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.退行演化（regressive evolution）指衍生性状的退化或丢失，其背后的遗传机制大多仍未明确，针对洞穴生物眼睛这类复杂结构的相关研究更是如此。在多种无眼动物中，视觉感光蛋白视紫红质（rhodopsin）似乎仍保留了功能性氨基酸序列。用以解释该蛋白功能似乎得以保留的假说主要有两类：一是保留光感知能力的选择压力较弱，二是视紫红质在昼夜节律与趋热性调控中发挥多效性作用。与之相反，本研究证实盲鳉科洞穴鱼类（amblyopsid cavefishes）的视紫红质功能约束已多次出现丢失现象：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保留了功能性视紫红质，但与地表支系相比，这些支系的非同义突变率显著升高，且此类突变对视紫红质的结构与功能影响更大。上述结果表明，盲鳉科洞穴鱼类的视紫红质功能已多次丧失。部分洞穴支系中仍存在功能性视紫红质拷贝，这一现象大概率可通过近期侵入洞穴环境后突变的随机积累得到解释。