The Galapagos Islands were formed by the eruption of volcanoes. Darwin was shocked at the broad expanses of black, hardened lava, and by the wildlife he saw living on it. Volcanic cones dotted the landscape. Scurrying or sauntering among them were marine iguanas, crabs, birds, lizards, turtles, and giant land tortoises weighing eighty pounds or more. The crew immediately set about gathering food: they killed eighteen tortoises on the first island they landed on, Chatham, and carried them on board. Darwin collected as much of the fauna as he could lay his hands on.

On September 23rd, they landed on another island in the Galapagos, Charles Island, where they found a small settlement. On the 28th they moved on to Albermarle, the largest of the islands. On each island Darwin gathered the species he found. He noticed that the birds that he had collected on Chatham differed from those he found on Charles and Albermarle, and he also heard the local residents claim that they could tell by looking at the shape of the shell which of the islands a tortoise had come from. But he was careless in his collecting, and for the most part he failed to label his species by the island on which he had found them, assuming for the most part that they were the same species on each island. The finches in particular bewildered him: there seemed to be different kinds, but as far as he could tell they mixed together in flocks almost randomly, and he could see no pattern in the differences.

There was no fresh water on the Galapagos, so the Beagle started to run low. Fortunately they ran into an American ship that generously gave water to tide them over. Stopping back at Chatham, they killed another thirty tortoises and some iguanas to serve as supplies for the voyage across the Pacific. Darwin also got a young tortoise, which he kept alive as a pet and living specimen. On October 20, 1835, about a month after arriving, they finally left the Galapagos and headed towards Tahiti.

It took about four weeks of sailing on the high seas to cover 3200 miles and arrive in Tahiti in mid-November. From there they went to New Zealand (December 19) and Australia (January, 1836), stopping in Tasmania (February 5) and at several points along the Australian coast. In Australia Darwin saw his first platypus up close and also managed to bag a rat kangaroo, though he was disappointed not to have caught a real one. He observed the differences between placental and marsupial animals, as well as the similarities: despite the radical differences in their reproductive systems, these two groups of animals seemed to be equally well adapted to their environments, and often in strikingly similar ways. In Tasmania he observed the marine life: corals, plants, and algae. As the Beagle moved into the Indian Sea he carefully studied the islands and reef formations he came across.

On May 31, 1836, the Beagle reached the southern tip of Africa, the Cape of Good Hope, and took a break on shore in Cape Town. Darwin was welcomed by the local scientific aristocracy, shown local geology and had a meeting with the eminent Sir John Herschel. He also received a letter that carried news that made him even more excited to return to England. Henslow had edited and published ten of his letters in a booklet that was receiving rave reviews from the scientific community. As the Beagle left Cape Town and started the long journey north to England, Darwin began organizing his notes and samples, knowing that after all his work he would still have an enormous task lying ahead of him when he reached England. He would have to make sense of about 1300 pages of notes on geology, about 370 pages on zoology, a catalog of 1529 collected species and 3907 other specimens. Fortunately he knew that his return was being awaited eagerly and that he would have support from the scientific community when he returned. Geologist Charles Lyell, whose Principles of Geology Darwin had faithfully read during the first few years of his journey, was enthusiastic about his discoveries, as was Adam Sedgwick, the professor with whom he had spent a summer month exploring the geology of North Wales. After stopping at several familiar points along the way north, including St. Jago where the Beagle had made its first landing five years before, they finally arrived in England on October 2, 1836.

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