BEACON Researchers at Work: Listening to the hyenas

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

Have you ever seen a group of hyenas take down a zebra? Or fight off a pride of lions? Ok, probably not, so you’ll have to take my word for it: one of these activities is striking in its silence, while the other is a deafening cacophony. Why does the pride of lions require more vocalizations than an observer can keep track of, while the zebra requires none? To whom are these vocalizations directed? Are the hyenas vocalizing to ward off fear, coordinate their movements, scare off the lions, or all of the above? These are just a few of the questions we are trying to answer in the Holekamp Lab.

In collaboration with the Miikkulainen Lab at the University of Texas in Austin, we are trying to determine how emotions and communication interact, leading to complex cooperative behaviors, such as hyenas pushing lions off of a kill. I, myself, am attempting to tease apart the answers to our questions about the communication that takes place during these striking interactions. Right now, that mostly means being out in the field with a microphone pointed at hyenas and trying to catch good vocalizations during the right kinds of interactions. Once my field season is over, it will mean pouring over 27 years of behavioral observations to pull out and quantify our behaviors of interest. (If you’re curious about how difficult that is, take a look at this video or the video below!)

Then, we will be able to determine what influences hyenas to cooperate in these dangerous interactions. Who recruits allies and why? Who stays quiet in the hopes of sneaking a snack from a lazy lion? Do loud whoops, giggles, and lows always precede a concerted rush (i.e. a mob) at the lions? Who participates in and leads mobs? Is there a difference between altercations over food and those that take place near hyena dens?

Work done by Tracy Montgomery will determine the hormonal correlates of these complex behaviors. From this, we hope to learn something about hormones, affiliative behavior, and communication, the roles they play, and how they interact with one another.

The Miikkulainen Lab is tackling this question from a computational perspective. They are creating a computational model that will mirror the behaviors we see in hyenas in the field. Through manipulation of the environment and which cooperation challenges the digital hyenas face, they aim to understand what allows the production of these complex behaviors in a digital world.

Eventually, we hope to have a better understanding of what mechanisms govern these complex behaviors. The ultimate goal is to determine how these complex communicative and cooperative behaviors have evolved, in an attempt to more fully understand how our own ability to communicate via language may have arisen. This ultimate goal will require the collaboration of a huge number of scientists in the fields of communication, cooperation, and cognition. In an attempt to jumpstart this field, the Cooperative Predator Vocalization Consortium has organized a symposium at the International Ethological Congress (Behavior2015) in Cairns, Australia. “This symposium will draw together contemporary research findings on the links between communication and social behaviour (including cooperation) of large predators. The symposium will synthesise a new approach to the study of the cognitive-communicative-social complex, and its implications for future research into the evolution of cognition and language.”

If you want to help us push the field of communication, cooperation, and cognition forward, please join us at Behavior2015 or contact me (kdslehmann@gmail.com) and Arik (arik.kershenbaum@gmail.com) about collaborating with the CPVC!

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BEACON Researchers at Work: Evolution in Action Exhibit at MSU Museum

This week’s BEACON Researchers at Work blog post is by MSU Museum Education Specialist Julie Fick.

Intro

IMG_1085Museums mean different things to different people. For me, the MSU Museum was a place where as a child I explored the halls with my family on Sunday afternoons. I remember winding through the Hall of Evolution, anxious to see the child mummy in her case, and climbing the marble staircase to stare in awe at the African elephant skeleton. Of course, the fact that my dad told us how he helped hold the bones while the curators directed the assembly of the behemoth was wildly impressive to an eight year old! These memories are clear and enduring, and it is this sort of wonderment and lasting impression that museum professionals aspire to develop in visitors of all ages.

The obvious question is, how is that accomplished? Having devoted most of my adult life to the education profession and for the past four years, museum education in particular, I can tell you that this is the challenge: providing a setting and an experience that plants a seed, prompts a question, inspires an investigation, or sparks an idea, all in the hopes that visitors carry away a little piece of the content you have shared with them.

Evolution exhibits at MSU Museum

Prior to 2010, the MSU Museum’s (MSUM) only exhibit area that dealt with evolution was the Hall of Evolution. Filled with fossil specimens and colorful – although outdated – murals that depict ancient life, this hall is a journey through geologic time in a traditional, “old-school” manner. Still popular with many and an historical treasure in its own right, this hall provides only partial coverage of evolution through what can be gleaned from the fossil record.

Fortunately, in 2010 the creation of the BEACON Center for Evolution in Action at MSU provided the motive and the means to create a new evolution perspective in the Museum. An exhibit area was designated the “Evolution in Action Gallery,” and the journey began. The purpose of the gallery was (is):

  • To inform audiences about BEACON’s mission and presence as a world-class NSF center at MSU
  • To increase public understanding of evolution
  • To showcase current evolution research being conducted here at MSU

IMG_1083When I joined the staff in 2011, the first phase of exhibit creation was basically complete. A suite of exhibit panels had been created; three to describe the BEACON Center and three to highlight Dr. Kay Holekamp’s hyena research. A mounted hyena specimen and a hyena skull were displayed in cases, and a touchscreen offered four videos to view.  

Over the course of the next eight months, I worked with scientists, designers, exhibition staff, and graduate students to create and install the third component of the gallery, Dr. Richard Lenski’s 50,000 generations of E. coli research. Five more panels were added, plus a video tour of the Lenski lab and an articulated skeleton of Nariokotome Boy – depicting what our ancestors might have looked like, 50,000 generations ago.

IMG_1090

In those months and since, I have learned that there are many challenges inherent in creating a museum exhibit; we faced several of them.

  • Choosing content – what are the “big ideas”, the visitor take-aways? If you try to include too much, visitors are overwhelmed. As a team, we struggled with copious amounts of text on the panels, suspecting that we were biting off more than most visitors could chew.
  • Delivering content – how do you get your big ideas across? Our solution was to install “wall words”; simple stand alone phrases that captured some big ideas: “We observe evolution in nature, in the laboratory, and with computers” (on a stand alone wall); “Social behaviors in organisms evolve” (on the hyena mural); and “Mutations drive evolution” (on the Lenski lab mural).
  • Design – how will you invite the visitor in and make him/her want to explore what you are presenting? How will you physically move them through the experience? We reconfigured the preliminary exhibit layout to consider what we wanted visitors to see first, installed color strips to match gallery components, and created a curved panel that suggested a starting place and a path.
  • Engagement – what could visitors do in the exhibit besides read text? At first, the only engagement options were to watch videos on two touchscreens and play a digital game on a third.

IMG_1076Phase two of our evolution exhibit was complete and everything fit together in the gallery: carefully chosen text – pared down from the scientists’ original submissions, two great specimens, clever graphics, all professionally designed. How would visitors react? What did they think of our gallery?

We asked them. In multiple versions and across several age groups, we asked visitors about their understanding of evolution (pre/post) and we observed their actions in the gallery. Data revealed what some of us suspected: visitors were not reading the text, they only sometimes watched the videos (and often only partially), and they were not playing the game long enough or understanding the concepts behind the game. It was apparent that we needed more and better ways to engage visitors.

Revamping the text panels was not an option in this case. So, over the next three years, we looked for ways to make the exhibit more engaging. We added: Mutation Station – a hands-on activity using Legos to represent segments of genetic code; See for Yourself – sealed plates of E. coli from actual competitions in the Lenski lab between ancestral and evolved bacteria, viewed under a lit magnifier; and a more active and easier to understand digital game, “Hungry Birds” (a project of Dr. Rabindra Ratan).

Another issue that we realized along the way was that nowhere in the exhibit – for that matter in the Museum – is there an actual explanation or description of what evolution is or the mechanisms by which it occurs. We were showing examples of outstanding research, but we lacked the primer to lay the evolution foundation for the visitor.

Evolution in Action Exhibit 2.0

The next phase, or EiA 2.0 as I call it, will address the above content concern as well as some of our earlier findings on the visitor experience. We will:

  1. Replace “Hyenas Rule” in the EiA Gallery with Drs. Ashlee Rowe and Matt Rowe’s work on venom evolution, featuring grasshopper mice and scorpions. We will use less text, more graphics, visuals and manipulatives.
  2. Create and install an evolution hub in the EiA Gallery that will create a solid foundation for visitor understanding of basic evolution processes and concepts. Variation, inheritance, selection, and time will be presented through simple examples and interactives.
  3. Create a visitor interactive station at the entrance to the science floor that connects the EiA Gallery with other natural science galleries in the Museum and provides the basis for interest and inquiry in evolution. Two large horizontal touch screens will offer state of the art, interactive technology that has been created for and tested in museums: Harvard’s FloTree, and either Karl Gude’s Tree of Life or Harvard’s Deep Tree. This station will invite visitors to explore evolution concepts such as common ancestry and tree-thinking when they first reach the science exhibits floor, prior to entering the EiA Gallery.

IMG_1091In addition to the newly featured research and the evolution hub, the EiA Gallery will contain a venue to “talk” to BEACON scientists and at least two new interactive games; Terry Soule’s Ladybug game (variation/selection), and Laura Crothers’ and Ammon Thompson’s Tree-thinking game (kid-friendly, build-a-tree). The 5E Learning model (Engage, Explore, Explain, Elaborate, Evaluate) will guide the creative process.

We will also approach evaluation a little differently. This time we will do “front end” evaluation regarding how material is presented and understood by creating a hub prototype and testing it with visitors. This, plus an array of summative evaluation measures with larger sample sizes will assess achievement of visitor learning goals as well as provide feedback regarding how visitors learn science in museum settings. 

As curator and project manager of the Evolution in Action Gallery, my goal is for EiA 2.0 to provide the venue for a deeper visitor understanding of evolution and a conduit for the connections that exist between our science galleries but have not been made obvious to our visitors. I am looking forward to this next chapter, to applying what I’ve learned, and to setting the stage for research in visitor learning in informal science settings.

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

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BEACON Researchers at Work: Soft robots

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

A nice sunny day for deploying a robotic fish in Wintergreen Lake at Kellogg Biological Station (KBS).

A nice sunny day for deploying a robotic fish in Wintergreen Lake at Kellogg Biological Station (KBS).

During my childhood, my favorite toys were the ones that I could create using scrap parts. When that was not fun enough, I used to teardown old devices at home just to see the type of mechanisms that were part of their functionality. There is no doubt that by exploiting my creativity and curiosity at early age I was delineating my future career as an engineer. Later on, when I was applying for college, robotics was my first choice without any hesitation. But how did I become part of BEACON?

In 2013, I was studying abroad in United States and I had the opportunity to work in the summer as an undergraduate research assistant at The Adami Lab. During that time, I have started investigating the application of evolutionary computational tools for evolving and transferring artificial brains to real world robots. By using Markov Brains, which are encoded networks composed of multiple probabilistic logic gates (more information in here: http://adamilab.msu.edu/markov-network-brains/), I was able to evolve controllers for line following robots in order to make them adaptive to changes in their work environment. The results of these experiments can be found in this page: http://alproductions.us/blog/2013/10/12/markov-brain-controllers-in-robots/.

The robotic fish GRACE sampling water columns for temperature and harmful algal blooms autonomously.

The robotic fish GRACE sampling water columns for temperature and harmful algal blooms autonomously.

Motivated to continue this previous work as well as due to collaborations between the College of Engineering at Michigan State University and the BEACON Center, I came back in 2014 to MSU to start a graduate program in Electrical Engineering. Now I am also part of the Smart Microsystems Lab (SML), which is focused on the design and control of novel materials and underwater robots. One of the projects in this lab, is a gliding robotic fish (GRACE), which is used for collecting and transmitting data from underwater environments, particularly, for sampling harmful algal blooms. Some field tests have already been performed at the Kellogg Biological Station (KBS) in the past few years (video: https://www.youtube.com/watch?v=7ybtkn1cdHs).

Finite element analysis of a soft joint and pneumatic actuated manipulator.

Finite element analysis of a soft joint and pneumatic actuated manipulator.

Autonomous machines like the robotic fish can have several limitations on their locomotion and sensory systems due to design constraints imposed by the type of materials used for their construction. Hard components are responsible for generating additional loads to a robotic structure as well as complexity in the assembling processes. Deploying a machine in a unstructured underwater environment, not only requires it to have precise sensing devices for detecting external features but also enhanced motorized mechanisms that facilitates its mobility. Constant design improvements are important since it allows the development of fitter autonomous systems.

A bidirectional soft actuator fabricated by 3D printing process.

A bidirectional soft actuator fabricated by 3D printing process.

When we look at nature, we can see that most organisms are composed of soft mechanisms such as tissues, muscles and organs. Due to this fact, most of the body dynamics and control are outsourced to the morphology and material properties of the organism such as the density, stiffness and compliance. We can then imagine a similar case for robots with an artificial version of these mechanisms. If we employ soft materials in robotics, would we be able to create autonomous machines that are compliant and capable to withstand damage, wear and large stress? Soft actuators and flexible sensors can be achieved through various methods such as soft lithography, photopatterning and 3D printing. In recent work, I have investigated the use of silicone-based and rubber-like materials for the fabrication of soft pneumatic bending actuators. These actuators are composed of a very flexible and stretchable hollow layer attached to a thin inextensible layer. By injecting any type of fluid in the chambers of the soft actuator, it will generate the desired bending motion. As part of my research, several prototypes have been simulated using finite element software as well as fabricated for physical experiments.

In a sense, the continuous deformation of soft materials allows the system to have infinite degrees of freedom. This material behavior enables a soft robot to achieve more complex motions and actions, similarly to the ones performed by some marine animals. The application of biological inspiration in the design of robotic systems is very important for the engineering field, since it promotes the advancement of new technologies in order to mimic the traits or behaviors found in different animal species. The investigation of novel materials and fabrication processes is necessary for designing state-of-the-art sensors and actuators for bio-inspired machines. For instance, by using a 3D printing process, I was able to fabricate a miniaturized stingray-like soft robot, which has a tethered pneumatic actuation system. However, if we want to build an entirely compliant autonomous system, the control unit and all additional components must also be capable to undergo large deformations while still being functional. These requirements and constraints bring a lot of opportunities for the discovery of innovative technologies, providing more impulsion to my current work.

A 3D-printed stingray-like soft robot for tethered actuation in underwater environments.

A 3D-printed stingray-like soft robot for tethered actuation in underwater environments.

Other challenges also include the exploitation of techniques for defining models or controlling algorithms for these elastomer based actuators. Since developing control methods for these soft bodies are non-trivial because of their high nonlinear dynamics, an evolutionary robotics methodology is another tool that might play a role for the design of robust controllers in conformable machines. This multidisciplinary research approach stimulates my creativity and problem solving skills, and it is very exciting to work in a community where different scientific fields benefit from each other.

For more information about Thassyo’s work, you can contact him at thassyo dot pinto at gmail dot com.

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BEACON Researchers at Work: The Original Social Gaming

This week’s BEACON Researchers at Work blog post is by University of Texas at Austin postdoc Tessa Solomon-Lane.

Me SCUBA diving in the kelp forests offshore of Catalina Island, CA to collect bluebanded gobies. The last dive of my dissertation warranted wearing a lab coat. Photo credit: Megan Williams & Jenny Hofmeister (2014)

Me SCUBA diving in the kelp forests offshore of Catalina Island, CA to collect bluebanded gobies. The last dive of my dissertation warranted wearing a lab coat. Photo credit: Megan Williams & Jenny Hofmeister (2014)

I can trace the beginning of my fascination with social behavior to the summer I was ten. That summer, I started volunteering as a teacher’s aide at an arts-based school for kids with learning and developmental differences. As I gained experience at the camp, the scientist in me started to recognize patterns and ask questions. One observation intrigued me most: seemingly independent of a wide variety of special needs, kids who could interact socially with other campers and adults seemed to have a particular advantage. There was an ease with which these campers moved through their day that we, as educators, struggled to instill in campers who didn’t already have that ability. In the long run, one teacher told me, these socially savvy kids would be fine. Although ‘fine’ is overly simple, and some social skills can be coached, I think there was an important kernel in my early observations that still drives my research today: members of highly social species who can play the social game well are likely to have an advantage.

Field biology beyond the playground. Fast forward to a college semester abroad in Australia when, for the first time, it clicked for me that scientific research was the way to ask and answer my persistent questions about social behavior and why individuals behave the way that they do. What led to this realization? I learned there were fish that changed sex depending on their social environment.

Most of the animals we encounter in our everyday lives —humans, dogs, cats, birds, and even zoo animals—are genetically either male or female. Males typically remain males for their entire lives, and females typically remain female. For many species of fish, however, sex is much more flexible. Females that produce eggs can transform into fully functioning males in just days or weeks (protogynous, sequential hermaphrodite). In species like grouper and clownfish, males can sex change into females (protandrous, sequential hermaphrodite), and there are even species that can change from female to male and back again (bidirectional, sequential hermaphrodite). This transformation can dramatically increase lifetime fitness and involves coordinated changes at multiple biological levels. The first changes occur in the brain and behavior of the sex changer. External morphology, such as coloration and genitalia shape, can also shift. Steroid hormones, particularly androgens and estrogens, are central to the reorganization of the reproductive system. And in the gonad itself, an ovary becomes a testis (or vice versa) through a combination of cell birth and cell death.

Remarkably, this whole transition is socially regulated. In a protogynous species, for example, female to male sex change occurs when a female establishes dominance in a social group. In nature, this might happen if the previous dominant male dies or if an all-female group forms. Within minutes of the social environment becoming permissive to sex change, the behavior of the dominant female changes. She may even take on the male role so rapidly that she performs male reproductive behaviors before she has sperm to release.

Why did sex changing fish set off a light bulb for me? Without a doubt, social behavior is critically important for all of the diverse social species found throughout the animal kingdom, including humans. But here were animals that, over the course of a single lifetime, must generate social behaviors appropriate for a low ranking female, a middle ranking female, a high ranking female, and even a dominant male! How do the fish accomplish this behavioral range and context specificity?

My field crew of undergraduate research assistants from Agnes Scott College: (left to right, back) Cierra Lockhart (2014), Megan Williams (2012-2014), Alma Thomas (2013-2014), and Alyssa Millikin (2014), with me in front. Taken at the Wrigley Institute for Environmental Studies on Catalina Island, CA.

My field crew of undergraduate research assistants from Agnes Scott College: (left to right, back) Cierra Lockhart (2014), Megan Williams (2012-2014), Alma Thomas (2013-2014), and Alyssa Millikin (2014), with me in front. Taken at the Wrigley Institute for Environmental Studies on Catalina Island, CA.

In my doctoral research, I addressed this overarching question by studying the bluebanded goby (Lythrypnus dalli), a bidirectional sex changer. I was fortunate to work in the field on Catalina Island, CA and in the laboratory at Georgia State University with a number of excellent undergraduate researchers, including two field teams I led from Agnes Scott College. Over the course of my dissertation, I formed many different kinds of social groups and watched hours upon hours of social interactions with the goal of understanding which factors affected social behavior and how. I formed social groups of different sizes and sex ratios, with adults and juveniles. Sometimes I selected females that were gravid and ready to lay eggs, gave individuals controlled social experiences, or chose fish with specific levels of aggression. In other experiments, I first implanted steroid hormones or injected neuromodulators, such as corticotropin-releasing factor and arginine vasotocin, into the brain. And like any good behavioral biologist, highly accurate reenactments of the behaviors I observed occasionally make their way into conference presentations and K-12 science outreach activities.

A male, juvenile, and female bluebanded goby (left to right).

A male, juvenile, and female bluebanded goby (left to right).

Male bluebanded goby caring for his eggs laid on the inside of the shell. The black dots are developing eyespots.

Male bluebanded goby caring for his eggs laid on the inside of the shell. The black dots are developing eyespots.

The good, the bad, and the adaptive. There is often an impulse to anthropomorphize animal social behavior and label behaviors as ‘good’ or ‘bad’ depending on their connotations for humans. But gobies are not tiny, underwater humans. Subjective classifications can impede our understanding of behavioral evolution because ‘good’ behaviors may or may not actually increase fitness. Furthermore, the fitness consequences of some behaviors, such as aggression, differ depending on the context and the species. Even the individual expressing the behavior can influence the outcome. In my research, I identified adaptive behaviors and successful individuals by directly measuring a component of fitness: reproductive success. For females, I counted the number of eggs she laid in the male’s nest, which ranged from 55 to 2,200 eggs per clutch. For males, I counted the total number of eggs (from multiple females) that hatched from his nest. The most productive male hatched 4,995 eggs in just 2 weeks! By identifying the strong connections between social behavior and reproductive success in bluebanded goby social groups, my research can provide insight into how these important behaviors evolved.

As a new postdoctoral fellow in the Hofmann Lab (cichlid.biosci.utexas.edu), my goal now is to go into the brain. Although I am no longer studying a sex changer, the African cichlid Astatotilapia burtoni is highly social and expresses fascinating and flexible social behaviors. I am excited to begin investigating how a highly conserved network of brain regions regulates the expression of adaptive, context-specific social behavior.

For more information about Tessa’s work, you can contact her at tksolomonlane at utexas dot edu.

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BEACON Researchers at Work: Same behavior, same genes?

This week’s BEACON Researchers at Work blog post is by University of Texas at Austin research associate Rebecca Young. 

Me as a teenager in 1996 (Austin, TX).

Me as a teenager in 1996 (Austin, TX).

From an early age I spent my time outside – chasing lizards, riding horses, and begging to go to a zoo. As this fascination matured I found it was the diversity of life, as Darwin so eloquently describes the “endless forms most beautiful and most wonderful”, which intrigued me most. Where does this variation come from? How are these differences generated during development?

Ironically, while my curiosity and decision to pursue a career in biology arose from a fascination with animal diversity, my study of biology is largely centered on what is shared among organisms. It is now known that the tremendous diversity of animal species on earth develop from remarkably conserved ‘toolkits’ of gene regulatory networks redeployed in context- and species-specific ways. In hindsight, some may argue this is not surprising. The foreleg of a horse and wing of a bat look and function differently, but at their core they are quite similar. Both are appendages, out growths from a remarkably similar bilaterally symmetrical bodyplan; their differences (e.g., their length, width, and arrangement of bones) can be achieved by changes in growth and adjustments in apoptosis during development. However, the underlying developmental and genetic similarities among organisms go beyond homologous traits like limbs – characters that occur in multiple species derived from the same ancestral trait. Developmental genetic similarities appear in non-homologous traits as well. For example, in cases of parallel evolution, where similar features evolve independently in multiple lineages, similar developmental mechanisms can be found (e.g., the electric organ in electric fishes). In some cases traits that have seemingly no similarities evolutionarily or functionally (e.g., human diseases and yeast phenotypes) can share gene regulatory networks (read about ‘phenologs’ here: http://www.phenologs.org/). That traits such as these, having no business being developmentally similar, are in fact “deeply homologous” – i.e., share gene regulatory mechanisms – is a principal discovery resulting from evodevo thinking in biology.

Paired monogamous and non-monogamous species used in our research.

Paired monogamous and non-monogamous species used in our research.

For the majority of its history, the field of evolutionary developmental biology has focused on morphological and physiological characters. However, other types of traits, such as behaviors, should likewise share gene regulatory mechanisms. My work as a research associate in the Hofmann Lab at the University of Texas at Austin (http://cichlid.biosci.utexas.edu/) asks whether similar behaviors, in this case monogamy, that have evolved independently in multiple taxa result from deployment of the same ‘deeply homologous’ gene regulatory mechanism. To answer this question we are taking a comparative transcriptomic approach. Specifically, we quantify expression of genes in the brains of reproductive males in paired, closely-related monogamous and non-monogamous species of voles, mice, song birds, dendrobatid frogs, and cichlid fishes using the next generation sequencing approach RNA-seq. By comparing neural gene expression between monogamous and non-monogamous species within a group (e.g., within voles) we can identify the genes that are up-or down-regulated in the monogamous species. If we do this in all of the groups we can identify the genes that are differentially regulated across all monogamous species examined. This is a jumping off point. From here, we can further examine this list of differentially expressed genes to identify groups of co-expressed genes. We can assess the known interactions and functions of the differentially expressed genes to identify the types of neurogenomic changes that accompany the transitions to monogamy in all of these groups generating functional hypotheses for future experiments.

Illustration of orthologs and paralogs.

Illustration of orthologs and paralogs.

Getting a list of genes differentially regulated in all these independent evolutionary transitions to monogamy is no small feat. Outside of the efforts required to recruit a consortium of experts who can provide the appropriate tissue for each of these distinct species, comparative approaches in next generation sequencing data analysis are in their infancy. To date, comparative ‘omics research has focused largely on closely related species. When studies do span large evolutionary distances they focus on model systems with well-developed genomic resources (e.g., a well-annotated, published genomes and functionally annotated genes) that facilitate comparisons. Much of our effort has focused on improving these approaches in non-model species like those explored for this project. One of the major challenges is identifying the ‘same’ (orthologous) genes in each species. This problem comes from differences in genome complexity across organisms. For example, gene, gene family, and whole genome duplications have occurred in some lineages and not others, meaning that quite often a gene has more than one copy – called paralogs. How can you compare expression of one gene in one species with two genes in another? To resolve this problem, I have worked in collaboration with the Center for Computational Biology and Bioinformatics (CCBB: http://ccbb.biosci.utexas.edu/) and the Texas Advanced Computing Center (TACC: https://www.tacc.utexas.edu/) to establish an analysis pipeline based on OrthoMCL (http://www.orthomcl.org/) in a high performance computing environment. Rather than focusing on individual genes, we use OrthoMCL to generate ‘orthologous gene groups’ that contain all of the paralogs for a particular gene. These gene groups are generated by comparing sequences within and between species. When gene sequences within species are more similar to each other than to genes in another species, they are grouped as paralogs into these orthologous gene groups. Expression values of the orthologous gene groups can be calculated and compared directly across species. This is not only critical for our research interests, but facilitates comparative ‘omics in general as next generation sequencing approaches are applied to more and more non-model organisms in a diversity of empirical and experimental contexts.

My 2 year old daughter at the Austin Zoo and Animal Sanctuary .

My 2 year old daughter at the Austin Zoo and Animal Sanctuary .

Right now the scientific pursuits that drive my curiosity are best explored indoors, in a lab or on a computer rather than in the field. Until my research takes me outside again, and from time to time it does (read about my other research directions here http://devoevo.ccbb.utexas.edu/), the observations of the beautiful and wonderful natural variation I have made on horseback as a teenager, in the field as a scientist, and exploring nature with my kids have generated endless questions on the developmental and evolutionary origins of animal diversity.

For more information about Rebecca’s work, you can contact her at youngrl at utexas dot edu.

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