Data from: Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid cavefishes (Teleostei: Amblyopsidae)

The genetic mechanisms underlying regressive evolution—the degeneration or loss of a derived trait—are largely unknown, particularly for complex structures such as eyes in cave organisms. In several eyeless animals, the visual photoreceptor rhodopsin appeared to retain functional amino-acid sequences. Hypotheses to explain apparent maintenance of function include weak selection for retention of light-sensing abilities and its pleiotropic roles in circadian rhythms and thermotaxis. In contrast, we show that there has been repeated loss of functional constraint of rhodopsin in amblyopsid cavefishes, as at least three cave lineages have independently accumulated unique loss-of-function mutations over the last 10.3 My. While several cave lineages still possess functional rhodopsin, they exhibit increased rates of nonsynonymous mutations that have greater effect on the structure and function of rhodopsin compared to those in surface lineages. These results indicate that functionality of rhodopsin has been repeatedly lost in amblyopsid cavefishes. The presence of a functional copy of rhodopsin in some cave lineages is likely explained by stochastic accumulation of mutations following recent subterranean colonization.关于退化演化——即衍生性状的退化或丢失——背后的遗传机制目前仍知之甚少，尤其针对洞穴生物的眼睛这类复杂结构。在多种无眼动物中，视觉光受体视紫红质（rhodopsin）似乎仍保留了功能性氨基酸序列。用以解释这一功能看似得以维持的假说包括：感光能力保留所承受的选择压较弱，以及视紫红质在昼夜节律与趋热性中发挥的多效性作用。与之相反，本研究表明盲鳉科（Amblyopsidae）洞穴鱼类的视紫红质功能约束已反复丧失：在过去的1030万年中，至少有三个洞穴支系独立积累了独特的功能丧失突变。尽管部分洞穴支系仍拥有功能性视紫红质，但与地表支系相比，它们的非同义突变率有所升高，且此类突变对视紫红质的结构与功能影响更为显著。上述结果表明，盲鳉科洞穴鱼类的视紫红质功能已反复丧失。部分洞穴支系中仍存在功能性视紫红质拷贝，这一现象或可通过近期洞穴定居后突变的随机积累加以解释。