Natural selection predominantly causes changes in populations. While it affects the frequency of various genotypes and phenotypes within those populations over time, it does not cause changes in individuals, as individuals do not evolve in response to natural selection. Instead, it is the population that evolves as advantageous traits become more common across generations.
So, the most accurate answer is: 3. populations. However, it's also notable that natural selection impacts both 1. genotypes and 4. phenotypes, as it works on the traits (phenotypes) that are heritable (genotypes).