I’ve been reading Sperm Biology: An Evolutionary Perspective; an engaging comparative look at, well, sperm biology. One fairly remarkable thing to me is that, while sperm evolve incredibly rapidly in morphology (at one point in the book, the claim is made that just about any animal can be distinguished visually by sperm cells alone), the precise genetic changes involved in this variation are entirely unknown.
Given that the human and chimp Y chromosomes have diverged massively, the rapid evolution of sperm, and the fact that many genes on the Y are involved in spermatogenesis, it stands to reason that there is a large amount of variation within current human populations (there is very little work on this, so direct evidence of this is hard to come by), and that some of the relevant genetic loci lie on the Y chromosome.
So how variable is the Y chromosome within humans? It appears this is largely unknown as well (outside of the markers used for ancestry testing and the like), largely due to the fact that its repetitiveness makes it difficult to genotype or sequence. Here’s the thought: Pacific Biosciences now claims to be able to generate quality sequencing reads of up to a few kilobases; this alone might be enough to overcome the repetitiveness of the Y. Is it time for a “HapMap” of the Y chromosome, and incorporation of this chromosome into association studies for relevant traits?
 random aside: many nemotodes, including C. elegans, have ameoba-like sperm, rather than flaggela. How many C. elegans genetics talks have I listened to without knowing this? Many.