Unrest continues among the Tuareg populations of the Sahelian and Saharan north. The Tuareg – who represent approximately 5 per cent of Mali's 13.5 million population – have traditionally opposed the central government in the capital Bamako, complaining of political and economic marginalization. Frequent droughts in recent years have contributed to growing hardship among these pastoralist communities. Following a Tuareg-spearheaded revolt in 1990–96, a decade of uneasy peace has recently seen two major outbreaks of insurgency or less well-defined violence. In early 2006, a former rebel, Ibrahima Ag Bahanga, subsequently integrated into the Malian army, deserted his post accusing the government of neglecting the northern region around Kidal. This led to an Algerian-brokered agreement in July, providing for boosted development initiatives for the region. More recently, in August 2007, there was a further outbreak of violence led by men loyal to Ibrahima Ag Bahanga. They kidnapped at least two dozen army personnel near the north-eastern desert settlement of Tendjeret. Although this appears to have been a one-off series of events linked to the cross-border smuggling trade in the region, the United States has viewed northern Mali as an area vulnerable to terrorism in recent years and has conducted training exercises with Malian forces.

Across the border in Niger, there remains a state of high tension between the government and the Tuareg-led Niger Movement for Justice (MNJ), including fire-fights with government forces leading to several deaths. The MNJ has repeatedly declared that northern Niger is 'a war zone' and has attempted to target the region's uranium extraction industry, including an attack on installations at Imou-Araren in April and the kidnapping of a Chinese contractor in July. The MNJ has also accused the uranium sector, spearheaded by the French conglomerate Areva, of long-term neglect of the environment and of the safety and interest of local, largely Tuareg, populations. In both countries, there is resentment towards Tuaregs from sedentary and southern populations. The marginalization of the Tuaregs is likely to be aggravated by the continuing desertification of the Sahel, a process likely to continue as global warming begins to bite. In 2007 Oxfam warned that changed rainfall patterns in Niger are contributing to worsening desertification, which, for indigenous people like the Tuaregs, means massive losses in livestock and food insecurity.

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