Evolution of the Y Chromosome


How did the human Y chromosome become so small relative to its X counterpart? 

Animation: To watch a truly fascinating video, click “Launch this resource” in box at top of article.

This animation depicts the 300-million-year odyssey of the sex chromosomes that began when the proto X and Y were an identical pair. Over time, structural changes in the Y chromosome resulted in its current form, which is specialized to trigger male development. The evolutionary timescale is represented by positioning the chromosomal remodeling events along an abbreviated vertebrate cladogram, a chart of evolutionary relationships.

Part 1. Sex chromosomes originated as autosomes

The sex chromosomes began as an ordinary pair of autosomes. During meiosis. chromosomes replicate their DNA, pair, and exchange genes (recombination; red lines). A mutation in the SOX3 gene produced the SRY gene, a critical determinant of maleness, on the proto Y. While the functions of SRY and SOX3 became very different over time, another gene, RPS4, retained a similar function on both the X and Y chromosomes.

Part 2. Inversions restrict recombination between the X and the Y chromosome

Inversions, which are internal recombination events, caused a rearrangement of genes on the Y chromosome. These rearrangements meant that large portions of the X and Y chromosome no longer recombined, which made the Y chromosome susceptible to deletions, and it decreased in size.

Part 3. Comparison of sex-chromosome recombination in males and females

After our lineage diverged from the ancestors of the monotremes, such as the duck-billed platypus, another inversion further scrambled the genes on the proto Y. In males, only the tips of the Y chromosome were left able to recombine with homologous genes on the X chromosome. In contrast, in females, recombination continued to occur across the full length of the two identical X chromosomes.

Part 4. Autosomal expansion of X and Y chromosomes

About 130 million years ago (Ma), an autosome donated a block of genes that extended the length of both the X and the Y chromosome. The X and Y were able to recombine in these expanded regions of the chromosomes. Subsequently, inversions rearranged the order of genes on the Y chromosome. Additional rearrangements occured almost exclusively on the Y. Without recombination to preserve its integrity, the Y continued to lose genes and, over time, shrank.

Part 5. An autosome contributed a copy of the DAZ spermatogenesis gene to the Y chromosome

Sometime after squirrel monkeys diverged from the primates that evolved into humans, an autosome contributed a copy of the DAZ spermatogenesis gene to the Y chromosome. The DAZ gene was copied and copied again and now the modern Y chromosome contains four identical DAZ gene sequences. The modern Y chromosome is about one-third the size of its X-chromosome partner.

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