ABI Development: Computational infrastructure for phylogenetic analysis in the R environment

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Over the past several decades, phylogenetic trees, the graphs that are used to represent the ancestor-descendant relationships between gene sequences, populations, or species, have become integral in scientific research across an increasingly widening range of biological disciplines such as ecology, evolutionary biology, molecular biology, comparative genomics, and development. Phylogenies too have begun to see application outside of biology in such diverse fields of study as comparative linguistics, anthropology, and forensic science. Meanwhile, the computational environment known as 'R' has developed into one of the leading platforms for scientific computing. The strength of R comes from the literally thousands of contributed function libraries (called "packages") developed and distributed for free by computational scientists and developers that are not members of the R core development team. Because of these contributions, R has grown into the preeminent software platform for manipulating, visualizing, and analyzing phylogenetic trees. That said, the capability to actually estimate phylogenetic trees from data in R remains relatively limited. The major objective of this award is to substantially extend the toolkit that is available to undertake phylogeny estimation in the R scientific computing environment. This toolkit will be built using an open development model and will be distributed as a free and open-source resource to the national and international scientific communities. Among the major advantages of developing software for scientific computing in R is that so doing dramatically facilitates scientific reproducibility by allowing all stages of the data analysis pipeline to be built into a single, fully reproducible workflow from open source components.This research will create new, open-source, and freely distributed software tools that will be of broad utility throughout the phylogenetic scientific community and beyond. The general goal is computational infrastructure development for phylogenetics in R. These investigators will focus on four specific objectives in particular: (1) the development and application of methods to compute distances between trees; (2) the development of new consensus and average tree methods; (3) the development of joint species-tree estimation methods based on likelihood; and, finally, (4) the application of visualization tools for sets of trees and phylogenetic networks. They focus specifically on these research objectives because they interact in particularly interesting ways and because they reflect areas in which substantial research is needed; however, research on these topics will likely result in unanticipated discoveries in fundamentally new areas. The award will also support postdoctoral and graduate training, the latter via an intensive, phylogeny methods boot camp for young developers. This training objective will be undertaken with the aim of helping to form the next generation of computational phylogenetic biologists and will target for participation graduate students from groups traditionally underrepresented in the sciences. Phylogenetic tools from this project will be hosted on the CRAN at https://cran.r-project.org/web/packages/phytools/index.htmlThis 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.