The year 2014 was punctuated by the election of President Joko Widodo, a youthful reformist popularly known as Jokowi, after a tense and divisive poll in July. Jokowi's win has been celebrated as a victory for democratic reform and religious pluralism in Indonesia after years of rising intolerance, raising hopes among the country's diverse indigenous populations and other minority groups. Jokowi campaigned under the national slogan 'Unity in Diversity', promising to curb escalating religious and ethnic tensions in the Muslim-majority country.

Indonesia has experienced a surge in religious intolerance under the 10-year rule of former President Susilo Bambang Yudhoyono, resulting in frequent violence against its Ahmadi, Christian and Shi'a minorities. According to the Setara Institute, attacks on religious minorities have skyrocketed since the government authorized two decrees restricting the right to worship freely in 2006 and 2008. This trend continued in 2014, with hardliners congregating in April in Bandung, West Java, to form the first ever 'Anti-Shi'a Alliance' calling for jihad against the minority, viewed as 'heretical' by extremists. A Shi'a journalist covering the event was reportedly detained, interrogated and assaulted by participants. Youdhoyono has been blamed for forging a political alliance with the Indonesian Ulema Council (MUI), which has relentlessly promoted a narrow and xenophobic interpretation of Islam. In January, the MUI urged police in Yogyakarta, Java, to monitor, freeze and disband organizations run by Shi'a Muslims. Ahmadis, who were branded 'deviant' by Indonesia's top clerical body in 2008, also face persistent social ostracism, harassment and arbitrary closures of their places of worship.

Activists have called on President Jokowi, who was sworn into office in October, to take a tough stance against extremist groups and their political allies. To his credit, Jokowi has already defended a number of minority politicians, including Christian Susan Jasmine Zulkifli and Shi'a Jalaluddin Rakhmat, against public outrage over their religious affiliations. The government has announced that it is drafting a new law to protect religious freedom, which will allow all religions to publicly practise their faiths and construct houses of worship. The new law is expected to replace previous discriminatory legislation, including Indonesia's controversial blasphemy law. Over 100 individuals have been jailed over the past decade for perceived religious offences under this draconian legislation.

Another crucial test for the new president is the bitter conflict in resource-rich West Papua province, where ethnic Papuan rebels have fought for independence from Indonesia for decades. Unfortunately, there has been little apparent progress in achieving a sustainable peace in the region since Jokowi took power, and security forces continue to perpetrate abuses against the indigenous population. In August, a prominent separatist activist went missing a day before a scheduled visit by then President Yudhoyono. His dismembered, bullet-ridden body was discovered floating in a sack off the Papuan coast six days later. Foreign media remain largely shut out from West Papua, which requires a special permit to enter. In August, two French journalists were arrested for reporting on the Papuan separatist movement on tourist visas. They were sentenced to two months in prison and later deported.

Dozens of peaceful activists were arrested in West Papua in 2014 amid regular reports of arbitrary killings, rapes and violence perpetrated by the Indonesian army. West Papua's independence movement is increasingly urban and educated, applying non-violent means to further their cause, with a growing number of youths using social media to campaign against the Indonesian occupation. In December, four high school students were killed when the military and police opened fire on a crowd of protesters in the eastern province. Jokowi was roundly criticized for his inefficient response to the incident. This follows anger over his decision to appoint former military strongman Ryamizard Ryacudu – notorious for his derisive attitude towards human rights defenders in West Papua and Aceh provinces – as the new Minister of Defence.

Indonesia's controversial transmigration programme – an initiative moving people from densely populated to less populated parts of the archipelago to counter rapid urbanization in Java – has fuelled anger and ethnic friction in West Papua. Six decades after this programme was first introduced by the Dutch colonial administration, ethnic Papuans now number less than 50 per cent of the population. The programme has led to increased marginalization of the indigenous population. According to the Institute for Policy Studies, indigenous urban youth in West Papua are twice as likely as migrants to have little or no formal schooling. Disparities in human development between the migrant-dominated urban areas and indigenous-majority interior are even more pronounced.

In May 2014, Indonesia's Human Rights Commission (Komnas HAM) launched its first national inquiry into land rights abuses committed against Indonesia's indigenous population. Over 2,000 communities have asked for investigations, according to the Indigenous Peoples' Alliance of the Archipelago (AMAN). Activists have called on Jokowi to publicly apologize to the country's indigenous peoples. This comes one year after a Constitutional Court ruling that invalidated the state's claim to millions of hectares of customary indigenous lands. Jokowi has pledged to improve conditions for Indonesia's 70 million indigenous people, although his government has yet to implement the Court's recommendations. A draft law on the rights of indigenous peoples has stalled in parliament, facing obstruction from Indonesia's controversial Forestry Ministry, which is currently being investigated by the Corruption Eradication Commission (KPK). Jokowi has since merged the Environment and Forestry ministries in an effort to improve sustainable practices, although environmental campaigners worry that this will dilute conservation policies.

Indonesia has one of the highest deforestation rates in the entire world, with a new study suggesting that 840,000 hectares of primary forest were felled in 2012 – twice as much as the historic global leader Brazil. This process has been accelerated by endemic corruption at the Forestry Ministry. In March, the former governor of Indonesia's Riau province was sentenced to 14 years in prison for issuing illegal logging permits in central Sumatra, which has already been devastated by the spread of palm oil and paper plantations. The former minister of forestry was questioned in a separate investigation.

Rapid deforestation and land confiscations have hastened the speed of urbanization among indigenous communities in Indonesia. For example, Dayaks – a constellation of non-Muslim peoples in Borneo – are increasingly migrating to bigger cities in search of better employment opportunities. Though the Indonesian government signed an agreement with UN-Habitat during the year committing to the promotion of sustainable urbanization, the government has not made specific plans on how Indonesia's myriad minorities and indigenous peoples will be incorporated into this process.

In Jakarta, Indonesia's capital, rapid urban growth has disproportionately affected certain ethnic groups. In particular, indigenous Betawi have been historically marginalized by the government's urban development projects. As Jakarta rapidly expanded into a sprawling mega-city, it engulfed Betawi farming villages on its periphery, turning them into isolated urban settlements. Thousands of Betawis have since been dislocated from their homes to make way for large-scale private or commercial enterprises, often forced into slum dwellings as land prices soar. Their culture and identity has come further under threat because of an influx of economic migrants to the booming capital. Many Betawis have had to abandon their traditional livelihoods, such as dairy cows, agriculture or batik production, and minority youths have struggled to find work, giving rise to ethnic-based urban gangs and criminal networks. In recent years the government has employed various strategies to promote Betawi culture in Jakarta. For example, when Jokowi was governor of Jakarta, he toyed with the idea of using Betawi architecture to boost tourism to the city. Another marginalized minority in Jakarta is Indonesia's ethnic Chinese, who faced acute persecution under military rule and continue to be segregated from other ethnic groups by the legacy of racism and violence since an outburst of anti-Chinese riots in 1998. However, this year saw the election of an ethnic Chinese Christian to the role of governor of Jakarta.

The Acehnese ethnic minority are known for their devout adherence to Islam and their long resistance to external rule. However, the strict interpretation of Sunni Islam in Aceh province has led to at least 20 churches having been closed in the province and 14 minority Islamic sects having been formally banned, fuelling insecurity among religious minorities. Women in particular have become increasingly marginalized in Aceh, since it was devastated by the Indian Ocean tsunami in 2004. Men have largely determined the recovery efforts, as well as the terms of the peace deal that ended Aceh's long-running struggle for self-determination and was reached as a direct consequence of the tsunami. The peace deal included the application of Sharia law, which has led to an erosion of women's rights and freedoms in urban spaces. Research suggests that these religious gender constraints are more harshly felt in urban areas than rural areas, with women's dress and behaviour more closely monitored – strictures that are felt especially by non-Muslim women.

Aceh's cities also received a disproportionate amount of humanitarian aid in the aftermath of the 2004 tsunami, aggravating an urban-rural divide in socio-economic development. This policy had a significant impact on thousands of survivors who had fled from coastal regions and urban centres to Aceh's conflict-torn interior and missed out on disaster relief. Banda Aceh had already been shielded from the worst of the fighting, even briefly emerging as a democratic space for the educated urban elite to resist the Indonesian occupation after the fall of Suharto. Five years after the tsunami, all traces of the disaster had been removed from Banda Aceh, while many rural areas lay neglected and abandoned.

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