Fiscal Year 2002 Awards

 

BIO Informatics Postdoctoral Research Fellowships

 

 

Fellow’s Name             Host Institution                         Research Area/Training Plan            NSF Award #

Title of Research & Training Plan

Abstract

Joshua I. Armstrong      Plant Gene Expression Center         Plant Developmental Mechanisms          0203281

 

Applying biological informatics and chemical genetics to explore developmental processes regulated by the plant hormone auxin

 

The plant hormone auxin arbitrates plant development at multiple levels. This research deconvolutes the complex regulatory network controlled by auxin and its effectors using small molecules, oligonucleotide microarrays, and bioinformatics. More broadly, it develops a general experimental and analytical framework for using chemical genetics and biological informatics to elucidate intricate signaling pathways in plants.

Sheri A. Church         Indiana University           Population Biology             0204160

 

Identifying rapidly changing genes and their impact on the speciation process in sunflowers through genome level sequence comparisons

 

If speciation is caused by adaptation to different environments, genes under strong selection for different adaptations may also be speciation genes. This study uses comparative analyses of genome sequences among sunflower species to identify genes on which natural selection is strongest and then tests to see if these genes are involved in speciation.

Anne E. Hall          University of Chicago                   Cell Biology                        0204327

 

Multi-species sequence comparison and compositional analysis of plant centromeres

 

This research seeks is to understand the composition, organization and evolution of centromeres--regions that mediate chromosome partitioning. Centromere sequences from relatives of the flowering plant Arabidopsis thaliana are being compared to assess sequence conservation and determine the types and abundance of sequence classes. This will distinguish rapidly evolving sequences from those exhibiting significant conservation.

Stephanie E. Hampton      University of Washington             Ecology              0204068

 

The effect of winter variability on biodiversity and community dynamics: analysis of long-term lake data

 

Strong contrast between winter and summer abiotic conditions annually provides distinctly different habitat within one location, promoting biodiversity. To determine effects of reducing this environmental heterogeneity, this research uses multispecies autoregressive analysis (MARs) to analyze complex seasonal community transitions, discerning biotic pathways through which winter conditions affect both summer and winter communities.

Jason J. Head      Queen Mary College, University of London and              Systematic Biology             0204082

National Museum of Natural History

Recovering the influences of environmental change on vertebrate faunas using a morphological phylogeographic analysis of recent and fossil erycine snakes

 

Morphometric analysis and robust statistics are being used to determine phylogeographic responses of recent and fossil erycine snake faunas to environmental transitions. This research examines the systematic levels at which fossils can be recognized by osteological variability, how reptiles respond to environmental changes through time, and the extent that fossils can predict faunal responses to anthropogenic environmental modifications, in order to define signaling mechanisms important to bacterial-fungal communities.

Wendy L. Hodges       University of California-Riverside             Systematic Biology         0204459

 

High-Resolution Imagery and New Visualization Tools for Reconstructing a Horned Lizard Ancestor

 

Complex images generated by high-resolution x-ray computed tomography are being combined with phylogenetic hypotheses and algorithms to estimate and visualize ancestral traits in a genus of lizards, Phrynosoma. The primary hypothesis, horn complexity increases along phylogenetic branches, is being tested by reconstructing ancestral morphology and visualizing changes from ancestor to extant species using comparative methods.

Jason H. Knouft              Washington University                  Systematic Biology             0204144

 

Investigation of factors influencing large-scale ecological and evolutionary patterns among Caribbean Anolis lizards

 

The research investigates macroecological patterns of body size, abundance, and character displacement in Caribbean Anolis lizards from a phylogenetic perspective. It integrates phylogenetic information on approximately 140 species, morphological data from specimens in museum collections from nearly 7,000 study sites, and landscape data from Geographic Information Systems (GIS) to examine factors influencing the diversification of these lizards.

Matthew J. McHenry         Harvard University                          Integrative Animal Biology               0204066

 

Modeling the dynamics of mechanoreception in fish
 
Fish can perceive mechanical vibrations even when water flows over the body during swimming. Both the swimming motion and mechanical stimuli generate forces on mechanosensory structures on the surface of the body. By integrating experimental and computational approaches, this work examines how these forces vary with stimuli and with the swimming motion.

Carrie L. Morjan                      Indiana University              Population Biology             0203687

 

Modeling the genetics of species using biological informatics: interactions of gene flow, selection, and dispersal

 

This simulation model uses parameters compiled from biological databases to evaluate the role of gene flow, selection coefficients and dispersal on the rate of allelic spread across subdivided populations. The research provides information on how species may remain cohesive at only a handful of major loci while simultaneously diverging at many minor loci, and has implications for explaining the relationship between macro- and microevolution.

Lydia P. Olander          Carnegie Institute of Washington        Ecosystem Studies                 0204210

 

Predicting the effects of land use change on nutrient limitation to ecosystem productivity and carbon storage in the humid tropics

 

Where land-use alters nutrient dynamics, nutrient impoverishment may alter recovery rates, maximum recoverable productivity, carbon storage, and water and energy fluxes. Current biogeochemical models have insufficient representation of phosphorus and other rock-derived nutrients often critical in tropical systems, and are unable to deal with rapid shifts typical of land-use change. This study develops mechanistic nutrient models at various spatial/temporal scales incorporating improvements into general biogeochemical models (Century/Terraflux) and testing predictions under various land-use scenarios.

Gail L. Patricelli                  Cornell University                           Animal Behavior                 0204291

 

The directionality of acoustic communication in passerine birds

 

The goal of the research is to develop a system for mapping the radiation of sound from vocalizing animals. The system is to be used to measure the directionality of different call types from passerine birds in open and forest habitats, and to test hypotheses about the functional significance of directionality in acoustic communication.

Matthew D. Potts          University of California-San Diego           Ecosystem Studies          0204070

 

Using Spatial and Species Explicit Forest Dynamics Models to Optimize Biodiversity Conservation in a Managed Landscape

 

Managing biodiversity in tropical forests requires solving an optimization problem that simultaneously maximizes biodiversity and timber value over time. This optimization problem is being solved through the development of sample based biodiversity indices, the development of spatial and species explicit forest dynamics models, and the quantification of the opportunity costs of biodiversity protection.

Noah A. Rosenberg        University of Southern California       Systematic Biology                0204057

 

Inferring evolutionary importance of genes from the shapes of multi-species gene genealogies
 
It is predicted that loci causally involved in divergences of incipient species have gene trees that are monophyletic within species and concordant with species phylogenies. This research develops coalescent-based probabilistic models to describe shapes of multi-species gene genealogies. These models are being applied to genomic sequence data to identify loci potentially involved in species divergences.

Tania Schoennagel       University of Colorado-Boulder           Ecosystem Studies               0203719

 

Modeling the influence of climate change on fire regimes and successional patterns in topographically diverse landscapes in the Rocky Mountains

 

Understanding the response of fire regimes to variation in regional climate and local topography is critical to predicting potential effects of global warming in forested ecosystems. This research combines dendrochronology and GIS techniques to model potential responses of fire regimes and successional patterns to plausible climate change scenarios within two national parks in the Rocky Mountains.

Michael W. Sears             Indiana State University             Ecology                              0204484

 

New procedures for modelling the thermal environment of small animals

 

The spatial and temporal distribution of thermal resources across landscapes influences the abundance and distribution of organisms. Existing techniques to evaluate thermal habitats do not adequately represent the complexity of most environments. Novel procedures are being developed to generate detailed, dynamic, thermal maps using artificial neural networks that incorporate thermographic imaging and microclimate data.

Harry A. Stern                Cornell University                    Biophysics                0204069

 

Computer simulation of lipid bilayer permeation

 

Phospholipid bilayer membranes regulate the transport of molecules into and out of the cell. Though most transport is assisted by channels or membrane proteins, passive transport directly through the bilayer does occur. A molecular-level understanding of membrane permeation can shed light on the blood-brain barrier, the mechanisms of anesthesia, and basic processes such as osmosis and the diffusion of oxygen and carbon dioxide. It may also assist in predicting the bioavailability of orally-administered drugs. The proposed research is the computer simulation of the permeation of small molecules through lipid bilayer membranes using recent algorithms developed for long-time molecular dynamics simulations.

Ted M. Townsend      University of Texas at Austin       Systematic Biology            0204451

 

Development and testing of genetic algorithms for inferring maximum-likelihood based phylogenies from very large, heterogeneous molecular data sets

 

Likelihood-based phylogenetic algorithms become very computationally expensive as data sets become larger. However, genetic algorithms offer an efficient alternative to existing methods. This project uses a large molecular data set to test the efficiency and accuracy of a recently developed genetic algorithm under various models of evolution and search conditions. The data are being used to construct a phylogeny of frogs.

Amy Vandergast      San Diego State University        Ecosystem Studies         0204447

 

Using Geographic Information Systems in spatially explicit analyses of population genetic structure

 

This research uses geographic information systems (GIS) to explore methods that incorporate explicit environmental information in distributional analyses of genetic variation within species. The investigations are focused in Southern California, where previous research has produced detailed environmental data layers and many genetic data sets for species in similar functional groups. It is being determined the extent to which landscape-level processes influence the creation, distribution, and maintenance of genetic biodiversity across this region.

Mark E. Welch           Vanderbilt University        Population Biology                     0204062

 

How much influence do the collateral effects of selection have on natural levels of genetic variation?

 

Genetic variance among populations, FST, is being measured at multiple mapped loci from specific linkage groups in Silene latifolia. The relationship between FST-values and genetic map distance is used to estimate the differential effects of selection across the genome, elucidating the overall effect of selection on population genetic structure.

 

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