ABSTRACT

Plants and animals have adapted to survive in a variety of extreme environments, and understanding these adaptations has the potential to aid in developing strategies to better withstand a changing environment. Despite their importance, much is left to be learned about the genes responsible for adaptations to extreme environments. This project investigates the genetic changes that are responsible for allowing animals to live in extreme environments. Cave environments provide natural laboratories to study how organisms can live without abundant food sources and in constant darkness. Cave animals have undergone shifts in their metabolism, sleep patterns, and sensory systems and can inform the understanding of these basic biological processes. This research will find commonalities in how organisms respond to extreme cave environments and asks specifically if some parts of the genome contribute to adaptation more so than other parts and if so, why those parts of the genome are unique. In addition, this work provides opportunities for international collaborations and for training the next generation of scientists in the classroom, in the laboratory, and across the world through interactive and virtual experiences.

Over 200 species of bony fish have adapted to live in cave environments, representing an unparalleled opportunity for comparative biology to uncover the genetic basis of dramatic trait shifts. Through using cutting-edge third-generation sequencing and newly developed population and comparative genomic analysis methods, this work will identify genetic variations associated with cave-derived traits within three species of cavefish that have close surface relatives: the Mexican tetra (Astyanax mexicanus), the cave Molly (Poecilia mexicana) and the Brazilian catfish (Aspidoras mephisto) to determine if the same genes and genetic changes underlie repeated evolution of cave adaptations. Genomic analyses across the teleost tree of life will also be performed to find common genetic changes across cave-adapted groups. By comparing both within and between species, this project will identify if mutational bias and mutational opportunity predispose regions of the genome to contribute to phenotypic change. Functional genomic tests using CRISPR-Cas9 will be employed to validate genetic changes found in cave species and test the impact of mutations on phenotypes.

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.

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