NSFDEB-BSF: Breaking Barriers to the Study of Traits that Affect Speciation and Extinction

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As new species arise and older species become extinct, life on Earth is shaped and re-shaped over many millions of years. Biologists seek to understand how particular traits of organisms---the size of an animal or the flower color of a plant, for example---affect the chances of giving rise to a new species or suffering extinction. This project develops computational tools to help identify traits that consistently affect speciation and extinction. It further applies the tools to understand the history of particular plant groups, including ones with agriculturally and economically valuable species. Undergraduate science opportunities and mentoring specifically target veterans of the armed services. A workshop and individual advising will equip young researchers with technical skills that are valuable for a variety of future careers. The international collaboration between American and Israeli labs will train students and postdoctoral researchers and hold workshops to build communities of young scientists working with phylogenetic comparative methods.Inferring trait-dependent lineage diversification from phylogenetic trees is difficult. There is currently a need for methods that are both powerful and reliable, and for tools to distinguish when methods perform well or poorly. In this project, two novel modeling techniques target weaknesses recently revealed in current methods. The first incorporates sequence evolution into models of trait evolution, to allow shifts in diversification rate to be explained by processes at both those levels. The second focuses on connections between diversification and trait shifts, rather than their values, to avoid the statistical problem of pseudoreplication. Two computational tools provided by this project improve the usage of existing and future methods. One is a community-driven database of benchmark tests to compare how methods perform across diverse scenarios. The other is a means of assessing model adequacy, to guide confidence in empirical conclusions and directions for future model development. Finally, this project investigates the macroevolutionary dynamics of two traits that have major effects on plant phenotypes and genotypes: breeding system and whole genome duplication. Methodological advances and expanded datasets provide the potential to make the strongest cases yet for the importance of species selection in shaping biodiversity.