Michael Phelps is an outlier. He is beyond the norm in a whole lot of key respects. Strong natural aptitude, strong motivation, fierce competitive spirit, willingness to work hard and capable of being coached.

Starting with outliers (Phelps, Tiger Woods, and so many more) and then comparing to some human norm, is how non sequiturs get started. Not to mention junk science.

I presume our ancestors would look at a river as something to cross at the most shallow section, rather than an opportunity to get their heart rate up.

Phelps is a sprinter. And logically, just how far would our ancestors have ever swum on anything approaching a regular basis? I'd say running is more natural to us. Of course if you're after fat loss then with the full body action, low injury risk and high thermal loads of being in water then being a swimmer can be effective. But Phelps doesn't represent chronic cardio to me - even the 400m medley is barely over 4 minutes.

Swimmers generally have higher body fat than their runner counterparts, so from that perspective, it's less ideal. See http://www.sportsci.org/news/compeat/fat.html. There's no scientific consensus on why that is generally the case.

Swimming also isn't weight bearing and won't do much for increasing bone density - swimmers have actually been found to have poor bone density compared to other athletes. See http://www.swimmingscience.net/2010/07/bone-mineral-density-in-swimmers.html

Michael Phelps is only one person. You can't draw any conclusions from that (just like you also shouldn't draw any definitive conclusions from looking only at Art De Vany, Mark Sisson, etc.).

Intuitively, our ancestors likely spent very little time in the water.

I would find it hard to believe that he doesn't do at least some weight training. I do not know of a swimming program that does not have it as a part. As a minimum, he would be using hand or feet flippers or a paddle machine.

I swam competitively for 15 years, including part of college. I was [clearly] nowhere near Phelps' level of competitiveness, but I was at a high enough level to know what general training is for elite swimmers. It definitely comes under the "chronic cardio" umbrella if you are concerned about that. For example, for the last seven years I swam I had two workouts a day, six days a week. All in all I spent about 30 hours at the pool each week. Most of that was in the pool, but we also did quite a bit of resistance and cross-training on deck, with medicine balls, running, and plyometrics. I did bodyweight exercises through high school and didn't get into actual lifting until college, but I assure you we did plenty of strength training along with training in the pool. I can't imagine Phelps only swims.

Also, for training purposes: Even our sprinters were at the pool about between 3 and 4 hours a day. Those of us who swam distance (especially me, as an open water swimmer), were at the pool at least five, sometimes in three sessions during school breaks.

One hypothesis as to why swimmers have a generally higher level of body fat than other elite athletes is that they're in a lower temperature of water and need the fat for insulation. Whether that's true or not, I have no idea. I hovered around 140 lbs and 14-15% BF the entire time I swam at my highest level. Note: I was a distance swimmer, not a sprinter. Most of the sprinters I knew had slightly lower BF% than the distance swimmers. I would guess that the distance swimmers tended higher because of possible higher cortisol levels, and would be similar to distance runners that way--but with significantly higher lean mass.