Opposite evolutionary effects between different alternative splicing patterns

Alternative splicing (AS) has been recognized as a mechanism of relaxing selection pressure on protein subsequences. Here, we show that AS may also yield contrary evolutionary effects. We compare the evolutionary rates of 2 types of alternatively spliced exons (ASEs)-simple and complex. The former does not change the boundaries of its flanking exons, whereas the latter does. By analyzing over 26,000 human-mouse orthologous exons, we demonstrate that complex ASEs have lower Ka and Ka/Ks ratio and higher Ks than constitutively spliced exons (CSEs), whereas simple ASEs have evolutionary rates to the opposite of CSEs. Our results indicate that complex ASEs are subject to stronger selection pressure than CSEs at the protein level, but the trend is reversed at the RNA level. Therefore, the previous view that ASEs accelerate evolution of protein subsequences needs to be modified.