Firstly, he was able to show that fossils of a small reptile called Mesosaurus were found only in South Africa and Brazil. These two places are now separated by the Atlantic Ocean, so how could Mesosaurus have lived in both locations? The chance of it crossing the ocean was very small and, if it had been able to cross the sea, why hadn't it been found in other places as well? To Wegener it seemed that the only sensible explanation was that South Africa and Brazil had been joined together at the time when Mesosaurus lived.
Secondly, he realised that the rocks in South Africa and south east Brazil were very similar, both in age and structure. This added weight to his theory that the places had once been joined together. Rocks are formed and laid down all the time around the world, but the type of rocks and their structures are controlled by local conditions. Similar rocks would have to form under similar conditions. If both rocks had formed in the same place at the same time, that would explain why they were the same.
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