David Baum - US grants

9419997 Baum The plant order Malvales contains ca. 5000 species of mainly tropical plants including several of economic importance (cotton, chocolate, okra, hibiscus). This study by Dr. David Baum of Harvard University and his colleague Dr. William Alverson will employ molecular techniques and analyses of plant morphology to study the evolution of the order, and in particular the phylogeny of certain groups at three nested levels. The placement of the order Malvales within the major dicot radiation of flowering plants; the placement of the family Bombacaceae (the kapok family) within the order; and relationships among the tribes and genera of Bombacaceae, are the three levels of emphasis. The molecular studies will involve the determination of DNA sequences from representative species of Bombacaceae and related Malvaceae, Tiliaceae, and Sterculiaceae, with emphasis on several chloroplast genes. In parallel the genera of Bombacaceae and relatives in the other three families will be studied for morphological characteristics, and the combined datasets will be used to infer phylogenetic relationships among the taxa. The resulting phylogenetic framework can be used to explain the great diversity of floral form within Bombacaceae and to account for evolutionary shifts in chromosome number and for geographical migrations through time. ??

9700876 Baum Graduate student Barbara Whitlock, under the direction of Dr. David Baum of Harvard University, is studying the neotropical plant genus Theobroma, the source of cocoa or chocolate, and its relatives of the tribe Byttnerieae of the Sterculiaceae family, for taxonomic and phylogenetic purposes. New collections in Central and South America will augment herbarium materials, and help improve understanding of morphological and geographic variation in the group. New molecular biology evidence is being gathered, from DNA sequencing of a chloroplast gene and of a nuclear gene, vicilinA, suspected to be involved in the flavor biochemistry of cocoa. The DNA data will be used to infer a phylogenetic tree for the c. 22 species of Theobroma and its close relatives. In turn, that genealogical perspective will guide further study of the origins of cauliflory in this and related genera, the formation of flowers (and fruits after pollination) along the trunk and main stems of the plant, as in Theobroma cacao, the commercial source of chocolate. Despite the commercial importance of cultivated cocoa, the taxonomy and phylogeny of the several species of Theobroma are not well studied, and new molecular methods applied to herbarium and freshly collected specimens will help improve classification and develop a phylogeny for the group. That knowledge will then help guide studies of the genetic and ecological factors affecting the evolution of cauliflory in tropical plants.

9876070 Baum This career development plan focuses on phylogenetics, the reconstruction and interpretation of the historical record of organisms. The research component is a study of historical relationships among the core Malvales, a group of approximately 3000 plants including such economically important species as cotton, chocolate, okra, durian, balsa, and jute. The teaching component involves courses at the college level and a workshop for high school teachers on phylogeny as a framework for teaching biological diversity.
The DNA sequence of five genes for representatives of Malvales will be determined. By comparing and analyzing these sequences and integrating information from plant morphology and paleontology, it will be possible to estimate historical relationships within the group. This will help clarify the timing and geographic context for the origin and radiation of core Malvales, as well as the historical mechanisms underlying floral diversity and pollination mechanisms in the group.
Courses taught will include one undergraduate course (Biological Diversity) and two graduate courses. An intensive workshop for teachers will be taught through the Center for Innovation in Urban Education, Northeastern University: The Tree of Life: Phylogeny as a Foundation for the Teaching of Organismic Biology. This will introduce teachers to phylogenetic trees using case studies (e.g., origin of whales, HIV phylogeny, origin of birds), debates (e.g., "life, by definition, exists only on earth"; "conservation is a phylogenetic problem"), and a hands-on project using skull characters to reconstruct history of the carnivores. We will also discuss how to bring these ideas into classrooms so as to improve biological literacy at the high school level.

9972647
Baum and Hileman

Recent studies focusing on model plant systems including the snapdragon Antirrhinum majus (family Scrophulariaceae) have identified individual genes affecting flower development, floral shape, and floral parts. Graduate student Lena Hileman, under the direction of Dr. David Baum at Harvard University, is investigating close relatives of the snapdragon in the genera Mohavea and Sairocarpus, to construct a molecular phylogeny of the species (mostly based on chloroplast ndhF sequences) in order to explore evolutionary changes in the floral development genes. The specific aim is to determine the genes that cause Mohavea flowers to have only two stamens as opposed to the four produced by snapdragon flowers. The search for the genetic basis of this difference is facilitated because a gene influencing stamen abortion, CYCLOIDEA (CYC), has been characterized in snapdragon. In snapdragon, CYC is expressed in one of the five stamen primordia and results in that stamen aborting (leaving four stamens to mature). Expression of CYC-like genes in the tetraploid Mohavea (where there may be multiple copies) will be studied in tissue preparations to see if these genes are expressed in early stages of the three aborted stamens. The work constitutes a fine-scale genetic dissection of the developmental control of floral characters used in the species- and genus-level classification of Scrophulariaceae plants.
Because plants of Mohavea are tetraploid (contain two complete genomes), they are expected to possess two copies of CYC and two copies of a closely related gene, DICHOTOMA (DICH). The project will include DNA sequencing of the members of the CYC/DICH gene family in order to provide information regarding molecular evolutionary changes in this gene family. Preliminary work has already identified four potential gene products, thus providing material for sequence analysis to determine whether some of the genes have been subject to stronger natural selection (as indicated by reduced rates of molecular evolution). By combining a detailed understanding of the selective history of these genes with studies of gene expression patterns, we will learn about the fate of duplicate genes during genome evolution and their role in morphological diversification.

9972612
Donoghue and Ree
Graduate student Richard Ree, under the direction of Dr. Michael Donoghue at Harvard University, is studying the phylogenetic relationships and patterns of evolution in morphological characters in the genus Pedicularis (louseworts, of family Scrophulariaceae), a northern hemisphere lineage of flowering plants that has undergone extraordinary diversification in the mountains of south-central China and neighboring regions. Conflicting taxonomic classifications of the numerous species in this genus (ca.. 500 described species in total) have resulted from differing emphases on floral features versus vegetative characters by taxonomists in their mostly intuitive assessments of similarity between species. The primary aim of the project is to test the hypothesis that major differences among classifications of Pedicularis reflect differential rates of evolutionary change in vegetative versus flower characters. Molecular data from nuclear and chloroplast DNA sequences, supplemented with morphological data, will be used to construct a phylogenetic (genealogical) framework for a sample of ca. 90 of the estimated 270 Asiatic species of the genus. Patterns and rates of character change will then be explored using methods of inferring ancestral states and assessing heterogeneity in rates across lineages.
The project is the first effort to apply modern, explicit phylogenetic methods to the study and interpretation of floral and vegetative diversity in the genus Pedicularis, and it will provide a framework for extended analyses on other species in the genus and in related Scrophulariaceae. Furthermore, the research targets one of the most species-rich regions in the eastern Himalayan biodiversity "hotspot" and hence will provide insights into the processes that have made this remote region the most diverse in the northern temperate zone.

0073299
Baum, Donoghue, and Davis
Malpighiaceae are a family of flowering plants that are an important element of forests and savannas in the Old and New World tropics. New World Malpighiaceae are pollinated by specialized oil-collecting bees (anthophorid females) and exhibit a highly conserved floral morphology despite tremendous diversity in fruit morphology and habit. These oil-collecting bees are absent from the Old World. Some Old World clades, like Acridocarpus, are presumed to be derived from New World lineages and they exhibit a combination of features associated with oil-bee pollination and with "buzz" pollination. These groups provide an opportunity to examine the consequences of the loss of specialized pollinators. The goals of this study by graduate student Charles Davis, under the direction of Drs. David Baum and Michael Donoghue, are (1) to infer the phylogenetic relationships within Malpighiaceae using chloroplast and nuclear DNA sequences, (2) to infer the phylogeny or genealogy of Acridocarpus species in order to examine patterns of floral morphological evolution associated with pollinator shifts, and (3) to document the pollination of Acridocarpus in African habitats.
Preliminary molecular data indicate that Old World genera of Malpighiaceae belong to several separate lineages, suggesting that morphologies associated with buzz pollination have evolved more than once independently. However, several areas of the phylogeny remain poorly resolved. Furthermore, several additional Old World lineages need to be added to existing datasets. Analyses of Acridocarpus using ribosomal DNA sequences reveal two major clades, one including species endemic to Madagascar and New Caledonia and the other consisting of species distributed across Africa. Oil glands appear to be entirely absent in species from Madagascar and New Caledonia, but appear in some African species. Fieldwork in Africa indicates that species of Acridocarpus are pollinated by large xylocopine bees that buzz the anthers, and the floral glands produce sugars rather than oils. Resolving the phylogeny of Malpighiaceae with additional chloroplast DNA sequences, along with sequences of a nuclear phytochrome gene, will clarify the origin and relationships of the Old World species. Further phylogenetic work will allow an evaluation of whether Old World species with similar morphologies have evolved independently, and whether such floral evolution is associated with the loss of oil-collecting pollinators. This study will shed light on the patterns and mechanisms of morphological change following a shift in pollination system.

A grant has been awarded to Dr. David Baum and Ms. Stacey Smith at the University of Wisconsin-Madison to investigate the role of habitat transitions and pollination systems in the diversification of flower form and color in Iochrominae, a group of 27 Andean species in the potato family, Solanaceae. Specifically, the research will examine the hypothesis that transitions to high-elevation environments are correlated with shifts to hummingbird pollination and the evolution of colorful, tubular flowers. Iochrominae occur at wide range of elevations, and they display a great diversity of floral morphologies and pollination systems, making them an ideal group in which to investigate this hypothesis. The study will be divided into three parts: reconstruction of the evolutionary history of Iochrominae, field studies of pollination, and biochemical analysis of floral pigmentation. Together, these components will make it possible to assess the extent to which elevational transitions are correlated with shifts in pollination systems and floral evolution.

Considering that topographical variation combined with plant-animal coevolution are thought to be responsible for the immense floristic diversity of the Neotropics, Iochrominae may serve as a case study of the process of adaptive radiation and diversification that has taken place in multitudes of neotropical lineages of flowering plants. Furthermore, this project will foster collaboration between North American and Latin American botanical institutions in trying to document and understand the floristic diversity of the Andes and the processes that have given rise to it.

0234118
Baum

The development of plants is controlled by meristems, areas of organized cell division and differentiation. Shoot meristems can take on either a floral or vegetative identity depending upon the activity of a set of meristem identity genes. Because flowers terminate shoot growth, the distribution of flowers, and hence the regulation of meristem identity genes, may have a profound affect upon plant architecture. Thus, it has been hypothesized that the architectural differences between species are largely driven by changes in meristem identity genes. In the proposed work we will evaluate the role of three meristem identity genes, LFY, TFL1, and AP1, in explaining why three species of the mustard/cabbage family (Brassicaceae) produce flowers from the basal rosette of leaves rather than on an elongated leafless stem (the inflorescence).

In previous work the PI studied LFY genes from three rosette flowering species, Ionopsidium acaule (Ia), Idahoa scapigera (Is), and Leavenworthia crassa (Lc). They used transformation to introduce LFY genes from these three species into plants of an inflorescence flowering species, Arabidopsis thaliana (that lacked a functional endogenous copy of LFY). They found that whereas Ia-LFY had no affect on plant architecture, the IsLFY and LcLFY genes tended to induce modifications to plant architecture reminiscent of rosette flowering, but they did not cause complete conversion to rosette flowering. This result suggests that evolutionary changes at the LFY locus contributed to the parallel evolution of rosette flowering in these species, but point to additional, as yet unidentified, genetic changes. The proposed work will include follow-up experiments on LFY aimed at determining whether the important differences between species are located in the protein-coding region or the adjacent regulatory DNA. Similar experiments with AP1 and TFL1 will be done to see if they may have contributed to the evolution of rosette flowering. Specifically, the goal is to clarify the molecular evolution of the genes and move them from the rosette flowering species into A. thaliana to see if they can induce rosette-flowering individually or jointly with the exogenous LFY genes.

This proposed study will shed light on how evolutionary changes in DNA translate into difference in the morphology of living species. In particular, the work will clarify: (1) the extent to which genetic changes are concentrated in a small set of developmental genes, (2) the relative importance of protein versus regulatory changes, and (3) the extent to which parallel evolution in independent lineages uses the same genetic toolbox. Additionally, the specific understanding of how plant architecture is regulated could ultimately have significance for efforts to modify crop plants to facilitate higher productivity and easier harvesting.

The research will contribute to the training of one graduate student and one postdoctoral scientist.

A symposium entitled "Regulatory genes and the evolution of plant phenotype" will be held at the Evolution 2003 meeting in Fort Collins, Colorado, June 25-29, 2004. The symposium will feature speakers at a variety of career stages from graduate students to full professors. The speakers will explore a number of topics related to the role of developmental regulatory genes in morphological evolution. Additionally, they will bring five undergraduates, primarily from underrepresented minorities, to the conference. The symposium will enhance communication among plant evolutionary developmental biologists and between plant and animal biologists.

Broader impacts: The conference will enhance the cohesion of the field of plant evolutionary developmental biology and support the career advancement of a number of young scientists. Additionally, the engagement of undergraduates in such a scientific conference will contribute to the recruitment of the best students (especially minority students) into the scientific career track.

0416096
Baum
Malvatheca is a group of about 2000 plant species that includes several economically important species (cotton, okra, kenaf, and balsa), united phylogenetically from the traditionally recognized cotton (Malvaceae), cocoa (Sterculiaceae), balsa (Bombacaceae), and linden (Tiliaceae) families on the basis of DNA sequence evidence. Most Malvatheca (more than 1700 species) are members of a group called the Eumalvoideae, which are primarily herbs and shrubs with a worldwide distribution. Prior work by Dr. David Baum and his colleagues suggested that the ancestors of Eumalvoideae were mangroves and coastal treelets that grew in Australasia; but only a handful of living species, the "Australasian grade," have retained this habit and distribution. The previous work also showed that the Australasian grade is likely descended from a group of Central and South American trees, the "Bombacaceous grade." The Eumalvoideae differs from the Australasian and Bombacaceous grade in the number of species it contains and in its extremely rapid molecular evolution (estimated at more than nine-fold that of the Bombacaceous grade). The proposed research, with colleagues Randy Small and Patrick Moss, aims (1) to use DNA sequences of plastid genes and the nuclear gene GBSSI to estimate when the Australasian grade arose, when and where the Eumalvoideae arose, and to shed light on the molecular mechanisms that may have led to accelerated molecular evolution and enhanced species diversification of Eumalvoideae; and (2) to use sequences of both plastid and nuclear DNA data to estimate the phylogenetic relationships within three important groups. These are (2a) Bombacoideae, a group that includes many large trees with spectacular flowers that grow in South and Central America as well as some African and Asian groups (e.g., the baobabs). The study will shed light on how the latter dispersed to Africa/Asia and will also clarify patterns of floral evolution. (2b) Matisieae, a group that includes ecologically significant understory trees from Central and South America. The study will shed light on the group's flower and fruit evolution. (2c) Malagasy Hibisceae, a group of putative relatives of Hibiscus that occur only in Madagascar. The study will resolve their phylogenetic relationships, which remain almost completely unknown, and will clarify when and from whence they arrived in Madagascar.
During the funding period the PI will continue teaching a workshop for K-12 teachers on phylogenies ("tree thinking") and will develop new curricular materials for this purpose. He will recruit undergraduate researchers through the University of Wisconsin Undergraduate Research Scholars program, which has a high proportion of minority/financial aid students. Additionally, the researchers will teach a course on modern methods in Madagascar and continue to maintain the Malvaceae pages at the popular Tree of Life website.

The slipper spurges, a group of 14 or so Mexican and Caribbean plant species, comprise the Pedilanthus clade within the large genus Euphorbia, in the poinsettia family (Euphorbiaceae). Euphorbia is characterized by having reduced flowers that are organized in a specialized inflorescence structure, called a cyathium. In the slipper spurges, the cyathium is often colorful and adorned with a nectar-containing spur, whose shape and size varies and appears to relate to the identity of pollinating animals. The slipper spurges are also remarkable for their great diversity in life form, from evergreen treelets of tropical moist forests to dessert succulents. Most slipper-spurge species have restricted distributions, 10 being local endemics in Mexico, and two extending from southern Mexico into northern Central America. However, one species, Euphorbia tithymaloides, has an extremely broad distribution: its eight recognized subspecies range from Florida to northern South America with populations throughout Mexico, Central America, and an arc of islands around the Caribbean. It has been hypothesized that the differentiation of E. tithylamoides around the Caribbean basin occurred along two fronts, forming a circle of populations of which the two ends meet in the Greater Antilles. If the two Greater Antillean subspecies occur in close proximity and behave as distinct species, then E. tithymaloides has the potential to be a ring-species. Very few examples of ring-species are known, most of them in animals, and they are of great interest for their potential to shed light on mechanisms of speciation.
The proposed research will study the evolutionary history of the entire Pedilanthus clade, and its association with geography. This will provide a framework to test evolutionary hypotheses regarding cyathium evolution, the origin of succulence, and switches to insect pollination in the group. Analysis of DNA sequences from nuclear and plastid genes, combined with studies of morphological variation, for the subspecies of E. tithymaloides will be used to test the hypothesis that E. tithymaloides constitutes a ring-species. The potential discovery of a new ring- species would help elucidate the roles of ecological specialization and reproductive isolation in the process of plant speciation. This study will also contribute to our understanding of Caribbean biogeography and will shed light on the systematics of a number of threatened species, potentially helping to establish conservation priorities.

The xeric scrublands of southern Madagascar support a number of charismatic and intriguing plant species, more than 90% of which exist nowhere else on earth. The proposed research will focus on the endemic genus Megistostegium and will utilize field and laboratory methods to clarify the evolutionary mechanisms at play in the group's diversification. Prior work has shown that Megistostegium is related to members of the genus Hibiscus that have radiated in arid regions of the island. Megistostegium contains three bird-pollinated species that are morphologically distinct from their close relatives (which appear to be either bird or insect pollinated). A particularly interesting situation occurs at the most southern tip of Madagascar, where all three currently recognized species occur in close physical proximity to each other yet remain morphologically distinct (M. Koopman, pers. obs.). This is intriguing given the fact that these species have overlapping flowering seasons and share the same, single pollinator, a small, green sunbird. There is also one undescribed species of Megistostegium in a remote valley 100 miles to the northeast, which is differentiated by an asymmetrical flower (M. Koopman, pers. obs). The aim of the proposed research will be to explore the genetic relationships, evolution and pollination ecology of Megistostegium. Fieldwork will determine the role of ecological barriers to pollen flow and seek evidence of reproductive barriers after pollination. Leaf tissue will be collected for molecular analyses and sequences for multiple nuclear genes will be produced to elucidate the extent of gene flow between the three forms and whether all three warrant species status (e.g., Is one a hybrid between the other two?).

This study will not only enhance basic systematic knowledge of an important group of species in a region threatened by anthropogenic habitat disturbance but has the potential to elucidate the ecological and genetic mechanisms that allow the coexistence of closely related species. Pollination biology at the species and population level has been shown to be of particular importance for the management and conservation of ecosystems. The pollination ecology of a vast majority of African plant taxa remains unexplored and this is especially true on the island of Madagascar. This project will document the pollination ecology of Megistostegium, which will help in planning community level sustainable management of pollinators and the forests they live in. Fieldwork will be conducted with one Malagasy student from the University of Antananarivo, Madagascar and will, thus, facilitate international scientific exchange.

The Integrated Biological Sciences Summer Research Program (IBS-SRP) for Undergraduates at the University of Wisconsin -- Madison aims to educate, encourage and prepare high potential students to pursue graduate study and careers in biological research, and to deepen their understanding of evolutionary theory. During this ten-week program students do individual research projects in faculty laboratories studying one of five areas: computational biology & biostatistics, neurobiology, cellular & molecular biology, plant biology, or environmental biology. These five, discipline-based groups of students and faculty form a large interdisciplinary learning community that explores connections across the students' research projects through evolutionary theory and the research process. In addition, the program fosters student professional development and builds cultural competency through workshops on science writing and presentation skills, preparation for graduate school, biological sciences research career opportunities, and ethics in biological research. Each student writes a research proposal at the beginning of the program and a final paper at the end. The paper is presented at a symposium for participants and other invited guests from the campus community. Students who are from ethnic groups underrepresented in biological sciences research, from low-income homes, first-generation college students, or attend small liberals arts colleges with limited research opportunities are especially encouraged to apply. For more information visit the program web site (http://www.wisc.edu/cbe/srp-bio/) or contact the program director, Dr. Janet Branchaw (branchaw@wisc.edu, 608/262-1182).

Knowledge of how changes at the genetic level cause species to have different features is still rudimentary. The proposed research will elucidate the genes responsible for differences in the architecture of wild relatives of cabbage (Brassicaceae). The genetic model species Arabidopsis thaliana produces flowers on an elongated portion of stem called an inflorescence. In contrast, species of Leavenworthia produce flowers on long stalks directly from the cluster of leaves close to the ground, the rosette. Prior NSF funded research has suggested that a gene called LFY changed during the evolution of Leavenworthia and that it may have played a role in the evolution of rosette flowering from inflorescence flowering. The proposed research we will further test this hypothesis by isolating the LFY gene from other rosette flowering and inflorescence flowering species and introducing them into A. thaliana. Additionally, other candidate genes that plausibly contributed to the evolution of rosette flowering will be studied. The characteristics of A. thaliana plants that contain single or multiple Leavenworthia genes we be used to determine which sets of genes played the most important role in architectural evolution. Lastly, the researchers will begin developing techniques for introducing genes into Leavenworthia, thereby allowing more powerful experimental tests to be used in the future. By clarifying the genetic basis of architectural evolution in Brassicaceae, the research will enhance understanding of basic principles of plant development. This information may help plant breeders more effectively manipulate crop plants and will provide insights into general mechanisms of developmental evolution. Additionally, the research program will provide valuable research opportunities for undergraduates and one minority graduate student.

The discordant signal obtained from analysis of different genes has raised new challenges for biologists. When contradictory evolutionary relationships are detected across different parts of the genome, it is difficult to recover and describe the history of a group of species. But this discordance among genes has also raised new opportunities: hybridization, gene flow, and other biological processes each leave their own signature in the pattern of gene tree variability. The goal of this project is to estimate the discordance between gene trees and the biological processes that have affected species and populations. An interdisciplinary team of statisticians, biologists and computer scientists will develop new and robust statistical methods for analysis of genes and species relationships.

The tools developed through this project will be implemented in a user-friendly program so that all phylogeneticists can utilize them. Software will be freely distributed to facilitate the utilization of these tools for the study of other groups of species. Undergraduate and graduate students will be trained at the interface between biology, statistics and computer science. Insights from this research will enhance educational modules in evolutionary theory at the undergraduate level and at K-12 teacher workshops.

PI: David A. Baum
IOS-1021930
The molecular mechanisms by which genes alter development when moved between closely related species

Available methods for isolating genes that cause closely related species to differ are limited by depending on the prior identification of candidate genes or on being able to hybridize the species and then isolate the causal differences. As a result, scientists are making slow progress towards the aim of identifying species-difference genes. This project is developing a new approach, transgenomics, which exploits the ease with which genes can now be moved between certain plant species. The project tests the effects of genomic fragments from Leavenworthia alabamica when introduced into Arabidopsis thaliana by transformation. These two species have many visible differences, yet are closely related. In prior work, more than 1200 A. thaliana transgenic lines were created that each contain a randomly selected fragment of DNA from L. alabamica. These were visually screened to identify DNA fragments that consistently alter plant form. For some cases where the transgenic plants resemble L. alabamica, the causal DNA sequences will be determined by testing subfragments for an ability to alter plant form. Additionally, the project will attempt to perfect the transgenomic strategy so that future experiments can proceed more efficiently with the aim of ultimately being able to screen an entire genome from a donor species in a recipient species' genetic background so as to identify genes that contributed to the differences between the donor and recipient. This work has the potential to rapidly advance our ability to determine which genes cause which traits and thereby to guide targeted efforts to design crop species with desirable agronomic features. In addition, this project will provide training to undergraduate students, a postdoctoral fellow, and a graduate student from a group underrepresented in science.

Species are the basic units of taxonomy, playing an important role in scientific communication and environmental policy. While the theoretical understanding of the species concept has advanced greatly, methodologies for the objective delimitation of species remain inefficient. This study by researchers at the University of Wisconsin - Madison and Iowa State University will develop new computational tools to make species delimitation more efficient. Their research will also address a central question in biology: What is a species? This study will use the genus Adansonia (the baobabs) as a testing ground for these methods. Baobabs are iconic trees of great cultural, ecological, and economic importance in Madagascar, continental Africa, and northwestern Australia, and are also a microcosm for many of the challenges that arise in species delimitation. The work will train undergraduate researchers, K-12 teachers, graduate students, and a postdoctoral associate at the interface of taxonomy, genomics, and computational statistics and provide several opportunities to establish international collaboration. Together, this research will provide new insights into Adansonia systematics and provide a new framework to facilitate species delimitation in diverse groups.

Species delimitation encompasses diverse methods that use genetic, morphological and other trait data to guide taxonomic grouping (placing organisms in hierarchically nested taxa) and ranking (deciding where taxa sit relative to the transition from tree-like relationships at higher levels to reticulate genealogies within populations). Species delimitation remains challenging in many groups due to polyploidy, introgression, and/or species with complex geographic patterns of morphological variation. However, opportunities for progress are offered by recent advances in high throughput sequencing technologies that facilitate rapid acquisition of multilocus DNA sequence data, and by new analytical methods for species level taxonomic problems. Using baobabs as a model, this study will develop a rapid and efficient experimental protocol using sequence capture technology and next-generation sequencing that will allow the application of different species delimitation methods. In addition to deploying existing analytical methods, the researchers will extend the Bayesian Phylogenetics and Phylogeography (BPP) method to formally incorporate morphology and geography. Further, they will add capability to the software program BUCKy for identifying cases where the data imply hybridization or introgression that could be applied in diverse groups of organisms.

With this award, the Chemistry of Life Processes Program in the Chemistry Division is funding Dr. David Baum and collaborators from the University of Wisconsin - Madison and Dr. David Eddington from the University of Illinois - Chicago to develop a microfluidic platform for the discovery of new, life-like chemical systems. There is a lack of knowledge about how new life-like chemical systems, having the capacity for reproducing and evolving, can emerge. The researchers are developing a device to screen complex chemical mixtures in order to find life-like systems that can grow over a mineral surface and can evolve more efficient growth over time. The goal of the project is the discovery of new life-like chemical systems, which would advance the understanding of how life originated on earth. The new experimental approach of this research is used to engage students and the public through presentations. It is also shared with diverse chemists, including high-school chemistry teachers, in a citizen-science effort to understand the nature of life's chemical origins.

This research project involves building a simple microfluidic device and an associated experimental paradigm for flowing a complex chemical mixture, in a stripe, over a mineral surface. This surface contains possible building blocks of autocatalytic cycles as well as inorganic or organic sources of energy. The stripe is displaced across the mineral surface over a multiple day experimental window. This experimental arrangement enables selection for adsorbed autocatalytic sets that can propagate themselves along the surface. Furthermore, if there is spatial variation in such autocatalytic systems, the device selects for variants that can more rapidly colonize newly encountered mineral. Among other analytical methods, X-ray photoemission spectroscopy is used to detect changes in the concentration of adsorbed carbon or nitrogen. Such changes would indicate an adaptive response to selection for enhanced colonization and growth. When new autocatalytic chemical systems are detected, their chemical composition is characterized.

This study explores the idea that the earliest adaptive evolution operated on self-amplifying cycles of chemical reactions, in contrast to most prior studies, which have assumed that evolution requires elements that carry information in the form of nucleic acids (DNA or RNA). Understanding how the origin of life came about is important because it shapes our expectations about life on earth as it exists today and because it aids us in making predictions about whether and in what form life may exist elsewhere in the universe. This project combines theoretical and laboratory research to address the fundamental question of how mixtures of chemicals could self-organize into evolving systems, as must have occurred during the origin of life. The project tests the hypothesis that interactions among multiple such cycles can change over time, similar to the way in which natural ecosystems change as species invade or go extinct, and that such chemical ecological change can gradually morph into more familiar gene-based evolution. In addition to helping explain how life came to be, the work will likely yield new computational tools for ecological and biochemical research and has the potential to lead to new strategies for chemical engineering. Moreover, the work contributes to breaking down boundaries between the fields of evolutionary biology, ecology, computer science, and systems chemistry. The research will bring together and train a diverse team of researchers whose primary expertise is in biology, chemistry, physics, or computer science. Lastly, this project will produce a set of educational resources, designed to make this new perspective on the interplay between chemistry, ecology, and evolution accessible to students across these fields.<br/><br/>The project entails three strands of theoretical research. First, the researchers will develop mathematical and computational tools for analyzing chemical or ecological networks and detecting adaptive evolutionary dynamics. Second, they will conduct analyses of digital ecosystems, composed of numerous digital species interacting in a virtual environment, to understand how patterns of species-species interaction and the spatial structure of the environment affect the capacity for ecological change to resemble evolution. Third, the team will use computer simulations of realistic chemical reaction networks to see if similar factors affect the emergence of adaptive behaviors in chemistry and ecology. These theoretical studies will be combined with laboratory experiments in which the chemical composition of complex mixtures that are driven out of equilibrium by periodic dilution using a flux of chemical food will be tracked over time using liquid-chromatography mass-spectrometry. Statistical analyses of the resulting time courses will be used to detect adaptive behaviors.<br/><br/>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.