Adults and larval dipterans live in nearly all habitats on land and in freshwater. Almost all adults are found on land and move about freely. However, louse flies spend most of their lives on their host animals. Dipteran larvae are found in fresh and brackish, or salty, water, wet soil and leaves, and other wet places. Some species live as external parasites on animals or bore through the tissues inside leaves. Larval shore flies live along the edges of hot springs and geysers where temperatures are more than 112°F (44.4°C). Others develop in pools of crude oil or inside the nests of ants, bees, and wasps. The pupae are usually found in the same habitats as the larvae. Aquatic species usually become pupae in the water, but species found along the water's edge sometimes prefer pupal sites away from water.

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