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

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Understanding the evolutionary relationships among organisms within the Tree of Life is essential for learning how life has evolved on Earth. By unraveling these interrelationships, the historical causes and consequences of biological phenomena ranging from disease to diet can be understood. Decades of research has shed light on many regions of the Tree, but still, many relationships are poorly understood. Recent technological advancements now allow biological researchers to collect DNA sequence data from the genomes of organisms on an unprecedented scale, and these massive data have the potential to untangle these difficult branching patterns in the Tree of Life. However, much remains to be learned about how genomes evolve across the many branching events of the Tree. This project will use these large DNA sequence data sets to study the branching patterns of evolutionary relationships in Strepsirrhine primates, a group that contains the highly endangered lemurs of Madagascar, and salamandrid salamanders, a diverse group of amphibians most commonly known as the newts. These two very different organismal groups will be used to answer questions about how different types of genes evolve at the molecular level as the lineages that contain them diversify and split over time. This will help evolutionary biologists answer the important question of which data from across the genome is best sampled to properly infer the organismal placement in the Tree of Life. This project will involve participants across multiple levels of education, including undergraduate, graduate, and postdoctoral researchers, as well as established faculty. This research will inform conservation planning of these two iconic organisms. Additionally the research will link with public outreach activities at the Duke Lemur Center and the North Carolina Museum of Natural Science. This research project will use next generation DNA sequence technology to sequence large portions of strepsirrhine primates and salamandrid salamanders genomes. These data will include hundreds of loci under positive selection as well as hundreds of loci from neutrally evolving parts of the genome. Analyses of these data will explore the ways in which massive data sets can be used in phylogeny reconstruction. The phylogenetic reconstruction will be focused within groups which have exhibited patterns of recent and rapid species radiations and contain branches that have challenged phylogenetic reconstruction. The researchers will assess the performance of genes under positive selection in reconstructing difficult clades. While the use of genes under selection is something typically avoided in molecular phylogenetics, properties of these positive-selection loci suggest that they may be an ideal source of phylogenetic information for the most challenging of branches. The loci under positive-selection will be annotated by gene properties thereby providing a tremendous wealth of gene ontology information. The researchers will assess the performance of functional classes of genes in phylogeny reconstruction to gauge whether particular functional classes of genes are better at recovering phylogeny. Overall, the results of this project will provide empirically-derived solutions to the phylogenetics community for how a genomic data can be used to solve challenging phylogenetic questions.