Strong selective sweeps associated with ampliconic regions in great ape X chromosomes
Kiwoong Nam, Kasper Munch, Asger Hobolth, Julien Y. Dutheil, Krishna Veeramah, August Woerner, Michael F. Hammer, Great Ape Genome Diversity Project, Thomas Mailund, Mikkel H. Schierup
(Submitted on 24 Feb 2014)
The unique inheritance pattern of X chromosomes makes them preferential targets of adaptive evolution. We here investigate natural selection on the X chromosome in all species of great apes. We find that diversity is more strongly reduced around genes on the X compared with autosomes, and that a higher proportion of substitutions results from positive selection. Strikingly, the X exhibits several megabase long regions where diversity is reduced more than five fold. These regions overlap significantly among species, and have a higher singleton proportion, population differentiation, and nonsynonymous to synonymous substitution ratio. We rule out background selection and soft selective sweeps as explanations for these observations, and conclude that several strong selective sweeps have occurred independently in similar regions in several species. Since these regions are strongly associated with ampliconic sequences we propose that intra-genomic conflict between the X and the Y chromosomes is a major driver of X chromosome evolution.
Haldane's Sieve 
Unfortunately pages 11-12 are missing from the pdf – I was trying to find out more about those ampliconic regions!
Have messaged Mikkel and Thomas about this.
Sorry for the missing pages. I have pasted their content below:
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Supplementary Information available online version of the paper.
Acknowledgments
We thank Brian Charlesworth, Andy Clark and Freddy B. Christiansen for comments to the manuscript. The work was supported by the EC funded FP7 NEXTGENE project (to T.M. and M.H.S.) and by the a grant from the Danish Natural Sciences Research Council (to M.H.S.)
Author contributions
K.N. and M.H.S. conceived and designed the experiments
K.N., K.M., A.H., J.Y.D., K.V., A.W., M.F.H., and T.M. performed analysis
K.M. performed simulations
G.A.G.D.P. contributed materials
K.N. and M.H.S. wrote the paper with input from all authors
Is the supplemental Information available?
Hi, I am not sure how to add it to arXiv, but I’ve told Kiwoong. Otherwise, email me mailund@birc.au.dk and I will send it to you.
Thomas,
One easy way to add it, is to just append it onto the end of your preprint.
Graham
I didn’t upload it, so I am not sure I can change it…
Thank you for the request.
I just resubmitted the full manuscript with supplementary to Arxiv.
Best,
Kiwoong,