Brownstein Chase D, Policarpo Maxime, Harrington Richard C, Hoffman Eva A, Stokes Maya F, Casane Didier, Near Thomas J
Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
Mol Biol Evol. 2025 Jul 30;42(8). doi: 10.1093/molbev/msaf185.
Genomes provide tools for reconstructing organismal evolution and larger Earth system processes. Although genome sequences have been jointly analyzed with geological data to understand links between biological evolution and geological phenomena such as erosion and uplift, genomic and natural history observations have seldom been leveraged to reconstruct the timescale of landscape change in cases where traditional methods from the Earth sciences cannot. Here, we reconstruct the genomic evolution of cave-adapted amblyopsid fishes. Although high-resolution computed tomography reveals the strikingly similar skeletons of cave-adapted lineages, our analyses of the genomes of all species in this clade suggest that amblyopsids independently colonized caves and degenerated their eyes at least four times after descending from populations that already possessed adaptations to low-light environments. By examining pseudogenization through loss-of-function mutations in amblyopsids, we infer that the genomic bases of their vision degenerated over millions of years. We leverage these data to infer the ages of subterranean karstic ecosystems in eastern North America, which are difficult to date using standard geochronologic techniques. Our results support ancient ages for imperiled North American cave biotas and show how genomes can be used to inform the timescale of landscape evolution.
基因组为重建生物进化和更大规模的地球系统过程提供了工具。尽管基因组序列已与地质数据联合分析，以了解生物进化与诸如侵蚀和隆升等地质现象之间的联系，但在地球科学的传统方法无法做到的情况下，基因组和自然历史观测很少被用于重建景观变化的时间尺度。在这里，我们重建了适应洞穴生活的洞鲈科鱼类的基因组进化。尽管高分辨率计算机断层扫描显示适应洞穴生活的谱系的骨骼惊人地相似，但我们对该分支中所有物种基因组的分析表明，洞鲈科鱼类在从已经适应弱光环境的种群中分化出来后，至少独立地四次进入洞穴并退化了它们的眼睛。通过研究洞鲈科鱼类中功能丧失突变导致的假基因化，我们推断它们视觉的基因组基础在数百万年的时间里逐渐退化。我们利用这些数据推断北美东部地下岩溶生态系统的年龄，而使用标准地质年代学技术很难确定这些生态系统的年代。我们的结果支持北美濒危洞穴生物群系的古老年代，并展示了基因组如何能够用于确定景观演化的时间尺度。
