Scott Hodges - US grants

The evolution of plant populations can be affected by natural selection, gene flow (genes entering the population from other populations), and genetic drift (chance events due to small population size). In order to understand how evolution proceeds, one must know how these different forces operate together. All of these are affected by which individuals are transmitting genes to the next generation. However, because movement of pollen from plant to plant is nearly impossible to follow, determination of which individuals are supplying genes is difficult. The technique of electrophoresis makes it possible to determine if a given individual could be the father of a particular seed. By applying this technique to seeds produced by all individuals in a population, a determination of which individuals are supplying genes to progeny can be made. Knowing the parentage of seeds will help explain how different forces affect the evolution of a population. In addition, information on how genes move through a population can be applied to agricultural systems. This informaton could be very beneficial when breeding for specific traits or when trying to reduce the amount of gene movement into or out of a particular area.

9726272 Hodges Two species of the columbine genus Aquilegia, A. formosa and A. pubescens, have very different floral morphologies and are predominantly pollinated by different animals. A. formosa has red, pendent, short-spurred flowers pollinated by hummingbirds and A. pubescens has white, upright, long-spurred flowers pollinated by hawkmoths. While these two species are fully compatible in controlled crosses, they rarely crossbreed in nature due to the differences in their flowers. The two species' distributions overlap in the southern Sierra Nevada mountains of California where narrow hybrid zones form. We will determine the number of genes responsible for the differences in floral morphology by utilizing techniques developed for animal and plant breeding. Because hybrid zones do occur where these species overlap, genes from one species that are not affected by natural selection can penetrate beyond the hybrid zone into the other species. However, genes that are affected by natural selection are prevented from penetrating the alternate species. We will determine how natural selection acts on each segment of the genome by measuring the degree it is able to penetrate beyond the hybrid zone. A major goal of evolutionary biology is to understand the genetic basis of traits conferring reproductive isolation. These traits are responsible for the generation and maintenance of biological diversity. Many scientists believe that most adaptive differences between species arise from the accumulation of many small genetic changes while others believe that they arise from a few changes with large effects. This issue has remained unresolved because detailed genetic studies have been limited to only a few model organisms. In addition, the number of traits and the proportion of the genome important for species isolation is unknown. By synthesizing genome mapping techniques with hybrid zone analyses a detailed examination of the genetics of specie s isolation will be possible.

Some birds, such as cowbirds and cuckoos, do not care for their own young but instead parasitize the parental efforts of other birds, their hosts, by laying their eggs in the hosts' nests. This social or "brood parasitism" depresses host reproductive output and some hosts have evolved defenses, such as removal of parasitic eggs. This study will determine the extent to which bird species retain host defenses when they are no longer parasitized by carrying out egg recognition experiments on populations that are not currently parasitized and by assessing levels of DNA sequence divergence to estimate the elapsed time since such populations became free of brood parasitism.

Whether an adaptation is retained in the absence of benefits is a fundamental question in evolutionary biology. The issue of the retention of adaptations is also vital to efforts to understand human nature as behavioral tendencies that were adaptive in the past but are no longer beneficial today may still be expressed, often to the detriment of society. Brood parasitism is significant to efforts to preserve biodiversity because some endangered host species are impacted by the losses suffered to parasitism. Currently, at least six endangered species are protected from parasitism by cowbird control programs that expend significant amounts of public funds. Understanding the extent to which egg recognition is retained in the absence of any benefits will reveal whether this trait has significant costs and will provide insights into the reasons some endangered hosts have not developed this behavior.

Adaptive radiations have long been recognized as prime examples of natural selection and speciation. To understand the processes that bring about these radiations requires a phylogenetic reconstruction of the relationships among the species. However, adaptive radiations usually occur extremely rapidly and therefore traditional methods of phylogenetic reconstruction often fail. The proposed research will investigate whether DNA sequencing of the 3'-untranslated region of multiple genes will provide the data necessary for the phylogenetic reconstruction of a particularly rapid adaptive radiation, that in the columbine genus Aquilegia. After sequencing the 3' ends of expressed genes, specific PCR primers will be designed to amplify both coding and non-coding gene regions. These gene regions will then be sequenced for multiple species of Aquilegia and a phylogenetic reconstruction will be made.

Understanding the processes that generate bio-diversity is essential to understanding how bio-diversity can be maintained. Adaptive radiations represent instances of remarkable diversification yet without information on the evolutionary relationships of their species, little progress can be made on understanding their origin. The proposed research will investigate a technique that would be applicable to reconstructing relationships for a wide range of taxa.

Convergent evolution provides a unique window into the process of adaptation. Replicated adaptations can range from morphological similarity to parallel molecular changes. Convergence at the molecular level may occur through either structural or regulatory changes and may be constrained by pleiotropic effects. The proposed research investigates the molecular basis for multiple convergent floral color adaptations to hawkmoth pollination. The degree of molecular convergence in the anthocyanin biosynthetic pathway will be determined using a combination of biochemistry, DNA sequencing and gene expression analysis. This study will determine the extent of molecular convergence and evolutionary constraint during adaptation, a fundamental process of evolution.

This study will have a direct impact on our understanding of how new adaptations arise. In a time of global climate change, organisms will be faced with unprecedented rates of environmental change. Their ability to adapt to these new environments will be of utmost importance in maintaining biodiversity. Evolutionary constraints on adaptations could partly determine the fate of many plant and animal species. A better understanding of the molecular basis for adaptations may help predict those species that are in peril of extinction and help guide conservation priorities to avoid extinctions due to global warming.

A grant has been awarded to Drs. Scott Hodges, Elena Kramer, Magnus Nordborg, Jeff Tomkins and Justin Borevitz (of the University of California, Santa Barbara, Harvard University, University of Southern California, Clemson University and University of Chicago respectively) to study adaptation to the environment in the columbine genus, Aquilegia. The evolution of life on earth has been punctuated by numerous examples of adaptive radiation. These dramatic events quickly create a large amount of biodiversity and are evidenced by rapid speciation along with morphological and physiological adaptations to numerous ecological niches. Species in the flowering plant genus Aquilegia have undergone a very recent adaptive radiation and present a unique opportunity to investigate the molecular genetic changes underlying adaptations. Species in this genus have spectacularly different floral morphologies with specializations to different pollinators. In addition, species differ radically in their habitats ranging from coastal forests to desert springs to the high alpine. Because any two species in the genus can be successfully crossed it is possible to dissect the genetic basis for essentially any trait in any species. By developing an array of molecular genetic resources for this genus, this project will provide the infrastructure for a host of studies by a broad community of scientists. Comparative genomic studies will be particularly amenable because Aquilegia is a member of the basal eudicot family Ranunculaceae, which is nearly equidistant between the eudicot model systems such as Arabidopsis and the monocot model systems such as rice. All of these studies will be facilitated by the fact that the genome of Aquilegia is among the smallest for a flowering plant at about 350 Mbp.

The specific goals of this project are to evaluate the genetic basis of three important traits, morphological adaptation to a specific pollinator, physiological adaptation for flowering time and adaptation to different soil/habitats. These goals will be accomplished by developing a physical map of the genome of one species of Aquilegia, A. formosa, along with a large-scale EST sequence database and a transformation system. The EST sequences will be localized to the physical map and used to construct oligonucleotide arrays for expression studies and array-based mapping of traits. Fine-mapping and cloning of a locus affecting flower orientation will be accomplished with array-based mapping along with association mapping and expression studies. To investigate the evolution of flowering time in Aquilegia, candidate genes will be cloned and their expression patterns and evolution will be characterized. To determine the genetic architecture for adaptations to different habitats, recombinant inbred lines from a cross between A. formosa and A. pubescens will be created, their breakpoints finely mapped and their fitness determined in each parental species' habitat.

Over the last several decades, the traditional fields of evolutionary biology, developmental biology and ecology have moved closer together both conceptually and technically. The newly synthetic field of modern Evolutionary and Ecological Developmental Biology, or Evo-Devo-Eco, is the result. Advances in Evo-Devo-Eco rely heavily on transferring and adapting technologies originally developed for use with traditional laboratory model organisms, in order to apply them to new and emerging model organisms. Presently, insufficient networking often leads laboratories working on non-traditional, yet promising, model organisms, to inefficiently and inadvertently duplicate effort when developing new protocols for use in their systems. Moreover, there is enormous untapped potential for the exchange of techniques, ideas, and knowledge to flow not just from established models to lesser-known systems, but also from the unique biology exposed by lesser-known systems to traditional models. This project will create a new research coordination network called EDEN (Evo-Devo-Eco Network). EDEN will facilitate new support networks and collaborations among laboratories that do not currently enjoy the large community resources of traditional model species. The four major activities of EDEN will be: (1) fostering active interchange of tools and techniques among labs working on emerging model systems; (2) training undergraduates in the field of Evo-Devo-Eco with a focus on emerging model systems; (3) documenting the tools and techniques used and developed in these organisms, and making them publicly available online for future users; and (4) promoting interactions across the Evo-Devo-Eco community through conference funding and the sponsoring of workshops. The advertising strategies and funding priorities of the network are designed to maximize accessibility by participants of underrepresented groups. The gender, ethnic, and career stage diversity of the EDEN core network group will serve as a visibly positive starting point for further increasing the diversity of the next generation of researchers.

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

This project is to replace a cluster of greenhouse bays on the UCSB campus. The current greenhouse has four bays, is old and decrepit, and is scheduled for demolition. The University intends to replace the existing facility with a new greenhouse complex located adjacent to the old. This will have three components: (1) a three-bay greenhouse on the site of a lath house that is to be demolished, (2) a small greenhouse what will maintain alpine conditions, (the ?Alpine House?), to be newly built on a currently open site, and (3) a second three-bay greenhouse to be built on a site that currently holds two small buildings that will be demolished. The alpine house is designed to simulate the temperature, light and humidity of high alpine environments. The first component is already under construction as a separate project. The current project is to construct the second and third components, and to finish the interior of two of the three bays in the first component to make them operational. The existing greenhouse will ultimately be demolished.

The new greenhouse facility will enable year-round controlled environments and provide many options for experimental research that are unavailable with the current greenhouse. It will be possible to control light, watering regimes, and temperature, and to determine their impacts on plant growth and reproduction. The replacement facility will make it possible to exclude (or include) pollinators, pests and herbivores, and thus enable ecological, genetic and evolutionary experimental research that requires a controlled setting. The facility will be used for research on the specific morphological, physiological, and demographic traits responsible for the maintenance of plant diversity; the identification of the genetic basis for adaptations to extreme environments and specific pollinators; tests of how attributes of the physical environment influence plant distributions, productivity, and phenology; and research on the genetic mechanisms underlying plant recognition and responses to a variety of stresses such as drought. Work will include studies of the genetic and environmental controls of the critical events of flowering time, pollination, seed production, and germination. These studies include the discovery and analysis of the morphological and biochemical changes in floral structure that drive pollinator specialization.

In addition to providing infrastructure for research, the facility will be used for research training of undergraduates, graduate students and postdoctoral associates. Research that is likely to have societal impacts includes research on invasive species and their biological control, and research into the genetic mechanisms affecting seed quality and germination (which is relevant to the mitigation of crop losses.) The facility will be used to advance the development of a new model genomic system that will be made available to the wider research community.

The campus has a number of activities designed to facilitate the recruitment and financial support of members of underrepresented groups, economically disadvantaged students, and highly talented undergraduates. Students in these programs participate in plant biology research and will be able to take advantage of research training opportunities in the new greenhouses. The University?s Center for Biodiversity and Ecological Restoration provides internship opportunities for undergraduates to provide hands-on botanical activities to students in local public schools.

Genetic variation between individuals is ubiquitous across the tree of life, and a requirement for both adaptive and non-adaptive evolutionary change. Processes that affect the genetic variation within species can affect their evolutionary potential. Geographic differences in the strength and direction of natural selection lead to local adaptation of populations and the maintenance of genetic variation at a species level, even when variation would have otherwise have been lost. Although this process has potentially dramatic consequences for adaptation by natural selection, its relative importance in shaping the evolutionary fate of species is unknown. Rocky Mountain columbine grows at high elevations in the Southern Rockies, a region characterized by strong environmental gradients such as summer precipitation (i.e. monsoonal rain in the south and almost none in the north). The proposed research will identify variable genetic regions through whole-genome sequencing of hundreds of individuals across the species? distribution, and patterns of genetic variation will be used to identify those regions that are experiencing geographically variable natural selection. Greenhouse experiments will test whether precipitation could differentially affect fitness of variants for one trait that shows geographic variation, flower color.

The proposed research will provide important insight into how environmental differences across a species range affect genetic variation at the whole-genome level. This relationship is critical to understanding how biological diversity originates and is maintained through time in the face of a variable and changing environment. In light of rapid global climate change, such an understanding takes on particular significance. Training of students will result from this work.

The body of a plant is made of just a few repeatedly produced structures, such as leaves and stems. However, these structures can vary tremendously in their shape both within an individual and between different species in predictable, consistent ways. This variation in shape is controlled by a combination of cell division and cell shape, which in turn must be controlled by variation in gene expression. The proposed research seeks to determine how complex shapes arise through development and the genes that control these processes. Thus this research will address the fundamental question of how organisms achieve the shapes of their bodies, which is critical to their survival. This research will also have broader impacts through the training of young scientists including undergraduates, graduate students and postdoctoral fellows with outreach efforts to recruit female and underrepresented minorities.

The nectar spur of Aquilegia is a complex three-dimensional structure that is recently derived and highly variable among species and, thus, can serve as a powerful model for investigating the control and evolution of complex organ shape. Nectar spurs develop via an early phase of localized, oriented cell divisions that create the prepatterned spur cup, which is then followed by a period of highly anisotopic cell elongation that gives rise to the final length and shape of the spur. Among the closely related and interfertile species of Aquilegia, variation in spur length and shape is generated by changing several developmental parameters: length is primarily controlled by cell anisotropy, which is in turn controlled by the duration of cell elongation; curvature is generated by varying cell elongation between the distal vs. proximal compartments of the spur; and circumference is controlled both by changes in cell anisotropy and cell number in the radial orientation. Thus, understanding the development and evolution of Aquilegia spurs will provide insight into all of these fundamental aspects of lateral organ development, which can provide new perspectives on the evolution of lateral organs more broadly across the angiosperms. The proposed research seeks to integrate multiple lines of study drawn from the fields of developmental genetics, evolutionary genomics/genetics, and biophysics. Specifically, the project will elucidate the fundamental genetic control of petal spur development, explore the roles of hormonal signaling and biomechanical strain in controlling spur development, use QTL-based approaches to identify the genes involved in the diversification of spur shape and use comparative genomic approaches to identify selective sweeps associated with the origin of nectar spurs.