Somalia begins appointing new government after picking Hassan Sheikh Mohamud as its first president elected on home soil in four decades

Somalia has begun appointing a new government after picking its first president elected on home soil in four decades.

Hassan Sheikh Mohamud has emerged as the surprise winner in a contest that had been marred by delays, intimidation and bribery. The 57 year old professor upset the favourite, incumbent Sheikh Sharif Sheikh Ahmed, who had spent heavily to retain the top job, in a run-off vote in Somalia's new parliament.

The departure of Mr Sharif Ahmed, who has been accused in UN reports of looting government budgets, could open the way for significant international funds to stabilise the war-ravaged Horn of Africa nation. Despite the presence on the ballot of leading politicians and warlords associated with the previous transitional administration, MPs opted for Hassan Sheikh, a relative political newcomer not linked to any armed factions.

The international community has been desperate to bring down the curtain on the tainted Transitional Federal Government (TFG) after eight years dominated by political squabbling and corruption. With the security situation in the country ruling out a direct election, the UN oversaw the appointment of an assembly of elders from Somalia's influential clans earlier this year. They in-turn picked a slimmed down new parliament who got to vote on Monday for a new president.

The process missed its 20 August deadline and officials involved reported death threats being made to members of a panel meant to vet the new MPs. However, strong opposition to another term for Mr Sharif Ahmed appeared to have united MPs from different clans and factions behind his remaining opponent, Hassan Sheikh.

The new president, who hails from the same Hawiye clan as his predecessor, has a strong following in the capital Mogadishu, where he remained through most of the last two decades of fighting. Those clan links have raised hopes that supporters of the outgoing president will not take up arms in response to his ousting. While in the city, the professor helped to found a private university which became one of Mogadishu's few success stories during the war years and has published a number of papers on the need for reconciliation and reconstruction in Somalia.

He nonetheless faces a herculean task in trying to establish Somalia's first effective national government since the 1980s. The Islamic militants of al-Shabaab have been in retreat for the last year but remain in control of large sections of south and central Somalia. There has been an uneasy truce between clan militias in the capital during the election campaign that could easily unravel. And he must come to some accommodation with the powerful northern region of Puntland and the breakaway region of Somaliland.

A moderate Islamist with links to Egypt's Muslim Brotherhood, the newcomer has been a vocal critic both of al-Shabaab extremists and the dysfunctional international engagement with his country – in particular the military spending aimed at curbing piracy. His critics have already accused him of lacking the political experience to keep the peace while his supporters point to his use of the clan system in winning the parliamentary vote.