Chimpanzee and Human Y Chromosomes Are Remarkably Divergent in Structure and Gene Content – Nature Letters

Here’s the abstract of some news which John Hawks describes as “really, really weird”:

The human Y chromosome began to evolve from an autosome hundreds of millions of years ago, acquiring a sex-determining function and undergoing a series of inversions that suppressed crossing over with the X chromosome1, 2. Little is known about the recent evolution of the Y chromosome because only the human Y chromosome has been fully sequenced. Prevailing theories hold that Y chromosomes evolve by gene loss, the pace of which slows over time, eventually leading to a paucity of genes, and stasis3, 4. These theories have been buttressed by partial sequence data from newly emergent plant and animal Y chromosomes5, 6, 7, 8, but they have not been tested in older, highly evolved Y chromosomes such as that of humans.

Here we finished sequencing of the male-specific region of the Y chromosome (MSY) in our closest living relative, the chimpanzee, achieving levels of accuracy and completion previously reached for the human MSY. By comparing the MSYs of the two species we show that they differ radically in sequence structure and gene content, indicating rapid evolution during the past 6 million years. The chimpanzee MSY contains twice as many massive palindromes as the human MSY, yet it has lost large fractions of the MSY protein-coding genes and gene families present in the last common ancestor.

We suggest that the extraordinary divergence of the chimpanzee and human MSYs was driven by four synergistic factors: the prominent role of the MSY in sperm production, ‘genetic hitchhiking’ effects in the absence of meiotic crossing over, frequent ectopic recombination within the MSY, and species differences in mating behaviour. Although genetic decay may be the principal dynamic in the evolution of newly emergent Y chromosomes, wholesale renovation is the paramount theme in the continuing evolution of chimpanzee, human and perhaps other older MSYs.

The rest of the content is behind Nature’s paywall, but Hawks offers some additional comment regarding the rest of the paper, specifically three options that might account for the unexpected gulf of difference, described within the paper thus:

Indeed, at 6 million years of separation, the difference in MSY gene content in chimpanzee and human is more comparable to the difference in autosomal gene content in chicken and human, at 310 million years of separation.

Option 1: Maybe nothing, Option 2: Massive changes in gene regulation, and Option 3: Hitchhiking, all of which is which is prefaced by this:

The Y chromosome was part of the initial chimpanzee genome draft, and was recognized then as a “clear outlier” in showing low human-chimpanzee sequence similarity (Chimpanzee Genome Consortium 2005). But it wasn’t obvious just how different it was because the relatively short sequencing reads aligned fairly well with the human draft. That comparison also seems not to have included the missing genes (they might have just been missed during sequencing), or duplications. Moreover, the Y chromosome includes a high fraction of repetitive sequence, including long front-to-back, or “palindromic” passages.

Only with very long reads with long overlaps is it possible to straighten out the large-scale sequence, and thereby detect sequence reorganizations and large copy number variants. This kind of intensive sequencing has so far been completed only for chromosome 21 and now the Y chromosome.

To read the rest of his commentary, just head over to Hawks’ Weblog.


Hughes JF and 16 others. 2010. Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature (early online) doi:10.1038/nature08700

3 thoughts on “Chimpanzee and Human Y Chromosomes Are Remarkably Divergent in Structure and Gene Content – Nature Letters

  1. About 25 years ago I have predicted this results (if you see a picture about chromosomes origins at my website you must understand it). Here at Amazon jungle we follow this wonderful research but we have a different interpretation about the final results. We understand that the evolutionary difference is all about the propensity difference between system’s state – where male has the propensity to be self-opened system and female to be self-closed system. I work with theoretical comparative anatomy between natural systems (from biological, Newtonian mechanics, atomic to galactic systems) and I found a model about the non-living ancestors of Y and X chromosomes. I understand that the idea of localizing the chromosomal phenomena in the astronomic dimension is a weird one, but I have accumulated too many evidences and the logics are rational. You can see in the figure below (which represents the formula or the diagram of Last Astronomic Universal Common Ancestor of all biological systems which was a closed system) how the Y phenomena is an opened door to evolution – at F4 (the male systemic function) the male has the choice to drive the flow of energy/information (F5) towards the female at the nucleus or to fire F5 to outside of the system. Meanwhile, the female at F1, localized at the center and so, the ruler or queen of the system, has the propensity to keep eternally this systemic closed state and drive the flow (F2 to F7) in a circular recycling process). Opened system means adventure, search, hunt, self-dissipation, less selfishness, then, it means faster evolution. Unfortunately I don’t know how to copy the picture here, then you can go to, click “Portuguese” and then, click “artigos”. Thanks by any comments…

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