ABOUT | PROGRAM | PEOPLE | CONTACT | DONATIONS
Internal Docs | Webmail
QUICK LINKS
About E&E
Program Faculty
Emeritus Professors
PhD Students
Master Students
Postdocs
Staff and Professionals
E&E Alumni




  Scan To Bookmark
E&E Department Faculty
H. Resit Akcakaya, Professor (CV)
Ph.D., Stony Brook University 1989
Applied ecology, conservation biology
Resit.Akcakaya[AT]stonybrook.edu
LS674, (631)632-8605
Akcakaya Lab Website
Research Summary:
My research focuses on developing and applying quantitative methods to address questions in conservation biology and environmental risk assessment. The following topics are examples of the types of questions that I am currently interested in:
Climate change impacts on biodiversity: I am developing methods that link climate change models, species distribution or habitat suitability models, and metapopulation models with dynamic spatial structure, to predict the vulnerability of species to global climate change.
Status and trends of biodiversity: I am interested in methods to quantify and analyze the threat status of species and trends in threat status, including quantitative methods for estimating spatial and temporal uncertainties in parameters used in threatened species assessments based on the IUCN Red List Categories and Criteria.
Species conservation: I use habitat-based metapopulation models to estimate the risk of extinction or decline, and to evaluate the chances for recovery with different management and conservation options.
Population dynamics: I am interested in developing new methods for modeling population dynamics, estimating model parameters, analyzing population declines, and validating extinction risk estimates.
Demographic toxicity: Currently, most assessments of the ecological impacts of pollutants use bioassays at the individual organism level. I am interested in developing standard methods that will allow ecotoxicological impacts to be assessed at the more relevant population and species levels.
For more information, see the Akcakaya Lab web site (see link above).
Stephen Baines, Assistant Professor (CV)
Ph.D., Yale University, 1993
Aquatic ecosystem ecology, ecological stoichiometry
stephen.baines[AT]stonybrook.edu
LS112, (631)632-1092
Baines Lab Website
Research Summary:
I am an ecosystem ecologist interested in how organism characteristics, ecological processes and factor acting over regional scales combine to shape aquatic biogeochemical cycles that involve carbon and trace elements. My current research foci can be divided into three areas.
First, I try to understand variability in the elemental composition of microscopic organisms that form the base of open water food webs - namely phytoplankton, bacteria and protozoa -- and how this variability may also influence nutrient cycles or the transfer of contaminant elements through food-webs. I do so with field and laboratory experiments using radioisotopes, biokinetic modeling of contaminant accumulation by organisms, ecological stoichiometric modeling of food-web and recycling dynamics and X-ray fluorescence microscopic measurements of the elemental content of individual plankton cells collected from nature.
Second, I study how the use of dissolved organic matter (DOM) as an energetic subsidy by aquatic consumer organisms can allow them to sidestep the negative feed-backs that typically occur in predator-prey systems, potentially leading to persistent reductions in the resource base upon which other consumer organisms depend. Because many toxic trace elements form complexes with dissolved organic matter, uptake of DOM by organisms also exposes them to contaminant metals and alters the movement of these contaminants through aquatic ecosystems. I am interested in how "bioavailability" of DOM varies over space and time, the sources of bioavailable fractions, and how the characteristics of the surrounding landscape may affect the susceptibility of lakes and rivers to transformative change by invasive organisms.
Finally, I use statistical analysis of long-term data sets to determine the degree to which the dynamics of neighboring ecosystems are synchronized by regional climate. This approach allows me to gauge the relative importance of extrinsic forces, local context and intrinsic dynamics as drivers of ecosystem variables. This question is important not only for the interpretation of long-term ecological data, but also generally in the effective monitoring and management of lakes, rivers and coastal embayments.
Michael A. Bell, Professor (CV)
Ph.D., UCLA, 1976
Contemporary evolution, evolutionary genetics
mabell[AT]life.bio.sunysb.edu
LS023, (631)632-8574
Bell Lab Website
Research Summary:
Mike Bell's research concerns patterns of morphological variation in time and space in the threespine stickleback fish, Gasterosteus aculeatus. This species complex is emerging as one of the premier systems in evolutionary biology because it exhibits extraordinary phenotypic diversity (Fig. 1) and has several qualities that make it easy to study. Threespine stickleback are widespread in north temperate and boreal regions and have invaded fresh water innumerable times from the ocean to found freshwater populations. Here they occupy diverse habitats and rapidly undergo adaptive radiation that is highly predictably in relation to food type, predation regime, water clarity, and other factors. Consequently, freshwater populations in similar habitats have similar phenotypes and can be used as replicate samples in comparative studies to infer selection mechanisms and the genetic and developmental basis of similar phenotypes in different populations. Stickleback reproductive and parental behavior have been studied for several decades, and extensive knowledge of morphology, behavior, and life history has been combined in studies of population biology and speciation. The first linkage map for threespine stickleback was published in 2001, and rapid progress is being made to develop specialized tools for research in stickleback genomics.
Bell's laboratory houses extensive research collections of threespine stickleback from Cook Inlet Alaska (Fig. 2) and fossil stickleback from Nevada (Fig. 3). The lab is well equipped to study variation of armor traits and body form, and fish can be reared for genetic analysis or to produce subjects for research in behavior and functional morphology. Bell's research interests include variation of armor phenotypes among lake populations in relation to environmental factors, patterns of evolutionary change on the time scale of centuries in fossils (Fig. 4) and generations in modern populations, relationships between ontogeny and morphological variation and between multivariate variation and multivariate evolution, and transmission genetics. He conducts field research in Cook Inlet, Alaska on modern populations and in west-central Nevada on fossil stickleback. Bell collaborates with genomists and developmental geneticists on the evolution of gene expression during skeletal developmental. By focusing on traits of a well-studied species from multiple biological perspectives, he is studying the interactions of phylogeny, environmental change, genetic architecture, development, and natural selection in determining patterns of phenotypic variation in time and space.
Liliana M. Dávalos, Assistant Professor (CV)
Ph.D., Columbia University, 2004
Phylogenetics, tropical deforestation
ldavalos[AT]life.bio.sunysb.edu
LS630, (631)632-1554
Dávalos Lab Website
Research Summary:
I’m an evolutionary biologist interested in the ancient history of biodiversity and its conservation. At my lab, we focus on how diversity in species and traits arises, and on helping shape policy to conserve ecosystems today and into the future.
Daniel E. Dykhuizen, Distinguished Professor (CV)
Ph.D., University of Chicago, 1971
Molecular evolution, phylogenetic analysis
dandyk[AT]life.bio.sunysb.edu
LS632, (631)632-8591
Dykhuizen Lab Website
Research Summary:
As a student of Richard Lewontin, I decided that it should be possible to test evolutionary hypotheses experimentally. I picked the common colon bacterium, Escherichia coli, because it could grow in defined medium with a generation time of one or two hours and because the genetics and physiology were well known. With this short generation time, competition experiments of fifty generations can be done from Monday to Friday, allowing a free weekend. The bacteria are grown in a chemostat, a continuous flow device that maintains a constant environment, so that the fitness differences of two genotypes can be measured to an accuracy of less than 0.5%. At first, I thought of bacteria as little fruit flies. But they are not. They are very different creatures. My primary interest in experimental evolution is to understand the causes of natural selection: What conditions in the environment act upon what types of genetic variation to produce natural selection. I, with Tony Dean and Dan Hartl, have established a predictive theory of natural selection linking differences in enzyme activity to differences in fitness in a simple environment (publications 1 and 2). This theory can be extended to more complex environments (publication 4). We are currently extending this work to look at the long-term evolutionary dynamic of specialization.
Sex in bacteria is very different from sex in animals or plants. Sex in bacteria has been separated from reproduction. Bacteria, rather than either being fully sexual or fully asexual, seem to have evolved an optimum level of sexuality or lateral gene transfer between lineages. Also, rather than mixing two lineages in equal proportions as animals and plants do, bacteria can transfer amounts as small as a few hundred bases to nearly half the chromosome. I showed that sexuality is important in E. coli (publications 3 and 5). I am now investigating the importance of lateral gene transfer in Borrelia burgdorferi, the cause of Lyme disease. B. burgdorferi has a very low rate of transfer of very small pieces of DNA, suggesting only the recombinants that have a selective advantage are seen in nature. I have an ongoing interest in species definitions and speciation in bacteria (publications 3, 6, and 10).
Recently, I have started to work on the population genetics of infectious disease bacteria. We have shown that only four of the seventeen clones (serotypes) of the Lyme disease bacterium found in the Northeastern United States cause chronic Lyme disease (publication 9). This simplifies vaccine development. Evgeni Sokurenko and I have developed the idea that evolution is important during a chronic infection (publication 8). We are studying the adaptation of type 1 fimbrae in E. coli during bladder infections (publication 7 and curent work). I am interested in being able to find every mutational change in the genome during adaptation, either in a long-term chemostat experiment or in an infected animal. In this way we can track evolution happening.
Walter F. Eanes, Professor and Chair (CV)
Ph.D., Stony Brook University, 1976
Molecular evolution, phylogenetic analysis
walter.eanes[AT]stonybrook.edu
LS634, (631)632-8593
Eanes Lab Website
Research Summary:
I work on the population genetics and molecular evolution of Drosophila as a model system. In general we are attempting to interface life history, populations genetics, pathway influences, and phenotypic effects of individual metabolic enzymes. We have a large database of metabolic enzymes involving glycogen, trehalose and triglyceride synthesis on D. melanogaster. This includes a sample of about 20 gene sequences (down through the glycolytic pathway) that allow us to identify specific amino aid sequences and recognized specific footprints in sequence data that allow inference about possible selective effects. We also have a set of population samples from Florida to Vermont that allow us to identify specific geographic patterns such as latitudinal clines. Using the P-element insertion series in D. melanogaster we have begun the functional knockout of specific genes in critical points. This has already allowed us to test specific effects of pathway activity variation and determine if individual steps have control over metabolic pool steady levels or possibly flux levels. The flux levels are assayed using NMR measurements using 13C stable isotopes. In addition we have an ongoing project funded by the NSF and in collaboration with Paul Schmidt at Penn to study the ecological genetics of the female reproductive diapause trait in Drosophila melanogaster. Our lab's primary role is in the QTL mapping and identification of the gene or genes responsible for this complex trait life history.
Douglas J. Futuyma, Distinguished Professor (CV)
Ph.D., University of Michigan, 1969
Evolutionary processes; evolutionary ecology; coevolution
futuyma[AT]life.bio.sunysb.edu
LS670, (631)632-1411

Research Summary:
Douglas Futuyma's research interests in evolution focus primarily on speciation and the evolution of ecological interactions among species. He has been a Guggenheim and a Fulbright Fellow, the President of the Society for the Study of Evolution, the American Society of Naturalists, and the American Insitute of Biological Sciences, the editor of Evolution, and is a member of the National Academy of Sciences. He is editor of the Annual Review of Ecology, Evolution, and Systematics, and is the author of the successful textbooks Evolutionary Biology and Evolution.
Most of his work has centered on the population biology of herbivorous insects and the evolution of their affiliation with host plants. Research on several species centered on genetic differences conferring adaptation to different host plants, and cast light on the evolution of host specificity. Recent work has focussed on whether or not constraints on genetic variation are likely to have influenced the phylogenetic history of host associations in a group of leaf beetles, and on the pattern of speciation in this group. Futuyma's students have worked on diverse evolutionary and ecological studies of insect-plant interactions and of speciation in insects.
Lev R. Ginzburg, Professor (CV)
Ph.D., Agrophysical Res. Inst. St. Petersburg, Russia, 1970
Theoretical ecology
lev.ginzburg[at]stonybrook.edu
LS610, (631)632-8569
Ginzburg Lab Website
Research Summary:
My attention has been focused on the foundations of population ecology. My most widely known work is a theory of predation (the ratio-dependent or Arditi-Ginzburg model) that is an alternative to the classic prey-dependent Lotka-Volterra and MacArthur-Rosenzweig models. A recent book, How Species Interact (Arditi & Ginzburg, 2012) summarizes our take on this proposed alteration of the standard view. Second in recognition has been inertial growth, or a quantity-quality, two-dimensional approach to population dynamics replacing the usual one-dimensional approach. This explanation of population cycles, based upon the material effect model, is the main point of the book Ecological Orbits (Ginzburg & Colyvan, 2004).
One of my interests in the last few years has been in metabolic ecology (Ginzburg & Damuth, 2008). I work on the idea that generation time is an essential fourth dimension of an organism in addition to the dimensions of space that it occupies. The 4D view provides a simple, unifying explanation for various observed slopes of metabolic allometries. Another recent interest of mine is an evolutionary theory of non-adaptive selection, the disappearance of unstable configurations (Ginzburg et al, 2010). I am currently writing a book (Non-Adaptive Selection, with John Damuth) which will explore the implications of this idea for macroecology.
Catherine Graham, Associate Professor (CV)
Ph.D., University of Missouri-Saint Louis, 2000
Biogeography, conservation biology, ecology
catherine.graham[AT]stonybrook.edu
LS636, (631)632-1962
Graham Lab Website
Research Summary:
Catherine Graham research is in two main areas: empirical work focused on landscape and behavioral ecology, with an emphasis on how human-altered landscapes affect ecological processes; and bioinformatics/geographic information systems modeling to examine how current and historical environmental factors affect patterns of species distribution. At a landscape scale she examines how landscape- and local-level factors influence patterns of habitat use by animals. Particularly, she is interested in bridging the gap between landscape and behavioral ecologists, who generally work at completely different scales. This disparity has resulted in a lack of empirical landscape-oriented behavioral information with which to develop a broad perspective on fragmentation effects. At a regional scale she is integrating museum data, environmental GIS layers, distributional niche models and phylogenetic information to better understand processes that may have led to current species distribution patterns. Catherine focuses on tropical systems and is currently collaborating with researchers from Ecuador, Colombia and Australia.
Jessica Gurevitch, Professor (CV)
Ph.D., University of Arizona, 1982
Biological invasions, plant population
jessica.gurevitch[AT]stonybrook.edu
LS638, (631)632-8590
Gurevitch Lab Website
Research Summary:
Prof. Gurevitch was the chairperson (from Sept. 2006 to Aug. 2012) of the department of Ecology and Evolution.
My research spans several traditional categories within the field of ecology. Most of my work involves the experimental investigation of fundamental ecological questions at the level of plant populations and communities. I am also interested in statistical applications in ecology, particularly in the design and analysis of ecological experiments. While my work has always been concerned with addressing questions of basic scientific interest, I have attempted to connect the basic research to issues with applied and conservation relevance.
Plant invasions: One major area of my research in recent years has been using field experiments to test which factors are most responsible for determining community susceptibility or resistance to colonization by invasive plant species in Long Island forests. Most studies on the ecology of invasions have been descriptive (whether quantitative or not), rather than experimental. Taking an experimental approach to this area of tremendous current concern and interest offers a number of compelling advantages, including the opportunity to disentangle and rank the importance of factors contributing to the success or failure of biological invasions. With my colleague Dr. Manuel Lerdau and several postdoctoral and graduate student researchers, we have conducted a series of experiments in which species introductions and manipulation of environmental variables (light and soil resources) test which factors are most important in facilitating or hindering invasion. The work has already confirmed some suspected relationships and presented a number of surprises. Invasion is positively associated with native species diversity, and with soil nitrogen and calcium. It appears that poor soil resources (but not light or disturbance) exclude invasive species from pine barrens communities, but light availability combined with soil resources are critical in allowing or blocking invasives in mixed hardwood forests. We have also examined the ties between the community effects of invasion and the effects at the ecosystem level by evaluating plant nutrient uptake, storage and recycling in leaf litter. This work is ongoing, and future research will focus on changes in plant functional groups in forests as a consequence of invasion and other global bioclimatological changes.
Pine Demography: Another major research interest concerns the demography of pines. I have studied the responses to fire of pitch pines, Pinus rigida, in Long Island pine barrens communities, including the globally rare dwarf pine plains, using long-term demographic data, tree rings, and modeling. Pitch pines depend upon disturbance (primarily fire) to regenerate, but severe fires after long-term fire suppression may have negative consequences for the recovery of these populations. This system offers the unusual and very exciting opportunity to work at the interface between population processes and community structure. The work also touches upon a number of issues related to general plant demographic responses to disturbance, as well as to fire management strategies for fire-prone ecosystems in a suburbanized landscape. With Dr. Fox, I have also worked on the demography of slash pines in Florida, and in the future plan to use a demographic approach to studying an invasive pine in Australia, P. radiata (Monterey or radiata pine).
Statistical problems in ecology: I have also worked on statistical aspects of experimental design and analysis in ecology. This work evolved out of my desire to design and analyze my own field experiments so that I could get the most information possible out of my hard-earned data. In response to the need for making more appropriate and sophisticated statistical techniques available to the ecologists, I co-edited a textbook on this topic (with Sam Scheiner), Design and Analysis of Ecological Experiments (1993, Chapman and Hall; 2nd ed. 2001, Oxford University Press). A major aspect of my statistical efforts has been the development and application of meta-analysis in ecology. Meta-analysis is the quantitative synthesis of the results of independent experiments. Borrowing from meta-analytic techniques in the social science and medicine, I have worked to introduce this approach to the fields of ecology and evolution since the early 1990's. I have both carried out meta-analytic syntheses of ecological research, and been involved in the development of the statistics of meta-analysis to make these methods more applicable to ecological data and ecological questions. In addition, I co-authored a software package for meta-analysis with the goal of making these techniques more accessible to ecologists (MetaWin 2.0, Rosenberg, Adams and Gurevitch, publ. Sinauer Assoc.).
Textbook: Finally, I co-authored a text book, The Ecology of Plants (Gurevitch, Scheiner and Fox, Sinauer Assoc. 2002) designed for upper-division college courses in plant ecology. The origins of writing a textbook grew out of my attempt in my own teaching to bring very current science to undergraduates in a vivid and understandable way, and to communicate my passion for the field.
Brenna M. Henn, Assistant Professor (CV)
Ph.D. Stanford University, 2009
Human evolution, population genetics, genomics
brenna.henn[AT]stonybrook.edu
LS640, (631)632-8600
Henn Lab Website
Research Summary:
My research lab investigates patterns of human genetic diversity and evolution by pairing genomic datasets with information about phenotype, language and prehistory. I am committed to understanding genetic diversity in under-represented populations and hypothesize that the determinants of phenotypic traits and disease in these populations may be influenced by alleles that are population-specific or generally rare. I am broadly interested in refining models of human migration and understanding the adaptive significance of healthy phenotypes such as life history traits, pigmentation and disease resistance. We are particularly focused on the complex demographic history of African populations. In collaboration with African geneticists, we currently work with Khoe-San populations at several field sites in the Kalahari Desert and Richtersveld to collect DNA samples, ethnographic data and basic phenotypes like skin pigmentation and height. By leveraging reduced environmental variability in these populations, low linkage disequilbrium and historic endogamy, we can jointly address questions regarding the genetic basis for different phenotypes and their evolutionary history. Are there loci of large effect for height and skin pigmentation? Are estimates of heritability for these phenotypes similar or different to estimates from cosmopolitan populations? Was the ancestral population of humans of short stature or tall? I have an interdisciplinary research background obtained during my Ph.D. in anthropology and as a postdoctoral fellow in human genetics, both at Stanford University, as well as industry experience in 'personal genomics'.
Jeffrey S. Levinton, Distinguished Professor (CV)
Ph.D., Yale University, 1971
Conservation biology, developmental evolution
levinton[AT]life.bio.sunysb.edu
LS680, (631)632-8602
Levinton Lab Website
Research Summary:
Jeffrey Levinton has done research on a wide variety of topics, all in the general area of marine ecology. His major interest is in relating feeding biology of marine bottom animals to population and community-level processes. Currently, he is working on feeding selectivity in suspension-feeding bivalves using flow cytometry and video endoscopy. In the last few years, he has also worked on the evolution of resistance to toxic substances and physiological adaptation of growth strategies to temperature regimes. Levinton has also done research on rate of evolution in the fossil record and maintains a strong interest in paleobiology. In collaboration with Gregory Wray, he is working on estimating the timing of the divergence of the animal phyla and has developed evidence against the Cambrian explosion hypothesis. He is currently doing simulations to understand the degree to which molecular data can confirm the notion of a Cambrian explosion. He is also working currently on the role of sexual selection and natural selection in the morphological evolution of fiddler crabs, and their relationship to phylogeny based on molecular data. His students have worked on related research topics, but also on grazing in coral reefs, chemical defense, and rocky shore ecology.
Levinton was a Guggenheim Fellow, a Fulbright Senior Scholar and is the author of a major text in marine biology and a monograph on macroevolution. He has served as an editor for The American Naturalist, Ecology, Ecological Applications, and was head of the Hudson River Fund Panel of the Hudson River Foundation. He is now an editorial advisor for Global Ecology and for the Journal of the Marine Biological Association.
Heather J. Lynch, Assistant Professor (CV)
Ph.D., Harvard University, 2006
Development and application of statistics
hlynch[AT]life.bio.sunysb.edu
LS113, (631)632-9508
Lynch Lab Website
Research Summary:
Dr. Lynch received her A.B. in physics from Princeton University in 2000, graduating summa cum laude and receiving the American Physical Society's LeRoy Apker Award for the best undergraduate physics thesis in the US. She continued her physics training at Harvard University, but after receiving her M.A. in Physics, decided to transfer into the Organismal and Evolutionary Biology Department to pursue her interest in statistical ecology. Under the advising of Dr. Paul Moorcroft, Dr. Lynch received her PhD in 2006 for her thesis "Spatiotemporal Dynamics of Insect-Fire Interactions". As a post-doctoral research associate, and then assistant research scientist, in Dr. William Fagan's lab at the University of Maryland, Dr. Lynch applied her expertise in the statistical analysis of complex ecological datasets to a range of problems including patterns of survivorship in mammals, biodiversity patterns in dendritic ecological networks, and the effect of reproductive asynchrony in defining the geographic range of the bagworm.
Dr. Lynch's research focuses on the development and application of statistics and mathematics to conservation biology. Her current research revolves around a large-scale vessel-based breeding bird survey program called the Antarctic Site Inventory, a project she manages in partnership with the non-profit research organization Oceanites. Her work to understand the complex spatiotemporal dynamics of Antarctic penguins, in particular their response to climate change on the Antarctic Peninsula, will bring a multitude of exciting opportunities for undergraduate and graduate students in the department. We are very excited about the strength in statistics and mathematics and added breadth in conservation biology that Dr. Lynch will bring to our department and anticipate that she will also strengthen connections between our group and others on campus.
Ross H. Nehm, Associate Professor (CV)
Ph.D., University of California-Berkeley, 1998
Science education, evolution education, cognition
ross.nehm[AT]stonybrook.edu
LS672, (631)632-7247
Nehm Lab Website
Research Summary:
The Nehm lab studies science learning, with a focus on biological concepts such as natural selection and evolution. Prior work has examined novice and expert reasoning strategies, psychometric evaluation of education instruments, science teacher belief revision, conceptual restructuring of folk-biological knowledge, and the comparative efficacy of educational innovations. Currently, the lab is developing machine-learning models for automated assessment of complex scientific practices (such as biological explanations). The lab has been supported by the National Science Foundation's EAR, CCLI, TUES, CAREER and REESE programs. For more information on this work, visit the Nehm Lab website (see link above) and the Center for Science and Math Education (www.stonybrook.edu/cesame/).
Dr. Nehm is a member of the Ph.D. program in Science Education at Stony Brook. He was the recipient of an NSF CAREER award, a teaching award from UC-Berkeley, a faculty mentoring award from CUNY, and was named an Education Fellow in the Life Sciences by the National Academies. He serves on the editorial boards of the Journal of Research in Science Teaching, the Journal of Science Teacher Education, and the Journal of Science Education and Technology; he also sits on the advisory boards of several NSF science education projects.
Dianna K. Padilla, Professor (CV)
Ph.D., University of Alberta, 1987
Aquatic ecology, applied ecology, conservation biology
padilla[AT]life.bio.sunysb.edu
LS618, (631)632-7434
Padilla Lab Website
Research Summary:
Dianna Padilla's major interests are (1) phenotypic plasticity, its relationship to morphology, and its significance in evolution; (2) plant herbivore functional ecology, especially the evolution of structural defenses of plants and the role of mode of feeding and morphological adaptations of herbivores, and (3) the patterns of spread and impacts of invading species in aquatic ecosystems. Her current research focuses on phenotypic plasticity of the marine snail family Littorinidae and ranges from determining the evolution of form and function of the radular feeding apparatus to studies of the phenotypic variation and function of littorinid radulae when snails are subjected to different foods or environments. She is also actively engaged in studies on the invasion of zebra mussels (Dreissena polymorpha) and other aquatic invaders. These studies include examining factors that influence the patterns of spread of invading species, particularly the movements of humans and the ecological impacts of invading aquatic species on both benthic species (gastropods) and the planktonic community and food web. She is also conducting collaborative work with scientists from the Former Soviet Union who have studied the Eastern European invasion of zebra mussels for more than 20 years. They are testing predictive models of the spread and ecological impacts of zebra mussels as well as summarizing decades of research that have not been previously available to non-Russian scientists.
Joshua Rest, Assistant Professor (CV)
Ph.D., University of Michigan, 2004
Genome evolution
jrest[AT]life.bio.sunysb.edu
LS676, (631)632-1916
Rest Lab Website
Research Summary:
Fitness Landscapes of Gene Expression
Related publications: Nonlinear fitness consequences of variation in expression level of a eukaryotic gene, Contribution of transcription factor binding site motif variants to condition-specific gene expression patterns in budding yeast.
We are measuring the extent that changes in the expression of genes result in changes in the fitness (reproductive capacity) of cells. We alter the expression level of a given gene using a repressible promoter, and measure the resulting fitness by competing the cells with altered expression against cells with normal expression. The result is an expression-fitness curve that indicates the precise relationship between expression level and fitness. The fitness curve for a gene predicts the amount of variation in expression among individuals in a population, where flatter functions are expected to show more variation.
We have completed measurement of the expression-fitness function for a gene, LCB2, that is essential for the production of sphingolipids in the cell. We are now using next-generation sequencing technology to scale up this analysis for a larger number of genes.
Variation in the Carbon Metabolic Network
Related publication: Coevolution trumps pleiotropy: Carbon assimilation traits are independent of metabolic network structure in budding yeast.
A goal in molecular evolution is to understand how evolution acts to integrate selective pressures from diverse and changing environmental parameters in light of constraints imposed by cellular architecture. We are taking advantage of the tremendous diversity for carbon utilization within the species Saccharomyces cerevisiae and S. paradoxus to investigate this. We are studying how sets of metabolic traits co-evolve, and what the effect of sharing of pathways of cellular systems among traits is on their co-evolution. We are taking advantage of natural variation in the number of carbon utilization traits to study whether the complexity of molecular pathways alters the effect of mutational input through canalization or mutational robustness.
Protein Interaction Stability, Degree, and Authenticity
We are investigating model-based integration among various types of protein-protein interaction data with the goal of robust inference of the degree, stability, and reality of individual interactions.
Phylogenetics and Horizontal Gene Transfer
Related publications: Massive mitochondrial gene transfer in a parasitic flowering plant clade, Horizontal transfer of expressed genes in a parasitic flowering plant, Sulfate activation enzymes: phylogeny and association with pyrophosphatase, Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages, and others listed here.
We use phylogenetic methods to detect horizontal gene transfer, to reconstruct ancestral protein and regulatory sequences, and to test biological hypotheses. We are particularly interested in statistical methods to reject or accept alternative biological hypotheses.
Interfering Interactions as a Driver of Regulatory Architecture
We are examining the extent that modularity is driven by avoidance of gain-of-function mutations, including avoidance of deleterious pairwise interactions. We artificially turn genes on at the same time to see if there is an epistatic cost for co-expression.
F. James Rohlf, John S. Toll Professor (CV)
Ph.D., University of Kansas, 1962
Biometry, geometric morphometrics, theory of systematics
rohlf[AT]life.bio.sunysb.edu
LS620, (631)632-8580
Rohlf Lab Website
Research Summary:
F. James Rohlf is a John S. Toll Professor and is a Fellow of the American Academy of Arts and Sciences and also of the American Association for the Advancement of Science. He is interested in the applications of mathematical methods and statistics (especially multivariate statistics) to problems in biology with emphasis on morphometrics and the theory of systematics. Along with Robert Sokal, he is the co-author of the popular text Biometry, now in its fourth edition.
Recent research has been concerned with the relatively new field of geometric morphometrics - using statistics to study variation in the shapes of biological structures its covariation with other variables. It is "geometric" because it involves a more complete capturing of shape than could be done with traditional ad hoc suites of measurements, ratios, and angles. Recent work has focused on some of the mathematical and statistical properties of morphological shape spaces as well as applications to primate evolution. For related information see the morphometrics web page.
Recent publications have included statistical analyses of the human microbiome, shell shape variation in Conus, and applications to optic neuropathy in humans.
John R. True, Associate Professor (CV)
Ph.D., Duke University, 1995
Genetics of species differences, speciation
jrtrue[AT]life.bio.sunysb.edu
LS114, (631)632-8600
True Lab Website
Research Summary:
My lab group is interested in the genetic and developmental basis of differences among closely related species and how natural and sexual selection bring these differences about. Our work centers on Drosophila melanin patterning as a genetic and developmental model system.
The laboratory is currently studying the evolutionary genetics of melanin patterning and male courtship behavior in the Oriental melanogaster species group. Several lineages in this species group exhibit male specific wing spots (Fig. 1). A recent phylogenetic analysis (Fig. 2) indicates that multiple gains or losses of male wing spots have occurred during the Oriental species group radiation. Intriguingly, species with the male wing spots also exhibit a striking wing display during male courtship. [To view a video of courtship in Drosophila elegans, in which much of our current work is focused, go movie page] D. elegans males also appear to use this display in male-male aggressive interactions [movie page]. Species that do not have male wing spots do not exhibit this behavior. We are currently surveying male courtship behavior throughout the Oriental melanogaster species group in order to understand how this novel behavior has evolved. For example, we would like to know whether the use of the male wing display in courtship evolved before or after its use in male-male interaction and whether specific elements in male courtship, such as circling the female, were prerequisites for evolution of the male wing display.
We are also studying the molecular genetic basis for naturally occurring melanism in D. elegans (Fig. 3). Populations of D. elegans from the northern part of its range (Taiwan, Japan) are dark black in color whereas southern populations (China, SE Asia, Indonesia) are light tan in color. This morph difference is controlled by a single, semidominant, autosomal Mendelian factor. We are in the process of fine-scale mapping of this locus with the ultimate aim of characterizing it at the molecular level. Melanic polymorphisms like this one in D. elegans are extremely common and insects but in no case has such a polymorphism been identified at the molecular level. Identifying the gene responsible for melanism in D. elegans will provide a crucial model for a general understanding of insect melanism at the developmental, genetic, and ecological levels.
Krishna R. Veeramah, Assistant Professor (CV)
Ph.D., University College London, 2008
Primate Comparative Genomics, Genetic Basis of Epilepsy
krishna.veeramah[AT]stonybrook.edu
LS616, (631)632-1101
Veeramah Lab Website
Research Summary:
Krishna Veeramah is a primate genomicist and population geneticist, who received both his B.Sc. in 2003, and Ph.D. in 2008 from University College London. His Ph.D., conducted under the supervision of Mark Thomas, examined the distribution of genetic variation in Africans. He then moved to UCLA as part of John Novembre’s lab where he looked at the genetic architecture of European population isolates. In 2010 he joined Michael Hammer’s lab at the University of Arizona in order to lead a project comparing patterns of genomic variation on the autosomes and X chromosome in apes. At Stony Brook his research will be focused on using genomic-scale data to understand the evolutionary genetics of human and non-human primates and conducting geographically fine-scale studies of human genetic variation in sub-Saharan Africa. He is also involved in projects examining ancient DNA from Migration Period Europe and the genetic basis of epilepsy.
Non-E&E Department Faculty Associated with the Graduate Program
Jackie Collier, Associate Professor (WEB)
Ph.D., Stanford University, 1994
Microbial ecology
jackie.collier[AT]stonybrook.edu
(631)632-8696
School of Marine & Atmospheric Sci.
David O. Conover, Professor
Ph.D., University of Massachusetts, 1982
Adaptation and natural selection of life-history traits
david.conover[AT]stonybrook.edu
(631)632-8667
School of Marine & Atmospheric Sci.
John Fleagle, Distinguished Professor
Ph.D., Harvard University, 1976
Primatology
john.fleagle[AT]stonybrook.edu
(631)444-3121
Department of Anatomical Sciences
Charlie Janson, Professor
Ph.D., University of Washington, 1985
Primate ecology and behavior, evolution of seed dispersal
charles.janson[AT]mso.umt.edu
Division of Biological Sciences,
University of Montana
Andreas Koenig, Professor
Ph.D., Georg-AugustUniversity, 1992
Primate behavioral ecology, social evolution
andreas.koenig[AT]stonybrook.edu
(631)632-1513
Department of Anthropology
Manuel Lerdau, Professor
Ph.D., Stanford University, 1994
Physiological ecology of metals, biological mechanisms
mlerdau[AT]virginia.edu
Environmental Sciences and Biology,
University of Virginia
Glenn R. Lopez, Professor
Ph.D., Stony Brook University, 1976
Marine ecology
glenn.lopez[AT]stonybrook.edu
(631)632-8660
School of Marine & Atmospheric Sci.
Stephen B. Munch, Assistant Professor
Ph.D., Stony Brook Univeristy, 2002
Life history evolution
steve.munch[AT]noaa.gov
(831)420-3909
School of Marine & Atmospheric Sci.
Massimo Pigliucci, Professor
Ph.D., University of Tennessee, 2003
Philosophy of biology, relationship between science
massimo.pigliucci[AT]gmail.com
Department of Philosophy,
CUNY Lehman College
Alistair Rogers, Scientist
Ph.D., University of Essex, 1998
Plant physiology, climate change
arogers[AT]bnl.gov
Environmental Sciences Department,
Brookhaven National Laboratory
Randall Susman, Professor
Ph.D., University of Chicago, 1976
Functional morphology, human evolution
randall.susman[AT]stonybrook.edu
(631)444-3125
Department of Anatomical Sciences
Patricia Wright, Professor
Ph.D., City University of New York, 1985
Conservation, primatology
patricia.wright[AT]stonybrook.edu
(631)632-7620
Department of Anthropology
Associated Research Faculty
Frank J. Turano, Research Assistant Professor
Ph.D., Stony Brook University, 1994

turano[AT]life.bio.sunysb.edu
LS035, (631) 632-8600

Research Summary:
Because of its confined physical limits and geographical position, Long Island is a test laboratory for many environmental issues that will face other areas of the country in the future. My primary research is concerned with compiling and understanding the Pre- and Post-European Contact Environmental History of Long Island. These studies utilize written cultural records as well as maps, art, graphics, photography, and oral history. This understanding is used to explore alternatives for contemporary environmental issues and produce documentary films.
Fredric V. Vencl, Research Associate Professor (CV)
Ph.D., Stony Brook University, 1977

fvencl[AT]life.bio.sunysb.edu
LS650, (631) 632-8609

Research Summary:
Two puzzles have long fascinated me: why are there so many species, especially of beetles, and has the evolution of novel traits, or suites of traits fostered the remarkable beetle diversification. I integrate phylogenetics, behavior, morphology, and chemistry with field experimentation to investigate the evolutionary ecology of firefly and leaf beetle defenses.
I investigate several questions that explore macro-evolutionary processes and patterns: (1) how novel traits ('key innovations') impact diversification rates; (2) what factors promote the recurrent evolution of ecological specialization; (3) whether and how sexual selection fosters speciation, and; (4) whether rates and quantitative patterns of behavioral, morphological, and chemical change during lineage diversification indicate escalation, or other directional trends in evolution.
My current work concerns quantification of the importance of proximate host choice behavior governing oviposition preferences of leaf-feeding beetles. I have tried to measure the impact on progeny survival of a female's oviposition choices of host leaves that vary in requisite chemical defense precursors necessary for her progeny's survival against predators. Other projects examine whether chemically-mediated, co-evolutionary interactions between hosts, host defensive chemistry, and predators have predictably guided herbivore dietary evolution. The relationship between allometric size variation in male secondary sexual traits, and mechanisms of female trait preference in fireflies is an ongoing subject of both field and laboratory study. With colleagues, I am currently investigating whether chemical exudates released by fireflies provide protection against nocturnal enemies such as bats, ants, and toads.
I also make contributions to the natural history, taxonomy, and systematics of fireflies (Lampyridae) and of leaf beetles (Criocerinae: Chrysomelidae).
CONTACT | CAMPUS MAP | DIRECTIONS | 650 LSB Stony Brook, NY 11794-5245 | Design&Webmaster: Fumio Aoki