Apropos of the recent drift vs. selection debates in regards to the driving forces of evolution, I thought I'd pass on this press release about the pervasiveness of neutral genetic elements. You can read the full provisional paper in PLOS Genetics:
Using sequence analysis and fossil dating, we also show a probable burst of integration of numts in the primate lineage that centers on the prosimian-anthropoid split, mimics closely the temporal distribution of Alu and processed pseudogene acquisition, and coincides with the major climatic change at the Paleocene-Eocene boundary. We therefore propose a model according to which the gross architecture and repeat distribution of the human genome can be largely accounted for by a population bottleneck early in the anthropoid lineage and subsequent effectively neutral fixation of repetitive DNA, rather than positive selection or unusual insertion pressures.
Razib,
I wish I had noticed this post a bit earlier. I was wondering what your thoughts were on the plausibility of the authors' scenario. If they're correct, tens of thousands of TEs, for example, that might otherwise have been selected out due to a reduction in population size that altered insertion/deletion/selection balance. (At least some large number that is well above and beyond the number that would have fixed without a drop in population size.) While their numts data was a new and interesting bit of info, I was a touch annoyed that they sort-of portrayed themselves as effectively the first group to entertain the notion that repetitive elements fix at higher rates when population sizes drop. This has been suggested numerous times in the literature, both for primates and other species. But beyond that, I've always had a bit of a hard time accepting at a gut level that so many (slightly) deleterious traits (whatever the level of increased slightly deleterious baggage due to low pop sizes) were tolerated in ultimately successful primate lineages and retained to this day. It's hard to buy, but I admit it's a fuzzy objection, and I can't rule out that scenario in any rigorous manner. It always seemed much more plausible that what is instead tolerated is the presence of more active source loci for TEs, etc. Yet their numts data, and its correlation with TE accumulation, does lend more creedence to the notion of a general increase of drift-related fixation due to weakened influence of selection. I still don't like it as an explanation for bursts in TE activity in particular, especially given the total number of loci involved (in many cases), but I was wondering if anyone else had thoughts on the matter.