Newsletter 2015-1 June 26, 2015

Mark Pagel, 2015 Darwin Day Speaker

Mark Pagel Does Darwin Day

Stony Brook's celebration of Darwin Day has become an important event in the life of Stony Brook University and we have been graced with a tremendous group of guest lecturers. Mark Pagel, F.R.S. and Professor of Biology at the University of Reading, U.K.  is one of the very most distinguished evolutionary biologists in the world and has made ground-breaking contributions to how we think about the evolutionary relationships of organisms and how their forms evolved. He has contributed strongly to our understanding of how to construct evolutionary trees and has applied these accomplishments to understanding the evolution of human language. 

Pagel's lecture was a fascinating introduction to the diversity and structure of human languages around the globe.  By reckoning our language into individual elements, he has used evolutionary principles to study how our language came to be so complex today, producing thousands of languages that are not mutually understandable by all of humanity. His work is very popular and he has given two well-received TED lectures. 

His audience filled the seats and every step, nook and cranny of the lecture theater. Overcoming a failure of our AV system, he managed to speak without a microphone and keep spellbound an audience of about 400. 

Krishna Veeramah Enters the Grave to Unfathom the Mystery of Barbarian Invasions Using Paleogenomics 

Few topics in European history are as controversial as the barbarian migrations in

The Assassination of Alboin, King of the Lombards by Charles Landseer (1856
to the Roman world at the end of Antiquity (~400 AD). Historians have debated for centuries the magnitude, nature, and impact of the movement of populations from the borders of the Roman Empire into its heart between the fifth and seventh centuries. For example were barbarian migrations the cause of the disintegration of the Roman Empire? How large and significant were these migrations? Did they replace local populations, simply dominate them, or rapidly merge with them?


The traditional sources used by scholars to answer these and other questions regarding what is commonly known as the Migration Period have been written sources and archaeological material. However, the development of 2nd generation sequencing has led to a revolution in the field of Paleogenomics over the past 5 year, allowing researchers to extract whole genomes from hominin specimens up to tens of thousands of years old. Therefore the Veeramah lab and historian Patrick Geary (Institute for Advanced Study, Princeton), in collaboration with a network of European paleogeneticists and archaeologists, are attempting to obtain genomes from thousands of Medieval specimens from across Europe in order to better understand the demographic history and social dynamics of the Migration Period.

As a starting point, they recently received an NSF Archaeology award to characterize ~300,000 genome-wide SNPs from the remains of 46 individuals found at a key 5th century Lombard-era cemetery in Szólád, Hungary. The Lombards were a Germanic people first identified as living along the shores of the Baltic Sea in the 1st century C.E but later residing in Pannonia (what is now Western Hungary, the Czech Republic, and Eastern Austria) prior to their entry into Italy in 568, where they established a vast kingdom that lasted for ~200 years. We will combine genomic, material culture and isotopic data in order to test whether the spatial arrangement of burials at Szólád is organized by genetic relatedness or some other aspect of social identity (e.g. warrior status). They will also be able to examineif there is evidence of admixture between genetically distinct populations within the cemetery and if so, if there is a relationship between certain archaeological signatures and long-term genomic ancestry. These inferences will allow Veeramah and his team to construct a model of the social system of a population associated with an important putative Lombard cemetery based on an unprecedented level of scientific characterization.

If this project is a success they will then be able to apply this approach to other cemeteries in order to also infer the dynamics of the putative Lombard invasion from Pannonia to Italy as well as further extend it to the migrations of other barbarian tribes. Veeramah's ultimate goal is to construct a genomic map of Migration Period Europe. Given that many modern nation states still trace their identify from these barbarian tribes, such a map would provide a powerful framework for understanding modern European genetic diversity from both evolutionary, population and medical genetics perspectives.


More information: See Krishna's Lab Page

Stickleback Conference to Meet at Stony Brook

The Eighth International Conference on Stickleback Behavior and Evolution will meet in the Wang Center of Stony Brook University from July 26 to 31, 2015. The Threespine Stickleback has long been a favorite of. In the late 1960s, evolutionary biologists discovered that the taxonomic confusion of stickleback systematics reflected rampant convergent evolution. Developmental geneticists were attracted by the skeletal diversity of this species in the late 1990s, and the first Threespine Stickleback genome sequence was released in 2006. 

Stickleback genomics was an important topic three years ago at the last Stickleback Conference. However, now genomics and molecular genetics have so thoroughly permeated research on behavior, physiology, ecology, evolution, toxicology, and parasitology of the Threespine Stickleback that genomic studies per se fill only a short session. So, the focus in the Stickleback Conference will be on traditional problems in biology that can now be illuminated by clever employment of genomic and molecular methods. 

Members and alumni of the Department of Ecology and Evolution, SoMAS, and other units in the College of Arts and Science will be welcome at sessions. Look for the schedule of papers for the Stickleback Conference in the next few weeks.
Contact Mike Bell ( for additional information.

Josh Rest

Josh Rest Lab Research Highlights: Variation in Metabolism and Gene Expression Levels


How do organisms survive in a changing world? Joshua Rest's lab is working to answer this question at the molecular level. Two of his lab's projects are highlighted here, examining metabolic variation among populations, and gene expression variation within populations. Rest is supported by a grant from the NIH.

Individuals show variation in which nutrients they can metabolize; for example, some people metabolize alcohol poorly. Rest and graduate student Dana Opulente used budding yeast (Saccharomyces cerevisiae) as a model to study why lineages isolated from different environments vary in their ability to use different nutrients. They found lineages that can utilize many different nutrients (from glucose to glycerol to glucitol), and also lineages that can utilize only a few. Rest and Opulente observed that lineages that utilize more nutrients grow and reproduce faster and are also more robust to the effects of genetic mutations. Using whole-genome sequences, they found that differences in this metabolic breadth are due primarily to changes in the number of copies of certain genes.. They computationally estimated the effect of this variation on the metabolic network, and found that strains that are mutationally robust also have network structures that are less sensitive to the loss of various network components.

Rest, along with doctoral student Chris Morales and technician Kash Bandlerage, are also investigating the consequences of "noisy" protein expression differences among individual cells in a population. "Noisy differences" means that levels of a protein vary among individual cells in a population even when the genotype and environment are identical. Using cells where a particular gene has been tagged with a fluorescent protein, they measured the growth rate of cells with very low or very high levels of expression. They found that, for many noisy proteins, the cells with extremely high or low levels of expression grow and reproduce much slower than the rest of the population. They also found that these noisy differences in expression level could last several generations. The team is now investigating whether cells with different noisy expression levels help the population better respond to environmental stresses, and whether there is genetic variation in the amount of noise.
Alumni and friends we hope you remember how important an early financial boost was in your graduate research. 
Please give to the Lawrence Slobodkin Fund for Ecological Research.
Give to the George Williams Fund for Student Research. Donate Now
Give to Ecology and Evolution Award for Student Excellence. Donate Now

How much? Suggested donations. Full professors: >= $200, Associate Professors: >= $100, Assistant Professors and Postdocs: >= $50 Please get used to giving annually. We need your help. Thanks so much!!
Our Spring 2015 PhD Graduates and Advisors

Ecology and Evolution spg 2015 Graduates
Left to Right: Fabrizio Spagnolo, Daniel Dykhuizen, Walter Eanes, Dana Opulente, Erik Lavington, Mary Alldred, Stephen Baines, Michael McCann, Dianna Padilla, Josh Rest 

E&E Events, Awards and Passages

Walt Eanes will soon be finishing his third term as Department Chair this summer, as he anxiously awaits the arrival of our new Chair Bob Thacker, a world renowned expert on symbioses between microorganisms and invertebrates and a central figure in the Sponge Tree of Life project. Walt has an active and exciting lab and is looking forward to finding out what is going on there very soon. We thank him for his literally tireless service.

Catherine Foley has been awarded the 2015 Science Policy award of the American Society of Mammalogists. Congratulations to Maureen Lynch who received a Tinker Foundation Field Research Grant of $2,500 to support her research on gentoo penguin acoustics in Argentina. Congratulations to Chloe Hae Yeong Ryu for receiving a grant from the Theodore Roosevelt Memorial Fund of the American Museum of Natural History. Elise Lauterbur was awarded a grant-in-aid of research from the American Society of Mammalogy and also was awarded a fellowship to attend the Summer Institute in Statistical Genetics of the University of Washington. 
Shyamalika Gopalan, PhD student, received a $2000 Boehringer Ingelheim Fonds travel award to train in ancient DNA laboratory techniques at the University of Mainz, Germany over winter break. Her training was successful and she has sequenced an early Neolithic dog genome. 
Gena Sbeglia, currently completing a year of fieldwork in Madagascar, has been awarded the Madeline Fusco Fellowship Award by the Graduate School.  Marisa Lim has been awarded a travel grant by the Society for the Study of Evolution to attend the Multiple Dimensions of Biodiversity Science symposium at the Evolution meeting. She was also awarded travel grants from the Stony Brook University Sigma Xi chapter and the Institute of Population Genetics for attending the Society of Molecular Biology and Evolution conference. 

Matthew Aiello-Lammens, who finished his PhD in Resit Akcakaya's lab about a year ago, has just accepted a position as Assistant Professor at Pace University, in the Department of Environmental Studies and Sciences. 
ShuDan Yeh, former student of John True, has accepted a tenure track faculty position in the Department of Life Sciences at National Central University in Taoyuan City, Taiwan. The Lindau Nobel Laureate Meetings has selected 
Laurel Yohe, student of Liliana Davalos, to participate in the 65th Lindau Nobel Laureate Meeting in Lindau, Germany. Only the, 650 most qualified young scientists from around the world can be given the opportunity to enrich and share the unique atmosphere of the Lindau Nobel Laureate Meetings.
Rodrigo Cogni is now Assistant Professor of Biology at the University of Sao Paulo, Brazil. Marianne Moore has accepted an Assistant Professor position at the Polytechnic campus of Arizona State University, Mesa. Kevin Shoemaker, a post-doc in Resit Akcakaya's lab, just accepted a position as Assistant Professor at the University of Nevada, Reno, in the Department of Natural Resources and Environmental Sciences. Minsu Ha, NSF Post-doc with Ross Nehm, accepted a position as assistant professor of biology education at Kangwon National University (South Korea). He will continue work on evolution education.

Mary Alldred, student of Stephen Baines, has received, a Junior Scientist's award to attend the Theo Murphy Discussion Meeting, "Elements, genomes and ecosystems: cascading nitrogen and phosphorus impacts across levels of biological organisation," in Buckinghamshire, U.K., hosted by the Royal Society. Mary has officially accepted a post doc to work on nitrogen cycling in Jamaica Bay with Chester Zarnoch at Baruch College.Mike McCann, student of Dianna Padilla, has defended his thesis on multiple states of lakes and has begun a postdoc at Rutgers. Recent graduate student from the Rest lab Niamh O'Hara was awarded two postdoctoral fellowships (!) - an NSF Postdoctoral Fellowship and a Runway Postdoc at Cornell Tech. She will be joining the Runway Postdoc program with the goal of launching a company to monitor the microbiome of hospitals to develop ways to combat hospital acquired infections. Dana Opulente (advisor Josh Rest) started a postdoc with Chris Hittinger at UW Madison working on ambitious project to sequence and analyze the genomes of every known species of Saccharomycotina yeast. Abby Cahill (advisor Jeff Levinton) started last fall a postdoc at the Station Marine d'Endoume, Marseille to work on genetic variation of Mediterranean invertebrates.

Heather Lynch has just been awarded a grant from NASA, entitled "Bayesian Data Model Synthesis for Biological Conservation and Management in Antarctica" and is being funded under NASA ROSES Earth Science Applications: Ecological Forecasting for Conservation and Natural Resource Management.Also Shawn Serbin and Lynch have been awarded a Stony Brook University-Brookhaven National Lab SEED Grant for the project "Three-dimensional structure and function for ecological monitoring using unmanned-aerial systems and computer vision". Liliana Davalos was awarded a NSF grant entitled "Collaborative Research: Chance or necessity? Adaptive vs. non adaptive evolution in plant-frugivore interactions." Ross Nehm joins Kostas Kampourakis (University of Geneva) and Alice Wong (University of Hong Kong) as the new editors of Science & Education. 

Distinguished Professor Daniel E. Dykhuizen officially retired last year, however both he and his lab have remained productive. Dan was the keynote speaker at the inaugural ASM Conference on Experimental Microbial Evolution in Washington, DC, highlighting the entire history of the field.  As for his students,
Omar Warsi successfully defended his thesis in September and is now at a postdoc with Dan Andersson at Uppsala University in Uppsala, Sweden.
Fabrizio Spagnolo defended in April and is currently a Postdoctoral Fellow at NYU School of Medicine investigating adaptation in Methicillin Resistant  Staphylococcus aureus with Bo Shopsin. 

Here is a question about E&E history from the last Newsletter
Which university has had the most E&E Ph.D.s join their faculty? Well it is a tie. The University of Pennsylvania has had Peter Petraitis, (Ph.D., 1979, advisor Jeff Levinton) Junhyong Kim, (Ph.D. 1992, advisor Lev Ginzburg),Dustin Briston (Ph.D. 2006, advisor Dan Dykhuizen). The University of Nebraska has Lawrence Harshman (Ph.D. 1982, advisor Doug Futuyma), Tony Zera (Ph.D. 1984 advisor Dick Koehn), and Guillermo Orti (Ph.D. 1995, but now at George Washington University).

A new question: How many E&E faculty have been Fulbright Senior Scholars? I don't know either!

Contacts: Chair Walt Eanes, Graduate Program Director Stephen Baines, or
the Newsletter Editor, Jeff Levinton