1987 — 1990 |
Hillis, David |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Evolution of Anurans: a Comparative Sequence Analysis of Ribosomal Dna |
0.915 |
1987 — 1993 |
Hillis, David |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Pyi: Interspecific Molecular Variation @ University of Texas At Austin
Dr. David M. Hillis's research interests concern the analysis of ribosomal genes of representatives of each of the families of frogs, as well as other amphibians. Such molecular techniques are extremely powerful as a means of recovering evolutionary history over the hundreds of millions of years of amphibian evolution. This work includes sequencing a portion of the 28S ribosomal RNA gene that contains numerous insertions (added lengths of genetic code). In addition, two other problems occupy Hillis's attention. First, he is involved in efforts to isolate and identify specific gene fragments from well-preserved 10,000 year old human remains found at Little Salt Spring, Florida. Second, he is studying the genetics of the highly polymorphic tree snail Liguus fasciatus, which has proven to consist of populations that reproduce with genetic recombination in some locations but clonally and without genetic recombination at others. Dr. Hillis's academic institution is the University of Texas at Austin. Funding is provided through a Presidential Young Investigator Award for a duration of five years.
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0.915 |
1993 — 1997 |
Hillis, David |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Phylogenetic Analysis and Simulations On Massively Parallel Computers @ University of Texas At Austin
This research is being conducted by Dr. David M. Hillis, a molecular biologist from the University of Texas. Dr. Hillis is well known for his studies relating to DNA sequence analysis. The current research is a natural extension of Dr. Hillis' past work and represents a major innovation, linking the utilization of parallel computers with a need for the development of more efficient software for analyzing the increasing amount of nucleotide sequence data. Software for DNA sequence analysis is being modified and developed for massively parallel computers in an effort to increase computation speed and enhance the assessment of available computer algorithms. Supercomputer manufacturers are currently emphasizing massively parallel architecture, and even smaller highly parallel computers are under production and/or developed. The development of software for biological analysis will contribute to both the scientific community and the newly emerging parallel computer industry.
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0.915 |
1993 — 1996 |
Hillis, David Kirkpatrick, Mark [⬀] |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Dissertation Research: Green Blood and Adhesive Pads: Evolution of Novel Adaptations in Lizards @ University of Texas At Austin
9311139 Kirkpatrick Several species of lizards from the South Pacific have green blood. This green coloration is the result of the accumulation of the bile pigment biliverdin. Bile pigments are toxic to virtually all vertebrates producing the pathological condition known as jaundice. An understanding of how these lizards are able to withstand large concentrations of biliverdin may provide insight into the pathological nature of bile pigments in other vertebrates including humans. This same group of lizards has evolved several different types of adhesive toe pads. These toe pads are so adhesive that they can climb on smooth vertical surfaces such as glass. By measuring the adhesive abilities of different microstructures for different species we can understand the relationship between different morphologies and mechanisms of adhesion. Knowledge of the evolutionary relationships of these lizards is critical to understanding patterns of morphological and physiological evolution. ***
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0.915 |
1994 — 1997 |
Bull, James [⬀] Hillis, David |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Dissertation Research: Experimental Molecular Evolution in Bacteriophage @ University of Texas At Austin
9411950 Bull This experimental study examines molecular evolution in recombinant DNA phages. The recombinant phage are constructed to specifically address two topics of interest in molecular evolution: 1) the molecular evolution of essential transgenes (phage capsid and assembly genes) and 2) the evolution of RNA polymerase-promoter interactions. Transgenic phage will be characterized at the molecular level via sequence analysis and at the phenotypic level via fitness levels. The fitness of transgenic phage is initially low, but increases rapidly when subjected to laboratory natural selections via serial propagation. After a response to selection for increased fitness is observed, the phage will be re- characterized at the molecular and phenotypic levels. Initial genetic manipulations will lead to specific expectations as to which genetic elements should evolve and how they will change over the course of evolution. This system of experimental molecular evolution in bacteriophage is a powerful new approach in evolutionary biology. Transgenic organisms have become increasingly popular in many areas of biology and industry. This project will for the first time directly address questions concerning how transgenes evolve, what their effects are on other genes, and how these combined molecular changes affect evolution of fitness at the organismal level.
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0.915 |
1995 — 1998 |
Molineux, Ian (co-PI) [⬀] Bull, James (co-PI) [⬀] Hillis, David |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Abr: Experimental Phylogenies For Testing Phylogenetic Methods @ University of Texas At Austin
9508987 Hillis Biologists have long been interested in the history of life, and the last few decades have been accompanied by major expansion in the areas of biology concerned with reconstructing these histories. There are now many different methods that can be used to reconstruct history, and there have been several new applications of the methods, such as discovering the US hantavirus and its animal reservoirs, as well as helping to determine whether health professionals infected their patients with HIV. An inherent difficulty in this important field of science is that there is usually no way to truly know the histories of the organisms being studied, hence it is difficult to know hmw often reconstruction methods fail. In the study proposed here, we will overcome that limitation. A virus will be grown in the laboratory to generate lineages with known ancestries. DNA sequences and other characteristics will be obtained from the resulting lineages. The success of reconstruction methods will be tested directly by comparing the estimated histories with the known histories. The data will also be studied for unusual properties that may thwart recovering history, such as the possibility of molecular convergence resulting from common selective pressures. %%% This study should impact the field of systematic biology both in establishing an empirical methodology for experimental phylogeny construction and in providing direct tests of phylogenetic inference methodology. ***
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0.915 |
1995 — 1997 |
Hillis, David Crandall, Keith |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Molecular and Morphological Systematics of the Australian Genera of Freshwater Crayfish (Decapoda: Parastacidae) @ University of Texas At Austin
9418425 Hillis and Crandall This award will support the travel expenses for three months of Dr. Keith A. Crandall to Australia. Dr. Crandall, along with Dr. David M. Hillis of the Department of Zoology at the University of Texas, Austin, are conducting collaborative research with Dr. Chris Austin of the School of Aquatic Science and Natural Resource Management at Deakin University in Warrnambool, Victoria, Australia. The study will provide information to assist in understanding the systematics and evolutionary biology of a family of freshwater crayfishes. The purpose of the travel is to collect a series of parastacid crayfish in preparation for a morphological/molecular study of their phylogeny. Once the phylogeny has been developed it will be used to test earlier hypotheses on phylogenetic relationships and biogeography. The study will also yield data that should be useful in conservation activities directed at these animals. Dr. Austin brings to the collaboration his expertise on the morphology of Australian crayfish and their geographic distribution. The American investigators have considerable contributions in molecular systematic techniques.
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0.915 |
1997 — 2000 |
Hillis, David |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Dissertation Research: the Evolutionary Persistence of Gynogenetic Lineages and the Role of Frequencey-Dependent Expression of Mating Behaviors @ University of Texas At Austin
9701135 Hillis One of the more puzzling genetic questions is how clonal species maintain themselves through time. Gynogenetic species are clonal animals that face an obstacle to long-term persistence because reproduction is dependent on males of another species. A gynogenetic species cannot persist in isolation; it must coexist with another species whose males it is capable of parasitizing behaviorally. However, simple population models of such interactions predict that gynogenetic species should rapidly become extinct. The existence of gynogenetic species indicates that these models are an insufficient description of reality. One factor that would allow the persistence of the gynogenetic species is frequency-dependent behavior. This investigation will examine frequency-dependent behaviors and their role in the maintenance of gynogenetic species. A mathematical model will be constructed that incorporates frequency-dependent mate selection, and then the model will be tested using two species of poeciliid fish: the gynogenetic specie and the species upon which it depends. The model will establish the levels of frequency-dependent mating that theoretically can result in a stable equilibrium of a gynogenetic species and the species upon which it depends. The experiments will determine if mate selection is frequency-dependent and if frequency-dependence is great enough to explain the coexistence of gynogenetic species and the species they parasitize.
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0.915 |
1998 — 1999 |
Bull, James [⬀] Hillis, David |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Dissertation Research: Synergistic Epistasis of Random Mutations: Experimental and Theoretical Approaches @ University of Texas At Austin
Bull 9801639 Mutations are always accumulating in an organism's genome. These mostly disadvantageous effects can only be removed by selection, that is, by the death or sterility of the individuals carrying the mutations. The genetic health of a population therefore depends in part upon how strongly natural selection is acting. If the genetics of an organism has a certain property, selection can become much more efficient at weeding out deleterious mutations. This study is attempting to see whether or not the genes of a very simple organism show this property, called synergistic epistasis. The term epistasis refers to the presence of an interactive effect between mutations. In this case, the effect of two mutations together is different than would be expected from merely adding the effects of each mutation by itself. Synergistic epistasis refers to the condition where the effect of two mutations is worse than the sum of the individual effects of each. (The opposite effect, where two mutations are less detrimental than the sum of their individual effects, is called antagonistic or diminishing returns epistasis). Synergistic epistasis has been postulated as a general property of genetic systems. It has been implicated as a possible driving force leading to the evolution of sexual reproduction, and has broad implications for the efficiency of natural selection. This study will look at a very simple organism, the bacteriophage PhiX174, to see if mutations behave synergistically or not. The advantages of using such a simple model system revolve around the fact that it is otherwise very difficult to know exactly which mutations are present, and how they interact. The proposed system will avoid this and other problems faced by previous studies that have looked for evidence of synergism.
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0.915 |
2000 — 2005 |
Ryan, Michael (co-PI) [⬀] Hillis, David Cannatella, David |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
The Evolution of Acoustic Signals of Frogs: Origins, Phylogenetic Information, Rates of Diversification, and Morphological Correlates @ University of Texas At Austin
9981631 Cannatella, Hillis, and Ryan The proposed research will integrate an important communication system, the advertisement call of frogs, with a phylogenetic approach in order to address the origin of frog vocalization, the rates of change in behavioral characters associated with vocalizations, and correlation of laryngeal shape change in the anatomical structures that produce the sounds. A formerly accepted phylogeny of frogs suggests that the earliest frogs did not have a well-developed acoustic signaling mechanism. According to a more recent hypothesis, the earliest frogs would indeed have had a well-developed communication system. These two alternative scenarios will be tested using more complete samples of species of the primitve frogs and larger samples of characters, from DNA sequences. There is a general bias that behavioral characters are more subject to change than other classes of data. The presence of intense sexual selection on the male vocal signal suggests that the footprint of history may be obliterated by rapid evolution of call characters. Thus, estimates of phylogenetic relationships derived from call characters will be very different from those derived from DNA sequences. The generality of this observation will be tested using complete DNA sequences of selected genes for five groups of frogs widely distributed throughout North, Central, and South America.
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0.915 |
2001 — 2009 |
Warnow, Tandy [⬀] Bull, James (co-PI) [⬀] Jansen, Robert (co-PI) [⬀] Hillis, David Linder, C. Randal |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Collaborative Research: Itr/Ap Reconstructing Complex Evolutionary Histories @ University of Texas At Austin
EIA-0121680 Warnow, Tandy J University of Texas at Austin
Collaborative Research: ITR/AP: Reconstructing Complex Evolutionary
Reconstruction of the evolutionary history of a group of organisms has changed the face of biology and is being used increasingly in drug discovery, epidemiology, and genetic engineering. Unfortunately, such reconstructions typically involve solving difficult optimization problems, so that even moderately large datasets can require months to years of computation. In addition, almost all evolutionary reconstructions presently assume that the historical pattern is one of strict divergence that can be represented by a binary tree. This assumption is frequently violated, especially by plants which often hybridize readily and thus produce networks of relationships.
This project brings together computer scientists and biologists from two institutions to develop new models and algorithms to address these two problems. Successful completion of this project will have an enormous impact by providing tools for reconstructing phylogenies of large datasets, and the first tools for inferring network models of evolution appropriate to hybridizing speciation. Such network models will alter how biologists think about speciation, while the development of methods for large-scale analyses will strongly benefit medical and pharmaceutical practice. Information technology will be advanced in fundamental ways as well, as the project will demonstrate how algorithm design and high-performance algorithm engineering can jointly solve very difficult discrete optimization problems.
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0.915 |
2001 — 2008 |
Jansen, Robert (co-PI) [⬀] Hillis, David Warnow, Tandy (co-PI) [⬀] Gutell, Robin Linder, C. Randal |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Igert: Computational Phylogenetics and Applications to Biology @ University of Texas At Austin
Phylogenetics , the study of the relationships among genes, individuals, populations, and species, forms the basis for all of comparative biology. This IGERT grant will support a comprehensive, interdisciplinary graduate training program in Computational Phylogenetics and Applications to Biology. The program involves 27 faculty participants from the computational and biological sciences at the University of Texas at Austin, and it will support 12 graduate trainees each year for five years. Two major research areas will be emphasized: computational phylogenetics and applied phylogenetics. Phylogenies provide a fundamental framework for all of biology, and present the computational scientist with many technical challenges. Computational phylogenetics is concerned with the computational aspects of phylogenetic inference, and applied phylogenetics uses estimated phylogenies to address a wide diversity of biological questions. The training program will involve a series of new and existing courses and seminars, a summer training program for students from underrepresented areas of science, co-advisement of each graduate student by one computational and one biological faculty participant, placement of students into well-established research groups in biology and computer science, participation in spring recruitment conferences and fall phylogenetics retreats, and opportunities for internships in the bioinformatics industry, national laboratories, and non-government organizations. The goals of this project are: (i) design and implement an interdisciplinary training curriculum for graduate students across computational and biological sciences that prepares students to understand and contribute to both sides of computational biology; (ii) stimulate interdisciplinary graduate research and interdisciplinary interactions in general between computational scientists and biological scientists that will lead to development and testing of novel approaches to unsolved problems in phylogenetics and their application to problems in biology; (iii) prepare trainees for their careers beyond graduate school and help them achieve visibility in the larger research community; and (iv) evaluate and improve the program in computational and applied phylogenetics to ensure its success beyond the proposed IGERT project. This program will create a unique collaborative environment for graduate students and faculty from the computational and biological sciences.
IGERT is an NSF-wide program intended to meet the challenges of educating Ph.D. scientists and engineers with the multidisciplinary backgrounds and the technical, professional, and personal skills needed for the career demands of the future. The program is intended to catalyze a cultural change in graduate education by establishing new, innovative models for graduate education and training in a fertile environment for collaborative research that transcends traditional disciplinary boundaries. In the fourth year of the program, awards are being made to twenty-two institutions for programs that collectively span all areas of science and engineering supported by NSF. The intellectual foci of this specific award reside in the Directorates for Biological Sciences; Computer and Information Science and Engineering; and Education and Human Resources.
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0.915 |
2001 — 2005 |
Amenta, Annamaria (co-PI) [⬀] Warnow, Tandy [⬀] Hillis, David |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
`Itr/Ap: Collaborative Research: Exploring the Tree of Life @ University of Texas At Austin
0121682 and 0121651 Amenta, Hillis, and St. John Defining and understanding the evolutionary relationships among species is fundamental to contemporary biology and the application of the comparative method in the life sciences. The results of such evolutionary research can be represented by a branching sequence of relatedness among species known as a phylogeny. Because of the geometric resemblance of a phylogeny to the branches of a tree, a phylogeny can be thought of as a tree of life. The proposed collaborative research by biologists and computer scientists at University of Texas-Austin and at CUNY-Lehman College in New York will provide specialized visualization and data mining tools to facilitate creation of a "Tree of Life" for all living organisms on the earth. This includes the development and refinement of algorithms to visualize and analyze multiple complex data sets for large numbers of species. More specifically, this project will: (1) integrate biological data through visualization and clustering techniques developed by computer scientists, and (2) apply these tools to taxa which comprise very large numbers of species with topologically complex and varied tree structures. The interdisciplinary team of biologists and computer scientists will integrate their newly developed software with existing computational tools in systematic biology, and make them freely available to and easily used by the scientific community. The project involves substantive efforts to provide undergraduates and students from under-represented groups with the opportunity to collaborate with scientists throughout the academic year and summer.
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0.915 |
2003 — 2005 |
Hillis, David |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Dissertation Research: Origin and Evolution of Polyploid Frogs @ University of Texas At Austin
Polyploidization is an increase in genome content by duplication of existing DNA or fusion of two species' genomes. Polyploidization events provide new material for natural selection to act upon. For example, genes with new functions may evolve or large portions of the duplicated genome may be deleted. The proposed research will focus on studying this phenomenon in gray treefrogs. Some gray treefrogs are diploid and have two sets of chromosomes, while the others are tetraploid and have four complete sets. Tetraploid frogs originated from diploid populations. Molecular data from different genes will be collected to determine (1) which diploid populations contributed to the formation of the tetraploids and (2) whether doubling of the genome content has changed the rate of evolution.
This study will have broad impacts by advancing the understanding of basic biological research and educating undergraduate and graduate students. Women are represented at both undergraduate and graduate levels. This cross-disciplinary genomics project incorporates phylogenetics, molecular evolution, and computer science with state-of-the-art techniques and equipment. Results will be published in scientific journals and presented at society meetings and in public forums. DNA sequence data will be made publicly available through submission to the GenBank database. Finally, this work addresses questions of relevance to agricultural crops, many of which have polyploid origins.
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0.915 |
2003 — 2008 |
Jost, Manda Zakon, Harold [⬀] Hillis, David |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Evolution of Neurotoxin Resistance in Pufferfishes and Relatives: a Comparative Genomic Approach @ University of Texas At Austin
One of the deadliest neurotoxins known is tetrodotoxin (TTX). TTX binds tightly to and blocks sodium channels in muscles, heart, and nerve causing paralysis and death. TTX is of biological origin and is produced by a striking variety of animals such as the blue-ringed octopus, the ghost crab, the California newt, and the pufferfish. In some species TTX is used to capture prey, in others for defense against predation. Because TTX circulates freely in the body of the animals that make it, these animals must evolve insensitivity to their own toxin. Some species of pufferfishes are more toxic than others, and that higher degree of toxicity is matched, obviously, with lower sensitivity of the tissues of those species to the toxin. One hypothesis is that the varying sensitivity of tissues to TTX among these species of pufferfishes likely resides in variation in the amino acid sequences of the proteins associated with the sodium channels. This project focuses on evolution of TTX sensitivity among pufferfishes by way of a mechanistic examination of the evolution of sodium channel proteins.
In order to reconstruct the evolutionary history of the sodium channel genes, the sequences of these genes will be examined from the pufferfish genome database. Next, the genes for three of the six sodium channels will be cloned and sequenced from a variety of related species exhibiting varying degrees of TTX sensitivity. Phylogenetic relationships among the pufferfishes are known. In addition, some related fish with varying degrees of TTX sensitivity, and some unrelated fish that are very sensitive to TTX will be examined. Sensitivity to TTX will be determined by measuring the amount of TTX that binds to tissue samples of brain, muscle and heart. A comparison of the sequences of these sodium channel genes will be made to identify particular amino acids in the sodium channel proteins that are different in those species that are highly insensitive to the toxin versus those that are not. From these data inferences may be drawn to reconstruct how particular mutations accumulated in the 3 genes during the evolutionary history of these species. Thus an understanding of how these genetic mutations influence TTX binding will be gained in the context of current thinking about how the toxin interacts with amino acids in the pore of the sodium channel.
This work on the evolution of pufferfish insensitivity to their own TTX is important for a number of reasons. First, TTX is classified as a weapons-grade toxin. Understanding how animals protect themselves against it may help in designing defense strategies against it. Second, TTX and related compounds are released by marine algae and cause the "red tide" which has a serious impact on fisheries industries and the marine environment. This project will help gain understanding about how some animals can protect themselves against this devastation. Third, because they have small genomes, the genome of the Pufferfish has been cloned and sequenced so there is a wealth of molecular data on this species. The present study will take advantage of that information. Finally, from a theoretical point of view, this is an intriguing question. Fish are known to have six different genes for sodium channels, so TTX sensitivity must have evolved more or less simultaneously in six genes. Understanding how toxin insensitivity evolved in pufferfish will be a model for how animals respond adaptively on a molecular level to environmental challenges. Very few studies have developed the mechanistic links between molecular variation, differential organismal performance, and relative fitness. The present study has great potential to forge those important links.
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0.915 |
2003 — 2009 |
Warnow, Tandy [⬀] Hillis, David Meyers, Lauren (co-PI) [⬀] Miranker, Daniel (co-PI) [⬀] Hunt, Jr., Warren |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Information Technology Research (Itr): Building the Tree of Life -- a National Resource For Phyloinformatics and Computational Phylogenetics @ University of Texas At Austin
This collaborative project aims to establish a national computational resource to move the research community much closer to the realization of the goal of the Tree of Life initiative, namely, to reconstruct the evolutionary history of all organisms. This goal is the computational Grand Challenge of evolutionary biology. Current methods are limited to problems several orders of magnitude smaller, and they fail to provide sufficient accuracy at the high end of their range.
The planned resource will be designed as an incubator to promote the development of new ideas for this enormously challenging computational task; it will create a forum for experimentalists, computational biologists, and computer scientists to share data, compare methods, and analyze results, thereby speeding up tool development while also sustaining current biological research projects.
The resource will be composed of a large computational platform, a collection of interoperable high-performance software for phylogenetic analysis, and a large database of datasets, both real and simulated, and their analyses; it will be accessible through any Web browser by developers, researchers, and educators. The software, freely available in source form, will be usable on scales varying from laptops to high-performance, Grid-enabled, compute engines such as this project's platform, and will be packaged to be compatible with current popular tools. In order to build this resource, this collaborative project will support research programs in phyloinformatics (databases to store multilevel data with detailed annotations and to support complex, tree-oriented queries), in optimization algorithms, Bayesian inference, and symbolic manipulation for phylogeny reconstruction, and in simulation of branching evolution at the genomic level, all within the context of a virtual collaborative center.
Biology, and phylogeny in particular, have been almost completely redefined by modern information technology, both in terms of data acquisition and in terms of analysis. Phylogeneticists have formulated specific models and questions that can now be addressed using recent advances in database technology and optimization algorithms. The time is thus exactly right for a close collaboration of biologists and computer scientists to address the IT issues in phylogenetics, many of which call for novel approaches, due to a combination of combinatorial difficulty and overall scale. The project research team includes computer scientists working in databases, algorithm design, algorithm engineering, and high-performance computing, evolutionary biologists and systematists, bioinformaticians, and biostatisticians, with a history of successful collaboration and a record of fundamental contributions, to provide the required breadth and depth.
This project will bring together researchers from many areas and foster new types of collaborations and new styles of research in computational biology; moreover, the interaction of algorithms, databases, modeling, and biology will give new impetus and new directions in each area. It will help create the computational infrastructure that the research community will use over the next decades, as more whole genomes are sequenced and enough data are collected to attempt the inference of the Tree of Life. The project will help evolutionary biologists understand the mechanisms of evolution, the relationships among evolution, structure, and function of biomolecules, and a host of other research problems in biology, eventually leading to major progress in ecology, pharmaceutics, forensics, and security.
The project will publicize evolution, genomics, and bioinformatics through informal education programs at museum partners of the collaborating institutions. It also will motivate high-school students and college undergraduates to pursue careers in bioinformatics. The project provides an extraordinary opportunity to train students, both undergraduate and graduate, as well as postdoctoral researchers, in one of the most exciting interdisciplinary areas in science. The collaborating institutions serve a large number of underrepresented groups and are committed to increasing their participation in research.
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0.915 |
2004 — 2009 |
Hillis, David Cannatella, David [⬀] |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Atol: Collaborative Research: Amphibiatree, An Integrated Phylogenetic and Phyloinformatics Approach to the Tree of Amphibians @ University of Texas At Austin
0334952 Cannatella and Hillis A grant has been awarded to Drs. David Cannatella and David Hillis at the University of Texas at Austin, as part of a four-institution collaboration, to study phylogenetic relationships of the living amphibians and their close fossil relatives. Living Amphibians are a prominent part of the Earth's vertebrate fauna and include three orders: the caecilians (Gymnophiona), salamanders (Caudata), and frogs and toads (Anura). Despite recent advances in discovering and describing their diversity, many critical questions in amphibian evolution remain unresolved and a fresh analysis of evolutionary relationships is needed to take new discoveries into account. Furthermore, the recent decline and apparent extinction of amphibians from many environments makes it urgent that we discover and classify the diversity present today. A team of seven investigators from diverse institutions (University of Texas at Austin, University of California at Berkeley, Harvard University, and the University of Kansas) and their colleagues will collaborate to resolve modern amphibian relationships. Field sampling in biodiversity hotspots will provide materials of new or previously unsampled lineages. Anatomical and morphological data from living and fossil forms will be combined with DNA sequences from a set of defined mitochondrial and nuclear genes for as many species as possible, and will be integrated with existing data sets. Analysis of these large data sets will be used to gain insight into such questions as repeated patterns of evolution, geographic patterns, and rates of evolution. Drs. Cannatella and Hillis will be responsible for coordinating the research amongst the different labs, with an emphasis on field work in South America and integration with nuclear and mitochondrial DNA data as well as overall coordination to construct a phylogeny from the combined and integrated molecular and morphological data. Understanding the evolutionary history of modern amphibians is critical for developing conservation strategies for amphibians as well as completing the vertebrate portion of the tree of life. The project will involve extensive student training and interaction with US and international colleagues. Communication with the public will utilize web resources, especially AmphibiaWeb, an existing site that will be expanded and further developed to provide information on all species of amphibians for professionals and the public at large. AmphibiaWeb will also provide training opportunities for students and senior professionals to enable them more effectively to communicate their findings.
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0.915 |
2005 — 2008 |
Hillis, David |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Dissertation Research: Polyploidy and Androgenesis in the Invasive Clam Genus Corbicula @ University of Texas At Austin
Two species of Asian clams have been introduced into North America. These clams have an unusual asexual mating system in which all offspring are clones of the father. During mating, sperm will cause the egg to eject the entire maternal genome-essentially parasitizing the egg. Competition experiments between species will determine whether one species has been able to spread through US rivers by parasitizing the other. Across all Asian clams, several species have this type of asexuality, while the rest reproduce sexually. Analysis of DNA sequence data will reveal similarities and differences between genes of sexual and asexual species of Asian clams. These comparisons will be used to determine whether parasitism of sexually reproducing species caused this asexual mating system to spread to new species.
Asian clams can become extremely abundant once established in an area, causing problems for industry by clogging water intake pipes. They also contribute to the decline of native American freshwater bivalves by displacing them in southern rivers and creeks. The outcome of these experiments will help provide information for the development of control methods. In addition, this research will increase scientists' understanding of what drives asexuality to replace sexual reproduction.
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0.915 |
2009 — 2011 |
Hillis, David Cannatella, David (co-PI) [⬀] |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Eager: Phylogenomics @ University of Texas At Austin
This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).
This project will investigate a novel method for producing large amounts of high-quality DNA sequence data for phylogenomic applications. The project will extend a strategy called "microarray-based genome selection" (MGS), which is capable of enriching a DNA sample for thousands of genes, to simultaneous enrichment across distantly related species. As a result, this study has the potential to address the remaining practical obstacles to microarray hybridization across species (cross-species hybridization) and result in hugely increased scaling of MGS technology. Such a scaling up will expedite the assembly of the Tree of Life and accelerate the adoption of next-geenration DNA sequencing technologies in many biological fields. Frogs, a diverse group broadly used in biology, will be the model group for this research.
This new genomic enrichment strategy will broadly extend the use of new sequencing technologies by accomplishing two main goals: 1) construction of significantly larger, cheaper and time-efficient molecular datasets, and 2) increasing the number of genetic markers in common across taxonomic groups, which will allow different parts of the Tree of Life to be merged together. The new lab procedures and design strategies will be published via a website and in peer-reviewed journals, further disseminating the MGS enrichment strategy to related disciplines, such as biomedical engineering.
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0.915 |
2013 — 2014 |
Hillis, David Wright, April |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Utilizing Likelihood Models For Phylogenetic Reconstruction From Discrete Phenotypic Characters @ University of Texas At Austin
Presently, there are two major methods for estimating phylogenetic trees from morphological data. In this study, researchers will simulate morphological data and use these data to to test the effectiveness of these methods. A strength of using simulated data is the ability to manipulate relevant parameters to create data sets that are relevant to many different types of researchers and scientific questions. The goals of this project are twofold: to provide practical recommendations and guidelines for best practices in estimating phylogenetic trees from morphological data and to understand the strengths and weaknesses of various methods for estimating phylogenetic trees.
Estimating a phylogenetic tree is a common way to understand the relationships among different groups of organisms. These trees can be used to understand the evolution of a trait, to test hypotheses of biogeography, or to infer other aspects of the evolution and ecology of organisms. Fossils are the only way that scientists can directly observe long-extinct organisms, making the study of fossil data a relevant practice, even as the price of DNA sequencing falls. The results from this project can be used to inform scientists about appropriate methods for inferring phylogenetic relationships from fossilized remains.
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0.915 |
2020 — 2023 |
Hillis, David Devitt, Thomas (co-PI) [⬀] |
N/AActivity Code Description: No activity code was retrieved: click on the grant title for more information |
Collaborative Proposal: Developmental and Genetic Pathways to Phenotypic Convergence in a Radiation of Groundwater Salamanders @ University of Texas At Austin
Cave organisms as unrelated as insects and salamanders often have shared features ? such as lack of eyes, pallid coloration, and elongated limbs. Life underground provides different challenges from life on the surface, and those challenges favor relatively rapid changes in appearance (and other, more subtle characteristics) at the population level. Those rapid changes lead to convergence in the appearance of many cave organisms, but the genetic and developmental processes that lead to repeated changes in different organisms are largely unknown. The Edwards Plateau of central Texas has an extensive, though fragmented, network of springs, caves, and aquifers that host numerous, diverse, underground salamanders. These salamanders attain reproductive maturity while retaining features (such as gills) that are characteristic of immature salamanders, and many of them show eyes reduced in size and development to varying degrees, along with other characteristics associated with living underground (e.g. an enhanced sense of smell). These characteristics have evolved independently and repeatedly in the various species, and this research will integrate information derived through a variety of approaches to shed light on the mechanisms that enable new structures and functions to evolve. This project is timely because in addition to enhancing understanding of the evolution of sensory systems, it will highlight and clarify the diversity of salamanders in central Texas at a time when human population growth and commercial development further threaten species that have been identified as being in danger of extinction. Finally, this project will serve as a platform to train numerous undergraduates in STEM research.
The researchers will use an integrative, hierarchical approach combining genetic, developmental, and phylogenetic perspectives to study the mechanisms that drive convergence in phenotypes of subterranean Groundwater Salamanders. Results from micro-computed tomography imaging, histology, transcriptomics, and exon sequencing will demonstrate the degree of morphological convergence in sensory systems (visual, olfactory, and lateral line) across subterranean lineages. Comparative transcriptomics will be employed to examine the developmental genetic mechanisms of organ system reduction and signatures of molecular convergence at the protein-coding level in sensory-system genes.
This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
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