Even today's broadest taxonomic groups originated in the distant past as diversifications of single species, the progeny of which then proceeded along their own evolutionary paths. While these ancient diversifications will never be observed directly, patterns and processes leading to radiations of taxa that exist today can be studied. Thus, in order to truly understand how the tree of life came to be, ways to analyze genome-wide data at lower taxonomic levels must be found. The research will address this goal by integrating new, high throughput sequencing technologies with modern evolutionary analyses. The potential of this method will be explored by applying it to a difficult problem - the resolution of systematic relationships and patterns of morphological evolution in New World representatives of the bat genus Myotis. However, while the focus of this work is a single bat genus, the method will be broadly applicable to any taxonomic group in which retrotransposons (self-amplifying, neutral genetic elements in the genome) have been active during the radiation of interest.

The methods to be developed have great potential in providing markers that are variable enough to resolve rapid radiations, while also being straightforward to analyze. Moreover, because this methodology is expected to be relatively inexpensive, it is anticipated that it will prove appealing to small labs that focus on resolving relationships among closely related species. The integration of multiple subdisciplines of Biology is often discussed but rarely realized. This project represents a unique attempt to integrate modern computational biological tools using genome level data and well established morphometric analyses. This project will contribute to the infrastructure of science by amassing tissue, skin and skeletal material that will fill gaps in terms of members of the genus Myotis and nontarget taxa. These materials will be deposited in a public repository (Museum of Natural History, LSU) and will be available in perpetuity to the scientific community. Finally, education and outreach to the local communities will be based on the investigation of a charismatic taxonomic group and will improve research and education in two traditionally underdeveloped states.

Project Report

Genomics, the sequencing and analysis of the entire genetic code of organisms, has the potential to improve our understanding of multiple fields within Biology. One of those fields is systematics, the study of evolutionary relationships. Unfortunately, genome-scale approaches to systematics have been limited to relatively broad taxonomic groups such as ‘eukaryotes’, ‘mammals’ or ‘land plants’. However, in order to truly understand the processes underlying evolutionary diversification, we must switch focus to lower taxonomic levels of genus and species. Unfortunately, gathering genome-scale data can be an expensive proposition. For this project we took advantage of two recent innovations to resolve both of these problems. First, next-generation sequencing technologies have made the generation of vast amounts of sequence data a realistic endeavor for a wide variety of researchers, not just major genome centers. Second, phylogenetic analyses based on transposable elements (TEs) have the advantage of being essentially homoplasy-free and able to inform us about even rapid diversifications. We combined these two innovations in an attempt to revolutionize phylogenetic analysis of large species groups. Within the project we proposed the following objectives: 1) Integrate next-generation sequencing technology with TE-based phylogenetic methods to transform TE-based analysis of species-rich taxonomic groups. 2) Determine the phylogeny of New World Myotis (Vespertilionidae) using two complementary methodologies developed as part of the above approach. 3) Employ the inferred phylogenies to evaluate mode and tempo of morphological evolution in general and to address the following questions in particular: The methods developed will be applicable to any eukaryotic clade harboring retrotransposons that were active during the time during which the taxa being studied diverged. Thus, the methodology has potential to transform large-scale phylogenetic analysis. Thus far, we have accomplished Objective 1 and are in the process of completing Objectives 2 and 3 with our co-PI, Richard Stevens, who has requested a one-year extension on his portion of the grant. We will continue collaborating with Dr. Stevens as we complete the project as a whole. The project concerns charismatic megafauna of great interest to the general public. Thus it has been high profile, resulting in a feature video on Science Nation (www.youtube.com/watch?v=kWHij0P-_F4). In PI Ray's laboratory, the funds provided by this project supported the training of one postdoctoral associate, three graduate students, four undergraduate researchers, and one high school science teacher. However, the effect of these funds did not end there. Funds have also supported nine publications and seven oral/poster presentations at national and international meetings. Four additional publications related to the project are either submitted to journals or are in preparation for submission. In addition, biological samples have been submitted to multiple museum collections as part of our efforts on the project. Finally, as mentioned above, broader impacts generated by the projects include the training of one postdoctoral associate, three graduate students (including two females), three undergraduate researchers (all female, two from underrepresented minorities), and one high school science teacher (female, and in a rural Mississippi district). In addition to these impacts, PI Ray and two graduate students visited the classroom of the participating teacher and trained high school students in basic molecular biology techniques while informing them about the project and its importance.

National Science Foundation (NSF)
Division of Environmental Biology (DEB)
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Program Officer
David Mindell
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Mississippi State University
Mississippi State
United States
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