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The chimpanzee Y chromosome is radically different from human

Robert W. Carter

Image iStockphoto Y-chromosome Adam and the Cambrian explosion

Do humans and chimpanzees share a common ancestor? Is there genetic evidence for our kinship? If we wanted to test this, where should we look? There are many candidate regions in the genome, but new data on the Y chromosomes of chimpanzees may have shaken them out of the evolutionary ancestral tree!

According to many evolutionists, the Y chromosome, the DNA sequence that makes men what they are, is supposed to be a degenerate leftover from our early evolutionary history. It is small and slightly twisted when in its condensed form, much of it is made of repetitive material, it contains relatively few protein-coding genes, and, since the corresponding X chromosome is so large, the Y chromosome was thought to not do very much. In addition, only a portion of the Y chromosome is different from the X chromosome (the “male specific Y”, or MSY).

Add some modern feminism to the mix, with its disdain for all things male, and one has a recipe for the relegation of the Y chromosome to the dustbin of history. One paper, published in 2009 (by two women, coincidentally), concluded there has been a dramatic loss of genes in the Y chromosomes of eutherians (placental mammals) and that the Y chromosome will eventually disappear if that loss continues.1 Of course, this is based on the belief that the X and Y chromosomes were once identical (there are, after all, two copies of all the other chromosomes) and that the Y chromosome is not a design feature. It also ignores the fact that every eutherian lineage still has a Y chromosome. They should have concluded that this little chromosome must be extremely important, since not one of the many species of placental mammals have lost it over the last 100 million years or so (using their dating scheme). Rather, they made some conclusions from faulty starting assumptions and decided the Y chromosome is vestigial. This is but one example of many that could be cited to illustrate this modern trend.

It turns out that the trend was wrong.2–5 From the findings of modern genetics, we have learned that the Y chromosome is a master control switch, affecting genetic expression of thousands of genes on all the other chromosomes. Its effects are so profound that it makes the difference between men and women. The Y chromosome is also very important for studies of heredity and evolution due to its mode of strict paternal inheritance.5 Using Y chromosome sequence data, one can build a family tree of Y chromosomes and use it to chart historical migration patterns of people across the world. Early work discovered that all human males have very similar Y chromosomes. This led to the conclusion that there was a single male ancestor for the entire world population, called Y-Chromosome Adam.6

Photo iStockphoto human and chimpanzee
Humans and chimps are very different and this is born out in comparisons of Y chromosomes.

A new study published on the Y chromosome of chimpanzees has surprised many. After a lot of work, the chimpanzee Y chromosome has finally been finished.7 This may come as a surprise to many who thought the chimpanzee genome was completed way back in 2005. Actually, the original chimpanzee genome construction was less than optimal as they did not sequence it to the same standards of the human genome. Rather, they used the human genome as a “scaffold” to reconstruct the chimpanzee genome. This created several problems and the worst being with the repetitive sequences. There are some considerable differences between the repetitive regions of the human and chimp genomes, and, since, the Y chromosome is extremely repetitive, the chimpanzee version was essentially left unfinished. Even today, the human Y chromosome is still only half-sequenced. The chimp chromosome was left in a worse state, but the current work mostly corrects the previous deficiencies.

Since Y chromosomes are small and since it is assumed they evolved from a larger chromosome, it is assumed that their evolutionary history included the loss of many genes. On top of this, the evolution of the Y chromosome is supposed to slow down as the chromosome loses more and more genes. This was not the conclusion of the paper, however, for they found remarkable differences between man and chimpanzee, including radical differences in the sequence and gene content of the corresponding MSY regions. Because of these huge differences, the researchers concluded that the chimpanzee has lost many of the MSY protein-coding genes, even entire gene families, since we supposedly diverged from the last common ancestor. Those are significant changes. David Page, who led the chimp Y chromosome sequencing project, said the two chromosomes are, “… horrendously different from each other … It looks like there’s been a dramatic renovation or reinvention of the Y chromosome in the chimpanzee and human lineages.”8

What are the differences? There are two main classes of MSY sequences shared between the two species: “ampliconic” and “X-degenerate” (humans also have “X-transposed” sequences, but the chimp does not). The X-degenerate regions of chimp and man differ by a full 10%. This is huge, considering the “99% identical” claim that we have heard parroted so often over the previous several decades. But this is only the beginning of the differences. To compare the ampliconic regions, they had to appeal to extensive rearrangement and “rampant” sequence gain and loss. Half of the chimpanzee ampliconic sequence, and 30% of the entire MSY, has no counterpart in the human MSY, and vice versa. These are sizable differences.

The 30% difference among human and chimp MSY regions was a shock. This amount of difference was expected between the autosomes of human and something like chicken (to use their example), and chicken is not even a mammal. Finding this much difference in one of the sex chromosomes was huge. When they looked at the gene content of the two respective chromosomes, they were additionally surprised to find that there were many fewer genes in chimp and many more genes in man, with “only two-thirds as many distinct genes or gene families as the human MSY, and only half as many protein-coding transcription units.” That is, they found huge differences in the number and type of genes on the two Y chromosomes and were forced to claim massive gene loss or gain as the evolutionary mechanism responsible. Design was not considered as a possible answer (of course).

To account for their data, they proposed several factors that led to the differences between chimp and man, including sperm competition (because less DNA per cell is supposedly an advantage for chimpanzee males, where lighter sperm might be able to out-swim those of a competitor), genetic hitchhiking (where deleterious mutations are carried along with favorable ones), and high rates of gene conversion (where similar sequences recombine within a chromosome, leading to sequence homogenization). Again, they did not consider design as a reason for the differences.

The idea that the Y chromosome is evolving at a high rate is based on the assumption of common ancestry. But there is an extremely low level of variation between human Y chromosomes, which would not be expected if they were mutating at a high rate, and so there is no real evidence for any evolutionary changes within these chromosomes. Most of the sequencing of the chimp Y chromosome was from a single male, however, so we do not know the divergence of chimps from one another.

What are the implications of this new information? First, for the evolutionist, the Y chromosomes must be evolving much more quickly than anyone imagined previously (“evolving faster” is ‘evospeak’ for “very different”). They are now going to have to apply mathematical models to try to demonstrate how a sequence can change extremely rapidly, including wholesale rearrangement of significant parts and the evolution of entire gene families in a relatively short amount of time, yet stay homogeneous within a species. This is going to be very difficult for them.

Second, for the creationist, we now know that the old “humans and chimps are 99% identical” canard is passé. Interestingly, a significant paper appeared in 2007 calling the 99% rule “a myth” and claiming that we have known for decades that humans and chimps were much more different.9 But this has been a significant and powerful evolutionary argument. How many people had their faith wrecked on those “mythical” rocks? Now we have half of the chimpanzee Y chromosome and learn that it is only 70% identical to human. This is evidence that humans and chimpanzees are very different. How different? To quote the famous geneticist, Svante Pääbo, “I don’t think there’s any way to calculate a number … In the end, it’s a political and social and cultural thing about how we see our differences.”5 This statement was made before the chimp Y chromosome data became available. If the number is incalculable, can we not jettison every evolutionary story of chimp-human common ancestry based on genetics? The new data on the chimp Y chromosome makes the case for common ancestry that much worse.

Published: 16 December 2010


  1. Wilson, M.A., and Makova, K.D., Evolution and survival on eutherian sex chromosomes, PLoS Genetics 5(7):e1000568, 2009. See also http://www.physorg.com/news167026463.html. Return to text.
  2. Hawley, R.S., The Human Y Chromosome: Rumors of Its Death Have Been Greatly Exaggerated, Cell 113:825–828, 2003. Return to text.
  3. Lemos, B., et al., Polymorphic Y chromosomes harbor cryptic variation with manifold functional consequences, Science 319:91-93. Return to text.
  4. 598-612, 2003. Return to text.
  5. Jobling MA, Tyler-Smith C., The human Y chromosome: an evolutionary marker comes of age. Nature Reviews Genetics 4:598-612, 2003. Return to text.
  6. Batten, D., Y-chromosome Adam? TJ [J. Creation] 9(2):139–140, 1995. Return to text.
  7. Hughes, JF, et al., Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature 463:536-539, 2010. Return to text.
  8. Buchen, L., The fickle Y chromosome, Nature 463:149, 2010. Return to text.
  9. Cohen, C., Relative Differences: The Myth of 1%, Science 316:1836, 2007. Return to text.

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