Love is in the air (or maybe it’s just bacteria)

This post is written by BEACON managing director Danielle Whittaker

Danielle Whittaker holding a black and white warbler at Mountain Lake Biological Station, Virginia

When we fall in love with someone else, is it because they are our soul mates… or is it because we like the way their microbes smell? We think a lot about the importance of physical appearance and the content of what we say. But when it comes to attraction, we may have less control over our preferences than we think.

Just like humans, birds are thought to rely on sight and sound as their primary senses, yet smell turns out to play an important role in choosing a mate. For the last decade, I have been studying how birds use odors as indicators of a potential mate’s suitability. Dark-eyed juncos (Junco hyemalis) are songbirds found throughout North America that spend the summer breeding in habitats with cooler temperatures, especially in the mountains or far north in Canada. Like most birds, they produce preen oil from their uropygial gland, located above the base of the tail. This oil, which they rub into their feathers while preening, is a source of odor that transmits information about an individual’s species, sex, breeding condition, and hormone levels. This odor also relates to individual reproductive success: males that smell more “male-like” have more offspring, as do females that smell more “female-like,” suggesting that these compounds are also communicating information about reproductive health or ability.

The preen gland is located above the base of the tail

Recently, my collaborator Kevin Theis (former MSU postdoc, now assistant professor at Wayne State) and I have been studying the source of these odors. While at MSU, Kevin studied the bacteria in hyena scent pouches. These bacteria produce the odors that hyenas use to communicate with each other. He suggested to me that symbiotic bacteria in the preen gland could also be responsible for producing junco odors. We decided to test this hypothesis by sampling the bacteria in and around the preen gland, and determining whether any of the bacteria present were capable of producing these compounds. We found that the preen gland is home to a very rich and diverse microbial community. Even better, using the Microbial Volatile Organic Compound database, we discovered that many of these junco bacteria are known odor producers. Two genera in particular, Burkholderia and Pseudomonas, are capable of producing over half of the compounds in junco chemical signals – and these two bacteria were very common and abundant in our samples.

Scanning electron microscope image of bacteria in a junco preen oil sample

Our next step was to test whether removing these bacteria actually changed the juncos’ smell. I injected a broad-spectrum antibiotic into captive juncos’ preen glands, and sampled them before and after treatment. Compared to control birds that were injected with only saline, birds receiving antibiotics had significantly lower levels of three volatile compounds – 2-tridecanone, 2-tetradecanone, and 2-pentadecanone. These three compounds are the same ones that are correlated with reproductive success, suggesting that symbiotic bacteria could be responsible for a chemical signal that’s important in junco mate choice. We are now in the process of sequencing the bacterial swabs from the birds in this study, to examine which bacteria were killed by the antibiotics and to identify candidates responsible for producing the compounds.

Female junco incubating eggs at Mountain Lake Biological Station, Virginia

We are also now studying how these symbiotic microbes are transmitted between individuals. We have found that nestling juncos have bacterial communities very similar to their mothers, and less similar to their fathers. This pattern makes sense because it’s only mothers that sit on the nest and keep the nestlings warm as they are growing, and microbes are shared through physical contact. We also found that the adult male and female pairs were more similar to each other than they were to other adults of the same sex – again, physical contact is the likely explanation. Our next steps are to examine more closely the effects of social behavior on individual microbial communities, and whether an individual’s odor reflects their social patterns.

So the next time you find someone attractive, stop for a moment and wonder why. Is it the way their blue eyes sparkle when they say something witty? Or could it be the scent of bacteria… maybe even bacteria they got from somebody else?

For more information:

Whittaker, D. J., N. M. Gerlach, S. P. Slowinski, K. P. Corcoran, A. D. Winters, H. A. Soini, M. V. Novotny, E. D. Ketterson, and K. R. Theis. 2016. Social environment has a primary influence on the microbial and odor profiles of a chemically signaling songbird. Frontiers in Ecology and Evolution 4:90.

Whittaker, D. J. and K. R. Theis. 2016. Bacterial communities associated with junco preen glands: ramifications for chemical signaling. In Chemical Signals in Vertebrates 13, eds. Bruce A. Schulte, Thomas E. Goodwin, and Michael H. Ferkin. New York: Springer International Publishing, pp. 105-117.

Whittaker, D. J., S. P. Slowinski, K. A. Rosvall, N. M. Gerlach, H. A. Soini, M. V. Novotny, E. D. Ketterson, and K. R. Theis. 2016. It’s what’s on the inside that counts… or is it? Microbial vs. physiological mediation of sexually selected chemical signals in a songbird. Oral presentation at Evolution 2016.

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Better Together: Of Hyenas and Men

This post is written by MSU grad student Zachary M. Laubach

“A guy needs somebody―to be near him. A guy goes nuts if he ain’t got nobody. Don’t make no difference who the guy is, long’s he’s with you. I tell ya, I tell ya a guy gets too lonely an’ he gets sick.”

– John Steinbeck, Of Mice and Men

Myself and Philomon, the head chef and camp manager of the Serena Hyena Camp. During my time in Kenya, I came to see Philomon as a source of social support and dear friend.

The notion that our social environment is important to our health and well-being is not new. There are profound and heartbreaking historical illustrations of how social interactions (or lack thereof) shape behavior and physiology. For example, adults who once resided in Romanian Orphanages, notorious for their depraved lodging conditions and neglect, exhibit severe psychoses and debilitating mental disease 1,2. Likewise, famous primate studies from the 50’s and 60’s demonstrated the importance of maternal touch and interactions with peers to healthy psychosocial development 3,4. However, despite the flurry of convincing correlative results linking the early social environment to future stress-related disease, the underlying molecular mechanisms remained poorly understood until the mid 2000s when Drs. Michael Meaney and Mose Szyf showed that DNA methylation (a stable epigenetic mechanism that alters gene expression without changing the nucleotide sequence) is both responsive to social stimuli and has a direct effect on stress phenotype. These scientists found that offspring born to mothers who did not engage in licking and grooming behaviors had higher methylation of the glucocorticoid receptor gene, which resulted in an inability to respond to elevated stress hormones. The elegant part of this study was that cross-fostering (e.g., switching the rat pups at birth between high licking and grooming and low licking and grooming moms) revealed that the effects of DNA methylation were not due to genetics, but rather, a direct effect of maternal care during the first few postnatal weeks 5.

My PhD research extends current knowledge of the relationships among the social environment, DNA methylation, and biological condition using data from Dr. Kay Holekamp’s population of wild spotted hyenas in the Masai Mara of East Africa, Kenya. You might ask, ‘Why spotted hyenas?’

A snapshot of Bart, a dedicated mom still nursing her nearly full-grown cubs. This photo highlights the extent to which hyena moms care for their young, even when they are rapidly catching up in size!

Several aspects of spotted hyena biology make them a powerful and relevant study population for my research interests. First, hyena cubs depend on their mothers for nourishment and protection through 2 years of age, presenting a window of opportunity to quantify a variety of novel measures of mother-offspring interactions. I am collaborating with Julia Greenberg, another PhD student in Dr. Kay Holekamp’s lab, to quantify patterns of maternal care using archived behavioral data. We are interested in the proximity of mothers to their young, time spent nursing, and frequency of grooming. Second, in addition to living in clans, hyenas hang out in cliques within each clan. Our detailed observational data regarding the number of individuals in a clique, the nature of interactions within group-members, and the amount of time spent together can be used to quantify unique aspects of a hyena’s social support system (see a previous post by Julie Turner). This notion that social support is critically important to well-being has been found in both non-human primate and human studies where both mothers and their babies are in better condition when social support is stronger 6–8. Finally, hyena societies follow a strict and well-defined rank system, which is of particular interest to me because it is analogous to socioeconomic status in humans; rank determines access to resources, friends, and mates. Thus, findings regarding the relationship between rank and stress phenotype in hyenas may be relevant to studies of socioeconomic position and health in humans.

A pile of hyena cubs keeping each other company, dozing off after a long bout of play.

Spotted hyenas are wild, gregarious, and perhaps not all that different from other social species (like non-human primates and even humans). Another reason why I am interested in this species is because most epigenetic research to date has taken place in highly controlled rodent and primate populations, limiting generalizability of findings to gregarious animals. Dr. Holekamp’s study population, therefore, represents a unique opportunity to explore how naturally occurring social behaviors correlate with epigenetic mechanisms and stress outcomes in a wild species exhibiting complex sociality. One huge hurdle that I’ve encountered thus far revolves around the task of carrying out epigenetics research in a species whose genome is not yet publically available (NB: the genome of the spotted hyena was sequenced and annotated years ago, but the Beijing Genome Institute has not yet released it). Fortunately, with the help of experts at the University of Michigan and at the University of Minnesota, I was able to sequence the region of interest (the glucocorticoid receptor promoter) using a technique known as multi-species alignment. In brief, I identified a sequence of hyena DNA that is comparable to the established target region in humans and rats. Next, I mapped the sequence to genomes of species in the same order as hyenas (Carnivora) – namely, the cat, dog, and walrus. Then, with a touch of bioinformatics, I sequenced the region in hyena DNA so that we could measure a comparable set of epigenetic marks to those identified in the rodent and primate literature. In addition to gene-specific epigenetic marks, I am also measuring genome-wide methylation content, which can be thought of as a proxy for an individual’s genomic stability and overall condition. Taken together, I hope that the measures of gene-specific and genome-wide epigenetics will shed light on how early social experiences shape adult phenotypes.

Preliminary results and what’s in store. Based on our initial work, which showed strong effects of a hyena mom’s rank on her offspring’s genome-wide DNA methylation, I suspect that inter-individual relationships and social status interact in ways that profoundly affect phenotype. The ways in which social experiences affect biology is relevant not only to health of individual organisms, but also has potential to impact how natural selection shapes phenotypes over time. The latter is of particular interest to me, as it implies that social experiences play a role in evolution. It is my hope that what we learn from animal models like hyenas, primates, and rodents will compel us to step back, and consider that humans are also merely animals whose behaviors, physiology, and health are shaped by social experiences. However, unlike other animals, we are uniquely endowed with the capacity to recognize the impact of our social experiences on our biology and how they may transcend generations. Knowing this should motivate social support, and the impetus to move beyond I-llness to WE-llness 9, especially in a world championed by individualism.

  1. Chugani HT, Behen ME, Muzik O, Juhász C, Nagy F, Chugani DC. Local brain functional activity following early deprivation: a study of postinstitutionalized Romanian orphans. Neuroimage. 2001;14(6):1290-1301. doi:10.1006/nimg.2001.0917.
  2. Kaler S, Freeman BJ. Analysis of environmental deprivation: cognitive and social development in Romanian orphans. J Child Psychol Psychiatry. 1994;35(4):769-781. doi:10.1111/j.1469-7610.1994.tb01220.x.
  3. Harlow HF, Harlow M. Learning to love. Am Sci. 1966;54(3):244-272. http://www.pitzer.edu/academics/faculty/banerjee/psyc109/readings/w1-Learn.PDF. Accessed August 21, 2014.
  4. Harlow HF, Zimmermann RR. The Development of Affectional Responses in Infant Monkeys. Proc Am Philos Soc. 1958;102(5):501-509.
  5. Weaver ICG, Cervoni N, Champagne FA, et al. Epigenetic programming by maternal behavior. Nat Neurosci. 2004;7(8):847-854. doi:10.1038/nn1276.
  6. Campos B, Schetter CD, Abdou CM, Hobel CJ, Glynn LM, Sandman CA. Familialism, social support, and stress: positive implications for pregnant Latinas. Cultur Divers Ethnic Minor Psychol. 2008;14(2):155-162. doi:10.1037/1099-9809.14.2.155.
  7. Silk JB, Beehner JC, Bergman TJ, et al. The benefits of social capital: close social bonds among female baboons enhance offspring survival. Proc R Soc B Biol Sci. 2009;276(June):3099-3104. doi:10.1098/rspb.2009.0681.
  8. Silk JB, Beehner JC, Bergman TJ, et al. Strong and consistent social bonds enhance the longevity of female baboons. Curr Biol. 2010;20(15):1359-1361. doi:10.1016/j.cub.2010.05.067.
  9. From an anonomysous quote.
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Kombucha: More Than Meets the Eye

This post is written by UT Austin undergrad researchers Katelyn Corley, Matthew Hooper, and Zachary Martinez

“What starts here changes the world.” This is the motto that we as students at the University of Texas at Austin have come to embrace and strive towards in our everyday lives. In 2016, we began conducting research at UT Austin. For most of us, this was the first time we conducted research. We also took part in iGEM (international genetically engineered machine), and attended the annual conference in Boston. Our research experiences broadly spanned topics including microbiology, molecular biology, and synthetic biology, but our main work in 2016 focused on studying the microbiome of kombucha, with an ultimate goal of creating a designer beverage by altering the kombucha microbial community.

Example of kombucha “brewed” in a test tube. The large mass at the top is a layer of cellulose, while the mass at the bottom and the stringy “material” throughout the tube are clumps of bacterial and yeast cells.

Example of kombucha “brewed” in a test tube. The large mass at the top is a layer of cellulose, while the mass at the bottom and the stringy “material” throughout the tube are clumps of bacterial and yeast cells.

Kombucha is a popular fermented tea beverage that is home to a variety of microbes, both bacteria and yeast. Many die-hard consumers of kombucha love its acidic qualities and its characteristic vinegar taste, while these same attributes are what often turn others away from the drink. More importantly, kombucha is commonly referred to by its producers as being healthy or “rejuvenating” due to the presence of probiotics that are said to aid in digestion. As undergraduate scientists, we are skeptical of these claims, particularly because no current scientific evidence supports them. To us, kombucha soon became a vast frontier full of gray areas and large unknowns. Is it healthy, and if so, what makes it healthy? If not, could we make it healthy? These questions are what continually drove us forward as both researchers and as members of a community who desire to put something good into the world.

So then what did we learn? Over the course of roughly 6 months, the three of us along with our team, studied the “mysteries of kombucha”. We first identified some of the microbes that are naturally found in the drink. Species of bacteria such as Gluconobacter oxydans and Gluconacetobacter hansenii became commonplace names in our lab as we characterized these organisms and attempted to genetically engineer them for future study. Another major contributor to kombucha that we identified was the yeast, Lachancea fermentati. Interestingly, we found two unique strains of this species in our samples of kombucha with different phenotypes, and both appear to be required for proper kombucha brewing. One grew more quickly, while the other produced higher amounts of CO2. This finding immediately intrigued us. Not only do an array of species of bacteria and yeast coexist in kombucha, but differences in members of the same species appeared to have evolved in the process! Differentiation in the species was a possibility that we had not considered at first. The community of organisms that exists within kombucha appears to have evolved in a way that was much more complex than we had initially imagined. Kombucha was not simply a tea drink that was commercially sold and consumed, but was an exciting example of the world of microbial communities, which possess aspects of evolution and symbiosis that are still not fully understood.

Members of the Austin UTexas 2016 iGEM Team (from left to right): Prachi Shah, Matthew Hooper, Zachary Martinez, Katelyn Corley, Stratton Georgoulis, Alex Alario, Ian Overman

Members of the Austin UTexas 2016 iGEM Team (from left to right): Prachi Shah, Matthew Hooper, Zachary Martinez, Katelyn Corley, Stratton Georgoulis, Alex Alario, Ian Overman

We had the privilege of presenting our research at the 2016 iGEM “Giant Jamboree” in Boston. This research competition is one of the most incredible opportunities offered to both undergraduate and post-graduate students in the field of synthetic biology. We spoke with other students who work in our field and shared many of our successes and difficulties along the way. Additionally, we had the chance to present our research on kombucha to scientists, who gave us feedback and additional suggestions for expanding our project in the future. Our future plans include studying how the microbial community changes during a single brewing cycle as well as how the community might collectively evolve over multiple brewing cycles.

The major take-away from this experience was that, there is still work to be done, but that it is important work. Many of us first saw this project as being fun and approachable, and though we still view our lab work in this way, we have now begun to see how the scope of this project extends into greater, more compelling fields of science. Kombucha offers immense outlets for exploring the limitations of synthetic biology, as well as in exploring the types of evolutionary changes that must occur to enable specialization and the coexistence of microbes. Additionally, if we were to create a “designer” kombucha beverage, we need to consider the potential evolutionary shifts that might occur as we alter the microbial community found within kombucha. The great part about science is that you never know where it will lead you. This project took us from a grocery store shelf holding a bottle of kombucha, to an international conference in Boston, to a situation where we are now beginning to see how our work could shed light on an area of science that is not fully understood. On behalf of the entire Austin UTexas iGEM team, we encourage others to never stop digging deeper into science.

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Social networks in spotted hyenas

This post is written by MSU grad student Julie Turner 

I’ve always loved animals. This love isn’t exactly unusual in young children, but my fascination and curiosity about animals has not wavered. Among my earliest memories as a toddler was catching turtles in my backyard because they were slow enough for me to grab. As I got older, I started reading everything I could about animals, starting with lions (like many kids who grew up in the ‘90s, I was enthralled with The Lion King—except in my case, the movie became a recurring theme in my life). While learning more about lions, I realized that I thought their family groups were fascinating! I moved on to reading everything I could about other animals that lived in family groups, which grew into an interest in animals that live in larger groups with complex relationships like bottlenose dolphins and orcas.

When deciding what to do after college, I knew I wanted to study animals with complex social interactions and came across a program that studied spotted hyenas in Kenya. Prior to learning about this program, the most I thought about hyenas was watching The Lion King. I figured that the portrayal of hyenas couldn’t be right—as wonderful as the movie is, it is not renowned for its biological accuracy. I started reading obsessively about a new species and found that hyenas are so cool! They live in groups called clans that consist of multiple families reaching up to 130 members. Like humans they live in fission-fusion societies which means that, though they’re all in the same clan, the individuals they associate with change as hyenas come together or split apart to be alone or join other individuals (Kruuk, 1972). Their societies are as complex as certain baboon species and vervet monkeys, which is rare to see in non-primate species, especially carnivores (Holekamp, Smith, Strelioff, Van Horn, & Watts, 2012). As it turns out, these social traits make hyenas a great animal to study if you’re interested in how lots of individual little interactions like greetings, aggressions, and hanging out go together to form a cooperative social group, otherwise known as sociality in animals. I am studying a small part of sociality, specifically how sociality develops in growing hyena cubs and what that means for them throughout their lives.

Figure 1. PhD candidate, Julie Turner, with a darted hyena in Kenya

Sociality, especially complex sociality, is surprisingly difficult to understand and even to observe. For instance, imagine you’re at work with your officemates or in a class of 100 people. You might have a general idea of who hangs around with whom, but would you know how often everyone associated with everyone else in the group? Could you name each person’s friends? Shelly may be friends with Max, but does Max consider Shelly a friend in return? Is anyone actively avoiding someone else? In studying humans, at least researchers can conduct interviews or give people surveys. So, assuming people are answering truthfully, these challenges are difficult but manageable. Now imagine that you want to be able to address these questions in an animal that doesn’t speak any language you may know or could easily learn (though we have researchers trying to learn how hyenas communicate right now).

One method scientists use to try to tease apart and try to explain complex relationships is using social network analysis (SNA). A social network isn’t just Facebook. A social network is a group of individuals or entities (businesses, classes, etc.) that are connected by relationships or interactions (associating together, being friends, writing papers together, etc.). Individuals are represented by nodes; relationships and interactions are depicted by lines between the nodes called ties.

Figure 2. Random network graph. Blue squares are nodes that represent individuals or other entities. The lines are ties that indicate which nodes are connected by a relationship.

Social network graphs, such as the one just described, help us visualize relationships that may be difficult to see simply by observing. These graphs are especially helpful with animals when we only can use observations of behavior to understand relationships and cannot rely on interviews and surveys.

So, we observe animals over enough time to see many interactions and then build a social network to represent relationships during that time period. Hyenas have the potential to have many different types of relationships. Let’s use this interaction as an example:

Figure 3. A picture of a typical hyena interaction with their names.

Here we have five hyenas in a session together where three individuals are acting aggressively towards another, and GALA is off to the side doing her own thing.

One type of relationship that social network analysis (SNA) can address is relationships that are undirected, also known as binary, like individuals just hanging out with each other. Though all five hyenas here are not necessarily interacting directly, they are all associating together. GALA can’t associate with HEL without HEL also associating with GALA. This association network would be represented as the following graph:

Figure 4. Undirected association network of the illustrative hyena interaction.

Or relationships can be directed, for instance, when one hyena acts aggressively to another, as when HEL, CHLE, and TICA are aggressive to IKA.

Figure 5. Directed aggression network of the illustrative hyena interaction. The direction of the arrow indicates who is being aggressive to whom.

Once relationships are graphed, we analyze aspects of these social relationships statistically through SNA. We can learn things like if one clan of hyenas is bonded by stronger relationships than another, or how one individual’s social role varies from another. I’m using SNA to look at how individual hyenas learn their social role or position in the clan and how that position then affects aspects of their life like their personality or longevity. We already have evidence that cubs “inherit” their mothers’ social network (Ilany & Akcay, 2016), but what does that mean for the cubs’ development? These questions are examples of what we are currently exploring in spotted hyenas. Learning more about the social lives of hyenas helps us to see that hyenas are much more than “nothing but slobbering, mangy, stupid poachers” (I just had to bring it back around to The Lion King).

References

Holekamp, K. E., Smith, J. E., Strelioff, C. C., Van Horn, R. C., & Watts, H. E. (2012). Society, demography and genetic structure in the spotted hyena. Molecular Ecology, 21(3), 613–632.

Ilany, A., & Akcay, E. (2016). Social inheritance can explain the structure of animal social networks. Nature Communications, 7, 1–10.

Kruuk, H. (1972). The spotted hyena: a study of predation and social behavior.

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Getting Mixed Signals: Exploring the Evolution of Disjunctive Signaling Games

This post is written by Peter Fetros, an undergraduate computer science research assistant at UI working with James Foster and Bert Baumgaertner

Peter Fetros explaining a section of their research poster presented at an undergraduate research conference

Peter Fetros explaining a section of their research poster presented at an undergraduate research conference

Signals are all around us. Most organisms use signals in order to communicate with one another. They might use them to tell others where the best food is, or possibly to warn them about approaching predators. However not very much is known about the evolution of these signals. How and why some signals are used while others are not, and how organisms decided to use these signals. I’ve always been interested in the ways that things communicate, from tiny organisms who emit chemicals to ward of predators, to humans and the thousands of different ways we choose to communicate information to one another. However, as a Computer Science Student I’m even more interested in finding a way to model these interactions in a meaningful way that will give us insight into how meaningful signals can evolve. Our current research explores how signals evolve over time and what that evolution looks like. We do this by modeling the interaction of “players” in something called a Lewis Signaling-Game.

A Lewis Signaling-Game in its most simple form consists of 2 players, a Signaler and a Receiver. In this game the player, or “agent”, who is designated as the Signaler first observes some world-state. The Signaler then chooses a signal to send to the Receiver based on the world-state it observed. After the Receiver receives the signal from the Signaler, The Receiver then chooses to perform an action based on that signal. If this action is the correct action for the world-state that the Signaler originally observed, they both get a payoff.

An example of this process in nature can be compared to the calls of Vervet monkeys. These monkeys have different vocal calls (signals) for when they see different types of predators, for example leopard, eagles, or snakes. When a Vervet monkey sees a predator (an observation) it will choose the call appropriate for this predator (a signal). It will make the call and then another monkey who cannot see the predator will hear it (Receiver). The monkey who hears the call will then have to decide how to properly avoid this unseen predator (choosing an action). In this example that might be climbing a tree in order to get away from a leopard prowling on the ground, running away from the comparably slow snake, or even hiding in a bush so the eagle can’t reach it. If the Vervet monkey chooses the correct action for the type of predator, it will get a payoff (not being eaten), However if it chooses the wrong action for the type of predator it will not get a payoff (get eaten).

To model these interactions on a large scale we model the Signaling-Game in a programming language called NetLogo. In our models we have a large population of agents that all pick a partner and then play the Signaling-Game. They start out not knowing what signal is correct to use for what world state it observed, as well as what action they should perform when they receive a signal. However, when they do choose the right action based on the world state the observer sees, they get a payoff in the form of an increase in their preference for choosing that signal again (if the player was a Signaler), or choosing that action (if the player was a Receiver) for that specific observation. After each game the agents randomly pick new partners and then play again. Eventually they do this enough so that they all agree on the same meaning for signals. When this happens we call it a signaling System.

There has already been some research into the basic Lewis Signaling Game and Signaling Systems. So what we are currently exploring is how these Signaling Systems evolve when we have observations that are disjunctive. Disjunctive observations are observations that the Signaler can sometimes make in which it doesn’t know the true state of the world. It might be World “A” or World “B”.

An example of this using the Vervet Monkeys might be when a monkey sees a rustling bush and doesn’t know whether it’s a leopard or a snake. Because it doesn’t know which it really is, it must somehow let the other monkeys know that there is a ground predator nearby but it isn’t sure what kind, all it knows is it isn’t an eagle. There are several ways it might do this. It may send a new type of call that means “Leopard or Snake” or it may just guess itself, and make the call for leopard or the call for snake depending on what it decides might be in the bush.

Ternary plot detailing the population preferences for the agents playing as Receivers

Ternary plot detailing the population preferences for the agents playing as Receivers

So far in our simulation we have discovered several different paths the evolution of these Signaling Systems may take. Sometimes the Signalers use a new kind of signal and sometimes they use the old signals while just making a guess at what the world state might be. We plot the results from the simulations on ternary-plots. These plots show the population’s average preference for a particular signal or action based on either the world-state it observed or the signal it received respectively. These graphs allow us to see how a particular preference changed over time at the population level.

If you have any feedback or questions about this research, please contact

Peter Fetros (Fetr0509@vandals.uidaho.edu), James Foster (foster@uidaho.edu), Bert Baumgaertner (bbaum@uidaho.edu) or Kelly Christensen (chri4898@vandals.uidaho.edu).

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Evolution & Ecology Activities at the 2016 SACNAS National Conference: STEM Diversity & Public Understanding

This post is written by Tracy Heath, Corrie Moreau, Alexa Warwick, and Felipe Zapata

The 2016 National Conference of the Society for the Advancement of Chicanos/Hispanics and Native Americans in Science was held last week in Long Beach, CA. This conference focuses on motivating, inspiring, and providing resources to underrepresented minorities pursuing careers in science, technology, engineering, and math (STEM) fields. The evolution and ecology activities sponsored by the BEACON Center for the Study of Evolution in Action and the Society for Systematic Biologists (SSB) were immensely successful. Four different events took place during the three-day conference: (1) field trips, (2) conversations with scientists, (3) a scientific symposium, and (4) the movie night. These events were organized by Alexa Warwick from the BEACON Center in collaboration with three members of the SSB council: Tracy Heath, Corrie Moreau, and Felipe Zapata.

Field Trips!

Neftali Camacho, collections manager of herpetology at the Natural History Museum of LA County shows SACNAS attendees preserved specimens in a behind-the-scenes tour of the herpetology collections. (Photo by C.S. Moreau)

Two separate field trips were organized to expose students to important resources for conserving, preserving, and understanding biological diversity. The first trip brought 25 participants to the Natural History Museum of Los Angeles County (NHM), led by Alexa Warwick from the BEACON Center and Corrie Moreau and Shauna Price from the Field Museum of Natural History. NHM is the largest natural history museum in the western United States, housing over 35 million specimens. Several of the young scientists commented that this was their first time ever at a natural history museum! During the trip the participants had behind-the-scenes tours of the collections housed at the NHM and heard about the science conducted by resident and visiting scholars. In particular, they were shown the herpetology collections by collections manager Neftali Camacho and toured the entomology collections with assistant collections manager Emily Hartop. The organization of this field trip was made possible by support from herpetology curator, Dr. Greg Pauly. After the tours, participants also had time to browse the fantastic public exhibits at the museum. 

A tour of the Rancho Santa Ana Botanic Garden with horticulturist Ashlee Armstrong. (Photo by T. Heath)

A tour of the Rancho Santa Ana Botanic Garden with horticulturist Ashlee Armstrong. (Photo by T. Heath)

The second field trip was to the Rancho Santa Ana Botanic Garden, which is the largest botanic garden dedicated to the conservation and study of California native plants and it houses the 10th largest herbarium in the United States of America. Our tour of the RSABG would not have been possible without the generous help of Dr. Lucinda McDade, Executive Director & Director of Research at the gardens. On this trip, Tracy Heath (Iowa State University) and Felipe Zapata (UCLA), brought 24 Sacnistas (SACNAS meeting attendees) to RSABG. The trip started with a welcome message by Dr. McDade and a quick overview of the visit for the rest of the day. Next, Dr. Naomi Fraga, Director of Conservation Programs, gave an exciting talk on the research and conservation activities going on at RSABG and shared her experience on becoming a researcher in a natural history collection. During her talk, Dr. Fraga also highlighted the multiple internship and volunteer opportunities available for students interested in plant ecology, evolution, systematics and conservation. The field trip continued with a tour of the Seeds Conservation Program, the Nursery Program (for restoration programs and the living collection), and the Grow Native Nursery. Several staff members, including technicians, volunteers and interns led these tours through different laboratories and greenhouses. Before lunch, horticulturist Ashlee Armstrong walked us through the garden grounds where she explained the different sections of the garden and talked about the different types of plants we were encountering. After lunch Mare Nazaire, Herbarium Collections Manager, took students to the herbarium where she explained the critical role of herbarium collection on biological research, and showed us some amazing specimens in mint condition such as one plant collected during Captain Cook’s trip in the 1700s. Loraine Washburn, Lab Manager and Conservation Scientist, showed us the molecular and anatomical lab facilities and described the exciting research that students and research staff are conducting in plant evolution, systematics and conservation. Irene Holiman, Library Specialist, led a tour of the library and archives where important and unique books are stored and available for researchers and the general public. Thanks to Dr. McDade and the staff at RSABG for an inspiring visit to one of the best Botanical Gardens in the country!

Conversations with Ecologists and Evolutionary Biologists

University of New Mexico undergraduate Ally Weidner learns about summer research opportunities at the University of Kansas from Dr. Rob Moyle. (Photo by T. Heath)

University of New Mexico undergraduate Ally Weidner learns about summer research opportunities at the University of Kansas from Dr. Rob Moyle. (Photo by T. Heath)

A signature event at SACNAS is the “Conversations with Scientists” program during which students have the opportunity to meet mentors in their area of interest in a small group setting. We had a great turnout for the event this year with a variety of fields within Ecology/Evolution represented.

 

Scientific Symposium: (Day and) Night at the Museum: Exploring Research in Ecology and Evolution behind the Scenes of Natural History Museums

The speakers and organizers: Tracy Heath, Seema Sheth, Andreas Chavez, Felipe Zapata, Corrie Moreau, Scott Edwards, Lauren Esposito, and Alexa Warwick. (Photo by C. Welch)

The speakers and organizers: Tracy Heath, Seema Sheth, Andreas Chavez, Felipe Zapata, Corrie Moreau, Scott Edwards, Lauren Esposito, and Alexa Warwick. (Photo by C. Welch)

In an earlier post, we described the motivation and the goals of this symposium. The symposium was very successful and we had over 50 attendees. Dr. Corrie Moreau (one of the co-organizers of the symposium) started the session with a brief description of the critical importance of natural history collections in ecology and evolution research followed by a talk on her personal path to becoming a museum researcher. Dr. Moreau described briefly two research projects going on in her lab, one on ant genomes and how in combination with museum collections these data have shed light on genome evolution, and one on ant micro biomes (microorganisms living inside ants) and how these data provide novel ways to study functional diversity. Building on his personal admixed background as a Chicano-Japanese American, Dr. Andreas Chavez shared his passion for studying the role of admixture in evolution and how hybrid zones in squirrels are excellent opportunities to study population divergence, natural selection and gene flow. In his talk, Dr. Chavez highlighted how animal skins housed in museum collections have been fundamental on his research program. Dr. Seema Sheth described how specimens available as herbarium collections are fundamental to answers questions she had developed since very early on her career. Dr. Sheth described how information on occurrence data can be used to study geographic ranges and ecological niches in rare versus widespread species, and how rates of niche evolution might relate to rates of phenotypic evolution. Dr. Lauren Esposito arrived straight from doing field work in the Bahamas to the symposium to share her story on becoming a researcher in a museum and integrating research with conservation programs. The last talk by Dr. Scott Edwards described the myriad ways that museum collections have permitted him and his students to explore the evolution of birds from biogeography to population genetics to the spread of zoonotic diseases.  

Corrie Moreau shares her personal journey as a scientist and research. (Photo by A. Warwick)

Students gathered around all of the speakers after the symposium! (Photo by F. Zapata)

Students gathered around all of the speakers after the symposium! (Photo by F. Zapata)

At the end of the symposium many attendees stayed and asked all the speakers multiple questions about their research and careers paths. It was an exciting symposium highlighting how important research collections are in advancing our knowledge of the diversity of life.

 

Movie Night!

The final Ecology/Evolution sponsored event at SACNAS was movie night. We showed five short films and one documentary to highlight research in Ecology/Evolution and the environmental and societal issues that such research can address. The 20+ attendees represented a wide range of fields from engineering to marine biology. Alexa Warwick organized and emceed the films and Noelle Beckman from SESYNC helped transition between the films. First we showed an HHMI film titled Got Lactase? The Co-evolution of Genes and Culture where scientists used genetics, anthropology, and chemistry to trace the evolution of lactase persistence in adult populations. Next was our featured documentary by Angela Sun, Plastic Paradise: The Great Pacific Garbage Patch. This film brings attention to the huge shift in our use of single-use plastics and the impact they are having on the environment and human health. The third film, Life of Every Color and Kind, was created by the Florida State University grad/undergrad group, ECOmotion Studios.This animated film was inspired by the classic 1966 paper by Dr. Robert Paine describing a rocky intertidal ecosystem in Washington State. The fourth film, Rules for the Black Birdwatcher, was actually a last minute addition to movie night after Ari Daniel mentioned it during the SACNAS plenary lunch on Friday. This short film features Dr. J. Drew Lanham, a writer, birder, hunter, and naturalist at Clemson University who considers “conserving birds and their habitat a moral mission that needs the broadest and most diverse audience possible to be successful.” Next we showed Conservation Bridge’s Biomimicry film, which provides clear examples of how humans have used nature’s best ideas to solve our own problems. The film also describes a novel conservation framework in which companies give back to nature by providing funding to the species/habitat that inspired their ideas. We concluded movie night with Pygids, a film featuring PhD student Tyler Corey from University of Nebraska-Lincoln and his arachnid study group, the amblypygi. This film was the 2016 winner of the annual Evolution Film Festival, and it was once again a big hit at SACNAS with its very catchy song! Overall, attendees thought the films were excellent and many reported that 80-100% of the content in each of the films was new to them. We highly recommend checking out these six films if you weren’t able to join us at movie night!

Looking to SACNAS 2017!

Next year, the SACNAS National Conference will be held in Salt Lake City, Utah October 19-21, 2017. The BEACON Center will continue to spearhead the organization of ecology/evolution activities with funding from SSB. If you have ideas for a symposium or field trip or questions about SACNAS activities, please contact Alexa Warwick, the BEACON Center’s Education and Outreach Postdoctoral Fellow. The SACNAS conference is inclusive and open to anyone who supports increasing diversity in science. We hope to see you in Salt Lake City!

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2017 Darwin Day Roadshow – Apply Now!

Starting in 2016, BEACON began collaborating with three scientific societies (ASN, SSE, SSB) to continue support for a variety of outreach opportunities that needed a new home after NESCent ended. Today we’re highlighting one of these opportunities – the Darwin Day Roadshow!

The roadshow is a way for scientists and educators to share their excitement about the science of evolution. Each year around the time of Charles Darwin’s birthday (February 12), teams of scientists talk to students, teachers, and the general public about their research in evolutionary science, their career path, and why evolutionary science is relevant to everyone. The roadshow has visited over 24 states so far since 2011!

We are currently planning for the 2017 Roadshow and are looking for local hosts, typically teachers! These hosts – known as ‘Darwin Day Scholars’ – work with the roadshow staff and scientists to design a set of activities that best serve their school and community. If you are a teacher or know of a teacher who may be interested, we invite you to read more about the roadshow on our website. The deadline for host applications for the 2017 Darwin Day Roadshow is Friday, December 2, 2016. HOSTS APPLY HERE!

A scientist visiting a classroom during a previous roadshow

If you are a scientist interested in participating in the roadshow, we would love to have you involved! Please fill out the ‘Roadshow Scientist’ application form HERE. The deadline for scientist applications for 2017 is Wednesday, December 21, 2016.

Any questions about the program can be directed to Alexa Warwick.

 

 

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Scientific Symposium at the SACNAS National Conference

The Society for Systematic Biologists and the BEACON Center for the Study of Evolution in Action have collaborated to organize a scientific symposium at the Society for the Advancement of Chicanos/Hispanics and Native Americans in Science national conference in Long Beach, California on October 14, 2016.

(Day and) Night at the Museum: Exploring Research in Ecology and Evolution behind the Scenes of Natural History Museums

Natural history museums house the world’s past and present biological diversity. Beyond the specimens and materials displayed to the public, these critical collections inform numerous research questions that seek to understand processes of evolution and ecology. This symposium offers a behind-the-scenes glimpse into the lives and research of museum-based scientists.

Speakers:

  • Corrie Moreau, PhD — How I Became a Rainforest Explorer: Ant Genomes to Microbiomes
  • Andreas Chavez, PhD — My personal experiences with admixture and what admixture can tell us about speciation and adaptation
  • Seema Sheth, PhD — Harnessing the power of herbarium specimen data for ecological and evolutionary studies
  • Lauren Esposito, PhD — Can arachnids save the planet? A journey through natural history and conservation
  • Scott Edwards, PhD — Using museum collections to study the genomics and evolution of birds

SACNAS is a national organization focused on increasing the proportions of underrepresented minorities in science, technology, engineering, and math (STEM) fields. In 2015, the National Conference was attended by 3,746 scientists from diverse backgrounds, with almost 60% of the participants members of ethnic/racial groups that are significantly underrepresented in STEM fields. This year promises to surpass 4,000 attendees!

For many people, a visit to a natural history museum may represent their first exposure to the marvels of science. What they may not realize is just how much scientific research is being conducted behind the walls and awe-inspiring displays. The goal of this symposium is to reveal the exciting biological research conducted within different major natural history museums across the US. By attending this session, participants will learn about the use of natural history collections in ecology and evolution research such as plant ecology, population genetics in mammals, avian comparative genomics, arachnid biogeography, and the interactions between ants and their gut microbiomes. Additionally, the speakers will discuss their paths as scientists and museum researchers, giving a behind-the-display glimpse from public natural history museums like the California Academy of Sciences and the Field Museum in Chicago, as well as university-affiliated museums/herbaria at UC Berkeley, Harvard, and Ohio State University.

For anyone attending the SACNAS conference, please join us on for the symposium on Friday, October 14, 10:15-11:45 in room 201B!

In addition to the scientific symposium, BEACON and SSB are also contributing the following activities to the 2016 conference:

 

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Meiotic Recombination: Crossing-over into Livestock Species

This post is by Kimberly Davenport, first year graduate student in Animal Science with Dr. Brenda Murdoch at the University of Idaho and Brenda Murdoch, assistant professor of animal genetics at the University of Idaho.

Kim Davenport

With each research project comes its own challenges, rewards, and quirks. My research project in Dr. Brenda Murdoch’s laboratory involves characterizing homologous recombination in different mammalian species. Homologous recombination is an extremely important process in gametogenesis that not only contributes to genetic variation but also ensures proper chromosome segregation during cell division in meiosis I. Errors due to failure or improper placement of recombination represent a significant contribution to aneuploidy, developmental disabilities, fetal loss and infertility [1]. Despite the importance, we know very little about the factors that control and/or influence global meiotic recombination in mammals.

Work in model organisms; yeast, fruit flies, and mice, have outlined the steps in the recombination pathway [2]. For example, we have gained insights on the sequential relationship of chromosome pairing, sister chromatid cohesion, synapsis and recombination. Meiotic recombination is initiated by a topoisomerase like protein (SPO11) that establishes breaks in the chromosomes. Chromosome breaks are resected with the aid of strand invasion proteins RAD51 and DMC1 and ultimately produce double Holliday junction intermediates. These are resolved as either crossovers or non-crossovers. The majority of non-crossovers are generated early in the pathway and only a subset of the breaks are resolved as crossovers. Crossover repair protein MLH1 localizes the majority of crossovers [3]. Interestingly, only a few of the breaks are resolved as crossovers and the rules that govern the frequency and sites remain unclear.

Over many years of research, scientists have identified a few general guidelines associated with meiotic recombination. First, one recombination event, or crossover, is required per chromosome arm pair for proper cell division. Second, we know from previous studies that the placements of recombination events are not random. Crossovers exhibit preferences in the genome called “hotspots” and experience “interference” in that one crossover cannot occur too close in proximity to another [4]. Third, crossover numbers have been shown to be sexually dimorphic (different between males and females) in many different species. And lastly, the number of crossovers is correlated with the size of the genome and number of chromosome arms (i.e. the more chromosome arms, the more crossovers are likely to occur).

Although recombination occurs in many different species, our lab focuses primarily on livestock species, specifically sheep and cattle. These two domestic species are not only important for agricultural food production, but also provides an interesting biological comparison and insight into how recombination has evolved in ruminants. While sheep and cattle have the same number of chromosome arms and a similar genome length, they do not have the same number of genome-wide recombination events. This poses a number of important questions about how genomic meiotic recombination levels are controlled in different domesticated species.

In the Murdoch lab we identify and characterize crossover events using our optimized immunohistochemistry method. This cytogenetic approach allows us to directly observe where chromosomes recombine through the microscope. We identify crossovers with an immunofluorescent antibody which specifically binds to MLH1, a protein that is known to be involved in repairing DNA breaks into crossovers.

Figure 1: Meiotic cross-overs in sheep and cattle. A) Representative images of MLH1 foci on synatonemal complex from a Gelbvieh bull (46 MLH1 foci), and B) Targhee ram (71 MLH1 foci) spermatocyte.

So, how do we get samples to collect the data we need? Much like a surgeon is on call for patients who need assistance, I serve as the “on call” graduate student for samples! Since we study primary spermatocytes, we require testicular samples from males who have reached puberty or older. However, finding males that have not been castrated provides a real challenge. Male sheep and cattle are usually castrated early in life to provide a safer working environment for both the animals and the people who care for them. Some males are kept intact (not castrated) for breeding purposes, but these are the few “best” animals. So, any time an intact male is at the end of his breeding career and is harvested for food, I retrieve a testicular sample. But there is one more problem: these samples cannot be frozen, and we need to extract the cells and fix them on microscope slides within 24 hours. Otherwise, the integrity of protein we use to identify crossovers degrades.

Prepping these samples is a race against time. If we receive the samples from a local source, I pick them up as soon as I get a phone call. If they are shipped overnight from elsewhere, I wait impatiently for the samples to arrive the next day. In a way, I am considered “on call” for receiving and prepping our samples. And since these samples only last for about 24 hours on ice, I prep them almost immediately upon arrival. It is exciting in our lab to receive a new sample because the data we collect from one ram or bull may be very different from another!

The reward for timely but precise preps of our samples is that we are able to learn more about the process of meiotic recombination, and impact the way the scientific community understands how genes are passed from generation to generation. Since meiotic recombination contributes to genetic variation, understanding differences as well as the mechanism behind the process gives us deeper insight into how genetic diversity is evolving.

References:

  1. Hassold, T., and Hunt, P. (2001). To err (meiotically) is human: the genesis of human aneuploidy. Nature reviews. Genetics 2, 280-291.
  2. Murdoch, B., Owen, N., Stevense, M., Smith, H., Nagaoka, S., Hassold, T., McKay, M., Xu, H., Fu, J., Revenkova, E., et al. (2013). Altered cohesin gene dosage affects Mammalian meiotic chromosome structure and behavior. PLoS genetics 9, e1003241.
  3. Baudat F and de Massy B (2013). Meiotic recombination in mammals: localization and regulation. Nature Reviews Genetics 14, 794-806.
  4. Jones, G.H., and Franklin, F.C. (2006). Meiotic crossing-over: obligation and interference. Cell 126, 246-248.
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