Douglas R. Taylor, Ph.D - US grants

9528966 Taylor The potential for cytoplasmic hyperparasites to influence the dynamics of plant-pathogen interactions will be the focus of this collaborative research project. The theoretical portion of the research has three o`jectives: (1) to identify conditions that allow the hyperparasite to invade a pathogen population, (2) to generate predictions on the effects that hyperparasite invasion has on plant-pathogen population dynamics, and (3) to generate predictions on long-term evolutionary dynamics of the plant-pathogen-hyperparasite system. Empirical studies will examine the chestnut blight system involving the American chestnut, the fungal parasite of chestnut, and a double stranded (ds) RNA hyperparasite of the fungus. One experiment will test predictions for the distribution of dsRNAs within chestnut populations, and the diversity of vegetative compatibility groups with and among fungal populations. A second study will evaluate the genetic interaction between the fungus and dsRNA in determining pathogen virulence. The relation between pathogen virulence and disease transmission rates will be evaluated in a third experiment. This work will determine the influence of hyperparasite infection on the relationship between virulence and transmission rate. The last experiment will test model predictions on the relative transmission rates of dsRNA-free and dsRNA-infected lines that allow dsRNAs to invade fungal populations.

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Taylor

So-called 'selfish genetic elements' are genes that enhance their own transmission across generations at the expense of the organism in which they reside. Often, there are other genes that suppress the effects of the selfish element. This antagonistic interaction between genes is known as 'intragenomic conflict'. Intragenomic conflict is thought to be of fundamental importance, perhaps influencing the origin of reproductive isolation, sex chromosomes, sex-ratio bias, repetitive DNA, and sex-determination mechanisms, among others. The perceived importance of these phenomena has grown recently as experimental studies have established their existence in a wide variety of taxa. Nevertheless, very few studies have examined the dynamics of intragenomic conflict or its historical importance in natural populations.

Silene latifolia is a dioecious plant with a sex-ratio polymorphism that closely resembles classic examples of intragenomic conflict in animals, but is more amenable to research in natural populations. This research focuses on two aspects of the sex-ratio polymorphism in Silene latifolia that are of general importance for understanding intragenomic conflict. First, the rates of genetic transmission of alleles that control the sex ratio will be measured in experimental populations set up in the field. Second, a phylogenetic analysis will evaluate the historical importance of intragenomic conflict in this system and the diversity of genetic mechanisms controlling the sex ratio.

The proposed experiments will make important contributions to our understanding of sex-ratio variation in nature, and the biological significance of intragenomic conflict. How often such conflicts arise and are resolved in nature is critical to our understanding of the origins of sex-determining mechanisms and the stability of Mendelian segregation itself. The educational component of this project focuses on expanding the role of laboratory research in undergraduate course curricula, and outreach programs to introduce the experience of research in university labs to secondary school students with career ambitions in science.

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Taylor

Gynodioecy is a condition in plant populations in which hermaphroditic and female individuals coexist. It arises when a mutation (called a cytoplasmic male sterility (CMS) factor) causes hermaphrodites to lose male function, with a concurrent increase in seed production. Understanding how gynodioecy persists is an ongoing question in the field of plant population biology. This project will combine molecular genetic markers and genetic crosses to ask how many different CMS factors exist in small natural populations of Silene vulgaris, and how those factors are distributed spatially. This will be combined with mathematical and computer models in order to understand how the extinction and recolonization of local populations influences the evolution of gynodioecy.

This project will be relevant to several broader scientific issues. First, CMS factors are an example of "selfish DNA". The studies of S. vulgaris will be one of the few to link molecular markers to selfish elements in nature. Second, the study of the genetics of small and fragmented populations is significant for conservation biology. This study of S. vulgaris will yield general information about genetic processes in small populations. Finally, gynodioecy is important for agriculture because it is used as a tool by plant breeders for increasing crop yield.

Intellectual Merit - Genes on autosomes, on sex-chromosomes, in mitochondria and chloroplasts, and those associated with transposable elements are inherited through different pathways and with different rules. Yet the occurrence of these elements within single individuals, whose phenotype they influence, creates complex evolutionary processes that influence phenomena such as chromosome evolution and genome restructuring. This planning grant has the goal of developing the angiosperm genus Silene and its associated pathogen Microbotryum as model systems for understanding the evolution and genetics of sexual reproductive systems. The Silene - Microbotryum community has successfully developed these species into model systems for the study of sex-determination and host-pathogen systems. The objective of this FIBR planning project is to organize this community around the development of a common set of genomic resources, to integrate the current workers in the field, and to reduce the duplication of effort in developing common resources. A research symposium will be held to achieve this goal and will include not only the scientists working on this system, but also a set of experts in genomics, molecular biology, and theoretical biology who share conceptual interests but work with other organisms. Subsequently, a workshop of the FIBR PIs will be held to develop the proposal itself. This project is centered on the strengths of this system with regard to answering questions that are not readily approachable in other model systems. These strengths include a broad range of systems within closely related taxa, intense knowledge of pathogen dynamics and its interaction with the reproductive system, and a profound understanding of the ecological and phylogeographic context of the evolutionary processes under consideration.

Broader Impact - This planning activity will draw together a diverse range of researchers representing a breadth of institutional types and a geographically disperse set. The research symposium emphasizes direct student and post-doctoral participation and builds on the ongoing outreach efforts of the principal investigators. The symposium and planning meetings will provide opportunities to develop further plans for enhancing educational and outreach opportunities as part of the anticipated pre-proposal. More generally, planning for the FIBR pre-proposal will include mechanisms to promote the integration of population dynamic and molecular approaches and help the career development of young scientists by crossing disciplines and emphasizing a broad and comparative approach.

Biological invasions represent one of the greatest threats to the preservation of biodiversity. In addition, the economic costs to the USA resulting from damage and control of alien organisms (e.g., zebra mussel, kudzu) amount to more than $100 billion annually. Surprisingly, very little is known about why species that are normally benign may suddenly become noxious pests following their introduction to another country or continent. While the emphasis of previous research recorded in the literature has been on ecological forces, the goal of this research is to explore the role that genetic changes play in the invasion process.

Using a combination of approaches, Taylor and Wolfe propose to study the genetics and origin of invasiveness in Silene latifolia, a plant that was introduced to North America from Europe. There are three goals to this research: 1) To examine the history of the invasion process and clarify the genetic consequences of the invasion process in terms of the amount and distribution of genetic variation. 2) To experimentally test for unique environmental patterns in North America that might promote the success of weedy species. 3) To use replicated experimental populations to test whether North American populations are genetically more invasive and the extent to which natural enemies limit invasiveness in Europe. This research will have broad significance for both understanding the origin of invasiveness and providing opportunities for career development of undergraduate students, graduate students and post-docs.

Invasive species are a worldwide problem, but the degree to which evolutionary processes influence invasibility is poorly understood. A fundamental question is how the process of invasion results in genetic changes that impact the fitness of introduced populations. Addressing this question is complicated by the fact that genetic changes can occur both as a consequence of chance events and by adaptation in response to natural selection. Little is known about the relative influence of these two distinct processes on the success of invaders. The proposed research studies a weedy plant native to Europe and introduced to North America about 200 years ago. Molecular tools will be employed to reveal how chance events during colonization shaped genetic diversity, and to identify the source areas in Europe from which invaders are descended. European and North American plants descended from the same ancestral sources will then be grown together in two experimental gardens within North America to analyze how divergence in adaptively important traits has occurred after controlling for underlying ancestry.

The impact of invasive species includes a heavy economic burden, with yearly losses for the U.S. in the billions of dollars. Thus the broader impact of this study will be to advance the understanding of how species become successful invaders, and help illuminate the basis of an important applied problem.

A central challenge in the field of molecular evolution is to elucidate the mechanisms that have produced the enormous diversity in genome organization, structure and function that exists across the tree of life. The proposed research will examine the role of mutation rates in differentially shaping genome evolution by comparing the mitochondrial DNA sequence, structure and function for two closely related species of flowering plants (Silene latifolia and Silene noctiflora) that differ more than 100-fold in mitochondrial mutation rates. For each species, the entire mitochondrial genome will be sequenced along with a sample of genes from the chloroplast genome (which does not exhibit any differences in mutation rate between the species), and patterns of RNA editing and intron splicing will be identified by sequencing cDNA. Given the many commonalities between the mitochondrial genomes of flowering plants and the nuclear genomes of multicellular organisms (such as the proliferation of non-coding DNA), the implications of this work will extend to the evolution and function of the nuclear genome.

Elucidating the dynamics of mitochondrial mutations is potentially important for understanding a wide variety of mitochondrial pathologies in humans and the mechanistic basis of cytoplasmic male sterility in plants, a phenomenon that is of great importance in agricultural systems. Annotated mitochondrial genome sequences will be of broader value to the Silene research community in diverse fields of study including breeding system evolution, metapopulation genetics, organelle transmission, systematics and molecular evolution. Also, the research will provide a valuable opportunity to train University of Virginia undergraduates in the modern techniques of molecular genetics and bioinformatics.

An insect society can serve as a hub of transmission for pathogens, commensals, and mutualists (symbionts), but transmission within a colony occurs between close relatives. If this consanguineous transmission is much more prevalent than between-colony transmission, selection may favor more benevolent symbiont strains in social hosts in comparison to solitary hosts, because high consanguineous transmission may couple the fitness of the symbiont to that of the host colony. To test this hypothesis, genetic covariances between social and solitary sweat bee hosts and their nematode symbionts are being measured to represent effective transmission. Effective transmission is a measure of within- versus between-colony transmission, and therefore provides a means to measure the coupling of host and symbiont fitnesses. Laboratory colonies of social and solitary hosts either with or without symbionts will be used to measure the impacts of infection on host fitness. This research will also determine if genetic covariances can predict the impact of a symbiont on its host.

This project will involve the training undergraduates, including students from underrepresented groups. Additionally, this research has direct relevance to the understanding of disease dynamics in social systems of all kinds, from humans to slime molds.

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).

Most organisms exist in populations that are distributed in irregular and often ephemeral patches. This research explores two fundamental consequences of this fact: the forces that create and destroy patterns of genetic variation across a landscape and how these spatial genetic patterns affect responses to disease epidemics and climate change. The research applies high throughput genomic tools to understanding the demographics and genetic dynamics in more than 800 spatially distributed populations. Objectives are to understand how the distribution of organisms in nature affects the establishment, persistence and proliferation of isolated populations, with a particular focus on disease epidemics and host resistance.

Understanding the genetics and ecology of interconnected networks of populations is of applied importance for conservation biology, management of genetically modified crops, invasion biology, and understanding the potential of species to respond to global change. The emphasis on disease dynamics and resistance also contributes to understanding the dynamics of human pathogens. The research involves training 10-15 undergraduate and graduate students in the interdisciplinary fields of ecology, genomics, and informatics, with training opportunities designed to enhance participation from members of under-represented groups.

In virtually all eukaryotic organisms, basic cellular processes depend on the function of mitochondrial genomes and their coordinated interaction with the nucleus. Understanding how and why mitochondria maintained their own genomes is a fundamental biological question. The rate of mutation has been hypothesized to be a driving force in the evolution of these genomes. The advent of high throughput DNA sequencing technology along with the recent discovery of extreme mitochondrial mutation rate variation among closely related species of flowering plants in the genus Silene presents an unparalleled opportunity to test the consequences of mutational processes in genome evolution. This project will produce complete mitochondrial and chloroplast genome sequences from multiple Silene species that vary more than 100-fold in mitochondrial mutation rate. These sequences will be used to test predictions regarding the evolutionary effects of mutation rate on genome size, structure and function. Furthermore, this research will identify and sequence nuclear genes that functionally interact with the mitochondrial genome to determine how mitochondrial mutation rate affects the nuclear genome.

The genomic information developed in this project will be a deliverable resource for the larger community of biologists working with the genus Silene, significantly enhancing its value as a model system for biological research. More broadly, increasing our understanding of mutational processes in the mitochondrial genome and nuclear/mitochondrial interactions will inform applied research into mitochondrial dysfunction. The research also generates numerous opportunities for training and career development in the emerging fields of genomics and bioinformatics and includes specific plans for K-12 outreach, undergraduate curriculum development and mechanisms for incorporating under-represented groups.

This project supports a collaboration between Dr. Douglas Taylor and his student, Mr. Peter Fields, in the Department of Biology at the University of Virginia, and Dr. Oscar Gaggiotti in the Laboratoire d?Ecologie Alpine at the University of Grenoble in France. This proposal will fund two long-term visits for Fields to the University of Grenoble in the Fall of 2011 and Summer of 2012. The collaboration will develop analytical and computational methods to analyze genetic data from natural populations. The proposed research leverages Gaggiotti?s expertise in population genetic analysis and software design and an unparalleled 24+ year metapopulation dataset of the angiosperm Silene latifolia. This collaboration is an exciting opportunity to refine statistical tools and ground truth population genetics methods with a long-term metapopulation dataset. The proposed research will allow for better understanding of the genetics of spatially distributed populations, or metapopulations. Additionally, the proposed research will parse out the relative roles of random and selective forces in shaping patterns of genetic diversity. Understanding evolutionary processes in metapopulations is of practical and applied importance for conservation biology, invasion biology, and for understanding potential responses to habitat fragmentation. In terms of deliverables, resulting software will be made freely available to researchers, being published under the GNU General Public License and distributed by the Free Software Foundation (http://www.gnu.org/licenses/).

This research project will expand our understanding of the causes and consequences of an unusual form of inheritance in plants, the transmission of organelles through pollen. A defining feature of cells with nuclei is the existence of organelles that have separate genomes. The nuclear genome is generally inherited from two parents. By contrast, the genomes of organelles, such as those in mitochondria, are nearly always inherited from the mother only. However, we know little about the frequency and cause of deviations from this general rule. Understanding the inheritance of organelle genomes is therefore important for understanding evolutionary processes. Using the plant Silene vulgaris as a model system, this project will explore the relationship between the geographic origins of the nuclear genome and paternal mitochondrial transmission, and the relationship between the physical structure of the mitochondrial genome and the propensity for mitochondrial genes to recombine, will be studied. This requires 1) sequencing several S. vulgaris mitochondrial genomes to document genome structure and identify genetic markers used to study recombination, 2) genotyping individuals from natural populations in order to estimate recombination, 3) conducting experimental crosses between individuals of varying nuclear and mitochondrial genotypes, and 4) genotyping their offspring to identify incidences of mitochondrial paternal inheritance.

In addition to furthering fundamental knowledge of plant mitochondrial genome biology, the results should be of applied significance. Plant breeders are concerned with developing CMS (cytoplasmic male sterility) resources because utilization of male-sterile individuals in breeding programs increases efficiency, and CMS genes usually reside in the mitochondrial genome. Studies of the inheritance of organellar genomes are also valuable because of concerns about gene escape from genetically modified organisms.

The plant flavonoid pathway forms distinct groups of chemicals responsible for several important roles, including pigmentation, plant defense, antioxidants, and sunscreen. An interconnected network of genes is responsible for the production of each flavonoid subgroup. Changes in gene regulation and subsequent flavonoid expression will be controlled by genes and enzymes that are shared among different branches of the pathway, suggesting that there may be trade-offs between flavonoid groups and therefore the related ecological functions. Next-generation sequencing in the form of multiple transcriptomes will be made of Silene vulgaris individuals taken from a reciprocal transplant experiment of high and low elevation plants (high and low UV-B environments) to test for adaptation to specific environments and flavonoid gene expression, which will be compared to chemical analyses of flavonoids. This will allow the consideration the entire flavonoid pathway simultaneously, in particular how increased expression of a specific branch affects the overall expression phenotype.
Studying the correlated traits of a metabolic pathway will shed light on the evolution of secondary metabolism in plants, illuminating how different points in gene networks can be subject to adaptive evolution and influence overall pathway development. Since flavonoids are ubiquitous, this research will be applicable to most plants. In particular, the proposed research will also expand on knowledge of plant adaptive divergence along UV-B gradients, shifts in which have been associated with human-mediated global change. This proposal also details using next-generation sequencing techniques in a natural setting and non-model organism, which may encourage further studies along those lines.

In nature, populations of organisms are generally clustered into distinct patches that, over time, exchange migrants and perhaps suffer extinction and later recolonization. The genetic consequences of this dynamic population fragmentation has been studied in theory, but experimental studies have lagged behind because of the large quantity of long-term data that are required. The proposed research will close this gap using nearly three decades of data collected from hundreds of populations of a plant (white campion) and an associated disease (anther smut). With these data, we will be able to follow the genetics of local populations as they are born, exchange migrants, and possibly go extinct. These observations are important for understanding how genetics affects extinction and colonization success. More broadly, understanding the dynamics of interconnected populations is fundamental to predicting how disease outbreaks can occur from local patches, how invasive species spread, or how the genetics of species can be altered when they are rare or occur in fragmented habitats.

The major objective of the proposed research is to follow the process of extinction and colonization in interconnected populations and study how these processes create and destroy genetic diversity. This proposal builds on a now 28-year study of the numerical dynamics of Silene latifolia (white campion) and its pathogen Microbotryum violaceum (anther smut). This project uses a long-term population genetic approach to characterize numerous colonization and extinction events and to follow populations through time. Methods used will include long-term monitoring (eventually more than over 800 populations for >30 yrs) and continued genetic sampling (eventually >15yrs). High throughput genomic studies of Silene populations will provide unprecedented resolution of changes in genetic divergence, the parentage of newly established populations, gene flow during population expansion or contraction, the genetic consequences of seed banks and the importance of inbreeding and genetic rescue for population persistence. Also, broad demographic shifts have occurred during the course of this study, opening up the potential to explore the population genetics of non-equilibrium systems of both the host plant and the disease. The Silene/Microbotryum system has become a model for numerous labs, and this research will provide a publicly available long-term data set of demographic and genomic data, living collections, and DNA samples. This study will provide scientific training in timely important fields of ecology, genomics, bioinformatics, and computational biology.