BEACON Researchers at Work: Exploring the evolution of navigation

This week’s BEACON Researchers at Work blog post is by MSU postdoc Frank Bartlett.

Frank BartlettOver the years, my research has focused primarily on understanding mechanisms of navigation behavior. My interest in navigation probably stems in part from my complete inability to navigate, often getting lost on campus or in my own back yard. Up until the last two years my investigations have addressed questions about visual navigation in hymenopteran insects -questions such as “What are the contents of visual spatial memory? “ and “How are these memories used to revisit familiar locations?” Such questions have a rich scientific history with published experiments dating back nearly a century. Much is now known about how a variety of animal taxa, ranging from roundworms to humans, learn about and move through their environments.

As much as we currently know about how navigation behavior works, very little is known about how it evolves. What constitutes the early beginnings of complex navigation strategies such as path integration and landmark guidance? What kinds of selective pressures influenced the evolution of navigation behavior? Questions of this nature have gone largely unasked. This is not surprising since the adaptive nature of directed movement often appears self-evident. In the case of attraction or repulsion in response to some environmental stimulus such as light or gravity, it is rather easy to imagine how and why such an ability evolved. But how do we go from simple oriented movement, such as phototaxis, to more sophisticated behavior such as path integration, which allows an organism to compute the direct homeward path from anywhere along the outbound route? (This ability has been demonstrated in a variety of animals ranging from insects to humans.) Organisms such as honeybees, ants, rats, pigeons, etc. display elegant behavioral solutions to deal with navigation in complex environments. However, it is very difficult to use biological systems to track the evolution of these abilities.

In order to formulate and test ideas about the evolution of navigation behavior, I have packed away my video camera and sunscreen and loaded Avida onto my laptop. The digital organisms in Avida provide an opportunity to examine the evolution of behavior over the course of hours and days rather than decades. It also provides explicit control over the environment allowing us to carefully define the behavioral task organisms must solve.

The first obstacle in my pursuit was to determine the physical and sensory capabilities of the organism. If one wishes to observe navigation, the organisms must first be able to move. To evolve any kind of interesting movement behavior the organism should have the ability to assess its environment including current position in the environment, condition or quality of the current position, the direction of movement, etc. To accommodate these requirements, we equipped Avidians with instructions that allowed forward movement and rotation as well as instructions to sense their current position in the environment. In addition we added an instruction that allowed the Avidians to sense their current directional heading.

Having settled on the organisms’ sensory and locomotor capabilities it was time to define the environment and the task. Avidians live in a grid world where they compete for space. They also compete for cycling time on a common processor, which allows them to execute their behavior. Under standard circumstances, all Avidians live and behave in a common grid. In our experiments the organisms lived and competed for space in a population grid but performed their behavior in a separate “state-grid.” The state grid was implemented to remove collisions and other complicating interactions among neighbors. We set up a rather simple foraging task defined by a single boundary. The state grid was divided into a northern resource half and a southern reproductive half. If an Avidian occupied a pink, northern grid cell and performed the sense instruction, it received a reward in the form of extra processor cycles. This extra processing power allows an Avidian to execute its behavior faster. A faster organism can move and reproduce more quickly than its neighbors and gain a competitive advantage. Collecting resources, however, was not enough to be successful at our task. Here is the rub: resource cells did not allow for reproduction. In order to successfully divide and generate offspring the Avidian had to occupy a southern, white grid cell. These cells provided no resource. So, the task required the organisms to evolve a move/sense behavioral strategy that put them into the pink zone to collect resource followed by traveling to the white zone to reproduce. This task is a simplified version of central-place-foraging seen in many biological organisms where the critter has to venture out to collect food and return home. Rather than “home” being a single point in the environment it is south of a “line in the sand”. Such a task mimics a intertidal zone where aquatic animals have to travel on shore to collect food but return to the water to avoid desiccation. Of course our digital organisms neither swim nor get wet!

We started the population with a single Avidian, placed facing north at the boundary of white and pink. This organism was equipped with a simple strategy (see Movie 1, above). In the movie the Avidian is represented with a dot for a head and a line for its body. When it flashes red it is executing a sense instruction. Our starting organism simply moved across the boarder and sensed to receive resource. It then turned around and moved to the white zone to divide. We turned this organism loose in the environment for 60,000 generations of mutation and natural selection. This took about 6 hours to complete, equating to about 1.5 million years in human generations. Movie 2 (below) shows the most successful behavior from this evolutionary run. This Avidian exhibits what folks here call “cockroach” behavior; following the walls of its environment and occasionally moving across the diagonal. Although this appears similar to the edge following behavior seen in many biological organisms the Avidian performs this strategy by simply moving without using a sense of direction.

It was instantly clear to us that these Avidians evolved a very simple strategy that exploited the geography of the state grid. To counter this chicanery, we modified the environment to provide no resource or reproductive area along the edges and diagonals of the state grid. The south is still the reproductive zone, represented by grey regions, while resource remains pink. White areas are a no-mans-land where the organism could neither collect resource nor reproduce (Movie 3, below). In addition, Avidians started their lives from random locations in the grid with a random facing. We seeded the evolutionary run with the cockroach from the last experiment and another 60,000 generations later a more interesting Avidian evolved. The dominant organism from this run evolved to use a sense of direction and had multiple distinct behaviors. Movie 3 shows the behavioral trace of this organism. Every time the Avidian flashes red, it is trying to collect resource. When it flashes green, it is sensing its current direction. How many separate movement behaviors can you categorize? (This organism evolved 4 separate behavioral modules)

In addition to the short generation time, another advantage of studying digital organisms is our ability to open up the hood and figure out exactly how they work. For example, even though our organism shown in Movie 3 appears to seek the northeastern corner of the state grid, it has no internal representation of the corner of its world. It simply executes a loop that moves it in the northeastern direction exactly 50 times. Although there is information from the environment via the directional sensor that could indicate when it reached the corner, this Avidian did not evolve to use it. Instead, both the corner seeking behavior and the resource collection behavior, which it spends the bulk of its time performing, are timed by a mechanism that monitors the continuous growth of its offspring. Each behavior is terminated when the Avidian’s offspring has grown to a particular length. So, rather than orchestrating behavior using cues from the environment, many of the Avidians evolved to make navigational decisions based on their life history.

These experiments are the beginning exploration of how complex navigation behavior might evolve. In these cases, both the organism’s sensory/motor capabilities are quite minimal and the environments of evolution are oversimplified. Currently we are developing more elaborate sensing and more intricate environments to develop hypotheses about how simple behavioral systems may evolve to solve more complicated tasks.

To learn more about Frank’s work, contact him at bartle47 at msu dot edu.

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BEACON Researchers at Work: A computer scientist, but also a biologist

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

“But wait – aren’t you getting your Ph.D. in Computer Science?” That’s a question that I have gotten used to hearing in my matriculation through graduate school. The short answer is yes, I am getting my Ph.D. in Computer Science, but I am also part of the Quantitative Biology program, and part of BEACON Center for the Study of Evolution in Action. With that said, I’m not your traditional computer scientist.

During my undergraduate career, I participated in several summer research experiences, one of which introduced me to the field of computational biology. My research project was to identify residues in proteins that are important for structural and functional purposes. The more important residues are usually conserved from one organism to the next. This conservation can be observed by mathematically modeling the protein and identical or similar proteins in other organisms. At that point in time, I had one biology class under my belt, and it wasn’t doing me any good. I started off with no idea of the biological implications of the data. That summer proved to be a pivotal point in my future research career because I developed an interest in the field of biology. As I was developing code to analyze biological data, I found it a bit tedious because I did not completely understand the problem. This lack of understanding fueled my interest in biology. I wanted to better understand the problem so that I could better process and analyze the data.

After that summer, I wanted a lab where I could work on computational science, as well as wet lab biological science. Michigan State University turned out to be a great fit. I found an adviser, Dr. C. Titus Brown, with joint appoints in Computer Science and Microbiology and Molecular Genetics. Since joining the Brown lab I have had the opportunity to learn of the growing pains of working in a wet lab, and it is a world of difference. There is no print function to determine if I set my parameters correctly, or to see if a block of my code is being executed. There are controls in biological experiments, but the margin for error is a lot smaller, and I learned this the hard way. However, once the balance shifts from “learning” to actually successfully completing an experiment, the sense of accomplishment makes everything worth it. 

Although there are long days and occasionally sleepless nights, I wouldn’t trade what I’m doing for anything. I’ve found that job that I would do for free – well, not free; I still have bills to pay. I get to go to “work” everyday and do something I enjoy. Currently I’m working on a cross-disciplinary evolution and development research project where I get to use my computational skills to analyze transcriptome data, and my wet lab skills to answer biological questions. There are two closely related species of Molgula, which are believe to be some of the closest related invertebrates to all vertebrates. The two species—M. oculata, and M. occulta—look very similar in their adult life, they sit on the bottom of the ocean and filter feed using their two siphons. Molgula fall under the phylum Tunicates. During development tunicates have a tadpole like stage that is similar to all vertebrates. The tailed tadpole phase is one of the key features that group tunicates and vertebrates into a group known as chordates. One of the species, M. occulta, has loss one of the key features that make it a chordate, and we want to find out why. In lab conditions the two species can be cross-fertilized and a hybrid forms with a tail about half the length of the M. oculata. Using the two species and the hybrid, we’re analyzing gene expression levels computationally and experimentally, in hopes of finding the gene regulatory network behind this loss of tail.

Another great opportunity that has come out of this project is the ability to travel and collaborate with other labs. I spend my winters in Michigan, which is great, seeing how much I love snow, and freezing cold weather, and I spend my summers in Washington or France. I have the privilege of working with Dr. Billie Swalla during the summer months, which has been a tremendous asset. I have learned a lot working under Dr. Swalla. The training I received in the Swalla lab was important to my development as a scientist, seeing that I come from a computer science background and wasn’t formally trained as a wet lab experimental scientist.

The way research is conducted has evolved. There is a strong push for collaboration and interdisciplinary research. I feel that I am being well prepared for this shift, and much of my preparation can be attributed to BEACON in some shape or form.  The experiences that I’ve had are not ones that an intercity kid from a public school typically gets, but because of my desire to uncover the unknown, I’m living a life I never dreamt of.

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

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BEACON Researchers at Work: Walk This Way

This week’s BEACON Researchers at Work blog post is by University of Idaho postdoc Anne Gutmann.

Anne Gutmann

In the classic Monty Python skit “Ministry of Silly Walks”,  the comedian John Cleese demonstrates a series of hilariously weird and wacky walks while maintaining the prim and proper demeanor of a British government official.  One reason Cleese’s “silly walks” seem so strange and comical is that although humans (and other animals) are capable of a wide variety of movements, they mostly use just a few typical gaits such as walking and running to move from place to place. But why do animals generally choose to use only certain common gaits and not a multitude of other uncommon, “silly” gaits?

As a scientist in the field of locomotion biomechanics my research addresses this question on two main levels: 1) the evolutionary level and 2) the muscular level. On the evolutionary level, I am interested in understanding how natural selection shapes animals’ bodies and gaits, and on the muscular level I am interested in understanding how the mechanical properties of muscles and tendons determine which gaits are possible and preferable for a given animal. For example, I might hypothesize that natural selection should favor animals that use energy-efficient gaits because animals that cannot obtain enough food to meet their energy needs risk starvation. However, to understand why certain gaits are more energy efficient than others, I must also examine how muscles and tendons function during locomotion. The most energy-efficient gaits might provide energy saving opportunities by allowing the tendons to store and return energy like springs or by allowing the muscles to function at the most efficient contraction velocities.

Desert kangaroo rat, Dipodomys deserti, in its natural habitat in Nevada

Currently, I am studying the evolution of bipedal hopping as a postdoc in Craig McGowan’s lab at the University of Idaho. My work is part of a collaborative project between the McGowan and McKinley labs (University of Idaho and Michigan State University respectively) which is funded by a BEACON seed grant. Our goal is to understand why animals as diverse as kangaroos, wallabies, kangaroo rats, and jerboas all hop. These animals span a surprisingly wide range of body sizes and habitats, but all have the same basic leg design and hop on two legs to move from place to place. One hypothesis is that hopping evolved as a means of producing the high accelerations needed to escape predators. However, differences in muscle-tendon architecture suggest that some hopping animals have evolved for energy efficiency rather than high acceleration. We will use an interdisciplinary approach that integrates biomechanics, computation, and physics-based simulation to understand how selective pressures shape the evolution of leg design and gait in these animals. Graduate students in the McKinley lab will use a physics-based simulator and evolutionary algorithms to determine which selective pressures produce bipedal hopping. I will develop a detailed musculoskeletal model of a kangaroo rat to determine the effects of muscle-tendon architecture on hopping dynamics. This process will include using micro CT scans to create a 3-D model of a kangaroo rat skeleton and doing careful dissections of kangaroo rats to determine the points at which the muscles attach to the skeleton. I will also collect mechanics data from real kangaroo rats to allow me to develop realistic simulations of hopping (kangaroo rat hopping uphill movie: http://www.youtube.com/watch?v=gORCCxPG_cU, kangaroo rat x-ray movie: http://www.youtube.com/watch?v=vfSbmR2VMeM). Once I have a detailed musculoskeletal model of a normal kangaroo rat up and running, I will adjust the leg design of this model to match the designs that emerge in the physics-based simulator. I can then use these modified models to compare the effect of different limb designs on muscle-tendon dynamics. This integrated approach will provide novel insight into why and how the musculoskeletal system of certain animals evolved for hopping.

Results from our study can be applied design biologically-inspired robots and prosthetic devices. Currently, most legged robots must move slowly and carefully to avoid falling over and have high energy requirements. Similarly, amputees often are forced to move more slowly than non-amputees because they must use more energy to walk and run. This can deter amputees from engaging in physical activity and reduce their overall quality of life.  Developing a better understanding of how kangaroos, wallabies, kangaroo rats, and jerboas hop will allow us to design agile legged robots that can navigate rough terrain quickly and efficiently and less-tiring prosthetic devices that will allow the wearer to walk and run at high speeds with ease.

For more information about Anne’s work, you can contact her at agutmann at uidaho dot edu.

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BEACON Researchers at Work: Teaching Kids about Evolution

This week’s BEACON Researchers at Work blog post is by University of Washington postdoc Heather Goldsby.

Heather GoldsbyInitially, I was planning on chatting with all of you about my actual research into studying division of labor using digital organisms. I’m fascinated by the questions and our exciting results. However, as I was sitting to write this post, I realized I really wanted to tell you about my recent outreach activities.

As scientists, we’re familiar with the sobering realities  — many kids don’t understand evolution, many kids think science is memorizing facts, many kids think computers are for geeks, many kids think scientists and, especially computer scientists, are all men. Nothing could be further from the truth (except for maybe the last one… but we should really work to change that), but how can we convince the average kid of that? Many of them have lost interest in science and computers long before freshman year when we have a chance to talk with them.

Think back, when did you become interested in science or computer science? For me, it was in high school. I went to a small high school and took a computer science class when I ran out of history classes to take, and my deplorable lack of musical talent made band or choir less than appealing. I immediately became addicted to the joys of problem solving with computers, and when the time came, enrolled in computer science as a college major. My interest in science arose much, much later when I learned science was about discovery, not just the names of rocks. I wish I would have discovered both at an earlier age.

Researcher with kids and laptopTo expose kids to the wonders of science and computers, we are partnering with teachers to bring an “evolution in action” program to elementary school and middle school kids. The program is simple. We spend the first few minutes discussing how computers are everywhere — in their (or their parents’) phones, gaming systems, household electronics — and are used for everything from school work to angry birds. The focus is on kids realizing that computers are extremely integrated into their lives and are used for more than geeky things. Next, we chat about how computers can be used to address some of the challenges that arise in studying evolution. Drawing upon the motivation for my own work, we talk about the tremendous amount of time it can take to watch evolution in the wild and how evolution in a computer works far more rapidly.  We also discuss how evolution produces animals that are more fit for their environment. We use examples the kids are familiar with (e.g., cheetahs, monkeys, etc.) to help them understand.

Abstract image

Figure 1: Ancestor image to evolve in Picbreeder

For the rest of the time, we split the kids into small groups where they work with a scientist to evolve either pictures (using http://picbreeder.org) or 3D objects (using http://endlessforms.com). I’ll describe the basic process using a picbreeder example, although endlessforms is similar. First, the group selects an ancestor picture to evolve (for example, Figure 1).  A panel of pictures appears. From this panel, the kids collectively select one or more parents for the next generation. Clicking the ‘evolve’ button produces the next generation. As part of this process, they can change the mutation rate from small to large and observe how similar or different the pictures are to their parents. The scientist working with the group uses this process to explain evolutionary concepts such as mutation, recombination, and selection. Because the kids themselves are interacting with the process by selecting the parents, the mutation rate, and letting things evolve, they gain a more intuitive feel for how evolution works. Some future twists we are adding to this process is having all the groups start with the same picture and then at the end comparing final products to see what selection under divergent environments (different groups) might look like.

Researcher with kids looking at laptopThus far, we’ve worked with first graders and third graders as part of a yearly event where students can sign up to visit different labs on campus. Some of the surprising things for us were: (1) The students are incredibly smart! During the discussion portion of the event, first graders have explained to us what predators and prey are. One student also informed us that the ancestor of a whale was a  land mammal that looked something like a hippo. (2) The kids have had tons of fun. Both years we’ve done this event our participants have groaned when they had to leave and have asked their sponsors if they could stay longer. Apparently, evolution in action won them over. (3) We, the volunteers, have enjoyed the event nearly as much as the students. There is something incredibly refreshing about sharing the wonders of science and computers with such a young audience.

In the upcoming weeks, we are expanding our outreach program to go visit the local schools working with 4th graders and 6th graders. This expansion lets us reach more kids close to the ages where they lose interest in science and computer science.

Next year, we hope to expand the program to include two additional sessions that target different aspects of the BEACON mission. Specifically, we’d like to expand our outreach to have three parts, where the first part is dedicated to traditional science, the second part is computer science used to address questions in science (the evolving pictures part I just described), and the third is using evolutionary computation to address engineering challenges, such as robots. I’m always looking for volunteers and would love to be able to share this program with other BEACON representatives who are interested in reaching kids in their own local area!

For more information, you can contact Heather at goldsby at uw dot edu.

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BEACON Researchers at Work: Understanding spatial genetic structure of martens and their prey

This week’s BEACON Researchers at Work blog post is by Michigan State University graduate student Paige Howell.

Paige HowellUnderstanding the processes that influence the spatial distribution of diversity is a long-standing goal in ecology and evolutionary biology. It has also always been an area of interest for me, both in the classroom and in my own research. A major theme of my research is identifying the processes that are most influential to the spatial genetic structure of individual species and communities of co-distributed species. In most taxa, dispersal is correlated with gene flow and consequently, it is a major contributor to population genetic differentiation. Dispersal ability and behavior are largely determined by the variety and spatial configuration of landscapes. Consequently, to understand the processes influencing how populations, species and communities are genetically structured requires consideration of the landscape features in which individuals exist and through which they disperse.

The emergence of landscape genetics as a synthesis of population genetics and landscape ecology has provided important advancements to our understanding of how dispersal and spatial genetic patterns are influenced by environmental features. To date, most research has focused on identifying physical landscape features (e.g., habitat matrix) or barriers (e.g., roads, waterfalls) that are correlated with genetic discontinuities. Identifying the environmental factors that most strongly affect gene flow and the spatial genetic patterns of different organisms has implications for basic research as well as conservation and management. For example, because of the potential influence of gene flow on the evolution of adaptation, evolutionary biologists are often concerned with understanding the processes governing gene flow. The dispersal ability of individuals between local sites may also impact the persistence of populations and so is an important study area for managers.

Unfortunately, I have found that most landscape genetic studies have ignored the potential impact of species interactions (e.g., density of heterospecifics, competition for food resources) on patterns of spatial genetic structure. Co-distributed species may respond differently or at different scales to the structure and spatial arrangement of landscapes. However, the dynamics of each species within the greater community are linked via ecological processes such as competition or predation. Ecological processes that are influential to the structure and function of biological communities are dependent on the intrinsic properties of each species as well as underlying landscape characteristics. Thus, incorporating measures of species interactions and physical landscape features at multiple spatial scales is crucial to understanding the spatial distribution of genetic variation for single species and communities of co-distributed species. A better understanding of the factors contributing to patterns of genetic diversity will enhance our ability to predict the probability of population, species, and community persistence in the face of changing landscapes.

Map showing distribution of marten and roads that impede gene flowThe community I’m working with now is a predator-prey system in the upper peninsula (UP) of Michigan composed of the American marten (Martes americana) and their small mammal prey (such as grey squirrels, voles). Previous research in my lab has developed genotypic data sets for American marten using neutral, microsatellite markers. Based on these data, three geographically distinct genetic clusters of American marten have been identified. Although individuals are continuously distributed across the landscape, the presence of genetic discontinuities suggests there are barriers to dispersal limiting the interaction between genetic groups. Based on all data from the UP, I am currently developing single species models of the associations between landscape (e.g., land cover, roads) and climatic (e.g., snow depth) features and measures of spatial genetic structure. In one such model, I tested whether a pattern of isolation by distance could explain the distribution of genetic variation in this species. Isolation by distance refers to the phenomenon that gene flow decreases with increasing geographic distance between groups and this results in higher genetic differentiation. Using a simple Mantel test to compare pair-wise geographic distances based on Euclidean distance and pairwise genetic distances based on inter-individual relatedness, I have detected a significant pattern of isolation by distance for marten over the entire study.

Because there exist a number of putative barriers to dispersal for marten in the UP, I was curious to see whether including any of these barriers in my model would improve my ability to explain genetic variation. The first barrier I have investigated is the presence of state roads and whether it contributes to the maintenance of genetic discontinuities within the population. Similar to models of isolation by distance, the spatial genetic structure of marten appears to be correlated with the presence of state roads as a factor influencing resistance to movement. However, the amount of genetic variation explained by either of these models is relatively low and incorporating other habitat features (e.g., landcover type, size of suitable habitat patches) may improve model fit.

While neutral markers like microsatellites serve as one measure of population genetic structure, I’m interested in looking at non-neutral markers as well. Certain phenotypic traits may be selected for in a population based on advantages they provide during dispersal through a complex mosaic of habitats. Phenotypic traits with high heritability may be used in addition to neutral markers as a proxy to evaluate the spatial distribution of genetic variation at non-neutral loci. Using a geometric morphometric approach, I will investigate whether spatial genetic structure in these animals is paralleled by morphological differences in skull shape.

As I mentioned earlier, I think it is critical to consider the species interactions that may be strongly contributing to the patterns of diversity of different species within a community. With marten, the diversity (e.g., beta-diversity in an ecological sense and intraspecific genetic variation) in their prey species may be one important factor. In some studies of community genetics, the genetic variation of one species has been found to predict the genetic structure of the other. The correlation of genetic variation in one species with another will depend on the strength of the ecological interactions linking each species and the shared responses of each species to environmental heterogeneity. At a more local scale where ecological processes, such as predation, are operating between marten and their prey, what factors are driving the observed patterns in spatial genetic structure? Is it the composition and configuration of habitat features, the spatial genetic structure of their prey, or a combination?

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

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BEACON exhibit and workshop draws teachers interested in Evolution in Action!

The Michigan Science Teachers Association held their 59th Annual Conference, Pure Michigan Science, in Lansing March 8-10, 2012 and a number of BEACONites attended, informing regional teachers about the exciting educational programs in development across our consortium.  

Melissa Kjelvik at the BEACON table

The BEACON Exhibit highlighted games and software being developed to help teach basic and advanced evolutionary concepts in the K-16 classroom. Melissa Kjelvik, a graduate student working with Drs. Getty, Hayes, and Soule, told teachers about the Lady Bug and Aphid game developed by Terence Soule from the University of Idaho. Melissa shared lessons she is developing for the K-5 classroom. Teachers also interacted with two EvoAPPS, Variation and Selection.  A collaboration between Stephen Thomas and Adventure Club Games, these games were designed for museum kiosk interactions, and specifically target common misconceptions and work to clarify how variation and selection are requirements for evolutionary change. Amy Lark, a graduate student working with the Avida-ED team, told teachers about this digital platform, showing the advantages of working with a program that shows evolution in action, and where students can carry out their own experiments.

Wendy Johnson talks about Avida-ED

In addition to the BEACON exhibit, Wendy Johnson, a teacher at Lansing Catholic, and part of the RET program through the College of Engineering last summer, gave a workshop on her use of Avida-ED in AP Biology. The high school teachers attending her workshop showed great enthusiasm for and interest in Avida-ED. The meeting room was over capacity and the participants were very engaged, and perhaps more importantly, excited about being able to give their students the opportunity to observe and test evolution in action rather than just lecturing. We anticipate holding a longer workshop for science educators in late August here at BEACON!

 

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

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

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

"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

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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