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.

退化演化（regressive evolution）指衍生性状的退化或丢失，其背后的遗传机制目前仍未被充分阐明，针对洞穴生物的眼睛这类复杂结构的相关研究尤为匮乏。在多种无眼动物中，视觉感光受体视紫红质（rhodopsin）似乎仍保留功能性氨基酸序列。目前用以解释该功能看似得以保留的假说包括：对感光能力保留的弱选择，以及视紫红质在昼夜节律与温度趋化中发挥的多效性作用。与之相反，本研究表明盲鳉科洞穴鱼类的视紫红质功能约束已多次丧失：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性突变。尽管部分洞穴支系仍携带功能性视紫红质，但与地表支系相比，它们的非同义突变（nonsynonymous mutations）率更高，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多次丧失。部分洞穴支系中仍存在功能性视紫红质拷贝的现象，大概率可通过近期迁入洞穴环境后突变的随机积累来解释。