Collaborative Research: Species tree reconstruction using neutral and non-neutral phylogenomic data.

We propose a research project with two broad aims: (1) to use phylogenomic data to generate a robustly resolved species tree for strepsirrhine primates, the most diverse higher-level clade of primates, and the most endangered clade of all mammals, and salamandrid salamanders, the 2nd most diverse family of salamanders. These systems are used to (2) assess the role of using various types of DNA sequence-based markers that differ in their molecular evolutionary and functional properties in the phylogenetic resolution of complicated, yet tractable phylogenetic radiations. This research will contribute to answering developing and pressing questions in the field of molecular phylogenetics as it moves solidly into the realm of phylogenomics. While questions and limitations surrounding the laboratory generation of genomic sequence data are rapidly fading away, new questions concerning the numbers and types of loci needed to answer challenging phylogenetic questions are quickly taking their place. Intellectual Merit: Our proposed research is built around three main objectives: First, we will assess the performance of species tree reconstruction for the strepsirrhine primate and salamandrid salamander systems using a large phylogenomic sample of neutrally evolving loci. Here we will explore the ways in which massive data sets (i.e., multiple hundreds of loci) can be used in species reconstruction, either in total, or as subsets of informative loci. Second, we will assess the performance of loci under positive selection in reconstructing difficult regions of the species tree. Here, we will tackle phylogenetic reconstruction within two focal strepsirrhine test clades and two focal salamandrid test clades, all of which have exhibited patterns of relatively recent and rapid species radiations and contain branches that have challenged phylogenetic reconstruction. While the use of genes under selection is something typically avoided in molecular systematics, properties of these positive-selection loci suggest that they may be an ideal source of phylogenetic information for the most challenging of branches to reconstruct: those featuring short durations of time and large ancestral population sizes. Finally, we will assess the performance of functional classes of genes in species tree reconstruction based on the annotated properties of phylogenomic loci. Here, we will capitalize on the tremendous wealth of gene ontology information, particularly available for primate genomes, to gauge whether genes within particular functional classes are better at recovering the species tree. Overall, the results of this project will be aimed at reconstructing phylogeny for two diverse vertebrate groups, and at providing empirically-derived solutions to the systematics community for how a phylogenomic approach can be used to solve challenging phylogenetic questions. Broader Impacts: Our proposed research will link together researchers across two major southeastern US research institutions and provide integrative training in genomics, phylogenetics, and molecular evolution at both the postdoctoral, graduate, and undergraduate level. The results of this research are expected to be highly informative to the molecular systematics community as it continues to experience massive changes in data collection and analysis. The data we will generate will have broad utility, beyond our research, including comparative genomics and larger meta-phylogenetic studies across the Tree of Life. Our research will strive to incorporate postdoctoral and student participants from underrepresented and minority groups. We will work with coordinators of the KY-WV Louis Stokes Alliance for Minority Participation (LSAMP) program to identify minority candidates from regional colleges and universities to fill undergraduate and graduate research positions, efforts that will complement the UK LSAMP program's goal to develop a "Bridge to the Doctorate" initiative. We will also work with curators and researchers at the NC Museum of Natural Sciences, and at the Duke Lemur Center, to coordinate a series of research talks and activities at the Museum and in the NC-Triangle community. The charismatic and conservation-related aspects of our study systems will provide an excellent backdrop for the educated children and adults about the importance of genomic technology and the analysis of genomic data in the basic sciences. Finally, the products of this research will contribute to conservation efforts for the world's most endangered mammals.