He monitored the foraging habits of the penguins by weighing them when they entered and exited a fenced off area. These weights told them how much food the birds were carrying year-to-year.
The changes in foraging were measured against conditions on the continent, such as the changing landscape or fluctuations in other species.
The Adelie population was in trouble because a warming world had reduced the amount of sea ice, which was the birds' main foraging ground.
The number of Adelie was expected to dramatically fall within 40 years because the penguins depended on sea ice to access krill, one of its food sources.
Dr Lyver said: "We expect to lose around 75 per cent of our colonies north of 70 degrees, and that equates to about 70 per cent of our Adelie penguin population.
"And there are similar predictions for emperor penguins as well. They could feel it even more acutely because they breed on sea ice."
But there was a confounding factor. The three Adelie colonies Dr Lyver was observing were breeding in record numbers. He believed there was a number of reasons the penguins were thriving.
Around the Ross Sea, sea ice was growing - a phenomenon believed to be caused by the cooling effect of the ozone hole.
In all other parts of the Antarctic, sea ice was retreating rapidly, and so too were penguin numbers.
Dr Lyver suggested that the increase in the local penguin population could also be the result of a fall in toothfish in the Ross Sea due to overfishing.
Toothfish and Adelie competed for the same food source: Antarctic silverfish. As toothfish were reduced, silverfish became more plentiful, making penguins more productive.
If this theory was confirmed, it would be highly significant because New Zealand operated three toothfish vessels in the Ross Sea each summer.
It also showed how seemingly small disturbances to an ecosystem could ripple out to many other species.
The next pattern Dr Lyver would watch was a possible decrease in krill quantities.
While the fishing industry was permitted to reduce the toothfish population by 50 per cent, the krill fishery could reduce this species by 75 per cent.
Dr Lyver said: "If you start introducing fisheries - you start removing krill out of that system - you're actually reducing a large part of the diet of the penguins."
"Krill is a keystone species for the Antarctic marine system. If you start impacting that, you are going to see far-reaching effects throughout the system."