The Beagle survey took five years, two-thirds of which Darwin spent exploring on land. He studied a rich variety
of geological features, fossils and living organisms, and met a wide range of people, both native and colonial. He methodically
collected an enormous number of specimens, many of them new to science. This established his reputation as a naturalist and
made him one of the precursors of the field of ecology, particularly the notion of biocoenosis. His extensive detailed notes
showed his gift for theorising and formed the basis for his later work, as well as providing social, political and anthropological
insights into the areas he visited.
On the voyage, Darwin read Charles Lyell's Principles of Geology, which explained geological features as the
outcome of gradual processes over huge periods of time, and wrote home that he was seeing landforms "as though he had the
eyes of Lyell": he saw stepped plains of shingle and seashells in Patagonia as raised beaches; in Chile, he experienced an
earthquake and noted mussel-beds stranded above high tide showing that the land had been raised; and even high in the Andes,
he was able to collect seashells. He theorised that coral atolls form on sinking volcanic mountains, an idea he confirmed
when the Beagle surveyed the Cocos (Keeling) Islands.
In South America he discovered fossils of gigantic extinct mammals including megatheria and glyptodons in strata
which showed no signs of catastrophe or change in climate. At the time, he thought them similar to African species, but after
the voyage Richard Owen showed that the remains were of animals related to living creatures in the same area. In Argentina
two species of rhea had separate but overlapping territories. On the Galápagos Islands Darwin found that mockingbirds differed
from one island to another, and on returning to Britain he was shown that Galápagos tortoises and finches were also in distinct
species based on the individual islands they inhabited. The Australian marsupial rat-kangaroo and platypus were such strikingly
unusual animals that he thought "An unbeliever... might exclaim 'Surely two distinct Creators must have been [at] work'."
He puzzled over all he saw, and, in the first edition of The Voyage of the Beagle, he explained species distribution in light
of Charles Lyell's ideas of "centres of creation". In later editions of this Journal he foreshadowed his use of Galápagos
Islands fauna as evidence for evolution: "one might really fancy that from an original paucity of birds in this archipelago,
one species had been taken and modified for different ends."
Three native missionaries were returned by the Beagle to Tierra del Fuego. They had become "civilised" in England
over the previous two years, yet their relatives appeared to Darwin to be "savages," little above animals. Within a year,
the missionaries had reverted to their harsh previous way of life, yet they preferred this and did not want to return to England.
This experience, his detestation of the slavery he saw elsewhere in South America, and other problems he found about such
as the effect of European settlement on aborigines in New Zealand and Australia, persuaded him that there was no moral justification
for the mistreating of others based on the concept of race. He now thought that humanity was not as far removed from animals
as his clerical friends believed.
While on board the ship, Darwin suffered from seasickness. In October 1833 he caught a fever in Argentina, and
in July 1834, while returning from the Andes down to Valparaíso, he fell ill and spent a month in bed. From 1837 onwards Darwin
was repeatedly incapacitated with episodes of stomach pains, vomiting, severe boils, palpitations, trembling and other symptoms.
These symptoms particularly affected him at times of stress, such as when attending meetings or dealing with controversy over
his theory. The cause of Darwin's illness was unknown during his lifetime, and attempts at treatment had little success. Recent
speculation has suggested he caught Chagas disease from insect bites in South America, leading to the later problems. Other
possible causes include psychobiological problems and Ménière's disease.