University of Michigan
Department of Ecology and Evolutionary Biology

Since Darwin, assembling an evolutionary tree that shows the relationships between all known species of life has been one of the grandest and most daunting challenges facing biologists.

Despite 150 years of effort, there's still no comprehensive tree of life, no single diagram that displays the links between all of the 1.8 million or so named species of animals, plants and microorganisms.

Now, with $5.76 million from the U.S. National Science Foundation, a group of scientists from across the country will attempt to complete the first rough draft of the entire tree of life in the first year of a three-year project called the Open Tree of Life.

This tree is expected to be a powerful tool that will enable scientists to interpret the patterns and processes of evolution and to predict the responses of life to rapid environmental change. NSF announced the award of first-year funding for the project last week.

The Open Tree of Life project is led by Karen Cranston of Duke University and has several sub-groups. University of Michigan computational evolutionary biologist Stephen Smith heads the group that will tackle the nitty-gritty details of piecing together all the existing branches, stems and twigs of life's tree into a single diagram.

Smith joined the U-M faculty in January as an assistant professor of ecology and evolutionary biology, his first university faculty position.

"This is a very complicated beast, and I'm really looking forward to the challenge," Smith said of the draft tree. "I really like taking on a problem that somebody, at some point, in a room that I've been sitting in, has said is not possible to do. And this is one of those instances."

The new information is expected to help enhance agriculture, identify and combat diseases (of humans and crops), conserve biodiversity, and predict responses to global climate change and to biological invasions.

Smith's lab will receive about $900,000 over the next three years for the tree project. He plans to hire two postdoctoral researchers and will include several graduate students.

"This is similar to when astronauts went to the moon and looked back at the Earth for the first time," Smith said. "It will be our first opportunity to see all of the organisms that we know on Earth. This is our moon shot."

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Caption: This evolutionary tree shows the relationships between more than 33,000 species of flowering plants. Trees like this will be pieced together to form an evolutionary tree of all named species of animals, plants and microorganisms as part of the Open Tree of Life project. Image credit: Stephen Smith

EEB graduate students Jen-Pan Huang and Tristan McKnight received Rosemary Grant Graduate Student Research Awards from The Society for the Study of Evolution. These awards assist students in the first two years of their Ph.D programs by enabling them to collect preliminary data or to enhance the scope of their research beyond current funding limits by visiting additional field sites, or working at other labs, for example. Professor Lacey Knowles is their advisor.

Huang is studying the Hercules Beetle to test the predominance of two competing mechanisms during population subdivision. Hercules Beetles have traits with different phenotypes that are governed by genetics and induced by environmental differences. By comparing phenotypic differences in these traits across multiple closely related populations/subspecies, Huang will estimate the speed and magnitude of evolutionary changes in non-plastic and plastic components of these traits.

McKnight is exploring dynamics of parallel evolution in the ecology and morphology in a pair of robber fly lineages using a combination of phylogenetic and ecological techniques. Robber flies (an understudied group of insects) are an interesting new system for exploring the creation of local communities from regional species pools and uncovering tradeoffs involved in adaptive radiations, according to McKnight.

EEB graduate student Rachel Cable participated in The Second Annual Spelling Bee for Honest Cheaters, Dirty Rotten Spellers, and Mustachioed Heroes in Ypsilanti recently to raise funds for 826michigan.

826michigan is a non-profit organization dedicated to supporting students aged 6 to 18 with their creative and expository writing skills, and to helping teachers inspire their students to write.

Cable teamed up with doctoral students Dan Gershman and Ahmed Tawfik from U-M’s Atmospheric, Oceanic and Space Sciences. They wore space costumes from a previous series of science writing workshops that Gershman and Kristen Mihalka (U-M AOSS) created and implemented at 826. The spelling bee team, The James Webb Space Spelloscope, raised $595.

The spelling bee was hosted by poet Raymond McDaniel and featured Ypsilanti Mayor Paul Schreiber and author Steve Amick.

“It was a great event that raised over $10,000,” said EEB graduate student Susan Cheng. “The proceeds will be used to support the organization's free programs for students, which include tutoring, writing workshops, and other in-school programs. It wasn't your typical spelling bee, the words were really hard! Rachel and Dan had to spell mulct and foumart.”

Cheng recently volunteered at a writing workshop called Robot PI:The Case of the Forgetful Firefighter at 826michigan where she played a character the students interviewed to figure out who the guilty party was. EEB graduate student Alison Gould has participated in a writing workshop helping students write stories. Cable, Cheng and Gould plan to stay involved with the organization.

As of May 1, 2012 Professor Mark Hunter has handed over the director’s reins for the Frontiers Master’s Program to Professor Tom Duda for a five-year term.

“We've just recruited our fifth cohort of students for a total of 21 students overall,” said Hunter, who was the director for the first five years of the program. “Graduating Frontiers students have joined doctoral programs at institutions across the U.S., including Harvard, Berkeley, UCLA, Minnesota and University of Michigan, among others.

"The program was conceived as a STEP project within the university's ADVANCE program,” he said. STEP stands for Strategies Toward Excellent Practices. “Deborah Goldberg, John Vandermeer and Beverly Rathcke were the ones who developed the idea for Frontiers and I was lucky enough to inherit the fruits of their efforts. And the support that we've had from Rackham – from Abby Stewart and from Janet Weis – has been spectacular. The Frontiers Program has been the result of a lot of work by many people."

"It's been a real privilege to work with Frontiers students during the past five years. They have increased the strength and the diversity of our graduate program and I have learned a lot from them.  It's reassuring to know that the program will in great hands with Tom Duda as director. Tom has put in a lot of work over the past few months to learn about Frontiers. He has some great ideas for leading the program into the future."

“As the founding director, Mark Hunter has done an absolute stellar job establishing the Frontiers programs with comprehensive mentoring and rigorous standards,” said EEB Professor and Chair Deborah Goldberg.  “I am delighted that Tom has agreed to be the next director and will be bringing his talents and creativity to the program.”

Loss of biodiversity appears to impact ecosystems as much as climate change, pollution and other major forms of environmental stress, according to a new study from an international research team.

The study is the first comprehensive effort to directly compare the impacts of biological diversity loss to the anticipated effects of a host of other human-caused environmental changes.

The results highlight the need for stronger local, national and international efforts to protect biodiversity and the benefits it provides, according to the researchers, who are based at nine institutions in the United States, Canada and Sweden.                                                                   

"Loss of biological diversity due to species extinctions is going to have major impacts on our planet, and we better prepare ourselves to deal with them," said Professor Brad Cardinale, one of the authors who is an ecologist in the Department of Ecology and Evolutionary Biology and the School of Natural Resources and Environment.  The study was published online in the journal Nature, May 2, 2012.

Caption: Researchers measuring the productivity of algae in a stream. Image credit: Brad Cardinale.

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The Detroit Free Press interviewed Professor Robyn Burnham in a travel article about Yasuni National Park in Ecuador that appeared May 14, 2012. Burnham’s quotes follow:

"Everyone on Earth should see the rain forest if they want to. It is precious; it is our lifeline to survival. Ecotourism may help if it can be strictly controlled."

"If everyone understood our connection to it at an organic level, we might be more willing as humans to sacrifice our comfort to save other species."

Read the Detroit Free Press article (Free DFP links expire after 30 days)

Captions: Afternoon rainshowers in tropical forests bring unexpected surprises.
Wooly monkeys (Lagothrix lagotricha) are commonly seen in Yasuní National Park by patient, quiet observers. Credit: Robyn Burnham.

Since Frontiers’ inception in 2008, four EEB Frontiers Master’s Program students have moved on to EEB’s doctoral program: Cindy Bick, Serge Farinas, Theresa Wei Ying Ong, and Senay Yitbarek.

Bick (2010 Frontiers cohort) is investigating questions pertaining to differential survival in a Pacific Island endemic species, terrestrial snails,with her advisor, Professor Diarmaid Ó Foighil. “In recent decades, the rich endemic tree snail fauna of the Society Islands (French Polynesia) has been almost completely extirpated by an introduced predator,” Bick said. “However, two snail species have differentially survived in the valleys of Tahiti and the goal of my thesis is to determine what factor(s) underlay this differential survival.

“I chose UM’s EEB program because of its outstanding depth in both ecology and evolutionary biology,” she said. “The faculty here is engaged in diverse and exciting research topics ranging from the origins of species to global climate change. Students get to be part of this exciting research. Fortunately, I found an advisor who worked on a research topic that I am highly interested in. The faculty and administration here are also very committed to fostering a supportive environment for its students.

“My undergraduate degrees were not in ecology or evolutionary biology and I was severely limited in the academic background that it took to succeed in an EEB graduate program. In the past two years as a Frontiers master’s student, I have been doing a lot of catching up. I have been exposed to a wide range of research topics as well as approaches in ecology and evolutionary biology. This exposure has enabled me to ‘fine tune’ my research interests and provide me with a foundation and competitive advantage to continue on to a nationally prominent Ph.D. program. This program also prepared me to navigate the mental and academic challenges of being a graduate student. Whenever I needed advice, there was always tremendous support from the EEB faculty and from diversity programs throughout the university.”

"Cindy has excelled in our Frontiers Master's Program and has proven to be a highly determined and intrepid researcher," said Ó Foighil. "I'm really pleased that she has picked us over Yale for her Ph.D. Given her interests in conservation biology,  Cindy is well positioned to make a big impact  (socially as well as scientifically) as a Polynesian woman scientist working in Oceania. We need to train talented young scientists just like her if we are to have any realistic chance of preserving representative fractions of these fragile island biotas."

Bick, who joins the Ph.D. program in the fall of 2012, was nominated for and received a Rackham Merit Fellowship, one of the largest and most prestigious awards for incoming students. The RMF recognizes entering students who have outstanding academic qualifications, show exceptional potential for scholarly success in their graduate program, and demonstrate promise for contributing to wider academic, professional, or civic communities. Farinas and Yitbarek are also Rackham Merits Fellows.

Regarding his decision to join EEB’s doctoral program, Farinas (2009 Frontiers cohort) said, “For me, it was a natural choice as I realized I had grown into a community here. There are so many great ecologists and the caliber of the work they do is amazing. Every day is a challenge. I have advanced greatly in knowledge and understanding since being here. Not only that, but I think the various other intellectual and social engagements that come along with this environment have caused me to grow quite a lot as a person.

“I feel the master's program was a solid preparation. Most of the time I felt like I was being treated like a Ph.D. student anyway. The expectations were quite high, but the mentorship was always there as a foundation.”

Regarding the experience of moving from Frontiers to the Ph.D. program, he said, “In all honesty, I don't feel like much has changed. Well, there's the additional stress of prelims of course, but the basic course is the same. I am trying to become the best and most well-rounded ecologist I can be. What I really look forward to, though, is more time to focus on deeper questions and building research that can answer them.”

Farinas will continue to study changing climate effects on plant communities. This summer he will focus more on questions of changes in nitrogen dynamics and the relationship to patterns of diversity. His advisor is Professor Deborah Goldberg.

Ong (2009 Frontiers cohort) chose to join EEB’s doctoral program because she really enjoyed working with her advisor, Vandermeer, and thinks that UM's theoretical ecology program and proximity to Detroit, which is currently the center of urban agricultural movements, was ideal.

“I found out that I was interested more in theoretical ecology and agroecology than conservation biology by going through the Frontiers program and being exposed to all sorts of research conducted at U-M,” Ong said. “Frontiers is a great program for deciding where to go next. It really helped me explore a variety of options, which helped me to decide what was best for me.”

Ong is currently investigating spatially-explicit ecological dynamics in urban gardens as part of Project Grow. Specifically, she is investigating the complex relationships between pea plants and other leguminous crops, plant pests (aphids) and the natural enemies of the pests (ladybird beetles and fungi). Ong and her collaborators will apply field, theoretical, and lab work towards understanding the patterns and mechanisms of pest and natural enemy dispersal through urban areas.  

Yitbarek (2008 Frontiers cohort) focuses on complexity, space, games, emergence, and assembly with his advisor, Vandermeer, and believes that there was no other place in the world than to join UM’s EEB department. “My choice for joining the Ph.D. program was relatively simple. I wanted to work with John Vandermeer,” Yitbarek said.

“Professor Vandermeer belongs to the last creed of world-class intellectuals and has made significant contributions to theoretical ecology as well as advanced this knowledge to the burgeoning field of agricultural ecology that sustains the livelihoods of millions of small farmers with the science of ecology.

“My training as a master student with John Vandermeer was aimed at helping me to discover things on my own, to challenge my own and others’ ideas, and to make mistakes, which in return gave me a much more profound understanding of the material at hand than any of the As I ever received in my life. In short, I became truly educated.”

As a Ph.D. student, Yitbarek is investigating the invasion dynamics of the little fire ant Wasmannia auropunctata, considered to be one of the world’s top 100 invasive pests. This species is not considered to be an invasive in its native range, but drastically reduces ant biodiversity outside of its native range. The question of why this is the case continues to be perplexing to many ecologists. By combining theoretical aspects of spatial competition, empirical analysis of competitive networks, and field observation in both Mexico and Puerto Rico, we hope to gain a deeper understanding of the invasion dynamics associated with W. auropunctata.

“Both Ong and Yitbarek have been great students, both during their master's career and now as Ph.D. students,” said Vandermeer. “The direction each of them has taken is a consequence of their experience as Frontier's students and I doubt they would have taken these tracks if it had not been for the opportunities offered them by the Frontier's program. In addition to the perspectives both bring to my lab with their distinct cultural backgrounds, they bring a diversity of intellectual engagement that has been exciting for everyone in the lab. This diversity of scholarly pursuit has been an incredibly important contribution of the Frontier's program to our department more generally.”

The Detroit Free Press interviewed Professor Ines Ibáñez about the record-breaking warm spring this year. The early warm-up can set up “an ecological mismatch,” though the final impact won’t be clear immediately, according to Ibáñez. Read the full article “Fahrenheit flip-flop means lots of bugs, buds and sneezes."

Biology freshman Matt Miyano won a ribbon for best poster presentation at the Undergraduate Research Opportunity Program (UROP) Spring Research Symposium. He presented his work in a poster titled “Assessing Forest Resilience with a Forest Accelerated Succession ExperimenT (FASET)” in April 2012. Miyano worked at the University of Michigan Biological Station and in the lab of Professor Knute Nadelhoffer lab this year as part of UROP.

His research seeks to quantify the resistance and resilience of available nitrogen and vegetation within a forest ecosystem from a girdling disturbance. Girdling is the complete removal of a strip of bark from around the entire circumference of tree trunk. By girdling early successional trees from 39 hectares of the UMBS’s Forest, FASET emulates disturbances, such as partial deforestation or an influx of tree pathogens. The goal of FASET is to assess how carbon and nitrogen cycling reacts across the forest ecosystem when secondary successional tree species replace primary, dominant trees. This research provided evidence for the resistance and resilience to disturbance of forest nitrogen cycling, which is important considering the anthropomorphic stressors that are being imposed on forests.

Two other undergraduate students who have been doing research in the Nadelhoffer Lab as part of the UROP were Ryan Chong and Nicole Dear. They have each been working on different aspects of FASET. 

Many other biology undergraduate students and EEB faculty take part in UROP each year.

EEB graduate students Celia Churchill and Wenfeng Qian won the 2012 EEB Outstanding Paper Award. Churchill’s cover story in Current Biology (October 2011), “Females Floated First in Bubble-Rafting Snails” and Qian’s “Balanced codon usage optimizes eukaryotic translational efficiency” in PLoS Genetics (March 2012) were selected by the review committee of Ya Yang and Sourya Shrestha, EEB postdoctoral fellows. 

Regarding the paper Churchill coauthored with her advisor, Professor Diarmaid Ó Foighil, and others, Yang and Shrestha wrote, “As the paper's opening states, it is indeed a challenge to explain drastic evolutionary changes mechanistically, and this paper – by providing phylogenetic evidence for a sequence of morphological evolutionary changes that shows how exactly neustonic (microscopic organisms that float on the surface of open water) bubble-rafting snails arose from its benthic (organisms living on sea or lake bottoms) ancestors – does that. The exposition is first rate, concise yet mostly accessible to non-experts, and the results are conclusive and impressive.”

Qian’s paper was coauthored with Jian-Rong Yang, former visiting student, Nathaniel M. Pearson, former postdoctoral fellow, Calum Maclean, postdoctoral fellow, and Qian’s advisor, Professor Jianzhi Zhang. The review committee wrote, “The paper attempted a very difficult question of the mechanisms behind codon usage bias. The authors used multiple arguments, including an elegant experimental manipulation in yeast. In the end, the author proposed a general evolutionary model that translation accuracy, coevolution between tRNA recycling and codon usage, and mutation and drift together determine the patterns of codon usage bias. The article is well written and well organized. The message is clear and convincing for evolutionary biologists in general.” 

Shrestha wrote, “Ya and I enjoyed reading five nominees for this year's outstanding student papers. The papers spanned a wide range of topics and employed various techniques, each making substantive contribution in their areas.”

Every year a graduate student paper is selected based on approach of study, scope of findings, and insights into questions of broad scientific interest using multiple lines of evidence. The winners will share the $500 prize.

Pictured: Wenfeng Qian and Celia Churchill