Jeffrey Morris, along with professor Richard Lenski and University of Tennessee collaborator Erik Zenser, proposes this explanation for why certain microbes may depend upon each other in a new paper in the journal mBio. The name “Black Queen” refers to the game Hearts, in which the Queen of Spades is a card generally avoided.

Check out the coverage in the New Scientist and io9.com!

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Introducing BEACON Distinguished Postdoctoral Fellow Joshua Nahum

Posted on March 29, 2012 by Danielle Whittaker

We are pleased to announce that Joshua Nahum is the first recipient of the BEACON Distinguished Postdoctoral Fellowship. He will be co-sponsored by Rich Lenski and Charles Ofria.

First, a little about Josh’s unusual background. Since early grade school, Josh has always had a strong interest in the sciences. Inspired by Bill Nye and excellent science teachers, he began to take classes meant for older students. As a high school sophomore, he began taking college courses at his local community college in chemistry and biology. With early aspirations about medicine and biology in general, he was able to graduate from high school at the age of 16 and enrolled at the University of Washington. Josh’s course work emphasised biochemistry and molecular biology, and in the span of only a year, he graduated with a Bachelors of Science in Biology. Upon concluding his undergraduate career, he began work as a technician in Ben Kerr‘s lab. A year later he entered UW’s graduate program (with Ben as his advisor). During his years at UW, Josh has worked with viral, bacterial and digital model systems in evolutionary biology.

His future work will involve the exploration of how and why organisms are evolvable. As BEACON is devoted to understanding and harnessing the force of evolution, comprehending the factors that determine evolutionary potential is crucial. By combining the merits of digital and microbial systems, he seeks to understand how contingency loci (regions of the genome with an increased mutation rate) may allow organisms to more rapidly adapt to new and/or changing environments. Contingency loci are often associated with genes involved in pathogenicity and virulence in microbes, as well as neurological disorders in humans. As such, understanding their putative role in enabling more rapid adaptation would yield a more accurate understanding of the nature of mutations with possible implications for medicine. Should contingency loci and other forms of biased mutation rates prove beneficial to evolution, they may also offer another avenue to improve the performance of optimizing applied evolutionary algorithms.

Josh will begin the postdoctoral fellowship at the end of 2012, with the first six months at UW (with Charles Ofria who will be on sabbatical). Afterwards, he will continue his fellowship at Michigan State University.

Josh Nahum has been an active member in BEACON so far, and we expect great things from him as a BEACON Distinguished Postdoctoral Fellow!

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BEACON Researchers at Work: Mathematical modeling of evolution

Posted on March 26, 2012 by Danielle Whittaker

This week’s BEACON Researchers at Work post is by MSU graduate student Masoud Mirmomeni.

Dog licking kitten on head

Photo from http://www.cuteheaven.com

I bet that the very first time you saw this kind of picture, an unconscious “ahh!” came out. Well, it worked on me. But now, I am seeing these kind of pictures under another perspective. 

Nature is full of sophisticated phenomena. Although some of these phenomena are known, partly known or remain mysterious, nature is beautiful. But it is all this complexity that makes nature beautiful, and on the other hand hard to analyze. This complexity is a result of many completely or partly unknown chemical, physical, biological, or sociological processes such as evolutionary processes. Evolutionary processes increase diversity at every level of biological organisms. Among interesting behaviors in living organisms, cooperative behaviors, especially altruistic behaviors, are more difficult to explain.

In evolutionary biology, a behavior is considered as an altruistic behavior when its organism benefits other organisms, at a cost to itself. One way to measure costs and benefits of a behavior is to look at the reproductive fitness, or expected number of offspring. Many species in nature behave altruistically. For example, dogs sometimes adopt orphaned kittens, squirrels, or even ducks! In many bird species, a breeding pair sometimes receives help in raising its young from other birds called “helpers.” These birds usually protect the nest from predators and help the breeding pair to feed the fledglings. In the presence of predators, vervet monkeys give alarm calls to warn their fellow monkeys – even if they put themselves in danger by attracting attention of predators to themselves. Even microorganisms can display altruism. For example, the slime mold Dictyostelium discoideum shows altruistic behavior when food is scarce. When food is plentiful, they live in soil as single cells, feasting on bacteria. However when starved, they form a multicellular fruiting body with a ball of spores at the tip. Around one fifth of them will die and become the stalk that lifts the spores above the ground as the result of this altruistic behavior, but the chance of dispersing to more favorable environments increase.

(a) William Donald Hamilton; (b) George Price

Evolution of altruistic behavior has been addressed by many researchers (e.g. R.A. Fisher, J.B.S. Haldane, W.D. Hamilton, G. Price, and D.C. Queller). Around 50 years ago, William Donald Hamilton proposed a theory to explain the evolution of altruism among relatives based on the idea of inclusive fitness. This theory is called Hamilton’s rule (HR), which is usually interpreted as specifying the conditions under which the indirect fitness of altruists sufficiently compensates the immediate self-sacrifice of altruists. Simultaneously, George Price presented the more thorough mathematical treatment given to this theory and developed the Price Equation. In his theory, Price shows how a trait evolves over time, depending on the trait’s fitness and the fidelity with which the characteristic is transmitted to the next generation. 

The Price equation was a simple, general, and profound insight into the nature of selection, and it was a new mathematical formulation for evolutionary change in the population. The novelty of the Price Equation is that it does not change the fundamental simplicity of evolutionary change; however by making a few minor rearrangements and changes in notation, the equation provides an easier and more natural way to reason about complex problems. It provides us a way to understand the effects that gene transmission and natural selection have on the proportion of genes within each new generation of a population. The Price Equation shows that the change in the fitness mean is proportional to the fitness variance. The Price Equation, given in equation 1, proposes a model that unifies all types of selection (chemical, sociological, genetic, and every other kind of selection):

wavg × Δz_avg = COV(wi , zi) + E(wi×Δz_i),

where w is fitness and z is a quantitative character, which can be anything such as complexity of species. This covariance equation shows that what matters in kin selection is not common ancestry, but statistical associations between the genotypes of donor and recipient. The Price Equation adds considerable insight into many evolutionary biology problems by partitioning selection into meaningful components. It’s an important theorem because it associates entities from two populations, called the ancestral and the descendent populations.

Photo of Masoud MirmomeniAs a Ph.D. student in Chris Adami’s lab, I am working on the evolution of altruistic behavior under William Punch and Chris Adami’s supervision. My main focus is to extend the Price Equation and Queller’s formula from their linear form to a generalized form based on information theory. By generalizing these theories to a nonlinear form. First we will have a better model for this nonlinear process. Then, we can address recent arguments about the validity of the Price Equation (refer to M. Van Veelen’s papers in 2005 and 2011).

Currently, I am trying to address the following questions:

“If the Price Equation is not valid, what would be the proper probabilistic model/equation that can properly describe the selection problem in general?”

“What is the best way to extend the Price Equation to hold for all populations?”

Screen shot of Avida populationI am using AVIDA to test the validity of the Price Equation. Because there is no assumption regarding the trait in the Price Equation, I chose the genomic complexity of AVIDIANs in the population as the trait (zi). The genomic complexity is defined based on information theory and Shannon entropy.

For more information about Masoud’s work, you can contact him at mirmomen at msu dot edu.

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BEACON Researchers at Work: The social lives of bacteria

Posted on March 19, 2012 by Danielle Whittaker

This week’s BEACON Researchers at Work post is by MSU graduate student Eric Bruger.

Photo of Eric Bruger in the labWhy play well with others when you can get away with just looking out for your own self-interest? This is a sentiment not only left to misbehaving children. Cooperative behaviors are difficult phenomena for evolutionary biologists to explain, in part due to the potential invasion of non-cooperating defectors into participating populations. The same can be asked about communication – why should robust, reliable communication be maintained over the course of evolution? On the surface, it would appear that natural selection alone would not favor the development and maintenance of these types of behavior. And as it turns out, microbes may present a great chance to examine these interesting evolutionary questions.

The extent of microbial diversity is truly astounding. I may be biased, but in my opinion microbes are unequivocally awesome. Seriously, they are spectacular in many regards for practicing and aspiring biologists. Not only do they exhibit countless interesting and novel features that impact global ecosystems and processes, they are also extremely tractable from an experimental standpoint. I became very interested in microbes as a bacteriology undergraduate at the University of Wisconsin-Madison when I began learning about the immense physiological potential they possess. But did you know that they also have elaborate social lives? It isn’t news that organisms other than humans, from ants to apes, are capable of social behavior. However, long ignored in the field of social evolution, it is now appreciated that microbes are seldom found in isolation and display an impressive array of social and cooperative behaviors. Bacteria are capable of a variety of group behaviors, ranging from competitive, such as the production of antibiotics and bacteriocins, to cooperative, such as producing secreted exoenzymes and iron-scavenging siderophores. These group behaviors do not merely affect the participating population of organisms and may, for example, extend to positive symbiotic or negative pathogenic interactions with hosts.

Flask of bioluminescent bacteriaNotable among these behaviors is quorum sensing (QS), a form of chemical communication that can mediate regulation of groups of genes. QS has evolved in many different groups of bacteria, including important plant and human pathogens. In QS, cells produce a chemical signal released from the cell, and a coevolved receptor that can detect the signal in other cells, thereby leading to altered regulation of many genes, resulting in expression of downstream behaviors. Although different lineages may vary in their regulatory network designs and system components, the underlying concepts are similar. QS is used to regulate numerous genes in bacteria including those important for virulence, biofilm formation, motility, and bioluminescence. Though well-studied at the molecular level, evolutionary explorations of QS are limited. QS is proposed to be a mechanism to promote cooperative behavior in bacteria, but it remains unclear how QS is maintained when non-cooperators potentially have higher individual fitness.

Currently, I am a PhD student in Chris Waters’ lab, where I work on a project that utilizes the gram-negative bacterium Vibrio harveyi. The primary focus is on the evolution of quorum sensing. Because it has a long-standing experimental history and a well-described quorum sensing system, V. harveyi is a great study system for these types of questions. A pathogen of numerous species of marine animals, V. harveyi causes significant economic damage each year to the aquaculture industry. Another notable feature of V. harveyi is its potential to produce light, or bioluminescence, by way of the luciferase enzyme. For our line of experiments, bioluminescence also serves as a great indicator that collective behavior is being turned on.

Generally, behaviors regulated by QS are not turned on when cells are at low density. Bioluminescence is carefully regulated in V. harveyi by the level of signal production, such that sufficient signal to induce bioluminescence gene production does not occur until a large number of cells (~108 cells/ml) are present. In this way, QS is hypothesized to serve primarily as an organizer for the types of collective behavior that may not be beneficial to individuals unless performed at a large group scale. However, there is also the potential that QS could provide benefits to cells in a manner independent of the collective behaviors they often regulate.

Performing these types of tasks that are costly to individuals sets the stage for a situation in which cheaters may emerge. In this context, a cheater is an individual whom does not contribute to a collective behavior performed within its resident population, but whom stands to benefit from that behavior being performed by others. Cheaters have been discovered in a variety of natural and artificial systems, often in respect to the production of public goods. We are attempting to address the question of how QS may be maintained by careful determination of costs and benefits inherent to QS. This is being done by performing long-term continuous culture experiments with wild type strains of V. harveyi capable of normal quorum sensing, as well as impaired mutants that mimic cells in perpetually locked low-density or high-density states. We are also pursuing genomic approaches to analyze changes arising in these lines over time in detail to the molecular level. In this way, processes that are entangled with QS regulation in ways not currently understood may also be discovered.

The costs and benefits of participation in QS and other collective behaviors may also vary depending on the surrounding social environment and the overall levels of resources. I plan to monitor this in dynamic fashion by tracking the stability of QS in populations propagated in relatively nutrient rich and poor environments. We hypothesize that altering the available types and levels of resources that V. harveyi is grown on should affect the stability of QS. Additionally, ecological interactions are being checked over through competition between different types of QS variants. In this way, we may be able to unmask the selective contributions of both resource levels for the maintenance of QS, as well as the importance of the specific QS components to the overall system.

Understanding the dynamics of QS in a model bacterial system has the potential for broad-reaching impacts. Application of general principles may allow for uses such as targeting QS for disruption to combat disease in plants and animals, as well as inducing desired QS-regulated behaviors for industrial production. Before that promise can be realized, though, steps need to be taken to supplement the current molecular understanding of QS systems with more information about their eco-evolutionary dynamics.

For more information about Eric’s work, you can contact him at brugerer at msu dot edu.

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BEACON co-sponsors math and science day for middle school girls at MSU

Posted on March 14, 2012 by Danielle Whittaker

MSU graduate student Michelle Vogel, writer of this post, was one of several BEACONites who participated in this event.

While the undergrads were vacant from MSU last week, local middle schoolers descended on campus to learn about science. The Graduate Women in Science along with BEACON and the Council of Graduate Students hosted over 100 middle school girls for a middle school math and science day. At the heart of the event were women faculty, graduate students and others sharing their love of maths, science and engineering fields with the girls. Dr. Stephanie Watts started the day off by sharing her love of science and her journey to becoming a faculty member.  She then challenged the girls to ask questions, discover what they were passionate about, and have fun. 

The girls then participated activities like wildlife forensics, where participants used skittles for karyotyping and even ran the ‘extracted DNA’ from the skittles on an electrophoresis gel. At “What’s your number? Blood Pressure,” our keynote speaker and her posse of female scientists taught several groups of girls how to take their blood pressure and talked about researching new blood pressure medications.  After participating in several of these types of activities, the day ended with an ice cream social and graduate student panel where the girls got to ask several of us about how we got to where we are and why we love what we do.

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BEACON Researchers at Work: Tadpole sibling rivalry

Posted on March 12, 2012 by Danielle Whittaker

This week’s BEACON Researchers at Work blog post is by MSU graduate student Sara Garnett. 

If you’ve grown up with siblings, you’re probably familiar with the potential for conflict. Deep down, you love each other and want the other to succeed, but that doesn’t stop you from competing for attention and other parental resources. It’s not just you; there’s an evolutionary basis to this balance between competition and cooperation among siblings. The pressure to compete for the resources needed to survive and produce offspring – the component we think of as direct fitness – is pretty simple to understand. If an individual is going to pass its genes on to the next generation, it needs to compete against others to get whatever food, habitat and mates necessary. If you’re only taking this direct fitness into account, you might expect that individuals will compete as intensely as possible to control these resources.

This isn’t always what we see, however, especially where relatives are concerned. Competition to pass on genes is a significant component of evolution, but a given individual isn’t the only one who has those genes. If it isn’t a novel mutation, at least one parent also has a copy, which means that it may also have been passed on to other siblings. Genes may also be shared as a result of common descent in half-siblings, cousins, grandparents, and other relatives, depending on how far back the gene is present.

What this means is that behaving in ways that help relatives survive and reproduce can also be an effective strategy when it comes to passing on genes. This is illustrated by Hamilton’s rule, which states that behavior benefiting a relative can spread in a population when the fitness cost to an individual who helps a relative is less than the fitness benefit that relative gains, adjusted for how closely related they are (that is, how likely they are to share genes). This adjusted fitness benefit for a relative can be considered to be the indirect part of the first individual’s fitness. When taken together with the genes passed on by producing offspring, both components make up an individual’s inclusive fitness. Thinking about ways to maximize this quantity, rather than focusing solely on direct fitness, can shed light on a variety of kin-directed behavior.

Common examples of Hamilton’s rule feature individuals performing some behavior that increases risk to themselves, such as ground squirrels that are more likely to perform alarm calls (and attract the attention of predators) if their kin are nearby, but similar motivations can also explain individuals refraining from behaving in a certain way. Restraint is often more subtle and difficult to detect than active helping, but it can be just as important. Amphibian species whose young develop as cannibal types or morphs are less likely to associate with siblings and, given the choice, prefer to consume unrelated individuals. In several species of birds, nestlings will beg more intensely in nests where average relatedness is lower, suggesting that they refrain from competing as much as possible with more closely related nestmates. Some plants even alter allocation to structures used to compete for limiting resources based on whether strangers or siblings are growing nearby. Investigating examples of such kin-discriminating behavior can provide insight into the strategies organisms use to maintain this balance between competition and cooperation, allowing them to maximize inclusive fitness.

I have been pursuing these types of questions as a Ph.D. student in Tom Getty’s lab, using American toad tadpoles as a study organism. Many pairs of adult toads may each lay thousands of eggs in a particular pond. While lacking any particularly complex social structure, the tadpoles (like some other species) form groups that are more likely to contain siblings than non-siblings. Because they cannot leave their birth pond until metamorphosis, any strategy to minimize direct competition with siblings cannot be based on avoiding siblings.  In this case, perhaps restraint is involved, with kin deferring to one another based on who benefits the most from a given resource in a particular set of circumstances.

A variety of population responses have been seen when tadpoles interact at high densities, but one common trend is for larger tadpoles to inhibit the growth of smaller conspecifics when competing for limited resources, probably through a chemical signal in the water. As there is evidence that chemical cues are used to recognize kin in some species, this may also be a way to communicate growth information to siblings. Although this could simply be a way for larger tadpoles to suppress the growth of their competitors, in some cases smaller tadpoles have been observed to perform better when grouped with kin versus non-kin. Rather than uniformly suppressing growth, larger individuals aggregating with kin may produce a signal that smaller siblings respond to by sacrificing resources to larger kin, who see a greater increase in marginal fitness benefits with additional resources, until the former have attained an adequate size. At this point smaller individuals, who now receive a greater fitness benefit from additional food, respond by using more food and increasing their growth rate. In this way, inclusive fitness and individual fitness are maximized for all siblings. For this to occur, the kinship and size structure of groups of tadpoles in nature must be predictable or detectable by some mechanism. On the other hand, unrelated tadpoles have no indirect fitness component to worry about and should always compete as intensely as possible, in order to maximize direct fitness.

My first step in addressing this question has been to investigate whether the conditions perceived by individual tadpoles affect their growth and development. To do this, I exposed tadpoles in individual enclosures to water from tanks containing either siblings or non-siblings receiving one of two food levels, then monitored several measures of growth and development until metamorphosis. By examining whether patterns differ across treatments and what form these differences take, I can gain further insight into what strategies may prove beneficial under various circumstances and how these strategies may have evolved.

For more information about Sara’s work, you can contact her at garnett3 at msu dot edu.

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BEACON Researchers at Work: Evolution of Cooperation in Artificial Systems

Posted on March 5, 2012 by Danielle Whittaker

This week’s BEACON Researchers at Work blog post is by MSU graduate student Daniel Couvertier.

Photo of Daniel CouvertierWe have all seen the wonders of evolution in the biological world. We have marveled at the great variety in the creatures that share the planet with us, and we have admired how they have adapted to overcome even the most extreme environments. We have also been surprised by the cooperative capabilities that many creatures, from lions to ants to bacteria, have proven themselves capable of performing. Of course, as humans we are no strangers to cooperation. We know that cooperative behaviors can allow a group of individuals to flourish and achieve things that would not be possible otherwise. We have, and continue to experience the benefits of this cooperation every day of our lives. However, every time I bear witness to cooperative acts among members of other species, I can’t help but be fascinated by them. I recognize that human cooperation requires elaborate communication, and issues of “trust” come into play. Is cooperation in the wild defined by the same (or similar) rules? Are creatures as simple as ants truly capable of understanding them? If not, how could such apparently structured and complex behaviors actually evolve without the individuals actively planning them out?

Wondering about these questions and researching their answers was an entertaining hobby, but being a computer scientist, I could only ever take a passive role in them. After all, what could a code-cruncher like me ever contribute to this field of natural sciences? I was involved in computer technology, which is probably the farthest thing from biology. I worked with sensor systems, networks, and robots, all of which seemed to have a large disconnect from the natural world. However, it soon became apparent to me that we were reaching the limits on human design potential. Problems were becoming too big and too complicated for us to come up with solutions on our own. Naturally, we allowed computers to start doing a lot of the work for us, but even that is bounded by the creativity of its human designers. Finally, we took a very important step—we applied evolution to the search of solutions for useful applications in technology. This effort, called evolutionary computation, has had many achievements. We have improved existing systems and developed new ones with little to no human intervention in the decision process. Also, we have been able to use digital life platforms to further our understanding of biology. This field bridged the gap between computer science and biology, and it is where I decided I wanted to be. In particular, I study the evolution of cooperation in groups of artificial agents in virtual worlds.

In my research I get to apply the principles we believe gave rise to cooperation in biology to artificial systems. However, since these systems are not natural, I am not necessarily constrained to all the restrictions that exist in the natural world. For example, in the real world, organisms cannot communicate across extremely large distances (such as miles), while in artificial systems, with the use of radio or data transmissions, this is not a limitation. My goal is to explore evolutionary applications in this new artificial world, where the rules and limitations of the environment are different, thus allowing evolution to take new, never-before-seen paths in its innovations.

I explore varying levels of heterogeneity in groups of digital organisms by considering them as being spread across a spectrum that ranges from purely homogeneous groups, to unbiased heterogeneity.

In particular, my work started off with my study of Biased Group Selection. In a group of real organisms, say lions, reproducing has a very high cost in terms of time and energy. As such, members of a pack may opt to allow misbehavers and cheaters to coexist with them simply because replacing these individuals with more well-behaving ones would not be cost-effective. However, in an artificial digital world, replacing an organism has no cost at all. I wanted to explore how a world in which the composition of a group is determined by different sets of rules would work. I studied this by establishing several group structures to evolve cooperative predation behaviors. In some group structures, all members were clones of each other (homogeneous groups) and in others, individuals varied amongst themselves at different levels (heterogeneous groups). We explored these variations by considering them to be part of a general spectrum that ranges from a homogeneous extreme to an entirely unbiased heterogeneous one. What we found was that evolving a group of clones results in solutions that are very refined, yielding a high performance. However, it turns out that it is hard for these groups to actually find a solution at all because all individuals are following the exact same evolutionary path. Heterogeneous groups, on the other hand, have more variety and can find solutions quicker. However, this variety does not allow the groups to get as good at solving their problems as their homogeneous counterparts because some individuals waste their time doing other things instead.

I am currently developing a new evolutionary system where organisms have the ability to alter their own genetic code, while still trying to achieve goals on a group level.

For my more recent work, I’m hoping to explore a different aspect of evolution in groups, in particular, self-evolution. While in the real world organisms cannot alter the genetic code that defines them (with the exception of some bacteria), this can be easily set up in a digital world. If I give my digital organisms the ability to alter themselves, how quickly could they adapt to a drastically changing environment? Will they be willing to share their genetic material with other group members? Can this type of self-altering behavior be sustained in the long run? These are questions that I wish to address in my new work for which I am currently designing and developing my own original evolutionary system. Currently, I am exploring the evolution of cooperative foraging where a group of individuals have to forage for food quickly enough to be able to reproduce, or risk getting wiped out by a competing group instead.

For more information about Daniel’s work, you can contact him at couverti at msu dot edu.

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BEACON Researchers at Work: What Makes an Attenuated Virus?

Posted on February 27, 2012 by Danielle Whittaker

This week’s BEACON Researchers at Work blog post is by MSU graduate student Evin Hildebrandt.

Photo of Evin HildebrandtWhile people are often all too familiar with those nasty virulent viruses that cause disease, attenuated viruses do not seem to be as well known as their nasty brethren. You may be wondering “So just what actually is an attenuated virus anyways?” In short, an attenuated virus is a virus which is no longer virulent and is unable to cause disease. Virulent viruses can become attenuated via serial passage by repeated passage through tissue culture to yield a virus which generally replicates very well in vitro, but has become attenuated, or “weakened,” in vivo and no longer causes disease. While the process of attenuation occurs in a variety of viruses, my project involves exploring what is the genetic basis for attenuation in Marek’s disease virus.

Marek’s disease virus (MDV) is an oncogenic herpesvirus that causes Marek’s disease (MD) in chickens, which costs over 1 billion dollars in losses a year, so controlling this disease is critical. Fortunately, there are multiple vaccines that have been introduced to prevent tumors and control MD over the years. Unfortunately, the reason that new vaccines have been required is that virulent field strains of MDV are evolving to greater virulence. The most effective vaccine available today is an attenuated virus that was created by serially passing a virulent strain repeatedly in vitro. While the process of in vitro attenuation has a well-known history in generating vaccines, the genetic basis behind what causes this change from virulence to avirulence remains unclear. Understanding what genes play a role in attenuation may allow for the design of more efficient vaccines, instead of relying on chance during serial passage to generate new vaccine candidates.

To identify what genes play a role in attenuation, three attenuated replicates were created by serially passing a virulent MDV BAC for 100 passages. MDV strains are often described as quasi-species, meaning that viral strains are not just one particular genotype, but are actually a mixture of genotypes that compose the viral population. Conversely, an MDV BAC clone contains only a single viral genotype in the entire viral population. Using an MDV BAC clone allowed us to determine if attenuation changes a strain’s phenotype through selection or mutation. If selection was the driving factor behind attenuation then avirulent genotypes already present in the quasi-species that replicate faster in tissue culture would dominate the viral population compared to de novo mutation generating new, avirulent genotypes. We expected that an MDV BAC clone would be unable to attenuate if selection primarily drove attenuation but de novo mutation would allow attenuation of even a 100% virulent BAC clone.

Workflow of experimental approachInitially, I was serially passing the three replicates every 5 days but progressively the time between passages decreased, eventually to passing the replicates every other day! While this dramatic change suggested that the viruses had become well adapted to in vitro growth and likely attenuated, I could not classify the serially passed replicates as attenuated without testing to determine virulence in vivo. Results of bird trials testing serially passed replicates showed that the MDV BAC clones did attenuate between passages 60-80, depending on the replicate. Since all replicates experienced a loss in virulence, this showed that de novo mutations are responsible for generating new, avirulent viruses and to attenuate the virus.

Since my goal is to identify the genetic basis of attenuation, I next needed to track down what mutations occurred in attenuated viruses compared to the virulent parental virus. Since the MDV genome contains only approximately only 100 genes and that the process of attenuation is such a reliable outcome following serial passage, we predicted there may be candidate genes responsible for attenuation shared in common among the attenuated replicates. Following Illumina sequencing of the attenuated MDV strains, we found 41-95 SNPs (depending on the replicate) in attenuated replicates compared to the virulent parental strain. While no identical, high frequency SNPs were shared among attenuated replicates at a nucleotide level, a much more promising picture emerged when considering the mutations at a gene level. Comparing nonsynonymous mutations that occurred in the same gene between the attenuated replicates revealed a very interesting candidate gene that contained multiple nonsynonymous mutations, many of which occurred at high frequencies, in all attenuated replicates. This gene, known as ICP4, contained between 3-8 nonsynonymous mutations (depending on the replicate) at various frequencies in ICP4. Some mutations occurred at frequencies as high as 40%, 60%, 80% in the viral population, and one SNP which was even completely fixed 100% in a particular replicate!

Looking at only this sequencing data from the attenuated replicates, ICP4 appears to be a very attractive candidate gene involved in attenuation, but considering the biological role of ICP4 helps to strengthen the case for the importance of ICP4 even more. Herpesvirus genes are classified as immediate early, early or late genes depending on when they are expressed. As an immediate early gene, ICP4 negatively regulates itself and other immediate early genes while activating early and late genes. One thought as to why ICP4 may be important in attenuation of MDV is perhaps mutations within ICP4 alter regulation of downstream genes, causing a widespread cascade effect in which mutations within ICP4 have a much wider impact than solely ICP4 itself.

Currently I am working on the next exciting step of finally making recombinant viruses in order to test how much of an affect candidate SNPs, especially ones within ICP4, have on virulence. Recombinant viruses will contain the attenuated version of a candidate SNP into an otherwise virulent MDV BAC background. These recombinant viruses will be tested for in vitro replication and disease incidence. This will allow us to identify what candidate mutations and genes affect MDV virulence, and possibly provide a starting point for developing and engineering new, beneficial vaccine candidates.

For more information about Evin’s work, you can contact her at hildeb35 at msu dot edu.

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