Tiger salamanders are used in a range of biological and biomedical research, with much emphasis placed on a single species, the Mexican Axolotl, due to ease of rearing and experimental manipulation. However, this species is just one representative of a large and diverse radiation of tiger salamanders. Collectively, this group can serve as a model system for research ranging from speciation to regeneration, but little is known about how many species actually exist and little is known about their natural history, evolution, development, and relationships. This research will leverage new molecular technologies and existing genetic data to provide a comprehensive assessment of tiger salamander species diversity across North America and place these species into a comparative framework to understand their evolution. Concurrently, there will be development of new statistical tools to identify genes that have been uniquely influenced by other factors, such as natural selection.
This research forges a strong link between statistical and biological research programs, an increasingly important form of collaboration as Biology moves further into the realm of genomics. Support and training of human resources will be provided at the postdoctoral and graduate level and persons employed by this grant will be integrated into a modern and multidisciplinary research program. This work will result in the collection of one of the largest set of genetic data at the level of populations for a naturally distributed organism.
A major goal in Biology has been to reconstruct the many ancestor descendent branches that make up the Tree of Life. For many years, molecular data, primarily in the form of DNA sequences, have served as an important source of information for reconstructing these historical relationships. Very recent technological advances now permit biologists to collect DNA sequence data from across the genome from nearly all organisms. However, biologists are just beginning to learn how these data should best be generated for biodiversity studies, and how they can be used in an effective and informative way to inform the reconstruction of the Tree of Life. In this project, one of the first "next-generation" phylogenetic studies was performed on a biologically important and species-diverse radiation of salamanders in North America, the Ambystoma tigrinum complex (commonly know as tiger salamanders and axolotls). Using DNA sequencing strategy known as parallel tagged amplicon sequencing, nearly 100 nuclear genes were sequenced from individuals representing populations and species from across the range of this salamander complex. These data have been used to clarify the geographic boundaries of species, and to reconstruct the ancestor descendent branches that define the history of speciation and adaptation in this group. More importantly, this study was one of the first of its kind to explore the importance, and limitations, of large genomic data sets in reconstructing regions of the Tree of Life. Working as a team of Biologists, Computer Scientists, and Statisticians, the participants on the project worked through numerous hurdles that come with learning how to integrate large data sets into analytical frameworks that have originally developed in the context of smaller data sets sampled from one or a few genes. This included the development of new informatic workflows to process the massive amounts of raw data generated by recently developed next-generation sequencing platforms, and the development of automated approaches for analyzing data from hundreds of genes. In addition, this project has fostered new perspectives on how results from these types of phylogenomic studies should be interpreted. This project involved training across multiple different and increasingly coupled disciplines, providing experience and training in next-generation sequencing and associated molecular lab work, mathematics and statistics, and high-performance computing. The participants gaining this experience included students at the undergraduate and graduate level, postdoctoral researchers, and the principal investigators, all of whom gained valuable experience in this rapidly changing field. This experience has proven to be timely and significant, as many participants in this project have since acquired new positions, including faculty positions at research institutions. This project also included research collaborators at additional academic institutions in Mexico and in the United States, providing a broader training base for all involved.
