Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan.
Mol Biol Evol. 2011 Jun;28(6):1769-76. doi: 10.1093/molbev/msq344. Epub 2010 Dec 20.
Reverse evolution is a widespread phenomenon in biology, but the genetic mechanism for the reversal of a genetic change for adaptation to the ancestral state is not known. Here, we report the first case of complete reverse evolution of two amino acids, serine and alanine, at a single position in RH1 opsin pigment for adaptation to water depth. We determined RH1 sequences of cichlid fishes from four tribes of Lake Tanganyika with different habitat depths. Most of the species were divided into two types: RH1 with 292A for species in shallow water or 292S for species in deep water. Both types were adapted to their ambient light environments as indicated by the absorption spectra of the RH1 pigments. Based on the RH1 locus tree and ecological data, we inferred the ancestral amino acids at position 292 and the distribution of the depth ranges (shallow or deep) of ancestral species of each tribe. According to these estimates, we identified two distinct parallel adaptive evolutions: The replacement A292S occurred at least four times for adaptation from shallow to deep water, and the opposite replacement S292A occurred three times for adaptation from deep to shallow water. The latter parallelism represents the complete reverse evolution from the derived to the ancestral state, following back adaptive mutation with reversal of the RH1 pigment function accompanied by reversal of the species habitat shift.
逆向进化在生物学中是一种普遍现象，但对于适应祖先状态的遗传变化的逆转的遗传机制尚不清楚。在这里，我们报道了 RH1 视蛋白中单个位置的两个氨基酸丝氨酸和丙氨酸完全逆向进化适应水深的第一个案例。我们测定了来自坦噶尼喀湖四个不同生境深度的慈鲷鱼类的 RH1 序列。大多数物种分为两种类型：292A 型用于浅水区物种，292S 型用于深水区物种。两种类型的 RH1 色素吸收光谱都表明它们适应了其周围的光照环境。基于 RH1 基因座树和生态数据，我们推断了位置 292 的祖先氨基酸和每个部落的祖先物种的水深范围（浅或深）的分布。根据这些估计，我们确定了两个截然不同的平行适应性进化：A292S 的取代至少发生了四次，从浅水区到深水区的适应，而相反的 S292A 取代则发生了三次，从深水区到浅水区的适应。后一种平行性代表了从衍生状态到祖先状态的完全逆向进化，伴随着 RH1 色素功能的反向适应突变以及物种栖息地转移的反向。
