Question

2. Use examples of molecular evolution and DNA sequences from lecture and the text to illustrate how you can test hypotheses of neutral evolution, negative selection, and positive selection.

Answer 1

answer ) The main tenet of the neutral theory is that the great majority of evolutionary changes at the molecular level are caused not by Darwinian selection but by random fixation of selectively neutral (or very nearly neutral) alleles through random sampling drift under continued mutation pressure. The theory also asserts that the majority of protein and DNA polymorphisms are selectively neutral, and that they are maintained in the species by mutational input balanced by random extinction rather than by "balancing selection."The neutral theory claims that the great majority of evolutionary changes at the molecular (DNA) level are caused not by Darwinian selection but by random fixation of selectively neutral or nearly neutral mutants. The theory also asserts that the majority of protein and DNA polymorphisms are selectively neutral and that they are maintained in the species by mutational input balanced by random extinction. In conjunction with diffusion models (the stochastic theory) of gene frequencies in finite populations, it treats these phenomena in quantitative terms based on actual observations.

Positive selection: also called (Darwinian selection) variants that increase in frequency until they fix in the relevant population. The selective pressure that leads to this fixation is termed positive selection. Positive natural selection is the force that drives the increase in prevalence of advantageous traits, and it has played a central role in our development as a species.As first articulated by Darwin and Wallace in 1858, positive selection is the principle that beneficial traits—those that make it more likely that their carriers will survive and reproduce—tend to become more frequent in populations over time . In the case of humans, these beneficial traits likely included bipedalism, speech, resistance to infectious diseases, and other adaptations to new and diverse environments.

In natural selection, negative selectionor purifying selection is the selective removal of alleles that are deleterious. This can result in stabilizing selection through the purging of deleterious genetic polymorphisms that arise through random mutations. Purging of deleterious alleles can be achieved on the population genetics level, with as little as a single point mutation being the unit of selection. In such a case, carriers of the harmful point mutation have fewer offspring each generation, reducing the frequency of the mutation in the gene pool.

The proportions of neutral, deleterious, and adaptive mutations and their selection coefficients can be estimated by various methods from variation within and between species. If all detectable amino acid and synonymous polymorphism is neutral, the ratio of amino acid to synonymous variation within species should remain constant regardless of a population's demographic history. However, this ratio should change as a function of frequency if some amino acid variation is under positive or negative selection. At allele frequencies on the order of the reciprocal of the effective population size, selection is ineffective and the relative proportions of neutral, deleterious, and adaptive variants correspond to their production by mutation. The relative number of deleterious to neutral mutations declines as a function of frequency in the population. Advantageous mutations, on the other hand, become enriched relative to neutral mutations in the high frequency portion of the distribution and in fixed differences between species. The effects of positive selection can be distinguished from negative selection only if an outgroup is used to infer whether a mutation is at, say, 5 or 95%. Many polymorphism studies do not make this distinction and so an excess of rare (low and high) compared to common single nucleotide polymorphisms (SNPs) cannot be attributed to just positive or negative selection. To estimate the fraction of DNA variation within and between species that has been under positive and negative selection we compare amino acid and synonymous polymorphism from two recent surveys of human DNA variation and from divergence between humans and old world monkeys.

Negative selection: Also called purifying selection, it means that selection is purging changes that cause deleterious impacts on the fitness of the host.