Certainly overweight dogs have more strain on their joints and organs than slim ones, but a larger dog has stronger bones and joints and bigger organs in proportion to its size, so this should not account for the shorter lifespans of larger dogs. I don't think anyone knows the reason for this, but it is a well recognised phenomenon.

I met a great dane owner who told me larger dogs hearts have to work harder to pump blood around compared to smaller dogs which is why they dont live as long

We had a jack russell (RIP Scamp) who lived to 18 1/2 yrs old before we had to have him out to sleep.
All of the labs we've had have lived shorter lives, but usually due to illness - cancer etc

Weird though, when you think in nature, larger animals (elephants, whales etc) live longer than smaller ones.

What do you mean by smaller ones? Smaller elephants and whales or a different animal that's smaller than it?

Maybe a smaller elephant would live longer than a bigger one - who knows. But we can't compare completely different animals together, as it isn't a fiar comparison.

Generally, smaller animals can live longer than larger animals of the same species.

Ok I know I keep putting up these links but this one seems really interesting.
Particularly the bit about reducing food intake, which is supposed to lengthen life expectancy.
Longevity, ageing, and life history of Canis familiaris

as with humans, many factors dictate length of life even in dogs. Stress plays heavily, along with activity level ie: high energy as opposed to dogs that are less energetic. I have been raising, breeding and rescuing dogs for 50 years and the one thing that studies do not take into consideration are the factors noted. My Miniature Pinschers (which have an average breed standard life span of 12 to 14 years) generally pass at about 14. I have had some including my current 17 year old that breaks the tradition. I have had a Malamute/Wolf who lived to be 16 and a Shepherd/Wolf who passed away at 17. Both of these dogs were over 170lbs. My Aussies averaged about 11 years. Much of this can be linked to their energy level. The Aussies and Pinschers by nature (if true to their breed) are naturally high energy dogs thus wore out sooner. My larger breeds were laid back and very calm and lived much longer. Breed standards with regards to life longevity has been based on studies for year and they are generally very precise so long as the breed complies with all the characteristics pertaining to it. Deviations from the common traits and characteristics can cause a change in these statistics with regards to how long a dog lives. Health, nutrition, exercise etc all play major roles in life expectancy but even when all are considered, you have to look at the breed itself then take into consideration the average along with the health, nutrition and exercise to determine if the dog will live to its breed expectancy ie: longer of shorter than. Size I have found has had no real bearing on the life expectancy of dog. Only taking in their natural life expectancy, providing proper nutrition, exercise and eliminating stress has proven to see an increase in most of mine, far beyond the age normally noted. It is documented that even humans that suffer from poor nutrition, lack of exercise and those who suffer from stress will not live as long as they would had they had proper nutrition, exercise and be stress free. In many cases many forget to look at the fact that like people, dogs can succumb to early death not from lack of healthy body but also from lack of healthy mind due to stress. This has been bore out from my years of experience with dogs. Majority of those who know me are always surprised out how long my dogs and cats live compared to theirs. In my case, I offer no unwanted attention on either. I do not force myself on them and in turn discovered years ago by doing this, they are more relaxed and will come to me wanting attention for brief periods of time. In addition, especially with my cats, all 13 know their names and will individually come to their names knowing that coming will be met with nothing more than a slight stroke of my hand down their back. No grabbing, no picking up or forcing to he placed in my lap. By letting them be dogs and cats, they seem to react in a more disciplined manner with very little training. This does not mean they do not need initial training and socializing but less are forced issues and more on realizing and accepting that they are not "children" but are dogs and cats and need to be that in order to be comfortable with themselves thus reducing a great deal the amount of stress that humans many times with realizing inflict on them.