Uncovering the function of host-associated microbial communities

Posted on October 25, 2017 by hageyt

This post is by MSU grad student Connie Rojas

Microbes colonize every surface of their hosts. Once established, they do not live in isolated patches, but instead form highly regulated, structurally and functionally organized communities, termed ‘microbiota’. Due to the interplay of the host’s immune system with its microbiota, many members are commensals or mutualists, performing functions critical for host health and physiology. In the human mouth, resident microbiota secrete antimicrobials and enzymes that contribute to oral health. In the mammalian gastrointestinal tract, microbiota synthesize vitamins, and supply the host with energy released from the fermentation of indigestible carbohydrates. In the human vagina, members of the microbiota produce lactic acid, which maintains a low pH environment thought to protect against infection. However, despite the explosion in microbiome research, we know very little about the additional functions microbes are performing within their hosts. We also do not know whether or how they have affected the behavior and evolution of their hosts.

The host generally maintains a stable microbiota. Stability ensures that beneficial symbionts and their associated functions persist over time. Host regulatory mechanisms like physical barriers, mucosal antibodies, and immune systems work to promote the growth of certain microbes, exclude others, and keep the microbiota in check. Furthermore, because some microbes are functionally redundant and can substitute for one another, community function can be retained despite shifts in composition. In fact, alterations to the function of these naturally occurring communities have been implicated in diseases like inflammatory bowel syndrome, type 2 diabetes, bacterial vaginosis, and colorectal cancer. Nevertheless, it is unknown the extent to which fluctuations in host and microbial environments, and resultant variation in the microbiota, can be afforded before these changes become detrimental. Years of research show that microbiota are often host species- and niche-specific, and across hosts, the microbiota varies with a myriad of factors like diet, age, antibiotic use, habitat, season, and environmental stressors. However, it is very likely that numerous other factors are driving variation in microbiota composition and function among hosts, and determining how this variation affects host phenotype is a key line of inquiry.

I study the gut microbiome of spotted hyenas! Photo Credit: Lily Johnson-Ulrich

My research seeks to understand the stability, composition, and function of the microbiota at various body-sites and elucidate the socio-ecological traits of hosts influencing its structure. While most microbiome research is conducted in humans and mice, typically within the context of host health and disease; I study these questions in wild spotted-hyenas (Crocuta crocuta). Due to their complex social behavior, hyenas are an excellent model system to explore how microbiota both influence host behavior and respond to host ecology.

Spotted-hyenas are large, social carnivores inhabiting much of Sub-Saharan Africa. They live in large groups, called ‘clans’, which are structured by linear dominance hierarchies, where an individual’s position determines its priority of access to resources. Their societies are also characterized by female dominance, male-biased dispersal, and a high degree of fission-fusion dynamics, such that individuals move freely among subgroups several times per day. Hyenas are reared in communal dens for the first 9mo of life, are weaned at 12-18mo old, and reach reproductive maturity at 24mo, although most females do not bear young until they are at least 36mo. In my current research, I am investigating how host factors like social dominance rank, group membership, and patterns of association affect hyena microbiota structure and function. Do individuals of varying social ranks differ in the stability and functional potential of their microbial communities? Are certain microbial genetic pathways lacking in one group vs. another? How similar are the communities, in terms of composition and function, of hyenas that associate very closely? Once again, can this variation have implications for host phenotype?

About to collect body-swabs and other biological samples from a hyena, after darting

We use next-generation sequencing technologies, mainly 16Sr RNA sequencing to profile the taxonomic composition of the microbiota, and metagenomic sequencing to characterize its function. From shotgun metagenomic data, it is also possible to infer microbial community dynamics. Populations of microbes, like members of any ecological community, cooperate and compete with each other, break-down and synthesize metabolites, and adapt rapidly to ever-changing environmental conditions. A recently developed mathematical framework by Sung and colleagues (2017) reconstructs community metabolic networks from metagenomic and available metabolic data. In these networks, the nodes represent major taxa, and the edges, which are color-coded, represent interactions (gray: cooperative; red: competitive; see Figure below). Metabolites that are imported and degraded by a species are shown in purple, and those that are synthesized and exported are in blue. I hope to use this framework to identify, for example, the molecules that are important for hyena gut community function, and evaluate whether the microbial community is dominated by competitive or cooperative interactions. Changes in community function and dynamics in response to extreme fluctuations in prey abundance (e.g. arrival of migratory wildebeest) will also be assessed this way.

The human gut microbiota metabolic community-level network constructed by Sung and colleagues (2017). Also, Connie’s dream figure.

Despite the interesting questions being asked, and the multitude of research on diverse host-microbiome systems being conducted, we still have a long way to go as a field. The things we do not know are too many to list. But I hope that revival of innovative culture-based techniques, advances in single-cell genomics, and development of more encompassing bioinformatics tools can help address the many existing gaps in our knowledge.

Reference

Sung et al. (2017). Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis. Nature Communications 8: 1-12.

 

 

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Judi Brown Clarke receives Sequoyah Fellowship medal

Posted on October 11, 2017 by hageyt

We are proud to announce that BEACON’s Director of Diversity, Judi Brown Clarke recently received a Sequoyah Fellowship medal making her a lifetime member of the American Indian Science & Engineering Society (AISES). The Fellowship is named in honor of Sequoyah, the great Cherokee Indian who perfected the Cherokee alphabet and syllabary in 1821, resulting in the Cherokee Nation becoming literate in less than one year. In this spirit, AISES Sequoyah Fellows are recognized for their commitment to the mission of “excellence in STEM” and to the entire American Indian community. They bring honor to AISES by engaging in leadership, mentorship, and other acts of service that support the students and professionals in the AISES family.

Judi Brown Clarke receiving a Sequoyah Fellow Medal at the 2017 AISES National Confernce in Denver, CO.

In addition, BEACON co-sponsored an Alaska Native (Haida) pre-college student who presented her summer research project about “Divergent Evolution of Shipworms and Clams,” and an undergraduate summer intern who presented her research “Curriculum Development Coupling Traditional Ecological Knowledge with STEM.”

Left to Right: intern Sarah Peele, Sonia Ibarra, Joseph Hilliare, Nevaeh Peele, Wendy F. Smythe, and Lauren Smythe.

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Beneficial bacteria in Oz

Posted on October 7, 2017 by hageyt

This post is by MSU grad student Colleen Friel

Pea fields (with yellow-flowered canola growing in the background) near Esperance, WA.

Increasing agricultural sustainability is an important research focus in the face of climate change, rapid population increase, and growing food insecurity. Synthetic nitrogen fertilizers have fueled a huge boom in agricultural productivity in recent decades, but they come with serious environmental consequences. Fertilizer manufacturing requires large fossil fuel inputs, and fertilizer runoff poses environmental and public health threats such as eutrophication of waterways and marine ecosystems, destruction of coral reefs, and algal blooms. For example, runoff from farms along the Mississippi River has led to a dead zone in the Gulf of Mexico that is 8,776 square miles, or roughly the size of the state of New Jersey.

One alternative source of nitrogen comes from the interactions between a subset of plants called legumes and specialized soil bacteria known as rhizobia. This interaction begins when plants growing in low nitrogen environments release a chemical signal from their roots. If this signal is detected by a compatible rhizobium, the rhizobium releases its own signaling molecules that initiate morphological changes in the plant root. Root hairs curl to encompass the rhizobium, and the plant houses the rhizobium in special organs called nodules. Inside the nodules, rhizobia convert atmospheric nitrogen (N2) to ammonia (NH3), which plants are able to use. In exchange, the plant supplies its rhizobia with sugars from carbon fixed during photosynthesis.

There is a wide range of outcomes in this interaction. Due to incompatibilities in signaling and other molecular events required for successful colonization, not all rhizobia can form nodules on all legumes. In addition, some rhizobia-legume combinations can form nodules but fail to fix nitrogen after nodulation. Evolutionary theory predicts that there is strong pressure on the rhizobia to cheat in a “tragedy of the commons” situation: since a single plant usually is colonized by a number of different rhizobial strains in the wild, each strain faces pressure to dedicate resources to its own reproduction rather than to nitrogen fixation for the plant. This trend is predicted to lead to a total breakdown of the mutualism, where all rhizobia fix little to no nitrogen for their plant hosts. However, this is not the case, suggesting that plants are able to control their rhizobial partners in some way and prevent this “cheating.” This might arise in the form of plants being able reward more effective rhizobia, punish less effective rhizobia, or select for more effective rhizobia during colonization.

The ability to select for more effective rhizobial strains is very important for the application of biological nitrogen fixation in agriculture. When rhizobia are used in agriculture, seeds are usually inoculated with a single rhizobial strain that has been shown to fix large amounts of nitrogen in combination with a given crop plant. However, this inoculant strain is frequently outcompeted by native rhizobia that are able to form nodules on the crop plant but fix little to no nitrogen for their host. Some legumes have demonstrated the ability to pick out the strains of rhizobia that effectively fix nitrogen for them, while excluding ineffective strains. However, not all legumes are very good at this, and we do not know what mechanism plants use for this purpose.

Making friends with the locals.

I spent the summer of 2016 at the Centre for Rhizobium Studies (CRS) at Murdoch University in Perth, Western Australia (WA) to study how plants select for effective rhizobia. Clovers are commonly used as forage crops in WA agriculture, since they are able to tolerate the challenges facing growers in WA, including low rainfall and acidic and sandy soils. The Mediterranean clover Trifolium purpureum and the South African clover Trifolium polymorphum are two such species. Both species have an effective native rhizobial partner that nodulates and effectively fixes nitrogen. If you inoculate one plant with the other’s effective rhizobia, the rhizobia will form nodules but will not fix nitrogen. If the plants are inoculated with a mixture of the two strains, the plant will pick out its effective strain and only form nodules with that strain, even if it is outnumbered 100:1.

To explore how the plants are doing this, we made bacterial mutants in which the gene for one of the proteins necessary for nitrogen fixation was deleted. We then inoculated these mutants onto the plants to see whether they were able to detect the ability to fix nitrogen, or if they used another marker to determine if a strain was an effective partner. We are also testing how the rhizobia strains react to the signals sent out by the plant and how well they are able to grow on the root systems of the different plant species. This will tell us if the the nodulation patterns we see are being determined by competition between the rhizobia rather than selection by the plant.. Understanding how plants select effective rhizobia can help make commercial rhizobial inoculants more efficient.

Planting Lebeckia in a field of nonwetting soil.

While I was in Australia, I traveled throughout much of WA, going 500+ km north of Perth to West Binnu, WA and going 700+ km southeast to Esperance, WA. During these expeditions, I assisted with field work for ongoing projects at the CRS. These projects ranged from assessing the negative effects of various pesticide treatments on rhizobial colonization in pea crops to planting field trials of the newly domesticated crop Lebeckia, which can grow in very sandy and unique nonwetting soils that plague parts of WA. It was an amazing experience to be able to interact with growers across such a large part of the country and learn how different agriculture is in Australia compared to the US. The landscape, flora, and fauna were shockingly different, and it was shocking to be able to drive for hours without seeing much evidence of humans. It was fascinating to learn how agriculture has adapted to the heat, low rainfall, and challenging soils present in WA. I look forward to using the knowledge, techniques, and relationships I developed in Australia to inform my work and increase our understanding of legume-rhizobia interactions.

 

 

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Frame your science to make it accessible, including for your representative

Posted on September 29, 2017 by hageyt

This post is by UT Austin postdoc Tessa Solomon-Lane. Tessa is working with Hans Hofmann (UT Austin), Travis Hagey (MSU), and Alexa Warwick (MSU) on public engagement at BEACON.

BEACON Congress resources (2017)

As a scientist communicating with the public, what if you want to go beyond sharing your science with an interested audience and advocate for Science? What if the audience doesn’t listen or believe you?

Tessa Solomon-Lane speaking at our BEACON Congress sandbox

At the 2017 Congress, we were excited to lead two public engagement sandboxes on topics specifically requested by BEACONites grappling with making their communication goals a reality: framing and public policy. Most scientists already engage with public audiences about STEM topics, from causal conversations to lab tours, blog posts, Twitter, and public talks. These interactions are fun, energizing, and rewarding. They can also be challenging. While many scientists engage because they want to share their science with interested audiences, situations arise when a scientist may want to change someone’s mind. Maybe there’s a vocal creationist in the audience. Scientists themselves may also seek out ‘controversial’ topics (e.g., vaccinations), audiences they disagree with, or complicated issues that do not have a one valid solution (e.g., climate change).

How does a scientist communicate effectively to these different publics? Our first sandbox focused on framing, a way of presenting information that appeals to and resonates with the audience, while ethically maintaining the integrity and accuracy of the science. This is one of the most important parts of effective communication, to the public or other scientists. The second sandbox focused on bridging the gap between STEM and public policy. There is a rapidly growing interest among STEM professionals to engage with public policy and policy makers. Our original data also show that BEACONites are interested in policy engagement; however, rates of engagement are relatively low.

How important is it that scientists engage with policy makers?

Here are some of the highlights from the sandboxes:

Build a Frame: Matching the scientific context to the audience

Frames are “interpretive storylines that set a specific train of thought in motion, communicating why an issue might be a problem, who or what might be responsible for it, and what should be done about it” (Nisbet, 2010).

To effectively frame a message, it is critical to identify your specific goals. What do you want your message to accomplish? Who is your audience, and what do they care about? Keep in mind that facts alone are not convincing! Researchers have debunked the Deficit Model, which imagines that if experts communicate information ‘correctly,’ then the public will automatically accept that information and take on those expert perspectives. It can be easy to forget that this approach does not work because it’s exciting to share data. Decisions about what content to communicate and how to frame it also brings up interesting ethical considerations. In building a storyline, think about what gets left out, what to simplify, and whether the resulting message remains accurate.

Delivery also matters. Humans are highly social animals, and relationships are important. Speak with respect. Be enthusiastic (if appropriate for the topic). Listen early and often. Meet people where they are and be able to go off script and have a conversation. Resist the temptation to view ‘quality of life’ frames as ‘dumbing down.’ Be humble about the skills we develop as scientists and take for granted. We recognize that science generates questions, but the public often wants answers. (Are eggs good for you, or not?!) Separating information from misinformation, or good science from bad science, is not a trivial task. Finally, not everyone wants to engage. Or your effort may not be worth it. Respectfully taking ‘no’ for answer can build trust and credibility, so not engaging can be a beneficial decision.

Bridging the gap between STEM and public policy 

Framing scientific messages for elected officials was the most requested topic at our UT Austin Public Engagement Workshop. There are many strategies for engaging with public policy and policy makers. Dr. Judi Brown Clarke, BEACON Diversity Director and former Lansing City Council president, running in the general election for Lansing mayor, provided insight on these questions, engagement strategies, and more.

Dr. Judi Brown Clarke speaking at our policy sandbox

To get started, know who represents you, from local to the federal government. These elected officials—or in reality, their staff—are who you will be engaging with. Know your audience and build a relationship with the staffers. Politicians hear from all kinds of lobby groups, and they should hear from scientists, too! You could advocate for the institution of science, basic research funding, and/or share the importance of your work. It is also critical to be solution-oriented. Scientists may make decisions based on data, but political decision-making is driven by money and special interest groups. The budget is a zero sum game. Why should money go towards your cause, not someone else’s? Representatives also don’t have the background or the time to be an expert in everything, so it’s important to be specific. For example, rather than expressing disapproval about draft legislation, hoping someone will learn from your teachable moment, provide specific changes to the text and explain your reasoning.

Beyond phone calls and emails, there are excellent opportunities to engage locally and build community relationships. Know your representatives’ positions on issues relevant to STEM fields, and support local candidates. You can offer to serve as a science ‘translator’ for local staffers who can make science accessible and correct misconceptions. You can also invite your representatives for a lab tour. It may surprise you who accepts the invitation! Finally, there are fellowships that place scientists in Congressional offices.

Of the 435 members in the House of Representatives, there is 1 chemist, 1 microbiologist, 1 physicist, and 7 engineers. However, more and more STEM professionals are getting involved in politics. Some are even running for office themselves! If you’re interested, check out 314Action, an organization started by chemist and breast cancer researcher Shaughnessy Naughton, to help scientists run for office.

Learn more from our framing and policy resources here. Resources include calls to action and approaches to engagement; how to’s and recommendations; science communication online toolkits, training, and resources; and STEM & public policy training and resources. We will also be running a day long workshop similar to our sandboxes at UT Austin in the spring of 2018.

Special thanks to our invited speakers Dr. Judi Brown Clarke, Dr. Rob Pennock, and Kim Ward and Jessi Adler, from the Michigan State Communications & Brand Strategy, who contributed to these sandboxes.

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Smells like Mean Sprit

Posted on September 24, 2017 by hageyt

This post is written by BEACON’s own managing director Danielle Whittaker about her work that has been accepted pending minor revisions in a special issue of Journal of Comparative Physiology A. 

Dueling Juncos ~ Junco picture from Cortes Island Canada. Photo courtesy of Island Light Photography

Fighting is risky – at best, it uses up energy and time, and at worst, it results in injury and death. But the potential rewards can be major, like food, territory, maybe even a chance to mate with another female. How does an animal decide when to take that risk, and when to skip it? The answer may be found in their opponent’s smell.

Fighting ability and aggressive behavior are often linked to testosterone. In most animal species, males usually have higher levels of testosterone than females, though there is variation in both sexes. Testosterone alone doesn’t explain variation in behavior and other linked traits, however. Hormones like testosterone function as signaling molecules that tell receiving tissues to turn certain functions on or off, like building muscle or changing levels of stress hormones. Androgen receptors in the tissues receive that message, and the strength of the tissue’s response to the message depends on how many receptors it has. For example, Dr. Kim Rosvall and colleagues at Indiana University found that the density of androgen receptors in the brains of dark-eyed juncos, a common songbird, was related to aggressive behavior in response to an intruder.

Is there any way that birds can get information about their potential rivals’ hormones and hormone receptors, in order to predict their behavior and decide whether or not to attack? A likely mechanism is odor. For nearly a decade, I’ve been studying how dark-eyed juncos and other birds use odor from preen oil, secreted from the uropygial gland and spread on the feathers during preening, to assess and choose mates (see past blog posts here and here). I teamed up with Kim Rosvall to study the links between odor, aggression, testosterone, and uropygial gland androgen receptors of these same birds.

Danielle Whittaker picking up chicks. (Note: these are not juncos.)

At Mountain Lake Biological Station in Virginia, we located breeding juncos on their territories. Each subject was either a female incubating eggs, or a male mated to a female who was incubating. Incubation is a time when the birds are likely to aggressively defend their territories, to ensure they are able to care for the nestlings when they hatch. We presented each bird with a junco in a cage (we call this a “simulated territorial intrusion”). The bird typically responds with aggressive behavior, like swooping over or dive-bombing the cage (“flyovers”) or, if it’s a male, singing at the intruder. Spending time close to the cage is also considered aggressive. We measured all of these behaviors and then captured the bird to take samples. We measured the testosterone levels in their blood, the volatile compounds in their preen oil, and the levels of gene expression of androgen receptors in their uropygial glands.

The odor of a bird predicted how aggressively that bird would behave towards an intruder. These odors are complex, with 15 or more individual components, like a perfume. Different components correlated with different aggressive behaviors, such that different aspects of an individual’s odor related to how many songs they sang towards the intruder (in males), how much time they spent near the intruder’s cage (in females), and how many times they swooped over the cage (in both sexes). This level of detail suggests that an astute rival could detect not only how aggressive their opponent may be, but also what type of response they would be likely to face.

Gas chromatography-mass spectrometry chromatogram of junco preen oil, showing volatile compound peaks. By Helena Soini, modified from Whittaker et al 2013

Next we looked at whether this relationship was due to testosterone and androgen receptors affecting that odor. We found that in males only, both circulating testosterone and uropygial gland androgen receptors interacted to predict that male’s odor. This relationship was not found in females, which suggests that maybe a different hormone is responsible for communicating a female’s likelihood of attack.

This study shows us that individual odor in birds contains a wealth of information for potential rivals as well as potential mates. The links between hormones, behavior, and smell suggests that this signal is “honest” and can’t be bluffed. For many years, people believed that birds had little to no sense of smell (and some still do), but more and more studies are debunking this idea. Similarly, humans are believed to have a poor sense of smell compared to other mammals… but I often wonder just how much of our judgments of each other, and the decisions we make as a result, are based on smell, without us even knowing it.

 

 

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UCI Summer Undergraduate Research Fellowship Program

Posted on September 11, 2017 by hageyt

This post is written by UC Irvine grad student Aide Macias Munoz

Adiya Moore, Aide Macias-Muñoz and Aline Rangel Olguin during a coffee break at the Ward Watt Festschrift

My advisor Adriana Briscoe is a Faculty Affiliate of BEACON, and I have been fortunate to be a member of this supportive community since starting my PhD in 2012. I appreciate that BEACON has many projects aimed at increasing diversity in science, some of which highlight the importance of mentoring at all educational levels. This summer our department of Ecology and Evolutionary Biology at the University of California, Irvine partnered with UCI Graduate Division to host North Carolina A&T students through the Summer Undergraduate Research Fellowship program. Graduate students from our department were assigned a mentee interested in working in our labs. Mentors were required to participate in a teaching seminar for an academic quarter aimed at learning techniques for effective mentoring. During this seminar, we discussed the importance of communication, differences between a mentor and advisor, and we designed a research project that complemented the students’ busy schedules. Aside from the research projects that we planned for our mentees, they were required to participate in classes such as writing courses, GRE prep classes, and presentation workshops.

Before her UCI visit, my mentee Adiya Moore and I communicated through email about her potential project in the lab. I shared with her NSF proposals that I had written for the particular project that she would assist with and two review articles relating to the project. She arrived to our lab ready to work. Upon arrival, we met to discuss the aims of the project, to plan a schedule, and to answer any questions that she might have. Her project was to investigate gene duplication, gene expression and cis-regulation of vision-related genes in Heliconius melpomene butterflies. Due to time constraints, she had to focus her analyses on a small subset of genes. During the first week, she learned how to use NCBI BLAST and MEGA to make gene trees and look for gene duplications. Next, I gave her gene expression data which she plotted and analyzed for our genes of interest. The rest of her time was spent identifying the location of these genes in a reference genome and looking for areas of open chromatin near these genes. Aside from learning bioinformatics tools, we worked in the lab to do DNA extractions and PCRs.

Adiya Moore standing by her poster at UCI summer research symposium.

In order to complete the project, I had already done some of the data processing and had output files ready for Adiya to work with. It was an interesting experience for me to examine ways in which someone else might learn best. Adiya was a quick learner, and I realized that an effective way was for me to show her how to do something and explain the rationale, then she did it with my supervision, and then she did it on her own. We met weekly to discuss progress and set goals and I checked in daily in case she had any questions. Since the summer program also required students to write a mock NSF proposal and scientific article, I shared my proposals with her to use as examples and I proofread her essays. Students also had to do a presentation at the end of the summer, so Adiya presented a talk to our lab during 3 separate lab meetings. I received good feedback from Adiya about the mentoring style that I employed over the summer. While she worked a lot on her own, I had beforehand talked with her about the project and taught her how to do what needed to be done, and I was always available if she had questions.

Our summer together ended with a lab trip to Colorado for a conference. The conference (Ward Watt Festschrift) took place at the Rocky Mountain Biological Laboratory, a site full of biodiversity and interesting research projects. Adiya, Aline –a visiting undergraduate student from UNAM, and I presented posters and discussed our research and career goals with faculty in attendance. Many professors were impressed by Adiya’s work and tried to convince her to continue in academia. Upon our return from the conference, Adiya did both a talk and a poster in a UCI symposium for summer research students. While her goal is to attend dental school, Adiya put in a huge effort to learn about our lab and to complete the project. It was an extremely rewarding experience to work in the lab with such a driven and self-motivated undergraduate.

Arches National Park- We saw this on our drive to Colorado.

Rocky Mountain Biological Laboratory

Aline Rangel Olguin, Aide Macias-Muñoz, and Adiya Moore exploring Emerald Lake during a conference break.

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Evolution, Science, and Religion

Posted on September 5, 2017 by hageyt

This post is written by BEACON’s Education Director Louise Mead

Evolution, Science, and Religion chapter in its entirety is available here.

I am an evolutionary biologist by training, and currently the Education Director at BEACON. I am also heading into my tenth year of teaching an online course titled “Teaching Evolution” for the NTEN program at Montana State University. These various roles often place me at the intersection of exciting research in evolutionary biology and the educational challenges that can be associated with teaching evolution. Perhaps because I was brought up in a Catholic tradition, I’ve always been interested in exploring ways people seek to integrate the domains of science and religion/spirituality with their experiences learning about evolution. For me, when I first learned about Darwin’s ideas about evolution in ninth-grade biology, it was as though the natural world, and even human nature, finally made sense. A course with Dr. Lynn Margulis on environmental evolution altered my entire relationship with science, allowing me to see the dynamic and tentative nature of scientific information. A new awareness of how science worked led me to pursue research, and a PhD in evolutionary biology, with Drs. Stephen Tilley and Laura Katz, studying the patterns and processes of speciation in a group of salamanders.

Experiences over the years led me to continue exploring spiritual questions and attempting to connect these questions and experiences with my understanding of the biological world. Over time, however, I realized these attempts to integrate supernatural explanations with science were unsatisfactory. Most of these ideas, when brought before a scientific framework of evidence-based reasoning, fell apart. Hence, the more I looked for connection, the more I realized the importance of keeping these realms separate. Religious/spiritual journeys are, by their very nature, personal and subjective. And while I have a personal scientific journey as well, scientific information is public, accumulates through a very specific process, is testable, and, perhaps most importantly, seeks to provide natural explanations for natural phenomena. I’d argue that any attempt to devise supernatural explanations for natural phenomena, or suggest science can validate or invalidate religious beliefs in general, diminishes both science and religion. Yet it is clear from polls about acceptance of evolution that many people need to find a way to accommodate these two ways of understanding.

Recently I was asked to write a chapter that explores the relationship between science and religion for an Evolution textbook. The result is a paper in which I explore how people’s worldviews influence both their understanding and acceptance of evolution. Hopefully, this exploration will provide an opportunity for students taking an Evolution course to engage in dialogue about the nature and process of science and how it is and/or is not compatible with religion. The chapter in its entirety is available here.

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Undergraduate Diversity at Evolution 2017

Posted on August 28, 2017 by hageyt

This post is written by Hollie Heape and MSU postdoc Alexa Warwick 

Fig. 1. UDE 2017 workshop and discussion panel

As an undergraduate research assistant through BEACON at Michigan State University, I was afforded the opportunity to study the efficacy of a travel award program to increase diversity in evolutionary science. In order to share some preliminary results of this study I spent five days at the annual Evolution Conference in Portland, Oregon, coincidentally my hometown. Here I attended both talks and poster presentations on a myriad of topics ranging from computational evolutionary biology methods all the way to queen ant aggression.

The conference began with a special undergraduate professional development workshop where undergraduate students gained insight and advice on various evolutionary biology career pathways (Fig. 1). I was fortunate enough to speak one-on-one with the presenters and gain a deeper understanding of their research. Each undergraduate student could also opt to be paired with two specialized mentors in the field the student showed an interest. Through this pairing, the students were able to create a personal connection with their mentor by spending time getting to know each other throughout the five days of the conference.

Fig. 2. Hollie presenting her poster at Evolution 2017

On the fourth evening of the conference, I presented a poster (Fig. 2) of my research in which I evaluated the efficacy of the Undergraduate Diversity at Evolution (UDE) Conference Travel Award program. This program has been running almost every year* since 2001 with the goal of increasing diversity in the evolutionary sciences (Fig. 3). This travel award solicits applicants around February each year and awards are made in late March or early April to undergraduates specifically chosen to diversify the field (see more at beacon-center.org/ude). In order to collect data from program alumni, an online survey was created and then sent to all applicants and awardees of the program since 2001. A total of 427 requests were sent out to undergrad awardees, applicants, and attendees, including emails to some current and/or past student advisors, as needed. So far we have received 150 completed responses**, which included 92 awardees (36% of the total) and 58 non-awardees (Fig. 4). As might be expected, most responses (84%) were from the most recent conference years (2010–2016). Some preliminary results are summarized below, or you can view the presented poster here.

Fig. 3. UDE 2017 travel awardees and some of their mentors

Most respondents are currently in academia, and the majority are still students. More females than males responded, although this proportion was representative of the applicant pool. Of the awardees who responded, almost half (43%) self-reported their ethnicity/race as white. This result raises a possible concern as the main focus of the travel award program is to increase the diversity within evolutionary sciences. However, this value was lower than the percentage of white non-awardees who responded (55%). Because ethnicity/race is not requested as part of the application we cannot determine what the expected response proportion would be. In addition, ethnic/racial diversity is not the only factor of diversity that is considered during the selection process, so this result does not necessarily indicate an issue.

Fig. 4. Summary of UDE alumni survey responses to date

When comparing the responses regarding receipt of awards in evolutionary science, 40% of UDE awardees had at least one other award whereas only 12% of non-awardees did. Although awardees reported more often than non-awardees that the field of evolution was very important their current position, the average ranking of importance was not significantly different. Of the respondents who attended at least one Evolution meeting, 88% made at least one new contact and 72% reported following up with at least one of these contacts within six months. Finally, 88% of awardees said they would not have been able to attend the conference without the UDE travel award. When asked what the impact of their participation was on their career success or path, the top two categories in terms of number of responses were: (1) networking with students and professionals and (2) reinforcing their career path in science and/or going to graduate school. For many it was also their first time attending/presenting at a scientific conference. Two example responses:

“The experience was transformative. I really connected with my mentor and he introduced me to lots of different scientists, helping me feel really engaged with the Evolution community. I also found presenting a poster at Evolution very empowering and I received validation early on that I am competitive enough to be a research scientist. It actually inspired me to pursue a PhD in Evolution.”

“My participation at UDE really helped understand the importance of studying Biology from an evolutionary perspective. In fact, it solidified my commitment to the field regardless of the profession I end up choosing.”

Even those who did not continue in the field still found it impactful in making decisions on their future careers, such as learning they didn’t want to continue in academia or reinforcing their goal in pursuing medicine. Approximately seven responses indicated little to no impact for a variety of reasons, and three said it was moderately impactful but they had already been accepted into a Ph.D. program. I will continue to analyze these data, along with my mentor, Dr. Alexa Warwick, in preparation for publication.

For me, my favorite part of the conference was the last night at the Oregon Zoo for the “super social.” During this event, I caught up with my fellow undergraduate friends and was even able to network while enjoying the beautiful backdrop of the zoo animals. The few days at Evolution 2017 were some of both the fast-paced, non-stop, and rewarding days of my undergraduate career. I vastly expanded my knowledge of evolutionary biology, while also gaining life long friends.

In terms of impact on my future career, I am currently heading into my third year at Michigan State with a major in Animal Science with hopes to attend Veterinary School in the near future, specializing in zoo animals. This research project was the first of my undergraduate career, and Evolution 2017 was the first professional conference at which I attended and presented. The networking opportunities and contacts I made at this conference far exceeded my expectations. Although not directly focusing on the veterinary profession, this conference allowed me the opportunity to talk to professionals who get the opportunity working to study species they love, which is something with which I can relate. My end professional goal is to work on rehabilitating species that are facing extinction in the wild, thus connecting my loves for veterinary medicine and ecology/evolution.

Funding for this project was provided by a BEACON budget request.

Notes:

*The Undergraduate Diversity at Evolution (UDE) Program will NOT be held as part of the Evolution 2018 meetings because it is a joint international meeting in Montpellier, France: http://evolutionmontpellier2018.org/. However, the program WILL continue in 2019 in Providence, RI, June 21-25. The application will be available by February 2019 at beacon-center.org/ude.

**If you were an undergraduate who applied for or received funding through the UDE program between 2001–2014, we would still welcome your feedback! Please email Dr. Alexa Warwick (awarwick@msu.edu) to receive a link for the survey (plus a $10 Amazon gift card as a thank you for your completed responses!).

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BEACON's Paul Turner honored at Yale University

Posted on August 22, 2017 by Danielle Whittaker

This post is written by MSU postdoc Zachary Blount.

Photo of Paul TurnerIn July, BEACON Faculty Affiliate Paul E. Turner was named as Yale University’s first Elihu Professor of Ecology and Evolutionary Biology. Named in honor of the school’s namesake, Elihu Yale, a philanthropist who provided critical support during its early years, the Elihu Professorships are highly prestigious and rarely granted.

It is hard to imagine anyone who could possibly deserve this honor as much as Paul. He stands as one of the leading stars of the experimental evolution community, and has been an excellent mentor to numerous among the rising generation that will carry the field forward. He has won a litany of prestigious fellowships, awards, and grants. In collaboration with his mentees and colleagues, he has made enormous contributions to science with his work using microbial and phage model systems. Some glimmering of his impact may be seen in the list of several dozen high impact papers that bear his name. Much of this work has been on fundamental evolutionary questions ranging from the origins of diversity, to pleiotropy, to epistasis, to the evolution of sex, to robustness and evolvability. He has also pursued extremely important, medically relevant research. Perhaps most importantly, he has been working to apply the insight he has gained over the years of fundamental work to the resurrection and development of phage therapy into what may well become a critical medical tool in this age of rampant antibiotic resistance. Indeed, this work has already saved at least one life. Over and above the research and mentoring, he has provided great service to the community, serving in administrative posts at Yale, as editor for a number of journals, on committees for the National Science Foundation and American Society for Microbiology, as organizer of conferences, including one of the best Gordon Research Conferences I ever attended, and even as a US delegate to global science workshops. Moreover, he has been tireless in his outreach to the community, and in his efforts to further diversity in science. As a researcher and as a citizen scientist, he is a model of what we should aspire to.

All those accomplishments might go to a lesser man’s head, but there is no worry of that with Paul, because his quality as a scientist is matched by his quality as a human being. He is remarkably humble, genuine, kind, approachable, and humane, without a single shred of pretense. This is perhaps most clear at conferences, where he is always a center of calm and good cheer, the brilliant fellow who is always smiling. It is certainly no surprise that his students and colleagues speak of him with genuine love and affection. As I recall, the first time I ever heard a story about Paul, it ended, “Paul’s the coolest.” That pretty well sums it up.

Go to http://turnerlab.yale.edu/ for more information about Paul Turner’s work!

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Africa’s next top animal intelligence model

Posted on August 15, 2017 by hageyt

This post is written by MSU grad student Lily Johnson-Ulrich

Spotted hyenas are found in just about every habitat in sub-Saharan Africa including human-disturbed areas and fully urbanized ones (i.e., cities) (Yirga Abay, Bauer, Gebrihiwot, & Deckers, 2010). While most large carnivores in Africa are decreasing in number, spotted hyenas are thriving. One reason for this inconsistency may be their high degree of behavioral flexibility; they’re dietary generalists eating everything and anything from termites to elephants (Holekamp & Dloniak, 2010). Spotted hyenas also exhibit social complexity and social cognition that are similar to the cercopithicine primates (a group that includes baboons and vervet monkeys) (Holekamp, Sakai, & Lundrigan, 2007). Living in novel or urban environments and complex sociality are factors that are thought to drive the evolution of large brains and intelligence in primates. This makes the spotted hyena an ideal model organism for confirming the relationship between these factors and cognitive abilities outside of primates.

I’m a graduate student in Dr. Kay Holekamp’s lab at MSU where Dr. Holekamp has been studying the lives of spotted hyenas for almost thirty years. This long-term data set provides a unique pool of information on hyena relationships that goes back several generations. I’m interested in looking at how social and environmental conditions may affect cognition in wild spotted hyenas in order to understand the adaptive function of intelligence in a natural system.

One of the things that we think makes humans unique is our large brains and intelligence (think human culture, innovation, science, and technology!). However, large brains are metabolically expensive and we’re still not sure just what the adaptive pay-off for extreme intelligence was in our ancestral environment. In today’s modern world, we no longer experience the same selective forces or live in the same habitat that we did when our large brains were evolving so it’s difficult to retrace the steps that led us to where we are today. I think it’s important to try and understand the adaptive function of intelligence because it can help us understand how to foster intelligent behavior such as creativity and innovation in today’s society. One way to try and understand both how our large brains evolved and how intelligence is adaptive is to take a look at its function in wild extant populations of other species that may share evolutionary pressures with ancestral humans, like spotted hyenas. In other words, we can try to understand the origins of intelligence by studying it in other species.

Figure 1. A hyena interacting with the multi-access box used to test innovative problem-solving. The box has four doors that a hyena may manipulate to retrieve bait from the interior.

For my graduate research I am testing two specific cognitive abilities that are related to intelligence, innovation (Figure 1) and inhibitory control (Figure 2), in three populations of wild spotted hyenas, one urban, one disturbed, and one protected. Innovation is the ability to solve a novel problem or solve a familiar problem in a novel way and. It has a strong relationship with brain size, behavioral flexibility, and also the ability to survive in novel environments across many animal taxa (e.g. Cognitive Buffer Hypothesis (Sol, 2009)). Cities are becoming more widespread and urbanization creates dramatic changes across a landscape, posing evolutionarily novel problems for animals to cope with. Spotted hyenas are among the few species that are actually able to thrive in urban environments and I suspect this may be related to their innovative abilities. To test this idea, I’m studying the innovative abilities of fully urbanized hyenas and comparing them to the abilities of hyenas in a fully protected national reserve and to those of an intermediate population. The intermediate population also resides inside a national reserve but the population’s boundaries overlap the border of the reserve and a growing human town where the impacts of tourism and cattle grazing are increasing.

Figure 2. A hyena successfully detours to the side of the transparent cylinder during an inhibitory control test.

Inhibitory control is the cognitive ability to resist a prepotent, but ultimately incorrect, response. In humans, strong inhibitory control in childhood is related to later life success (Meldrum, Petkovsek, Boutwell, & Young, 2017). Inhibitory control is thought to be important to other cognitive abilities like innovation, because it allows individuals to “stop and think” prior to making a decision (Hauser, 2003). In the social world of spotted hyenas, each group member is part of a linear hierarchy, or “pecking order” that determines access to food. An alpha female and her children are at the top, followed by other females, and then the males are at the bottom. Adult male hyenas fall at the bottom of this hierarchy because male hyenas will leave their natal clan when they reach sexual maturity and join a new clan in search of mating opportunities while female hyenas remain in the clan they were born in (and benefit from the support of their mother and sisters). Male hyenas, on the other hand, when they join a new clan don’t have the support of family members they had in their natal clan and they begin their new lives at the very bottom of the social hierarchy along with other immigrant males. At the bottom of the hierarchy individuals must inhibit all aggression towards higher ranking clan members or risk strong retaliation (Kruuk, 1972). Since all male hyenas are “doomed” to live their adult lives as the lowest ranking members of a clan we suspect that they will possess better inhibitory control than female hyenas. If so, it would support the idea that many advanced cognitive abilities evolved in challenging social contexts, an idea known as the Social Intelligence Hypothesis (Dunbar, 1998).

In sum, I hope to examine if individual hyenas with better inhibitory control are also more innovative and if these two cognitive abilities are related to the environment hyenas live in or if they are related to social factors such as group size, sex, and rank. Ultimately, I plan on relating variation in both innovation and inhibitory control to heritability and fitness. If variation in innovation and inhibitory control is heritable and related to annual reproductive success this would suggest that evolutionary selection is currently acting on cognitive abilities in spotted hyenas. I hope that my research can shed light on where and why intelligence is adaptive, which in turn can give us clues about where and why human intelligence might have evolved. I also hope to highlight the fact that many animals, even distantly related ones, share many of the same cognitive abilities with humans. Increasingly, it looks like the difference between human and non-human animal minds is one of degree, not kind.

Dunbar, R. I. M. (1998). The social brain hypothesis. Evolutionary Anthropology: Issues, News, and Reviews, 6(5), 178–190. http://doi.org/10.1002/(SICI)1520-6505(1998)6:5<178::AID-EVAN5>3.3.CO;2-P

Hauser, M. D. (2003). To innovate or not to innovate? That is the question. In S. M. Reader & K. N. Laland (Eds.), Animal Innovation. Oxford University Press.

Holekamp, K. E., & Dloniak, S. M. (2010). Intraspecific Variation in the Behavioral Ecology of a Tropical Carnivore, the Spotted Hyena. In Behavioral ecology of tropical animals (1st ed., Vol. Volume 42, pp. 189–229). Elsevier. http://doi.org/http://dx.doi.org/10.1016/S0065-3454(10)42006-9

Holekamp, K. E., Sakai, S., & Lundrigan, B. (2007). The spotted hyena (Crocuta crocuta) as a model system for study of the evolution of intelligence. Journal of Mammalogy, 88(3), 545–554.

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

Meldrum, R. C., Petkovsek, M. A., Boutwell, B. B., & Young, J. T. N. (2017). Reassessing the relationship between general intelligence and self-control in childhood. Intelligence, 60, 1–9. http://doi.org/10.1016/j.intell.2016.10.005

Sol, D. (2009). The cognitive-buffer hypothesis for the evolution of large brains. Cognitive Ecology Ii, 111–134.

Yirga Abay, G., Bauer, H., Gebrihiwot, K., & Deckers, J. (2010). Peri-urban spotted hyena (Crocuta crocuta) in Northern Ethiopia: diet, economic impact, and abundance. European Journal of Wildlife Research, 57(4), 759–765. http://doi.org/10.1007/s10344-010-0484-8

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