In many species the nucleotide diversity differs between the

In many species the nucleotide diversity differs between the autosomes and X-chromosome. For example, in humans the average neutral nucleotide diversities are: autosomes = 1 times 10^-3 per site, X-chromosome = 0.6 times 10^-3 per site. a. How do you explain the difference level of diversity of the autosome and X-chromosome? b. How would you determine which of your explanations was correct In contrast in African D. melanogaster the relative neutral diversities are: autosomes = 1.8 times 10^-2 and X-chromosome 1.8 times 10^-2 per site. How might you explain this pattern given your explanation above?

Solution

Answer:

2. a. The X chromosome has a different inheritance pattern from the autosomes, direct interaction and potential conflict with the Y chromosome, and fewer copies than the autosomes.

Natural selection may thus act differently on the X chromosome. It has been found recently that the X chromosome contains megabase-sized regions that are almost without variation in most species. No such regions are found on the autosomes.

So, it has been suggested that independent and very strong selective sweeps are the only plausible explanation for these observations It has been hypothesize that the targets of these sweeps are multicopy testis-expressed genes in a genetic conflict with the Y chromosome for transmission to the next generation.

b. The experiments which can be used to validate the above explanations are:

i. Analysis of polymorphism and divergence data:

To contrast diversity patterns between autosomes and X chromosomes, the analytical dataset can be divided into exonic, intronic, and intergenic regions, followed by the estimation of the nucleotide diversity, , for each functional category in each (sub)species.

If lower diversity around these regions are more pronounced for the X chromosomes than the autosomes, then it can illustrate positive correlation between distance to genes and the ratio of X to autosome diversity.

ii. Analysis of X-linked ampliconic regions:

To test whether ampliconic genes are associated with lower diversity in regions around them, nucleotide diversity () can be contrasted in the flanking regions of the amplicons (100 kb and 1 Mb) with the rest of the X chromosome.

c. Although fruit flies have both X and Y chromosomes, the Y chromosomes is mainly involved in producing sperms and does not confer maleness. Sex determination in Drosophila melanogaster is through the ratio of X chromosomes to autosomes. Thus, both types takes part in the sex determination process and are interdependent. This phenomenon can explain similar types of selection pressures on these sets of chromosomes leading to an equivalent realtive neutral diversities.