More people moving to Amazonia usually mean more deforestation. Regionwide, most deforestation is due to clearing for agriculture, but in some areas of Madre de Dios, deforestation for alluvial gold mining has surpassed agriculture as the primary cause. Logging – legal and illegal – is also common in the region. In Brazil, clearcutting precedes agriculture. In Peru, logging is more selective, with loggers targeting particular valuable trees. Nevertheless, studies show that selective logging is more destructive than it appears. Studies show that for every tree felled for timber, at least 10 more fall around it or are cut to build logging roads. Selective logging also changes the species composition of the forest and can affect biodiversity in the long run.

Between 2000 and 2005, about 27,151 sq km (10,480 sq ml) of forest was cleared annually in the Amazon basin, according to the U.N. Environment Program. And the pace is increasing. The deforestation rate in 2007 had increased 15 percent over that of the previous year. Deforestation results in habitat fragmentation, changes in ecosystems and loss of biodiversity. Studies have found that species diversity is greater in primary forests than in secondary forests or plantations. Despite all the scientific research done in Amazonia, we still know so little about the region that many species are probably disappearing before scientists even know they are there.

Protected areas offer some safeguards against destruction, although resource extraction is permitted in some areas and a shortage of park guards in many countries leaves parks and reserves vulnerable. Among them, eight of the nine countries that share the Amazon basin (not counting French Guiana) have 168 protected areas, totaling 784,100 sq km (302,700 sq mi), an area nearly twice the size of the US state of California. Brazil has 100 areas, totaling 420,000 sq km (162,200 sq mi), while Peru is second with about one-fourth that amount of land in 15 protected areas in Amazonia.

Some environmentalists and government officials are betting that carbon trading schemes to provide incentives for avoiding deforestation will give both public and private conservation efforts a boost in the Amazon basin. There is growing support for a proposal known as REDD (Reducing Emissions from Deforestation and Forest Degradation) and an expanded model known as REDD-plus, which would include compensation for protected areas. Some industrialized countries, such as Norway, are providing carbon-offset funding to encourage South American governments to conserve their tropical forests, but there are still many questions about how REDD or REDD-plus will operate in the marketplace.

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