Collaborative Research: A genomic-architecture-aware approach for resolving a taxonomically complete phylogeny of parrots

The tree of life is a powerful tool for understanding evolution that can also be used for research on medicine, wildlife management, and agriculture. However, recent studies indicate that genes transferred between species can make it difficult for scientists to build an accurate evolutionary tree or understand the relationships between species. This project will use parrots, one of the most endangered and illegally trafficked groups of animals, to better understand how often species transfer genes and how that impacts scientists’ ability to accurately build an evolutionary tree. The researchers will collect genetic data, including sequencing genomes, for all parrots. These data will be used to build an evolutionary tree of parrots and answer questions about gene transfer between parrot species. This data will also be used to aid conservation efforts by developing forensic DNA barcodes that will help law enforcement correctly identify illegal products made from endangered parrot species. The project will build collaborations between forensic scientists and natural history museums, provide training and mentoring for students through early-career researchers, and share findings with the public and scientific communities. To estimate accurate phylogenetic trees in the genomic era, the effect of genomic architecture (the structure, organization, and content of a genome) on phylogenetic signal must be understood. Large-scale phylogenetic methods often do not account for gene flow, nor do they address the interaction between genomic architecture and phylogenetic signal, which can lead to well-supported but inaccurate evolutionary relationships. Using the global radiation of parrots as a focal system, this project will reconstruct a nearly complete time-calibrated phylogeny of the clade to assess gene flow across an entire radiation and predict genomic regions prone to biasing phylogenetic estimates. The researchers will generate new genomic resources, including five chromosome-level reference genomes and genomic-scale markers for over 400 previously unsampled taxa. The project aims to test the following hypotheses to make general predictions about the factors causing gene tree discordance and to inform a species-level taxonomic revision: 1) non-monophyletic species are a common feature across the parrot evolutionary tree; 2) non-monophyletic species and weakly supported relationships are associated with a higher prevalence of gene flow that spans millions of years; and 3) genomic architecture is relatively conserved across the parrot radiation and can be used to mitigate the effects of gene flow in phylogenetic inference across temporal scales. This work will offer a high-resolution view of the interaction between phylogenetic signal, gene flow, and genomic architecture in parrots, and demonstrate how this framework can be used for improved taxonomic classification and wildlife management. This 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.