A central controversy in current exercise science essentially boils down to endurance vs strength. What do you get out of (for example) sprinting vs. distance running? Is one or the other not only not as good, but actively bad for us? Perhaps even more importantly, why do each of us who sprint or lift weights or ride bikes a hundred miles do it - is it entirely for life extension? Or mostly for meditation?
I've waded into this a few times before, most recently here. Normally I don't care, except that a subset of the high-impact sprinter/lifter types have taken it on themselves to purge the exercise world of endurance-sport apostates. Evolutionary approaches have a great deal to offer this debate, and both sides have employed evolutionary arguments. And of course there are myriad other vitally important questions impacted by investigations into recent human evolution, in fields ranging from medicine to literature to philosophy.
One of the central questions in human evolution is whether human culture has "fed back" to impact our evolution. For the curious and/or scientifically-minded, U of Wisconsin Anthropologist John Hawks has hands-down the best blog focusing on recent human evolution and on feedback cycle of impact of our own culture. Actually, the question is becoming less central because the near inevitable consensus is yes.
Examples? 1) East Africans and Arabians have more efficient versions than the rest of us of a drug detoxification enzyme that operates best on alkaloids found in East African and Middle Eastern food. 2) Human skeletons have become more gracile (delicate) over the past hundred thousand years, paralleling the physical changes that follow domestication in other species of mammals. 3) Europeans and West Africans have much higher rates of lactose tolerance because they started using milk as a diet staple earliest. These are all genetic changes resulting from the impact of cultural behaviors transmitted down the generations. Almost seems like common sense, in retrospect. If you're still not convinced, you better check your doctors' credentials because they're teaching us this at UCSD medical school too.
So what does any of this have to do with the endurance/strength debate? Everything. While the vast majority of genes in humans are the same across the whole species, a few of them do differ. This is why we're not all clones of each other. Some of those differing genes have a geographic patterning (for example, skin and hair coloration); some don't. For some differences we've figured out an obvious adaptive value (anemias as malaria-resistance in tropical regions); for some we haven't.
One recently discovered difference is in alpha-actinin, a protein critical for muscle function. Muscles are fascinating molecular machines (actinin is in the Z-line in that animation), and as you might expect, changing the parts in machines usually isn't a good idea. There are different sub-types of alpha-actinin, and most mutations in most sub-types are just plain bad. That is, they cause a disease. There is one curious one, however: sub-type #3 is disappearing from humans, at least in some parts of the world. Some people are lacking it entirely. If you're African, there's about a 10% chance that you're missing it. But if you're European or Asian, odds are 50% (presumably similar odds for everybody else not African). Fortunately there's no disease if you're missing it because sub-type #2 takes over. The thing is, when you see a difference like that between different populations, that's a big red flag. It often means something is going on, in terms of natural selection.
Here's Where It Starts to Get Cool
Looking at where we find people missing this gene today, as well as taking information from surrounding DNA, it looks like about starting in Asia around 33,000 years ago, this gene was selected for. Why is that a big deal? Because it means that not only was it not harmful, but there was some reason that people missing this gene did better. (About this time is when people are starting to jump up and down and shout Well what does the goddamn thing do but don't worry, we're getting there.) Based on these same methods, it looks like the gene made its way into Europe about 16,000 years ago. The timing is interesting because humans began leaving Africa en masse about 40,000 years ago, right when the famous language gene FoxP2 started spreading - that's important because it correlated with a paleolithic industrial revolution, in the sense that suddenly tools became more specialized and refined. Because we also know a) the ancestors of modern Indo-European speakers dispersed from the Eurasian steppes starting no later than 6,000 years ago, and b) there was still a big ice sheet over much of Europe and the Eurasian steppes 33,000 years ago, preventing people from moving into Europe until it retreated. Consequently I would bet that what we're seeing is the selection of some muscle-related trait post-Africa FoxP2 positive ancestors of steppe-dwellers, including the ancestors of today's Indo-Europeans (and probably at least Altaic speakers).
It Gets Really Cool Here
So what does the alpha-actinin-3 deletion do? What has been found is that in competitive sprinters and weight-lifters, very few people are entirely deleted. In fact it seems that the higher up you go in the competitive world, the less likely it is you could carry the deletion. So there is some phenotypic effect, at least at the margins of human activity. But it's still hard to imagine why not being able to lift heavy weights or run fast would actually be selected for, unless...
This Is the Coolest Part
...unless there's another effect. It turns out that a) mice who have alpha-actinin-3 knocked out show a greater endurance capacity, judging by metabolic markers, and b) the effect is seen in female endurance athletes, who are more likely to have the deletion than the general population. It hasn't been seen in males, not yet anyway (one of many things I'd love to do my med school research project on). [Added later: I have now had my genome screened for a host of functional polymorphisms, by 23andMe. It turns out I am an alpha-actinin-3 knock-out homozygote. I don't have any functional copies. So it's no surprise I'm a much better endurance runner than sprinter.]
Long story short: deletion of this protein correlates with better aerobic performance at the cost of extreme feats of strength. Why would that have been selected for starting 33,000 years ago? Because suddenly our ancestors found ourselves on some enormous plains, with less fruit but better tools and herds of game. Ambush hunting (or running away from large African predators) would have been less useful than chasing down game over miles and miles, a practice that can only evolve in predators smart enough to develop persistence - like humans. What we're seeing in our genes is selection for high-endurance long-term physical activity. As I've pointed out before, there are groups of people in the world who still do this, or did until the recent past (Khoi-San, i.e. Bushmen, and Navajos being two examples).
So why am I happy? The core of the paleo diet and/or high impact sprint/lift people seems to be that greater health is to be had from those types of exercises because they more closely match the behavior of our pre-agricultural ancestors. This view seems increasingly wrong, unless they want to discount the evolution that's taken place since the spread of FoxP2 turned us into cognitively modern humans - and we started doing things that fed back to impact our own evolution. After all, there must be some reason that the deletion was selected for. And anyway, I'll trade in the ability to work up to an 800 lb. clean-and-jerk for being able to run 15 miles easily enough that it's meditative. Because the most important point in all this is that distance running is a hell of a lot more fun.
This post was inspired by an entry at PZ Myers's blog.
 MacArthur et al. Loss of ACTN3 gene function alters mouse muscle metabolism and shows evidence of positive selection in humans. Nature Genetics 39, 1261 - 1265 (2007)
 Lek et al. The evolution of skeletal muscle performance: gene duplication and divergence of human sarcomeric alpha-actinins. Bioessays 32(1):17-25. (2009)
 Yang et al. ACTN3 genotype is associated with human elite athletic performance. American Journal of Human Genetics 73(3):627-31. (2003)