BEACON | An NSF Center for the Study of Evolution in Action

Introducing BEACON’s New Science Outreach and Communication Postdocs

Posted on January 19, 2016 by hageyt

This post is by MSU postdoc Travis Hagey.

Late in 2015 BEACON advertised for an Evolution Outreach and Education postdoctoral fellowship. As a result of that posting, we would like to introduce three new postdocs, Dr. Wendy Smythe, Dr. Travis Hagey, and Dr. Alexa Warwick. These new BEACONites will be focusing on diversity outreach (Wendy), communicating BEACON’s research to the public (Travis) and evolution education and outreach (Alexa). We encourage the BEACON community to reach out and strike up new collaborations, taking advantage of the skills and resources these new postdocs bring.

Dr. Hagey studying the ecomorphology of Anolis lizards in the Dominican Republic.

To introduce these new postdocs to the BEACON community, we will be featuring blog posts dedicated to each of their goals and research interests. Today we are focusing on Dr. Hagey. Travis completed his Ph.D. with Dr. Luke Harmon at the University of Idaho in 2013 investigating the evolution, mechanics, and ecology of gecko adhesion (Fig. 1). Travis continued his gecko research at UI for two years as a BEACON funded postdoc As BEACON’s Science Communication Fellow, Travis will be taking over the public communication aspects of BEACON, including the BEACON blog. As result, all blog related inquiries should be directed his way. Travis will also soon be looking for additional blog posts, so if you haven’t ever written one or it has been a while since your last update, take this opportunity to get your research out into the hands of the public.

Travis will also be managing BEACON’s Facebook, Twitter, and yearly newsletter. If you have research, upcoming events, or other information that you think should be featured, please let him know. Public science outreach and communication is an important part of science research. It’s also important to BEACON and NSF. If you have been thinking about public science outreach activities or have one come coming up, let Travis know and he can help get the word out. In addition to disseminating the research occurring at BEACON, Travis will also be collaborating with Jory Weintraub on the Sixth Annual Evolution Film Festival Video Contest. The application deadline to submit your short evolution-themed films is coming up at the end of May! Finalists will be screened at the Evolution 2016 conference.

Travis will also be continuing his previous research working with gecko adhesion. This research blends evolution, mechanical engineering, and ecology. The main questions of Travis’ research focus on how animal performance works and why animals are shaped the way they’re shaped. This research combines work with live animals, biomechanical simulations, and (if he’s lucky) fieldwork to observe animals using their natural habitat.

A 3D reconstruction of Gekko gecko adhesive structures using micro X-ray CT.

Travis is currently investigating the use of high-resolution 3D reconstructions of morphological structures using a suite of different approaches (Fig. 2, confocal microscopy, micro and nano X-ray CT, and photogrammetry). Travis is also working with engineering simulation approaches such as finite element analyses and combining evolutionary and mechanical simulations in software like Open Dynamics Engine. Whenever you mention 3D reconstructions you also have to consider 3D printing! How cool would giant 3D printed gecko toes be?

Travis also has experience with evolutionary comparative methods, fitting models of trait evolution such as Brownian Motion and the Ornstein-Uhlenbeck models. If you’ve got questions, are interested in collaboration, or want to chat about biomechanics let him know.

Posted in BEACON Researchers at Work, BEACONites, Education | Tagged BEACON Researchers at Work, Biomechanics, Education, evolution, Outreach | Leave a comment

Receiving Advice, Exercising, Tweeting, Chairing & Networking at Conferences

Posted on January 13, 2016 by hageyt

This post is by UT Austin graduate student Rayna Harris. Also posted on Medium.

Fig. 1. This image and the above quote were taken from Steal Like an Artist by Austin Kleon, my new favorite book.

This blog post is based upon my experience at the 2016 Society for Integrative and Comparative Biology Meeting. These are my thoughts about what works best with regards to giving/receiving advice, live tweeting, chairing symposia, networking with people who don’t know you, and prioritizing exercise.

Remember, all advice is autobiographical.

“…when people give you advice, they’re really just talking to themselves in the past.” — Austin Kleon

I hear people giving and receiving lots of advice at conferences. Most of the time it’s really good and given in good faith, but it’s not always the best advice. What works for me might or might not work for you or vice versa. Hopefully you will find some useful bits of information herein.

Fig. 2. Is including a handle, hyperlink and photo overkill? Maybe, but this was my most popular #SICB2016 tweet.

Tweets with handles, links, or photos are better.

Live tweeting has its pros and cons. I enjoying following the hashtag of a meeting, but I don’t enjoying having my normal Twitter feed bombarded by live tweets. I’m not the only one who thinks it’s wise take the time to find accompanying hyperlinks and twitter handles for your tweets, but here’s my rationale.

When I use the speaker’s twitter handle, it lets the speaker know I liked the talk, and maybe she/he will be the first to retweet it. When I link to a paper, my tweet shows up on Altmetric (like this). When I add an image, it catches people’s eye and is more likely to be used in Storify (like this).

I takes time to do these things, but I think your followers will appreciate the effort.

Fig. 3. The audience has been staring at this title for 5 minutes already, so I like to say a little more about the speaker instead.

When chairing a session, provide details about the speaker.

Pretty much everyone in the audience has already read the title. To avoid redundancy, I prefer to introduce the speaker by providing some or all of the following details:

Name, current institution, and current lab
Their supervising PIs from grad school and postdocs
A one sentence description of the research

These details provide a better picture of the speaker’s background and interests than when simply saying their name and talk title.

Networking = talking to people with shared interests that may /may not already know you.

I’m not sure what networking means for most people, but I think networking means talking to people about share interests. At conferences, I think it’s important to strike a balance between talking with people you already know and talking with people you might like to know. My desired outcome could range from having a good conversation or meeting new people to strengthening relationship with colleagues or gaining the recognition of future employers. If talking to people you know is the easier option, how should one go about networking with people you don’t know?

A few ways I network with people who don’t know me yet

I introduce myself to whoever my PI is talking to. I’ve met dozens of scientists and a few program officers this way. Bonus: It’s easier for this new acquaintance to remember what lab I’m from the next time we meet.
When presenting my poster, I specifically ask 1) what caught his/her eye 2) if they know any of my co-authors and/or 3) are familiar with the places where I do my research. When we find common ground, we’re much more likely to converse later in the conference or in my career.
When I find myself next to a speaker while in line for coffee/beer/food, I casually say that I enjoyed the talk (if I did) and why. For me, this is a much more natural way to engage with a speaker than approaching them immediately after a talk when others are eagerly waiting to ask questions.
I walk straight up to people and introduce myself. I usually do this when I have a question or want to say that I think they are awesome! This requires some confidence and grace, but I have managed to strike up some good conversations and made new colleagues this way.
I participate in workshops. Workshops give you the chance to talk and listen to a diverse group of people on topics of shared interest. I actually get to know people this way and frequently chat with them later. Bonus: The setting can perk you up if you were falling asleep during a previous talk.
I chair a session. This is a great way to get people to see your name and hear you speak. It requires the confidence to speak in front of a large audience, but there is little one-on-one conversation.
I co-organize social events, and it’s awesome! I’ve done this twice (in 2014 with Sarah Davies and 2016 with Suzy Renn). We used Evite to invite our colleagues and passed out printed invites to new acquaintances. Because two people were organizing, we were able to bring together a people from different circles to promote cross-disciplinary networking.

Fig. 4. Left) Approaching people who know my PI. Middle) Finding common ground during a poster session. Right) Group discussion duing a student/postdoc workshop

Fig. 5. Left) Long-time colleagues reminisce. Middle) A bar filled with scientists with shared interests. Right) Intermingling of people from different labs.

Prioritize exercise.

It is really easy to let a conference disrupt one’s regular workout routine, but it’s important to not left the meeting consume your life or detract from your health.

Fig. 6. I’m doing #YogaCamp with Adriene Mishler this month. I borrowed a mat from the hotel fitness center for my yoga practice.

When I allocate 30 min or so to exercise, I have so much more energy than when I don’t. I was proud of working out for 4 of the 5 days in Portland, but I wish I had hit 5 for 5.

I find it’s easiest and best to knock it out early in the morning. Alternatively, I suggest turning happy hour into a workout hour… I know that reduced drink and food prices are enticing, but it’s really hard to exercise in the evening if the drinking started at 4 pm.

Comments

I’d like to hear your thoughts and perspectives, so feel free to make comments on the version of this blog posted on Medium. Thanks for reading!

Posted in BEACON Researchers at Work | Tagged networking, Scientific Conferences | Leave a comment

Avida-ED for classroom research

Posted on January 4, 2016 by Danielle Whittaker

This post is by MSU postdoc Mike Wiser. Reposted from the DevoLab blog.

Laboratory components are often integral parts of both K-12 and college science courses. I certainly had a lot over the course of my science education; 5 courses with labs in high school, 8 in college. But for the overwhelming majority of them, I was essentially following a recipe and doing by rote things which had already been done and where the answers were already known. It was only in science-fair-style projects that I typically had any control over the questions I was asking, or how I would go about trying to answer them. But science education doesn’t have to be like that. Inquiry-based science practice is a growing part of the recommendations for science education (1,2). Thankfully, computational tools are making these practices more accessible.

Jim Smith presents his students’ inquiry projects at BEACON

Avida-ED provides a great platform for students to do actual scientific research within the settings of a course on general, population, or organismal biology. Students have the ability to explore questions which they devise themselves, in part because they do not have the cost associated with consumable materials that most natural science experiments do. Further, because computational data can be generated so much more rapidly than physical experiments, students can perform exploratory work to generate hypotheses, and then gather sufficient data to test them. We have found inquiry projects work well when students work in small teams.

Classroom assessment studies from the Avida-ED group have shown a benefit to students conducting their own active research projects using this software. Students have to grapple not only with defining questions and designing experiments, but also with figuring out what data to collect, how to analyze this data, and how to present findings to others.

How does one go about using Avida-ED for classroom research projects? Great question; that’s what this post is about to lay out.

Within Avida-ED, there are several parameters that are easy for the user to change, including:

World Size (which influences population size)
Mutation Rate
Which tasks are rewarded
Which organism(s) is/are used as the ancestor

Likewise, there are multiple different responses that users can track. These range from some very simple ones, such as:

Fitness, Merit, or Gestation Time at a given time point
Whether any organisms in the environment perform a given function
How many organisms perform any given function

To more complex ones such as:

Maximum Fitness, Merit, or Minimum Gestation Time in the population
Number and complexity of tasks performed by the most fit organism
Relative abundance of descendants from different ancestors

To ones that require real-time monitoring of populations like:

Time at which a function was first observed
Whether new tasks appear in a background already performing many other functions
Whether gain of a new function involves loss of a previous task

Undergraduates present posters of Avida-ED research to faculty and graduate students

Part of the scientific process involves first being able to show a correlation between an outcome and a set of conditions. Therefore, I highly encourage students to pick a single parameter to manipulate at a time, and a single measured response to use for a particular experiment. Once a correlation is established, researchers can then gather additional evidence to test not only correlation but also the causation that is implied – changing a parameter leads to a different outcome, so therefore the parameter likely contributes to the outcome. The fewer parameters we change, the more confident we can be that the difference in the results flows from a specific change we made. It is especially instructive for students to be able to run experiments of this sort to see for themselves how evolutionary processes can produce adaptations. Instructors may find value in a simple demonstration for a class where the instructor changes many parameters at once, gets a different result, and then asks the class which of the parameters they think contributed to the difference and how they would be able to tell.

Overall, programs like Avida-ED offer a way for students to pose real questions (and deal with all of the challenges in figuring out what data to collect, how to interpret it, etc.) just as researchers regularly face in their work. This takes a class experience from being essentially an exercise in recipe-following – a “lab experience” in name only — to an activity where they engage in authentic science practice. In a later post, I’ll outline some of the basic types of data analysis likely to be relevant to a wide range of introductory research questions.

NGSS Lead States. (2013). Next Generation Science Standards: For States, By States. Retrieved from http://www.nextgenscience.org/
Vision and Change in Undergraduate Biology Education: A Call to Action. Retrieved from http://visionandchange.org/finalreport/

Posted in BEACON Researchers at Work | Tagged Avida-ED, Digital Evolution, Outreach, undergraduate education | Leave a comment

BEACON Researchers at Work: #SummerofKBS

Posted on December 21, 2015 by Danielle Whittaker

This week’s BEACON Researchers at Work blog post is by 2015 REU student Douglas Page.

My time at the Kellogg Biological Station working as a BEACON/NSF sponsored REU was an amazing opportunity to not only conduct research in the field of ecology and evolutionary biology, but it also gave me a chance to network with others who share my interests. Over the course of the program I worked in the Conner lab conducting plant research that has helped me to understand evolution and ecology. This summer has shaped me in ways I never thought possible. At first I didn’t know what to expect coming to Michigan from North Carolina, but after settling in I saw that Michigan has a lot to offer. I finally got to go to Chicago and Lake Michigan for the first time, camped on the beach, hiked through the Northern woods and so much more. I believe what has affected me the most here at my time at KBS are the friends I have made here.

Although we have only been here for a short time, all of us have become closer than I thought we could be. As our time here at KBS comes to an end I have come to realize how much of an honor it was to be a part of everything this place stands for. Looking back on this experience has made me feel pride in both myself and the work that I have done here. I hope to return one day to KBS; maybe as a researcher or graduate student. However, until that day comes I’ll accept taking the lessons I have learned here with me where ever I go. I understand the importance of programs such as this to the community and how vital it is for students like me to take advantage of them. By being here I feel like I am on a path which will take me closer to my goals in life. For example, I have begun to contact various Long Term Ecological Research (LTER) sites around the country to apply for different opportunities thanks to the support I got from the program at Kellogg Biological Station. I was not only made aware of the existence of these scientific centers, but people shared their experience on what I could do to better my chances of participating in them.

I have enjoyed my time here with so many new ideas and experiences I will remember for years to come. While I will miss my time and my friends here at KBS, I feel confident to move on in my endeavors in both my career in science and life in general. The adventures I have had really shaped me for the better, which I hope to instill in others as I lead by example. I am grateful for my opportunity to work and learn at the Kellogg Biological Station. Lastly, I would like to say to all the people who have made this summer one to remember, thank you and I hope to see you again.

Posted in BEACON Researchers at Work | Tagged BEACON Researchers at Work, Kellogg Biological Station, plant biology, Research Experiences for Undergraduates, REU | Leave a comment

BEACON Researchers at Work: How to Grow an Animal

Posted on December 14, 2015 by Danielle Whittaker

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

Axolotl, also known as Mexican Salamander.
Image Credit: “Axolotl ganz” by LoKiLeCh – Own work. Licensed under CC BY-SA 3.0 via Commons https://commons.wikimedia.org/wiki/File:Axolotl_ganz.jpg#/media/File:Axolotl_ganz.jpg

Meet Sal* the Salamander. Sal, like all of his kind, has a unique gift. He can regenerate his limbs, if you cut one off! This unique ability of salamanders has fascinated generations of scientists from Aristotle to Charles Darwin. And yet, there are many, many questions about this process of regeneration that we still do not understand. Primarily, how does the regenerating limb know what size it has to grow to? How is the correct final organ size achieved in the face of developmental growth perturbations and changes in environmental conditions? These questions form the basis of my research here at Michigan State University.

I study developmental growth regulation in the common fruitfly, Drosophila melanogaster, an organism that may seem far removed from salamanders, humans and other large animals that we are more familiar with. However, the signaling pathways regulating growth are conserved all the way up from fruitflies to higher animals—in fact, most of these signaling pathways were first discovered in Drosophila. Consequently, any discovery of novel developmental mechanisms in Drosophila is of interest not just to fly biologists, but to the broader scientific community of developmental biologists. Moreover, the wealth of genetic tools available to manipulate growth and development in Drosophila is unparalleled, making it an excellent model system to answer challenging questions of developmental growth control.

Diagrammatic representation of developing imaginal discs in Drosophila larva and the organs they develop into in the adult fly. (Klug and Cummings, 1997)

Drosophila is a holometabolous insect, meaning it undergoes complete metamorphosis during its life cycle—passing through 4 different life stages: embryo, larva, pupa and adult. Unlike other animals, the adult does not grow in size, and therefore, the final body and organ size depends on growth of organ precursors (called imaginal discs in Drosophila) during the larval period. To put it simply, the larval phase of growth can be likened to growth and development through childhood and adolescence before entering adulthood.

Two important factors regulate the final organ size achieved at the end of development: the duration of growth and the growth rate. Naively, one would expect that longer the developmental time, the greater the final size. In the context of larval development, perturbing the growth of one of the imaginal discs actually results in an increase in the total developmental time—presumably to allow the growth perturbed organs to “catch up” (Parker and Shingleton, 2011; Stieper et al., 2008). However, despite this increase in developmental time, the other unperturbed imaginal discs do not overgrow—in fact they reduce their growth rate to match that of the growth rate of the perturbed imaginal disc. Thus, growth rates appear to be coordinated among different organs so that, at metamorphosis, the final organ size is correctly proportioned in relation to the body and the rest of the organs.

Diagrammatic representation of the wing imaginal disc with the shaded areas showing the two compartments of the disc.

But what about growth coordination within an organ? If you could perturb the growth of one part of an organ, would the growth rate of the other unperturbed part also be reduced? This was the question that I was interested in answering when I started my PhD. In order to answer this question, we focused our attention on the wing imaginal disc, which ultimately forms the wing and most of the thorax of the adult fly. I generated larvae in which the two halves of the wing disc (called compartments) seemingly had different rates of growth; one compartment that grew slowly due to a defect in the protein production machinery, and another compartment which grew at normal or near-normal rates. We then looked at their relative rates of growth throughout development by measuring the sizes of each compartment in larvae sampled at various points in larval development. We found that similar to coordination between organs, the unperturbed compartment reduces its growth rate to match that of the growth perturbed compartment.

What’s most exciting however, is that both intra- and inter-organ growth coordination during development seem to be regulated not by organ-specific mechanisms but by a common systemic mechanism, involving the hormone ecdysone. Ecdysone is an insect hormone that regulates metamorphosis through different stages of the insect life cycle. Research from our lab suggests that ecdysone functions not just as a molting hormone, but also functions as a regulator of imaginal disc growth rates during development. This suggests that in Drosophila, developing organs rely not just on organ-specific mechanisms to ‘perceive’ and reach their final size, but in fact respond to systemic cues as well.

While most of the research that I have described here is focused on Drosophila, I would like to emphasize, that the basic developmental mechanisms discovered in this model organism are by no means unique to it. In fact, there is considerable evidence to suggest that localized growth defects also cause growth retardation and developmental delays in humans. For example, in children suffering from chronic inflammatory diseases such as Crohn’s disease there is a systemic growth hormone insensitivity. Consequently, these children also suffer from stunted growth and severe growth retardation (Sanderson 2014). Therefore, the utilization of systemic signaling mechanisms in the maintenance of “correct” organ size appears to be an evolutionary conserved mechanism present not just in your common -run-of-the-mill fruitfly but in all animals.

References:

Parker, N. F. and A. W. Shingleton (2011). “The coordination of growth among Drosophila organs in response to localized growth-perturbation.” Dev Biol 357(2): 318-325.

Stieper, B. C., M. Kupershtok, M. V. Driscoll and A. W. Shingle

ton (2008). “Imaginal discs regulate developmental timing in Drosophila melanogaster.” Dev Biol 321(1): 18-26.

Sanderson, I. R. (2014). “Growth problems in children with IBD.” Nat Rev Gastroenterol Hepatol 11(10): 601-610.

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

Posted in BEACON Researchers at Work | Tagged BEACON Researchers at Work, development, developmental biology, Drosophila, growth | Leave a comment

BEACON Researchers at Work: The Evolution of Cooperation by the Hankshaw Effect: A Big Thumbs Up for Cooperation!

Posted on December 7, 2015 by Danielle Whittaker

This week’s BEACON Researchers at Work blog post is by University of Washington graduate students Katie Dickinson and Sarah Hammarlund and postdoc Brian Connelly.

Brian Connelly, Katie Dickinson, and Sarah Hammarlund are all thumbs!

Hold your hand out in front of you and examine it closely. Five digits, four fingers and a thumb… What a useful appendage, the thumb! You can give a friend an encouraging thumbs-up or maybe a death sentence in a gladiator coliseum with a thumbs-down. You can twiddle your thumbs during a boring seminar, thumb wrestle with your brother, tend your garden with your green thumb, or stick out like a sore thumb. We use our thumbs to text and type and write, to hold a spoon, to touch. But arguably the most important use for a thumb is to hitchhike.

Humans can hitchhike to get to Burning Man, robots can hitchhike around the world (http://m.hitchbot.me/), and even genes can hitchhike during evolution. In the case of genes, a trait can become more common if it is genetically linked with another trait that is favored by natural selection. Otto and Hartfield[i] have shown that even costly, maladaptive traits can survive by “genetic hitchhiking.” One such costly trait is cooperation.

Evolutionary biologists including Darwin have been puzzled by the evolution of cooperation. We would expect natural selection to favor selfish individuals that maximize their own fitness. In contrast, cooperative behaviors benefit others at a cost to the cooperator. Furthermore, cooperators continually face the risk of being exploited by “defectors,” individuals that don’t cooperate but reap the benefits of cooperation. So how did cooperation come to be so prevalent in our world?

One way for cooperation to succeed is through genetic hitchhiking. If cooperation, a costly trait, becomes linked to an adaptive trait (one that increases survival in a harsh environment, for example), cooperation can hitchhike with that trait. For this to work, the selective advantage of the adaptive trait must outweigh the cost of cooperation. This process has been demonstrated to support both yeast[ii] and bacterial cooperators[iii]^,[iv].

The challenge with genetic hitchhiking is that cooperators and defectors are equally likely to gain these adaptations through mutation. Once one type gets lucky and catches a mutational ride, it leaves the other in the dust. So how can cooperators consistently get a thumbs-up? We have recently been exploring ways in which cooperators can actively increase their chances of gaining adaptations.

One way cooperators can more reliably catch a ride is by sticking together. When cooperators preferentially interact with other cooperators, their growth is boosted by the benefits of cooperation. With more growth comes more mutations, and each mutation offers an opportunity to gain an adaptation. By working together, cooperators increase their chances of hitchhiking—they are now much more likely catch a ride than defectors. So in a sense, cooperators have larger thumbs—they are more visible to passing cars and therefore have a higher likelihood of catching a ride with an adaptive trait.

We call this phenomenon the “Hankshaw effect” after the fictional character Sissy Hankshaw from Tom Robbins’ novel Even Cowgirls Get the Blues. Hankshaw was born with extremely oversized thumbs. She’s teased for her thumbs as a child and has trouble even just buttoning up her sweaters, but she eventually discovers that her thumbs make her an excellent hitchhiker. For Hankshaw, a trait that is an impairment becomes her salvation on the open road. We constructed a model to see how the Hankshaw effect might allow cooperators to hitchhike their way to success[v].

Cooperation and the Hankshaw effect. Although equally present in the beginning, cooperators are quickly driven to extinction when they are not more likely to gain adaptations than defectors (above). However, when cooperators improve their chances for gaining adaptations, they can hitchhike along with these non-social traits to dominance by the Hankshaw effect (below). The ride abruptly ends once cooperators become fully adapted, and adapted defectors eventually take over.

We found that the Hankshaw effect can allow cooperators to consistently hitchhike and escape the threat of defectors, but only as long as there are beneficial traits to be gained. Once cooperators become fully adapted to their environment and the ride ends, mutations create equally-adapted defectors that take over. This makes the Hankshaw effect only temporary.

However, if the environment changes and new opportunities for adaptation are created, the ride may not be over for cooperators. And if environmental change continually occurs, then cooperators can be maintained by the Hankshaw effect as long as there are opportunities for adaptation.

We have taken this idea one step further and allowed organisms themselves to change the environment instead of passively waiting for change to occur. We found that this “niche construction”[vi]^,[vii] can allow cooperators to create opportunities for adaptation that keep the ride going indefinitely[viii].

When the environment changes (at each vertical line), creating a continual supply of potential adaptations, cooperators can continue to hitchhike and are maintained indefinitely.

Although at first, from an evolutionary perspective, cooperation seems like a losing strategy, there are ways that cooperators can succeed. Maybe Sesame Street had it right: “Cooperation—Makes it Happen.”

[i] Hartfield, M. and Otto, S. P. 2011. Recomination and hitchhiking of deleterious alleles. Evolution, 65: 2421–2434. doi: 10.1111/j.1558-5646.2011.01311.x

[ii] Waite, A. J. and W. Shou. 2012. Adaptati

on to a new environment allows cooperators to purge cheaters stochastically. Proc. Natl. Acad. Sci. USA 109:19079-19086.

[iii] Morgan A.D., B. J. Z. Quigley, S. P. Brown, and A. Buckling. 2012. Selection on non-social traits limits the invasion of social cheats. Ecol. Lett. 15:841-846

[iv] Asfahl, K. L., J. Walsh, K. Gilbert, and M. Schuster. 2015. Non-social adaptation defers a tragedy of the commons in Pseudomonas aeruginosa quorum sensing. ISME J. doi:10.1038/ismej.2014.259.

[v] Hammarlund SP, Connelly BD, Dickinson KJ, Kerr B. 2015. The evolution of cooperation by the Hankshaw effect. bioRxiv. doi:10.1101/016667.

[vi] Odling-Smee, F. J., K. N. Laland, and M. W. Feldman. 2003. Niche construction: the neglected process in evolution (No. 37). Princeton University Press.

[vii] Laland, K. N., F. J. Odling-Smee, and M. W. Feldman. 1999. Evolutionary consequences of niche construction and their implications for ecology. Proc. Natl. Acad. Sci. USA 96:10242- 10247.

[viii] Connelly, B. D., Dickinson, K. J., Hammarlund, S. P., & Kerr, B. 2015. Negative Niche Construction Favors the Evolution of Cooperation. Evol. Ecol. doi:10.1007/s10682-015-9803-6.

Posted in BEACON Researchers at Work | Tagged bacteria, BEACON Researchers at Work, Biological Evolution, Cooperation, genetic hitchhiking, genetics, mutations | Leave a comment

BEACON Researchers at Work: Source-sink population dynamics facilitate plasmid host range evolution

Posted on November 30, 2015 by Danielle Whittaker

This week’s BEACON Researchers at Work blog post is by University of Idaho postdoc Wesley Loftie-Eaton.

With all the thanks to BEACON for funding and Dr. Eva M. Top for her support and guidance, my latest foray into the world of plasmids explores a question that I have been thinking about for nearly a decade: How, and under what conditions does plasmid host range evolve when the plasmids do not encode any genes obviously beneficial to the host or when there is no strong external selection for their maintenance?

For the non-(micro)biologists reading this, plasmids are self-replicating DNA molecules that occur in bacteria and are quite often capable of spreading horizontally between diverse bacterial genera, making them central to horizontal gene transfer and rapid bacterial adaptation. With that said, we generally tend to study plasmids in context of their role in spreading antibiotic resistance genes and virulence factors between pathogenic bacteria. The focus on this phenomenon is driven by the immense public health threat brought about by antibiotic resistance (Kahrstrom, 2013; Obama, 2014). As a result, most of our efforts to understand the evolution of plasmid persistence and consequently host range include (periodic) conditions that render the plasmids beneficial to their hosts, such as the presence of antibiotics to which the plasmids encode resistance (Bouma and Lenski 1988; Modi et al. 1991; Modi and Adams 1991; Dahlberg and Chao 2003; Dionisio et al. 2005; Heuer et al. 2007; De Gelder et al. 2008; Sota et. 2010; San Milan et al 2014a; San Milan et al. 2014b; Harrison et al., 2015). While there is no arguing the contribution of plasmids towards the spread of antibiotic resistance genes and virulence factors, we have to remember that many plasmids in nature lack genes that encode host-beneficial functions (Brown et al. 2013, Loftie-Eaton and Rawlings, 2012). Because these so-called ‘cryptic’ plasmids lack an obvious benefit to their host there is no strong external selection for their maintenance and thus it is unclear what conditions can facilitate evolution of their host range.

Fig. 1 An illustrated hypothesis of how genetic variation in the genome of a plasmid from a source host can facilitate greater persistence in a sink host. Plasmids with mutations that lead to increased persistence in the sink hosts are indicated in green, whereas plasmids with mutations that are deleterious/neutral in the sink population are indicated in red.

Borrowing from ecological source-sink theory my colleagues and I have formulated a hypothesis that may help us understand ecological conditions that facilitate plasmid host range evolution in the absence of strong external selection. In source-sink theory a source is a habitat in which the net birth rate within a population is positive, whereas a sink is a habitat in which the net birth rate is negative and population persistence relies on immigration from a source (Pulliam, 1988). Evolutionary source-sink theory predicts that adaptation to a new habitat is unlikely to occur if the reproductive rate in that environment is low. However, given sufficient genetic variation from a source population, mutant alleles may increase reproductive success in the sink habitat following immigration (Dennehy et al, 2010). The “habitat” of a plasmid is its bacterial host. A source host of a plasmid is thus a bacterial species in which the plasmid is capable of long-term persistence, whereas a sink host is a bacterial species from which the plasmid is rapidly lost due to high segregational loss, reduced host growth rates brought about by high plasmid cost, or inefficient horizontal spread. However, from previous research we know that as little as one mutation in the plasmid can result in increased persistence (Sota et al, 2010; Loftie-Eaton et al, submitted). Thus we hypothesize that genetic variation in the genome of a plasmid from a source host can facilitate greater persistence in a sink host (Fig. 1).

Fig. 2 Source-sink population dynamics to study plasmid host range evolution can be achieved and controlled in chemostats. This is done by creating an environment that precludes the source host from growing while allowing for continuous growth of the sink host. In such an environment the only way for the plasmid to propagate is to transfer to the sink host before the source host is diluted out. In theory, plasmids with sink-beneficial mutations that conjugated from the source to the sink will be able to persist for a longer period of time than the ancestral plasmid or plasmids with sink neutral/deleterious mutations. Plasmids with different alleles are indicated in different colours.

To test our hypothesis we put together a team with experience in microbiology, ecology, evolutionary theory and mathematical modeling and devised an experimental design that is driven by explicit theoretical predictions to be tested using empirical and computational methods. The plasmid we are using is a cryptic conjugative plasmid that was isolated from the pathogenic bacterium Bordetella pertussis (causes whooping cough; Kamachi et al., 2006). The source host that we are using is an E. coli that is quite capable of maintaining the plasmid in the absence of strong selection, whereas the sink host, Shewanella oneidensis, is not (Yano et al., 2013). The source host, however, is an auxotrophic mutant whose growth can be selectively inhibited by excluding a nutrient essential to it, but not to the sink host. Thus, in a constantly diluting environment such as a chemostat in which the source host cannot grow, the only way for the plasmid to persist is to conjugate to and propagate in the sink host (Fig. 2). However, since the plasmid is maladapted to the sink host it will not be able to persist for long unless, in accordance with our hypothesis, there are mutant alleles in the genome of the plasmid that allows for increased reproductive success in the sink host. Based on current estimates of the parameters describing persistence of the plasmid in a monoclonal population of the sink host, our preliminary modeling predicts that mutant alleles in the plasmid genome that b

ring about a 10% decrease in plasmid cost or a 100-fold decrease in segregational loss rate can, in either case, result in the plasmid persisting 500 generations more than the ancestral plasmid in the sink host, thus supporting our hypothesis in silico.

For me, as a plasmid biologist dabbling in evolution, this project is super exciting. We will for the first time provide experimentally derived insight into the evolution of host range of cryptic plasmids. But moreover, having a tractable source-sink experimental system combined with computational methods will open avenues to empirically test different theoretical source-sink migration dynamics. For example, our results will guide future studies with other bacteria and plasmids and diverse experimental conditions, including growth in biofilms, to explore how source-sink and other population dynamics can explain some of the observed abundance of plasmids in natural bacterial populations. This is important because to successfully control the spread of antibiotic resistance, which is rapidly becoming a global health crisis, we need to understand the persistence, spread and evolution of all plasmids, not just resistance plasmids.

Acknowledgements

This work would not be possible without my excellent team members which includes Dr. Eva Top and Genevieve Metzger at the University of Idaho, and Dr. John Mittler and Jacob Bayless da Costa at the University of Washington, nor would it be possible without funding from BEACON.

References

Bouma J. E., R. E. Lenski. Evolution of a bacteria/plasmid association. Nature 335:351-352.
Brown, C. J., D. Sen, H. Yano, M. L. Bauer, L. M. Rogers, G. A. Van der Auwera, and E. M. Top. 2013. Diverse broad-host-range plasmids from freshwater carry few accessory genes. Appl Environ Microbiol 79:7684-7695.
Dahlberg C., L. Chao. Amelioration of the cost of conjugative plasmid carriage in Eschericha coli K12. Genetics 165:1641-1649.
De Gelder L., J. J. Williams, J.M. Ponciano, M. Sota, E. M. Top. Adaptive plasmid evolution results in host-range expansion of a broad-host-range plasmid. Genetics 178:2179-2190.
Dennehy, J. J., N. A. Friedenberg, R. C. McBride, R. D. Holt, and P. E. Turner. Experimental evidence that source genetic variation drives pathogen emergence. Proc Biol Sci 277:3113-3121.
Dionisio F., I. C. Conceição, A. C. Marques, L. Fernandes, I. Gordo I. The evolution of a conjugative plasmid and its ability to increase bacterial fitness. Biol Lett 1:250-252.
Harrison E., D. Guymer, A. J. Spiers, S. Paterson, M. A. Brockhurst. Parallel compensatory evolution stabilizes plasmids across the parasitism-mutualism continuum. Curr Biol 25(15):2034-2039.
Heuer H., R.E. Fox, E.M. Top. Frequent conjugative transfer accelerates adaptation of a broad-host-range plasmid to an unfavorable Pseudomonas putida host. FEMS Microbiol Ecol 59:738-748.
Kahrstrom, C. T. 2013. Entering a post-antibiotic era? Nat Rev Microbiol 11:146.
Kamachi, K., M. Sota, Y. Tamai, N. Nagata, T. Konda, T. Inoue, E. M. Top, and Y. Arakawa. 2006. Plasmid pBP136 from Bordetella pertussis represents an ancestral form of IncP-1beta plasmids without accessory mobile elements. Microbiology 152:3477-3484.
Loftie-Eaton, W. and D.E. Rawlings. 2012. Diversity, biology and evolution of IncQ-family plasmids. Plasmid 67:15-34.
Loftie-Eaton W., H. Yano, S. Burleigh, R. S. Simmons, J. M. Hughes, L. M. Rogers, S. S. Hunter, M. L. Settles, L. J. Forney, J. M. Ponciano, E. M. Top. Evolutionary paths that expand plasmid host-range: implications for spread of antibiotic resistance.
Modi, R. I., J. Adams. 1991. Coevolution in bacterial-plasmid populations. Evolution 45:656-667.
Modi R. I., C. M. Wilke, R.F. Rosenzweig, J. Adams. Plasmid macro-evolution: selection of deletions during adaptation in a nutrient-limited environment. Genetica 84:195-202.
Obama, B., The White House, Office of the Press Secretary. 2014. Remarks by the president in state of union address Washington, D.C.: Retrieved from http://www.whitehouse.gov/the-press-office/2014/01/28/president-barack-obamas-state-union-address.
Pulliam, H.R. Sources, sinks, and population regulation. Amer Nat 132:652-661.
San Millan A., K. Heilbron, R. C. Maclean. Positive epistasis between co-infecting plasmids promotes plasmid survival in bacterial populations. ISME J. 8:601-612.
San Millan A., R. Peña-Miller, M. Toll-Riera, Z.V. Halbert, A. R. McLean, B.S. Cooper, R. C. MacLean. Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids. Nat Commun. 5:5208.
Sota, M., H. Yano, H. M, Julie, G. W. Daughdrill, Z. Abdo, L. J. Forney, and E. M. Top. Shifts in the host range of a promiscuous plasmid through parallel evolution of its replication initiation protein. ISME J 4:1568-1580.
Yano, H., L. M. Rogers, M. G. Knox, H. Heuer, K. Smalla, C. J. Brown, and E. M. Top. Host range diversification within the IncP-1 plasmid group. Microbiology 159:2303-2315.

For more information about Wesley’s work, you can contact him at wesleyl at uidaho dot edu.

Posted in BEACON Researchers at Work | Tagged antibiotic resistance, BEACON Researchers at Work, Biological Evolution, Bordetella, E. coli, horizontal gene transfer, modeling, plasmid, Shewanella | Leave a comment

BEACON Researchers at Work: Soft-bodied animals and soft-bodied robots

Posted on November 25, 2015 by Danielle Whittaker

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

In recent years, robots are becoming more accessible and almost an integral part of our lives. They are not seen as only industrial machines which are used for welding and assembling vehicle components anymore. Many robots can now be used at home for domestic tasks (vacuums, pool cleaners, lawn mowers), for personal assistance (companion robots), or just as toys for recreational activities (small flying drones). Moreover, medical facilities are now equipped with modern robotic devices for tele-operated surgical processes as well as wearable robotic suits for human rehabilitation exercises. Since humans are interacting more closely with robots we should ask ourselves: How should we design robots that offer safety to humans and that are able to work in unpredictable environments?

Figure 1. The soft humanoid robot Baymax from the animation “Big Hero 6.”
Source: http://www.awn.com/animationworld/don-hall-and-chris-williams-talk-disneys-big-hero-6

The Disney’s Marvel-inspired “Big Hero 6” movie has a charismatic robot with irresistibly cute personality which address the aforementioned issues. In this plot, Baymax (Figure 1) is an inflatable health care robot companion created by a brilliant robotics student, Tadashi Hamada. His soft form provides him the ability to deform when moving across unstructured environments as well as to absorb the energy generated from any collision. Because of its compressible structure, he is able to safely interact with humans at any level. These unique characteristics are based in a novel approach to robotics defined as “soft robotics.” As one of its goal, soft robotics seeks the creation of machines that are more adaptable and animal-like in their capabilities.

Figure 2. Octopus vulgaris.
Source: http://blogs.scientificamerican.com/octopus-chronicles/there-are-plenty-of-octopuses-in-the-sea-mdash-or-are-there/

Biological systems are largely comprised of soft materials [1]. In animals, compliant materials are fundamental for the mechanical design of their body, which has coevolved during many generations with their nervous system and formed a completely integrated neuromechanical system. In changeable and complex environments, animals can use these soft components to their advantage. The body softness enables surface conformation, stress distribution and reduction of impact force, as well as entrance into very small apertures for shelter or hunting. For instance, an octopus (Figure 2) can be seen as a biological demonstration of how effective behavior in nature is directly connected to the morphology of the body. Since it is a soft invertebrate, it can adapt the shape of its body to the environment, squeezing through gaps smaller than its unconstrained body. Furthermore, it can extend its arms very quickly to reach, grasp and manipulate objects. Its arm articulates the shape by shortening, elongation, bending, or torsion, and forces can be distributed by localized or global stiffening [2].

It is important to consider that soft biological organisms also have some limitations. Since their body do not contain any rigid structure to support their own body weight, soft animals are usually small in size. Large soft invertebrates are only found in water or underground, where they can use the surrounding medium as their support structure. In addition, due to their highly deformable tissue, they cannot exert large initial forces or move the entire body with great speed. These important lessons of the morphology and functionality
of compliant structures in nature are essential for building soft robotic systems.

Figure 3. Octopus-like soft robotic manipulator.
Source: Laschi, Cecilia, et al. “Soft robot arm inspired by the octopus.” Advanced Robotics 26.7 (2012): 709-727.

Soft robotics literature is flourishing and becoming vaster every day [3]. The development of soft muscle-like actuation technologies is one of the major challenges in the fabrication of fully soft-body robots. As shown in Figure 3, an interesting bio-inspired soft robotic manipulator is based on the anatomy and mechanics of octopus arm [4]. The exterior part of the soft robotic arm is comprised of a plastic fiber braid, whereas shape-memory alloy (SMA) springs are disposed longitudinally and transversally, as in muscular hydrostats. These metal alloys are capable of undergoing a certain strain and subsequently recover their original shape when heated, generating local deformations in the soft robotic arm.

Mimicking soft animals requires investigating the most suitable technological solutions, such as materials, sensors, actuators and control schemes. With bendable and adaptable machines, we would be able to deploy robots in harsh and unpredictable environments or disaster situations. In the future, these soft machines could also play a role in space exploration. A group of researchers have recently proposed a concept of a soft robotic eel with electrodynamic power scavenging designed to explore the seas of Europa, a Jupiter moon [5].

By studying how animals use soft materials to execute complex motions as well as perform everyday tasks in unpredictable environments, we can achieve helpful insights for designing new technologies for robotic applications in human assistance, search and rescue, environmental monitoring and medicine. The natural world can show the potential capabilities of soft robots. Many advances in soft robotics will be realized from the collaboration among several disciplines such as mechanical, electrical, materials science, bioengineering and computational evolution.

References:

[1] Trivedi, Deepak, et al. “Soft robotics: Biological inspiration, state of the art, and future research.” Applied Bionics and Biomechanics 5.3 (2008): 99-117.

[2] Kim, Sangbae, Cecilia Laschi, and Barry Trimmer. “Soft robotics: a bioinspired evolution in robotics.” Trends in biotechnology 31.5 (2013): 287-294.

[3] Rus, Daniela, and Michael T. Tolley. “Design, fabrication and control of soft robots.” Nature 521.7553 (2015): 467-475.

[4] Laschi, Cecilia, et al. “Soft robot arm inspired by the octopus.” Advanced Robotics 26.7 (2012): 709-727.

[5] Gilster, Paul. “Soft Robotics for a Europa Rover”. http://www.centauri-dreams.org/?p=32620

For more information about Thassyo’s work, you can contact him at thassyo at ieee dot org.

Posted in BEACON Researchers at Work | Tagged BEACON Researchers at Work, Evolutionary Applications, evolutionary robotics, soft robotics | Leave a comment

Today's Google Doodle features hominid evolution!

Posted on November 24, 2015 by Danielle Whittaker

Here at BEACON, we’re of course excited to see today’s Google Doodle (archived here) celebrating Lucy, the Australopithecus afarensis fossil discovered in 1973. However, BEACON’s Education Director Louise Mead points out, “I usually love the Google doodles, but the one for today, acknowledging the fossil Lucy, Australopithecus afarensis, does much to contribute to misconceptions about a linear evolution. They need to add the branches representing common ancestry!”

Hey Google – we fixed it for you!

Posted in Uncategorized | Tagged evolution, google, hominid, misconceptions | Leave a comment

BEACON Activity in China

Posted on November 20, 2015 by Danielle Whittaker

BEACON Director Erik Goodman just returned from a 13-day trip to China, where he met with BEACON-collaborating teams in Shanghai’s Tongji University and at Shantou University in Guangdong Province. In Shanghai, the Tongji researchers also met with MSU Horticulture Prof. Erik Runkle and BEACON ECE graduate student José Llera. The MSU team is working with Prof. Lihong Xu and his students, postdocs and technicians on developing greenhouse control systems based on multi-objective evolutionary computation.

The goal is to develop control strategies that can maximize crop yield while minimizing energy expenditure. Unlike typical greenhouse controllers that fix daytime temperatures at an “ideal” set-point and nighttime temperatures at another set-point, the new controller would base the temperature to be maintained at any time on a model of the crop’s environmental response and on the external weather conditions, allowing energy to be traded off against production depending on weather conditions. China is constructing many new high-tech greenhouses that could be controlled by such technology, including the Dushi Green greenhouse on Chongming Island (near Shanghai, see pictures below) that is about 340,00 sq. ft. and uses the latest in Dutch greenhouse technology, including heat pumps, intra-canopy LED lighting, automatic movement of crop beds, several types of screens, and other devices. While in Shanghai, Prof. Runkle also gave a talk for the Shanghai Society of Agricultural Engineers dealing with supplemental greenhouse lighting technology. The Tongji and MSU members of the research team shared ideas on ways to simplify the model of the greenhouse microclimate and crop growth, as the more traditional models require too much computational time to be used realistically in evolution of a controller. Once back at MSU, the team will continue to work with Prof. Xu’s student, Leilei Cao, who is a visiting scholar in BEACON for two years.

L to R: (greenhouse manager), Prof. Xu, Prof. Goodman, Prof. Runkle, Chenwen Zhu (former BEACON visiting scholar), (greenhouse employee), Prof. Ruihua Wei.

After the Shanghai visit, Goodman went on to Shantou, China, where he collaborates with Prof. Zhun Fan of Shantou University. They have collaborated for many years on the use of genetic programming for mechatronic design, and now are working in the more general field of evolutionary robotics. Prof. Fan has an excellent laboratory with many students designing robots, including one for potential application in greenhouses such as the ones being designed by Prof. Xu. He uses multi-objective evolutionary design to optimize robot design and robot trajectories. Fan’s and Goodman’s collaborators include Prof. Han Huang, South China University of Technology, Xinye Cai, Nanjing University of Aeronautics and Astronautics, and Hailin Liu, Guangdong University of Technology. This team is seeking funding for a new State Key Laboratory to be located at Shantou University, promoting further collaborative research on robotics, multi-objective evolutionary optimization, and medical image processing. Prof. Liu just returned from BEACON to Guangzhou, but plans to return to continue his work at BEACON in 2016.

Prof. Cai leads a discussion with Prof. Fan’s students and Prof. Goodman (far left).

Returning to Shanghai, Prof. Goodman then went with his long-term collaborator Prof. Meng Yao, of East China Normal University, to visit cities in Chongming Island and just north of the Yangzi River, nearby Yuelai, in Jiangsu Province. Leaders in both locales are eager to host development of R&D activities, offering proximity to Shanghai, but with much more favorable conditions in terms of population density and environment. A future research facility for Prof. Yao’s work may be located on Chongming Island.

Posted in BEACON Researchers at Work | Tagged china, Evolutionary Applications, Evolutionary Computation, evolutionary robotics, greenhouses, international, multi-objective optimization | Leave a comment