Brian Charlesworth wrote a review of Mike Lynch's The Origins of Genome Architecture, in which Charlesworth argues that sexual reproduction can explain many of the features Lynch claims evolved under nearly neutral processes (doi:10.1016/j.cub.2008.01.008). Not to be left out of the party, Deborah Charlesworth has chimed in with her opinion, and it's much more critical of Lynch than her husband's (doi:10.1017/S0016672308009282). The main thesis that Lynch has been presenting in both this book and some of his recent papers is that many features of eukaryotic genomes (introns, complicated cis regulatory regions, lots of non-coding DNA) arose via relaxed constraint due to small population sizes, not adaptation.
In her review, Deborah Charlesworth takes Lynch to task for not devoting enough of his discussion to within species polymorphism. Additionally, she argues that comparisons between distantly related taxa are limited by confounding variables. By ignoring recent studies that have identified evidence for selection on large portions of some genomes (and by excluding some important tests for selection, e.g., the McDonald-Kreiman test), Lynch paints a biased picture of what we know about adaptive evolution at the molecular level. However, Charlesworth does make the point that Lynch's book is not the be all and end all of genome evolution; rather, it is designed to get the reader to consider other explanations besides adaptive evolution when explaining genomic features.
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Thanks for pointing out the review. The DOI link to Debra's article does not seem to work. Where did the review appear? I think that the Charlesworths are right that comparisons between distant taxa are not the way to proceed with this, but such comparisons are useful for hypothesis generation. Overall I liked the Lynch book, as it gives a framework that can be tested/discussed. Plus adaptive hypotheses of genome evolution often seem to gain ground without much testing or population genetics intuition.
I am also interested in this article but I could not get via the DOI nor some searches, could you replace the link please. Thanks for pointing it out.
Guys, I've updated the link. It's in Genetics Research. See here.
Thanks (PS it is Deborah not Debra, sorry to nitpick).
Thanks, it's fixed.