Massive Differences Found Between Chimp And Human Y Chromosomes

I'm publishing Lizzie Buchen's very clear Nature report in entirety. David Page's group have been fascinated by the evolution of the sex chromosomes and their painstaking sequencing has paid off in this revelation as to just how different the Y chromosome is between chimps and humans. This seems to be another case of how species "churn" their genomes differently. The Y chromosome has suffered from relative gene loss in the chimp and gene gain in the human. The majority of the genome evolution seems to have occurred in a section of so-called palindromic sequences which appear to have been duplicated many times. Rapid duplication of genes, or DNA sequence including genes, has historically been very difficult to pick up by standard sequencing techniques. Because the duplication has occurred relatively recently - within approx. 6 million years, the dupes are all very similar and so the sequencer cannot tell them apart as dupes. However more painstaking, and modern, sequencing techniques have revealed the extent of this duplication. The advantage of dupes to genome evolution is that natural selection can act differentially on any dupe, perhaps creating new genes with a different function. In the case of the Y chromosome this has certainly to do with sperm production and particularly "sperm wars" between males in species where the female multiply mates, creating competition in her reproductive tract between the sperm of a number of males. Sperm competition is far more pronounced in chimpanzees than humans.

The fickle Y chromosome

Chimp genome reveals rapid rate of change.

Lizzie Buchen

The male sex chromosome, long dismissed as the underachieving runt of the genome, has now been fully sequenced in a common chimpanzee. And comparison with its human counterpart — the only other Y chromosome to have been sequenced in such detail — reveals a rate of change that puts the rest of the genome to shame.

The common chimp (Pan troglodytes) and human Y chromosomes are "horrendously different from each other", says David Page of the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts, who led the work. "It looks like there's been a dramatic renovation or reinvention of the Y chromosome in the chimpanzee and human lineages."

Sex chromosomes evolved some 200 million–300 million years ago, but the chimpanzee and human lineages diverged only 6 million–7 million years ago. Comparisons of the chimp and human genomes suggested that not much has changed between the species since1.

But those analyses excluded the Y chromosome, much of the genetic sequence of which is made up of palindromes and elaborate mirrored sets of bases that elude standard whole-genome sequencing techniques. Portions of the chimp Y chromosome were sequenced a few years ago2,3, but the full landscape is only now available, after Page and his team precisely sequenced large segments of the chromosome, then stitched them together. They report their findings in a paper published online in Nature on 13 January4.

As the earlier studies had suggested, many of the stark changes between the chimp and human Y chromosomes are due to gene loss in the chimp and gene gain in the human. Page's team found that the chimp Y chromosome has only two-thirds as many distinct genes or gene families as the human Y chromosome and only 47% as many protein-coding elements as humans. The remainder of the chimp and human genomes are thought to differ in gene number by less than 1%.

Even more striking than the gene loss is the rearrangement of large portions of the chromosome. More than 30% of the chimp Y chromosome lacks an alignable counterpart on the human Y chromosome, and vice versa, whereas this is true for less than 2% of the remainder of the genome.

Even the portions that do line up have undergone erratic relocation. In the only other chromosome to have been sequenced to the same degree of completeness in both species, chromosome 21, the authors found much less rearrangement.

"If you're marching along the human chromosome 21, you might as well be marching along the chimp chromosome 21. It's like an unbroken piece of glass," says Page. "But the relationship between the human and chimp Y chromosomes has been blown to pieces."




The rapid evolution of the Y chromosome is not a total surprise, because the Y chromosome has no partner during cell division and so largely avoids the exchange of DNA that occurs between partnered chromosomes and keeps modifications in check. "It's expected that they are going to be more different than the rest of the genome, but the extent of it is pretty amazing," says geneticist Christine Disteche at the University of Washington in Seattle.

The Y chromosome is also prone to change because most of its characterized genes are involved in producing sperm, which are at the frontline of reproductive fitness, particularly in chimps; receptive females will often mate with many males in one session, so the male with the most virile sperm has the highest likelihood of success.

"The Y is full of surprises," Page says. "When we sequenced the chimp genome people thought we'd understand why we have language and write poetry. But one of the most dramatic differences turns out to be sperm production."

References

1. The Chimpanzee Sequencing and Analysis Consortium . Nature 437, 69-87 (2005).
2. Hughes, J. F. et al. Nature 437, 100-103 (2005).
3. Kuroki, Y. et al. Nature Genet. 38, 158-167 (2006).
4. Hughes, J. F. et al. Nature doi:10.1038/nature08700 (2010).

Source: Nature
http://www.nature.com/news/2010/100113/full/463149a.html

Gene-Culture And The Setoronin Transporter Gene

In the penultimate chapter of NOT A CHIMP I try to lay some foundations for a proper bio-social approach to the study of the evolution of human social behaviour through the evolution of several prominent neuro-transmitters. In particular, I reported that the "short" allele of the serotonin transporter gene had been implicated in creative dance in the context of proto-religious collective human mystical experience. I also reported the finding that variability in short, long and extra-long repeat versions of this gene were more prevalent in more demonic societies typified by long-range geographical distribution - like rhesus macaques and humans. Further research has also implicated the short allele of this gene in anxious, depressive and occasionally violent personality traits.

In this interesting open paper in Proceedings of the Royal Society B, Joan Chiao and Katherine Blizinsky fill in another aspect of this growing picture by associating the short allele of the serotonin transporter with gene-culture evolution of collectivistic traits in human society.

As the authors say: "A fundamental way in which culture shapes human behaviour is through self-construal style, or in how people define themselves and their relation to others in their environment. In particular, cultural psychologists have identified two primary styles of self-construal across cultures: individualism and collectivism. Individualistic cultures encourage thinking of people as independent of each other. By contrast, collectivistic cultures endorse thinking of people as highly interconnected to one another. Individualistic cultures emphasize self-expression and pursuit of individuality over group goals, whereas collectivistic cultures favour maintenance of social harmony over assertion of individuality. Self-construal style affects a wide range of human behaviour, including how people feel, think, perceive and reason about people and objects in their environment, and their underlying neural substrates."

However, there is one other important ingredient in the mix - disease. Previous work, they report, has shown that the S allele is selected for in those cultures with great history and contemporary prevalence of disease-causing pathogens like malaria, typhus and leprosy. The S allele appears to be linked with collectivism and the authors posit that a cultural norm of collectivism could help to protect against the run of disease by enhancing conformity and parochialism. It would seem that this would leave many cultures open to affective disorders but in highly collectivized societies, for instance in Asia, this seems not to be the case. Their answer? " Here we propose that by favouring social harmony over individuality, collectivistic cultural norms may have evolved to also serve an adaptive, ‘anti-psychopathology’ function, creating an environmental niche that reduces the risk of exposure to environmental pathogens, such as chronic life stress, for group members. Consistent with a gene-by-environment (GxE) theory of affective disorders, reduced exposure to chronic life stress for individuals living in collectivistic relative to individualistic cultures would then cause reduced prevalence of affective disorders among genetically susceptible individuals. Hence, culture variation in the epidemiological prevalence of anxiety and depression is likely due to geographical variation in the cultural adoption of collectivistic social norms." So, collectivism helps fight disease and protects against the downside of the S allele - affective disorder.