Y Chromosome- An Evolutionary Curiosity

The X and Y chromosomes are an odd couple. But the Y reads more like a rule-breaker of human genetics; most of it refuses to recombine, more than half of it consists of tandem repeats of satellite DNA and it's not a prerequisite for life (females don't have or need one). So why bother with a chromosome that tells us about 50% of the population (assuming a 1:1 sex ratio)? Since it passes directly from father to son, its sex-determining role means it is specific to males and haploid. It contains vast numbers of unique SNPs and has some notable exceptions such as 2 pseudoautosomal regions that do recombine with the X as well as euchromatin sequences (which are loosened during interphase). Largely escaping recombination, the Y can bequeath haplotypes which are passed down a robust phylogeny (changes only via mutation) and can be used to trace back the most recent matrilineal ancestor, Y-chromosomal Adam. A gene called SRY (sex-determining-region-Y), derived from SOX3, which transcribes a protein to activate the formation of the testes, such is the origin of the sex-determining role. We can infer that the sex chromosomes started off initially as a matched pair (due to the identical telomeric sequences at the tips, which can engage in recombination); during the course of meiosis (the process of gamete formation), the homologous chromosomes align and exchange segments, subsequently sending off a copy of an autosome and and a sex chromosome to each cell. Other indications that Y and X were once alike include the non-recombining sites on the Y, most genes in this region have corresponding duplicates on the X. What makes the Y-chromosome an evolutionary curiosity is that its profound lack of recombination it makes it more prone to accumulating mutations and then decay; something must have happened to cease the exchange of DNA between the X and Y. The Y forfeited its ability to exchange DNA with the Y in discrete stages; firstly, a strip of DNA flanking the SRY gene spreads down the chromosome. But only the Y decayed in response to the loss of X-Y chromosome recombination, in contrast to the X which in females undergoes recombination when a pair of copies meet during meiosis. So what then could explain away the interruption of recombination between the X and Y?

As the early Y tended to exchange segments, a portion of DNA experienced an inversion (effectively turning the sequence upside down) relative to the X and since a prerequisite for recombination is that analogous sequences are aligned, any inversion would prevent interaction between the two regions. Comparative genomics unveils that autosomal precursors of the X and Y were unbroken (intact) in reptilian species before the mammalian lineage began . But monotremes like platypi were among the earliest to speciate and have a SRY gene aged back to 300 million years. X-inactivation followed (in which female embryo cells arbitrarily shut down a majority of the genes in one of the 2 X-chromosomes) to compensate for the degeneration. If we reduce the whole human population to two people (one man and woman), together this couple carries four copies of each autosome and three X chromosomes and a single Y. The effective population size of the Y can be therefore predicted to be similar to that of haploid mtDNA, 1/3 that of any X and 1/4 that of any autosome. Hence, we can expect much lower rates of diversification in the Y than any other region of the nuclear genome. We can predict is to also be more subject to genetic drift (random changes in frequency of haplotypes) and such drift would act as a catalyst for the differentiation between aggregates of Y-chromosomes in different populations.