Final answer:
Natural selection operates on the heritable traits of populations to increase or decrease the prevalence of certain alleles. However, it does not act on individual alleles, and its effectiveness can be limited due to factors like linkage disequilibrium and existing genetic variance. The net effect of an organism's alleles on fitness is what ultimately matters for selection.
Step-by-step explanation:
Natural selection is a cornerstone principle of evolutionary biology that acts on a population's heritable traits. This process, termed adaptive evolution, selects for beneficial alleles that increase an organism's fitness and thus their likelihood to reproduce and pass on their genes. However, natural selection does not directly act on individual alleles but rather on the organism as a whole. An organism may have a mix of beneficial and deleterious alleles, but it is the net effect on the organism's fitness that influences which traits are passed on to the next generation.
One limitation of natural selection is the phenomenon of linkage disequilibrium, where some alleles are physically close to each other on the genome and are therefore inherited together. Moreover, evolution acts on the phenotype—the observable characteristics influenced by the genotype and the environment. The environment cannot differentiate between genotypes if they result in the same phenotype, which is why natural selection cannot favour a homozygous individual over a heterozygous one if they share the same traits.
Ultimately, natural selection is constrained by a population's existing genetic variance, the new alleles that arise, and the environment's selectively pressured ecosystem. It offers insights into how populations adapt to their environments, but it does not create 'perfect' organisms, nor does it act on non-heritable traits or acquired characteristics. An allele that negatively impacts fitness may still be passed on if it occurs in an individual with an overall adaptive phenotype.