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The USGS Gap Analysis Project (GAP) grew out of biologists’ response to the need to complement species-by-species management in dealing with widespread habitat loss. 

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A new approach was needed that could provide clear, geographically-explicit information on the distribution of native vertebrate species, their habitat preferences, and their management status, in order to determine “gaps” in biodiversity protection.

Until the late 1980s, there was little information on ordinary species. Their habitat needs had not been systematically documented, and there was little information about their overall distributions on lands that were being managed for conservation. There was no standardized classification system for species assemblages, and no institutional capability to develop or use the kind of information needed to manage biological diversity as a resource.

The gap analysis process itself was conceived in the 1980s, by J. Michael Scott, at the University of Idaho. He developed methods to assess endangered birds in Hawaii and began by mapping the distribution of each species individually. Then he combined data on individual species to create a map of species richness throughout the island.  Until this approach was developed there was no broad scale way to assess the level of protection given to areas rich in biodiversity.  The results of this analysis led to creation of the Hakaiau Forest National Wildlife Refuge, in one of the areas of highest species richness.

In the late 1980s, Scott and other researchers at the University of Idaho Cooperative Fish and Wildlife Research Unit initiated an Idaho Gap Analysis Project as a first pilot project under the auspices of the U.S. Fish and Wildlife Service.

Following two years of methods development, the program was launched in 1989 as part of the U.S. Geological Survey under the title, Gap Analysis Program (GAP). GAP is now known as the Gap Analysis Project.

A wide range of tools and procedures are now available from GAP, including standards for classifying natural vegetative communities, extensive databases of species, land cover and protected areas, and documented methods to apply GAP information to everyday resource decisions and long-range planning. Today, GAP is operational nationwide and has enjoyed significant international interest.