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At the same time as the mammals were diversifying on land, they were also returning to the sea. The evolutionary transitions that led to the whales have been closely studied in recent years, with extensive fossil finds from India, Pakistan, and the Middle East. These fossils chronicle the change from the land-dwelling mesonychids, which are the likely ancestors of whales, through animals such as , which was still a tetrapod but which also has such whale-like features as an ear capsule isolated from the rest of its skull, to the primitive .

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The History of Animal Evolution - University of Waikato

However, despite the fact that the mammals had what many people regard as "advanced" features, they were still only minor players on the world stage. As the world entered the Jurassic period (213 - 145 million years ago), the dominant animals on land, in the sea, and in the air, were the reptiles. Dinosaurs, more numerous and more extraordinary than those of the Triassic, were the chief land animals; crocodiles, ichthyosaurs, and plesiosaurs ruled the sea, while the air was inhabited by the .

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Dinosaurs spread throughout the world - including New Zealand, which had its own dinosaur fauna - during the Jurassic, but during the subsequent Cretaceous period (145 - 65 million years ago) they were declining in species diversity. In fact, many of the typically Mesozoic organisms - such as ammonites, belemnites, gymnosperms, ichthyosaurs, plesiosaurs, and pterosaurs - were in decline at this time, despite the fact that they were still giving rise to new species.

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New Zealand, by virtue of its isolation and its relatively recent geological development, was not the centre of any novel evolutionary development. However, many of the species that date back to Gondwanaland, or that arrived more recently as migrants, have undergone significant adaptive radiation in their new homeland. Some of the best examples of this can be related to the major ecological changes that accompanied the Pleistocene Ice Ages.

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The trend towards a cooler global climate that occurred during the Oligocene epoch (33.7 - 23.8 million years ago) saw the appearance of the grasses, which were to extend into vast grasslands during the subsequent Miocene (23.8 - 5.3 million years ago). This change in vegetation drove the evolution of browsing animals, such as more modern horses, with teeth that could deal with the high silica content of the grasses. The cooling climate trend also affected the oceans, with a decline in the number of marine plankton and invertebrates.

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Like the plants, animals evolved in the sea. And that is where they remained for at least 600 million years. This is because, in the absence of a protective ozone layer, the land was bathed in lethal levels of UV radiation. Once photosynthesis had raised atmospheric oxygen levels high enough, the ozone layer formed, meaning that it was then possible for living things to venture onto the land.

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The mass extinction at the end of the Cretaceous period, 65 million years ago, wiped out the dinosaurs along with every other land animal that weighed much more than 25 kg. This cleared the way for the expansion of the mammals on land. In the sea at this time, the fish again became the dominant vertebrate taxon.

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Throughout the Pleistocene there were about twenty cycles of cold glacial ("Ice Age") and warm interglacial periods at intervals of about 100,000 years. During the Ice Ages glaciers dominated the landscape, snow and ice extended into the lowlands, transporting huge quantities of rock with them. During these periods the South Island was extensively glaciated, and there were small glaciers on the Tararua Ranges and Central Plateau. Because a lot of water was locked up in ice, the sea levels dropped during the glacials (up to 135m lower than at present). Extensive land bridges joined the main and many offshore islands, allowing the migration of plants and animals. During the warmer periods large areas became submerged again under water. These repeated episodes of environmental fragmentation drove rapid adaptive radiation in many NZ species, especially (but not exclusively) the alpine plants.