BEACON Researchers at Work: Genetic and Environmental Basis of Trait Loss, or, How to Lose a Trait: Organismal Spring Cleaning Edition

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

Samuel PerezThe study of morphological traits, physical features that are directly observable and measurable, is important for the study of evolution, and play a central role in Darwin’s theory of natural selection. Organisms interact with their environment using their morphological traits to do tasks like obtain energy from limited resources, avoid predation, maintain homeostasis, and reproduce. The traits involved in these tasks often have differences between individuals (variation) in a population, and some traits have more variation than others. If those morphological differences lead to differences among individuals in the number of offspring, then natural selection results and evolution at the population level can occur; this process is known as adaptation.

However, if a formerly-adaptive trait no longer contributes to the fitness of a population, perhaps due to changing environmental conditions, then what happens to that trait? In that case, there can be two possibilities: either the trait will become reduced and lost as it accumulates mutations and resources are invested in other, more essential features that can contribute to adaptation, or the trait can be modified towards a new function. A striking example of trait loss in animals is the loss of flight, which has occurred in two major groups of animals that have developed flight (insects and birds). Some insects have lost their wings altogether, while penguin wings have been co-opted for swimming.

A.thaliana flower. Note that pollen from the mature short stamen does not reach the pistil (center) part of the flower.  Pic: Jürgen Berger/Max Planck Institute for Developmental Biology, Tübingen, Germany

A.thaliana flower. Note that pollen from the mature short stamen does not reach the pistil (center) part of the flower.
Pic: Jürgen Berger/Max Planck Institute for Developmental Biology, Tübingen, Germany

I’m interested in knowing how much variation is observed in a trait undergoing loss at the population level, the genetic basis of trait loss, why nonfunctional traits are sometimes maintained, and how formerly adaptive traits can be shifted towards new functions (co-option). I study trait loss in the model plant Arabidopsis thaliana (thale cress), of the Brassicaceae family, which has almost 4,000 species and includes species like mustard, cabbage, canola, and radishes. A conserved feature in Brassicaceae is that flowers have four long stamens (male reproductive parts) and two short stamens.

 

However, A. thaliana produces more than 98% of its seeds through self-pollination, and the short stamen anthers, where the pollen is produced, never come near the stigma, where the pollen needs to be deposited to fertilize the seeds (see picture above). Previous experiments by Anne Royer in which short stamens and long stamens were removed showed that the short stamens do not contribute significantly to self seed production, making it an example of a nonfunctional trait. Anne also showed that the short stamens have begun to be lost in some populations of A. thaliana, and this loss exhibits a latitudinal cline in the native European range: stamen loss is common in the Mediterranean but rare in Scandinavia.

A. thaliana flowers with six stamens (left), five stamens (center), and four stamens (right).

A. thaliana flowers with six stamens (left), five stamens (center), and four stamens (right).

Many animal and plant traits that exhibit a latitudinal cline also show an altitudinal cline as well; lower latitudes correspond to low altitudes, and higher latitudes correspond to lower altitudes due to similarities in climate. To see if this is true for stamen loss in A. thaliana, I counted short stamens in 15 natural populations from N.E. Spain that ranged from 109-1688 m in altitude. I found that, in parallel to the latitudinal cline, populations at lower altitudes had more short stamen loss than populations at higher altitudes (see graph below). These parallel latitudinal and altitudinal clines suggest that there is a common source of natural selection at work, either directly on short stamens or through a correlated trait.

Mean short stamen number (±1 SEM) from 15 populations in N.E. Spain. Quadratic fit in red is provided.

Mean short stamen number (±1 SEM) from 15 populations in N.E. Spain. Quadratic fit is provided in red.

One of the advantages of studying lines from multiple populations of Arabidopsis thaliana is more potential for phenotypic and genetic variation across floral traits. Green circle diameter = 1.9 cm.

One of the advantages of studying lines from multiple populations of Arabidopsis thaliana is more potential for phenotypic and genetic variation across floral traits. Green circle diameter = 1.9 cm.

I also measured stamen loss from a series of inbred line crosses between two populations from Sweden and two populations from Spain to look at the genetic basis of stamen loss across the whole genome. We found that there was genetic variation in stamen loss within one of the Italian populations. The F1 generation showed evidence of recessive genes underlying stamen loss, the F2 and backcrosses suggested that there were epistatic interactions between the genes responsible for stamen loss. The gene interactions may be slowing the evolution of stamen loss even when genes have additive effects.

My thesis research will focus on furthering the understanding of the selective and genetic mechanisms underlying stamen loss. I will examine the fitness effects of stamen loss, both direct effects through costs of production of short stamens, as well as correlated traits that may be involved with adaptation to high altitude and latitude. I will conduct genome-wide association mapping studies (GWAS) using the whole-genome sequence data to look for the genes responsible for the latitudinal cline in stamen loss.

For more information about Sam’s work, you can contact him at perezsa4 at msu dot edu.

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BEACON Researchers at Work: Discussing evolution is fruitful: Or, Why I don’t shut up about evolution

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

southAs a woman raised in the South, and now returning to it as I finish my dissertation, I am reminded of a gem I have heard come out of more than one Southern mother’s mouth: “If you can’t say anything nice, don’t say anything at all”

As I always interpreted as “Just don’t be mean,” I found wiggle-room in this statement: If it has to be ‘not mean,’ it could also be neutral. I could say things that described a process that were neither mean nor nice, merely factual.

Taking the approach of neutrality, I’ve had a host of fruitful, meaningful discussions. Talking about things has helped me to uncover the framework of my thoughts, my misconceptions, and my assumptions in real-time. I believe we can grow, individually and as a society, through examining our thoughts, and those of others, through such conversation.

However, despite the benefits of discussion in everyday life, do these benefits extend to classroom discussion, particularly for tricky topics, like evolution?

In the case of evolution, some might shy away from discussing it at all; after all, various misconceptions about evolution run rampant, originate often from first encounters with the topic, and can even be instilled by teachers. Given the additional, resistant religious and political climate toward evolution in certain regions, it can be intimidating for teachers to bring up evolution in the classroom. If you find yourself in that position, I urge you: discuss it anyway.

Not only is the teaching of evolution supported by several national science education standards, tons of evidence also shows classroom discussion to have many benefits. Among them, classroom discussion helps expose students to importance of team work and cooperation, foster the inclusion of under-represented groups, and facilitates knowledge exchange between students. These discussions are helpful in exposing common misconceptions which students may later challenge as a first step in gaining new knowledge. And now, we have evidence to support that discussion (*not* debate) of the science of evolution can be used as a tool to increase student understanding of evolution and experimental biology.

I was privileged to work with Dr. Mark Tran (formerly MSU Zoology; now new faculty at Blue Ash College in Cincinnati- go Mark!) and Dr. Gail Richmond(Teacher Education, MSU) on a project that addressed how upper-level college biology student’s evolution knowledge and misconceptions changed after a discussion-based course. The overall theme of this particular course was physiological adaptation to the environment, thus evolution was critical for students fully understand the course topics.

As a baseline, first we tested students to see what they knew about evolution prior to the discussion course. We asked open-ended questions of varying complexity to test their understanding of evolutionary processes both generally and with respect to the specific topics to be covered in the course.

Then, for the duration of the semester, the class met weekly for 50 minutes. Each class session was designed to foster peer-to-peer dialogue about course topics and related weekly readings. Students met in small groups and convened as a class answer previously constructed discussion questions as led by graduate teaching assistants (TAs) and fellow students (under TA guidance). Finally, at the end of the semester, we re-tested the students.

peacock

An overused, but classic, example

Here’s what we found: Students consistently struggled with adaptation and how it is connected to evolution (namely, adaptation and evolution do not occur in a single organism over its lifetime, and evolution is not always adaptive). These misconceptions were widespread, even among students who *had* previously taken an evolution course (talk about a let-down!). However, improvement after discussion was apparent for certain topics, in particular for students who had yet to take an evolution course.

In short, students increased in their ability to define evolution, as well as to distinguish that populations can evolve without adapting, but not the reverse. Students also showed a greater ability to distinguish between observational and manipulative research methods.

Thus, discussing evolution can be used as an effective tool in evolution education. Our results stress the need for instructors to address their students’ preconceived ideas on evolution and dispel misconceptions at the start of courses, if not at the start of student’s classroom exposure to evolution. Furthermore, our results also show that students found discussions to be intellectually stimulating, and increased their interest levels in science. And, given that students who had not taken an evolution course made greater gains in knowledge (compared to students previously enrolled in an evolution course), discussions on evolution may actually work best for early-career students before they take courses specifically covering evolution.

So, I beg you, discuss evolution with students. Discuss evolution with friends, family—anyone that wants to learn about the science that connects us all. And if you need help, see some of the resources below or ask a friendly BEACONite to help you out. Just drop us a line, and start the discussion. 

For more, see our paper here:

Tran, M.V., Weigel, E.G., and Richmond, G. (2014). Analyzing upper-level undergraduate knowledge of evolutionary processes: Can class discussions help? Journal of College Science Teaching 43(5): 80-90.

Link: http://www.cirtl.net/files/Tran,%20Weigel,%20and%20Richmond%20JCST%202014.pdf

See also these fantastic evolution education materials, including games, comics, cool videos designed to engage students: 

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

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BEACON Researchers at Work: Of Moths and Math

Octavio CamposThis week’s BEACON Researchers at Work blog post is by University of Washington graduate student Octavio Campos.

We can all appreciate the beauty and diversity of flowers. After all, they come in so many different shapes and sizes – not to mention colors – that there’s bound to be something that appeals to everyone’s taste. Even for the dark and broody among us there is the Black bat flower! But although flowers hold strong symbolic meanings for people all over the world, their vast variation in appearance is thought to have been greatly influenced by their need to attract particular species of animals for the purpose of efficient pollination, and therefore efficient reproduction. Moths, bats, bees, and hummingbirds (and even some small rodents), for example, benefit from consuming the energy-rich nectar that many flowers produce while inadvertently transferring pollen between flowers as it sticks to their fuzzy bodies. 

Manduca sexta, a crepuscular hovering hawkmoth with long proboscisIf you really stop to think about it, drinking the nectar from a flower isn’t exactly the easiest way to making a living out there. Some animals can only feed from flowers by hovering in front of them. That by itself is a hugely complicated process that demands an impressive amount of coordination and control. On top of that, some hovering animals such as hawkmoths must be able to insert their proboscis, which is a hollow drinking straw-like appendage that serves as their mouthparts, into a very narrow opening in the flower in order to reach the nectar reservoir. Bear in mind, the proboscis can be from one and a half to three times the length of the animal itself! Imagine holding a rubbery, flexible pole that was 15 feet long and trying to precisely touch the bullseye of a dartboard, and you might begin to appreciate the scope of this challenge. And to make things even worse, many (but not all) hawkmoths do their foraging at night or dusk and dawn, when light levels are extremely low.

Some of the variation in flower shape in nature.  Adapted from http://theseedsite.co.uk/flowershapes.html

Some of the variation in flower shape in nature. Adapted from http://theseedsite.co.uk/flowershapes.html

Given the challenge that hovering animals must face when attempting to feed from flowers, I was interested by whether certain shapes of flower might be able to help the moth find the nectar source. For example, some plant species have flowers whose petals more or less resemble a flat disk, while others have petals that form the shape of a trumpet, funnel, or bowl, and anywhere in between. Intuitively, it might make sense flowers that are more trumpet and funnel-shaped might be able to better guide the long proboscis of hovering hawkmoths toward the nectar reservoir of a flower. After all, the military seems to have come to a similar solution in the context of mid-air refueling of military aircraft. During this process, a fuel hose with a cone-shaped tip is presented by a fuel tanker to another aircraft trailing behind it. The trailing aircraft, seeking to be refueled, will attempt to dock with the fuel hose via a long-thin probe. Having a cone at the tip of the fuel hose effectively makes the tip of the fuel hose bigger, thus providing a larger target for the refueling aircraft to aim for.

Flat disk flowers should be the most difficult to exploit while more "trumpet-shaped" flowers should be easier for moths to exploit

Flat disk flowers should be the most difficult to exploit while more “trumpet-shaped” flowers should be easier for moths to exploit

A trumpet-shaped 3D-printed flower (ABS plastic), with shape parameters specified by a mathematical equation

A trumpet-shaped 3D-printed flower (ABS plastic), with shape parameters specified by a mathematical equation

The trouble is that, as a scientist, I would like a quantitative way in which to investigate flower shape and its supposed affect on pollinator foraging ability. In other words, how can I describe flower shape using numbers instead of phrases such as, “funnel-like” and “disk-like?” The solution that my collaborators and I settle upon was to reduce the vast complexity of floral 3-dimensional shape into as few key “traits” as possible and then describe those traits using a mathematical equation. If you can do that, then you essentially have an equation for numerically specifying any imaginable flower shape that you can think of. And the beauty of such an equation is that 3D printers can be used to make a real-life sculpture of any particular combination of shape “traits” specified by the equation. For example, my flower shape equation can specify four aspects of floral shape: flower length, width at the outer edge of the petals, width of the central nectar reservoir, and, most crucially, the degree of curvature of the petals. If you give me any four numbers, one for each of the four flower traits, then I can use my shape equation and a 3D printer to make a plastic prototype of that hypothetical flower!

Now we’re getting somewhere… 

Image from infrared video of a hawkmoth (lower left) foraging on one of the 16 artificial flowers in this 16-flower array.  There are two distinct flower shapes in this array, 8 of each.

Image from infrared video of a hawkmoth (lower left) foraging on one of the 16 artificial flowers in this 16-flower array. There are two distinct flower shapes in this array, 8 of each.

What all of this allows me to do is to design artificial flowers of varying but precisely defined shapes and then make them using a 3D printer. I then take these artificial flowers and attach tubes filled with sugar water (which is all that flower nectar actually is), and then I expose these flowers to visitation by real pollinators, hawkmoths in this case. By carefully documenting the order in which these flowers are visited and for how long, I can gain insights into how floral shape influences pollinator foraging ability! Ultimately, I hope that my data can be used down the line to investigate how (if at all) animal visitation has influenced the evolution of flower shape diversity throughout the millions of years of flowering plant history, bringing my research back full-circle. Flowers have captivated human senses for millennia. We are quite capable of altering many aspects of floral appearance through careful selective breeding. But we aren’t the only “choosy” ones out there. Thanks to my flower shape equation, we can begin to take some initial steps in figuring out how influential the “birds and the bees” are at determining the evolution of floral shape… Time will tell!

For more information about Octavio’s work, you can contact him at eocampos at uw dot edu.

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BEACON Researchers at Work: Notes from the field

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

Kenya2Month041It never ceases to amaze me how returning to place after years away results in this dizzying contradiction: so much has changed, but everything feels the same. Four years ago, I was a Research Assistant for the MSU Hyena Project. I lived in a tent and collected behavioral and demographic data every morning and evening for ten months. The data I collected became a small piece of the dataset Professor Holekamp and her research assistants and graduate students have been gathering for 26 years. Four years later, I have returned to Kenya as one of those graduate students and so much has changed. 

I have been mentally preparing for my return to Kenya since I started graduate school in the fall of 2012. With all of that advance thinking, going back to Fisi Camp (fisi is Swahili for hyena) didn’t start feeling real until my supplies started arriving a couple of weeks ago. I will be studying hyena vocal communication and unfortunately, this means I need a LOT of equipment. I need recording equipment to record the hyena’s calls. I need speakers to play the recorded sounds back to the hyenas. Plus, I need all the memory cards, hard drives, and batteries to keep all this equipment running (and I won’t bore you with all the underwear, personal field gear, and charging cords that are necessary for life in camp). 

The three speakers I tested, with a cantelope for scale.

The three speakers I tested, with a cantelope for scale.

The speakers were an adventure all by themselves. I have a lot of requirements and received advice ranging from “Anything will work” to “Nothing will work except custom speakers made by an expert” and “There is no way you will find speakers like that without having it plugged into external power.” I had a few brief panic attacks in the midst of this fiasco. In the end, I purchased three different portable, battery operated speakers and tested all of them out.

The Klipsch speakers (the medium-sized ones in the picture above) ended up being the perfect combination of battery powered, amplitude, and sound clarity. With my back turned to them, it was easy to believe I had a hyena whooping behind me. If I can fool myself, then the hyenas should be fooled too (at least for a little while). 

Once you have devices that run on batteries, you need batteries to go with it. Suddenly, you feel as if you’ve given a mouse a cookie. Now that you have rechargeable batteries, you need a battery charger, and then you need to something to run those chargers. Our solar power in camp isn’t always reliable and we always have a ton of people using it. This made a solar set-up necessary. The last thing I want is to have good weather, no mud, great hyena cooperation, and no background noise, only to find that the recorder batteries have died. I ended up getting a lovely, compact set-up that includes a solar-powered battery and a rugged solar panel. 

On top of my own supplies, there were some other things we needed for camp. Add all this together and you get the craziness that ensued in my living room for a week:

Just half of the boxes that arrived at my house.

Just half of the boxes that arrived at my house.

Two sets of recording equipment, plus their cases.

Two sets of recording equipment, plus their cases.

This is only a portion of the mess. After this I got too embarrassed to take pictures.

This is only a portion of the mess. After this I got too embarrassed to take pictures.

Luckily my roommates are also researchers so they tolerated the mess. Eventually, I packed everything into five very full, very heavy bags. 

And I was ready to fly out!!

Now, I find myself in Kenya, this place I called home for ten months. It still feels like home, but so much has changed! The hyenas are different (although I was surprised to find there were a few I still recognize), the park itself has transformed, and camp and the nearby town have grown considerably. But, the most important difference is the data I am collecting will be critical for my dissertation. I will succeed or fail based on their quality and quantity. 

As I mentioned, my research here focuses on the vocal communication of the spotted hyena (Crocuta crocuta). I hope to help us begin to understand the evolution and the function of vocal communication in the complex social world that hyenas must navigate. No pressure, there. But, in the end, even if the stakes are higher and that crossing I used every day four years ago is now impassable, this tent I am typing from still feels like home. Not all that much has changed.

If you’re interested in reading more blog posts from Kenna and the MSU Hyena Project, check out their blog at msuhyenas.blogspot.com!

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BEACON Researchers at Work: The role of resource mutualisms in plant adaptation to abiotic environments

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

Tomomi inoculating hog peanuts with rhizobia

Tomomi inoculating hog peanuts with rhizobia

When you get thirsty, what do you do? You simply get something to drink, right? Plants don’t have the ability to move like animals, so they had to come up with other strategies to deal with stress like drought, heat stress, and salinity. For example, they can reproduce and disperse seeds to less stressful habitats or they can associate with other organisms, such as symbiotic microbes, that can “help them out” when times get tough. Although the second strategy has received very little attention, there is increasing evidence that interacting species, particularly microbial symbionts, are capable of facilitating plant adaptation to stress.

Ecologically, there is lots of evidence supporting that microbial symbionts can facilitate a plant’s tolerance to abiotic stress. For example, resource mutualists, such as arbuscular mycorrhizal fungi and nitrogen-fixing bacteria, can help plants acquire nutrients and can help mitigate the effects of drought and low pH. Evolutionarily, genetic variation in microbial symbionts may even facilitate plant adaptation to local environments. Given their short generation times, genetic diversity and dispersal ability, rapid evolution of microbial symbionts may facilitate adaptive plant responses to environmental stress.

Can you find nodules in the roots?

Can you find nodules in the roots?

My research focuses on whether soil bacteria make it possible for plants to adapt to and live in different habitats. One type of soil bacteria, called rhizobia, infect the roots of plants from the Fabaceae family (a.k.a legumes). Once inside the root, they form “root bumps,” called nodules. Rhizobia live inside the root nodules and convert nitrogen in the atmosphere into ammonia, in a form that legumes can use (like a natural fertilizer!). In turn, legumes provide photosynthetic carbon to the rhizobia. Rhizobia therefore can help plants grow in areas where they might not live otherwise. But just like human relationships, plants and rhizobia may not be compatible, or one of the partners may not be even available! For example, rhizobia may not survive or convert nitrogen effectively in certain environmental conditions, like dry soil or shade. Using a native legume called the hog peanut (Amphicarpaea bracteata), I study how mutualism between plants and rhizobia are affected by environmental stress.

In particular, I test whether rhizobia mediate plant adaptation to soil moisture, a well-characterized stressor to plants that also is known to influence plant-microbe interactions. I’m interested in three specific questions: 1) Are plants locally adapted to soil moisture conditions? 2) Do resource mutualists contribute to plant adaptation to soil moisture? 3) What plant traits drive adaptation to wet vs. dry environments?

Reciprocal transplant experiment in progress

Reciprocal transplant experiment in progress

I am currently conducting a series of field and greenhouse experiments to test these questions. I don’t have all the answers yet, but so far I have found soil moisture affects nodulation and benefits that rhizobia provide to plants. I also found that there’s genetic variation for symbiosis-related traits (e.g. nodulation, nodule size) among plant genotypes, suggesting the potential for plants and rhizobia to co-evolve in response to soil moisture. My goal of this project is to expand our understanding of the mechanisms behind local adaptation in two ways. First, I will examine whether symbiotic mutualists are contributing to local adaptation to soil moisture. Given the intimate relationships between plants and symbiotic microbes, it is likely that rhizobia play a role in plant adaptation. Second, I will identify environmental factors driving local adaptation and phenotypic traits under selection, which are critically important to understanding the cause of natural selection and variation in selection among local habitats.

High school students from KAMSC conducting an experiment testing the effects of fertilization on soybean-rhizobia interactions.

High school students from KAMSC conducting an experiment testing the effects of fertilization on soybean-rhizobia interactions

Sam Peters (high school student from KAMSC) working on his independent project in winter 2013

Sam Peters (high school student from KAMSC) working on his independent project in winter 2013

Plant-rhizobia as educational tool: Along with a research on plant-rhizobia interactions, I have shared my excitement for this topic with middle school and high school students. For example, through a BEACON education project, I had an opportunity to mentor a motivated high school student from Kalamazoo Math and Science Center on his independent project, testing whether rhizobia from different soil nitrogen have evolved differently to benefit the plants. I also worked with Brad Williamson, a former president of National Biology Teachers, to create a guided inquiry biology lesson, using the plant-rhizobia symbiosis as a model system (in review for The American Biology Teacher). In this lesson, students gain experience in scientific methods by coming up with hypothesis, designing and conducting experiments, to making claims based on the data they collect. We think that the plant-rhizobia interaction is an excellent system to teach inquiry-based science at high school and college levels.

For more information about Tomomi’s work, checkout her website at tomomisuwa.com or contact suwatomo at msu dot edu.

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