Shedding light on the evolution of a blind cavefish

The subterranean world of caves often gives rise to unique character changes in species that live in darkness, leading to troglomorphic traits such as loss of pigmentation, giving them a pink appearance, and loss of eyes. Studying these cave-adapted species offers a window into evolutionary processes, as selective pressure (or relaxed selection) in caves is often strong and well-understood. Scientists are particularly interested in whether these evolutionary changes are the result of natural selection adapting the animals to their unique environment, or whether they result from genetic drifta random shift in gene frequencies that can occur in isolated populations. Two hypotheses have been proposed: (1) troglomorphic traits may arise from a lack of natural selective pressures in caves, or (2) these traits provide an adaptive advantage in cave conditions, possibly due to effects, where one gene affects multiple traits. This study will investigate to what extent each hypothesis explains the evolution of these adaptations in cave-dwelling organisms. Our research will focus on a cyprinid fish from the Hajar Mountains in Northern Oman: Garra longipinnis, which has both surface populations and a troglomorphic cave population which occurs only in the Al Hoota cave system and is of rather recent origin (0.8 to 0.1 Myr ago). By comparing the genomes of cave and surface populations of G. longipinnis, and a closely related species (G. sharq), we aim to elucidate how the peculiar cave characteristics arises. First, we want to understand whether genetic differences between cave and surface populations are due to adaptation to cave life or random changes. Additionally, we aim to investigate whether the genetic changes in the cave populations are due to new mutations or due to shifts in existing genetic variation. Finally, RNA-sequencing will allow for a comparison of gene expression across various forms and life stages to determine whether changes in protein-coding genes or gene regulation contribute to the troglomorphic traits. This work will provide deeper insight into the genetic and evolutionary mechanisms underlying the fascinating adaptations of cave organisms, advancing our understanding of how extreme habitats shape life.