EDGE CMT: Genomic characterization of mammalian adaptation to frugivory

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PROJECT SUMMARY Overview: A comprehensive molecular understanding of how mammals ascertain complex traits to adapt to specific environments remains largely unknown. Here, we will take advantage of comparative and functional genomics to systematically dissect dietary adaptation in mammals using frugivory as a model. Mammals evolved from a common dietary ancestor to have an extremely broad range of diets. Amongst these, frugivorous adaptation is of particular significance, as fruit-eating arose in multiple lineages within primate and bat orders. Frugivorous adaptation is also of general interest as diets rich in sugar increase risk for diabetes and metabolic disease in many mammals, including humans. Conversely, frugivorous primates and bats can eat large quantities of fruit/sugar without apparent disease consequences. Supported by recent advances in genome availability and genomic technologies, we plan to take a systematic approach to uncover frugivorous molecular factors by: 1) carrying out comparative genomic analyses of primates and bats to identify sequences that were specifically accelerated in frugivorous species combined with a wide-range of genomic techniques, including RNA-seq, ATAC-seq, ChIP-seq and combined single-cell RNA-seq and ATAC-seq on metabolically pertinent insect and fruit bat tissues; and 2) functionally validate frugivory-associated sequences using cell-based gene assays, massively parallel reporter assays (MPRAs) and swapping these sequences into mice. Our work will comprehensively identify the molecular components leading to frugivory and functionally characterize the genes, regulatory elements and pathways involved in this complex trait. Intellectual Merit: As bats and primates encompass broad dietary ranges, and the evolutionary distances within each order are sufficiently small, they offer ideal models for comparison within each group and between groups to analyze the genetic determinants of dietary specializations. In addition, the use of mouse genetic engineering can allow for functional validation of genetic candidates. We plan to not only identify protein changes that lead to phenotypic differences but also gene regulatory elements that have been shown to be important drivers of morphological change and the evolution of new traits. We have all the needed reagents in place to carry out this project, including necessary bat and primate genomes as well as tissues from both insectivorous and frugivorous bats, fasted and treated or untreated with fruit, and phenotypically relevant bat and primate cell lines for MPRA. Importantly, we have all the needed expertise in our lab, routinely carrying out comparative and functional genomic assays, MPRAs and mouse engineering. With our resources and proficiency, we are in the apt position to advance understanding of the complex trait that is frugivory and ultimately genotype-phenotype relationships. Broader Impacts: This research will improve genotype-phenotype predictions with regards to diet and environment and genetic factors elucidated here have the potential to assist therapeutic developments for people with metabolic diseases like diabetes. Thus, this work will have broad-ranging impacts across disciplines of comparative biology, gene expression, bioinformatics, molecular ecology, molecular evolution and human disease. We already have numerous collaborations with several scientists established from this project, which are discussed in further detail in the project description. PI Ahituv and members of his lab working on this project will contribute to the design of teaching modules from this work. This includes teaching both at UCSF in graduate courses and at San Francisco State University (SFSU) both in undergraduate and graduate courses, where PI Ahituv and his lab members have been actively involved in teaching for years. The lab has also been enthusiastically expanding outreach through the UCSF Science and Health Education Partnership (SEP), educating at local public K-12 schools and the Bay Area Science Festival and will use project materials and findings for these. The Ahituv lab has trained over 30 undergraduate students and 10 high school students, primarily from ethnic groups lacking sufficient representation in STEM. PI Ahituv will continue to offer internships for these students to learn the details of genome analysis and manipulation through this project and encourage careers across the aforementioned disciplines through inclusive mentorship.