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While the Highlands and Islands are part of Scotland and share some common history with their southern kin, the ethos north of the Highland Boundary Fault is distinct, reflecting a different landscape and offering a different spin on historical events.

Scotland's earliest inhabitants were hunter-gatherers, who began arriving about 6000 years ago from England, Ireland and northern Europe. The Neolithic era, around 3500 BC, brought a new way of life with agriculture, stock breeding and trading. The Iron Age reached Scotland in around 500 BC, heralding the arrival of Celtic settlers from Europe. In the Highlands, which escaped Roman influence, the Iron Age lasted well into the Christian era.

Scotland, which was known as Alba, became dominated by two indigenous Celtic tribes, the Picts and the Britons. From the 6th century AD they were joined by a third Celtic tribe, the Scotti from northern Ireland (Scotia). Despite their differences, all these tribes had converted to Christianity by the late 8th century, at which time a new invader appeared. Raiding Norsemen in longboats arrived in the 790s, and for almost 500 years they controlled the entire western seaboard. The Picts and Scotti were drawn closer by the threat from the Norsemen and by their common Christianity. A royal marriage between the two tribes saw a Scott become king of Alba, and thereafter the Scotti gained cultural and political ascendancy, and Alba eventually became known as Scotia.

In the 11th century, Malcolm III and his English queen founded the Canmore dynasty of able Scottish rulers and introduced new Anglo-Norman systems of government and religious foundations. David I adopted the Norman feudal system, granting land to great Norman families in return for their promise of protection. Feudalism was eventually grafted onto the old kinship-based system, and enormously powerful clans were created. Meanwhile, inaccessible in their glens, the Highland clans remained a law unto themselves for another 600 years. A cultural and linguistic divide grew up between Gaelic-speaking Highlanders and the Lowland Scots who spoke Lallans, a language made up of English, Norse and Gaelic constituents.

The 17th century brought religious differences and civil wars. While there was an overall struggle to establish independence from Rome, Scotland was also divided between the Presbyterians, who shunned all ritual and hierarchy, and less-extreme Protestants who were more like the Anglicans south of the border. The wars left the country and the economy ruined, and anti-English feeling ran high. Graham of Claverhouse raised a band of Highlanders and in 1689 routed the English troops at Killiecrankie, near Pitlochry. In 1692 people were horrified by the treacherous massacre, on English government orders, of MacDonalds by Campbells in Glen Coe. The event became Jacobite (Stuart dynasty) propaganda that still resonates today.

Following the Act of Union of 1707, which united England and Scotland under a single parliament, the Jacobites, who never received much support outside the Highlands, rebelled. In the uprisings of 1715 and 1745 they attempted to replace the Hanoverian monarchy with Catholic Stuarts, notably James Edward Stuart (the son of the exiled James II, and known as the Old Pretender) and Bonnie Prince Charles Edward Stuart (James Edward's son, who was given the moniker the Young Pretender). Following the disastrous Jacobite defeat of 1745, the government banned private armies, wearing the kilt and playing the pipes. Many Jacobites were transported or executed; others forfeited their lands.

By the mid-19th century, overpopulation, poverty and the potato famine of the 1840s led to the tragic Highland Clearances. People were forced off the land and shipped or tricked into emigrating to North America, Australia and New Zealand. Those who remained were moved to small holdings known as crofts. Rents were extortionate and life for the crofters was extremely precarious. Common grazing ground was confiscated for sheep or deer. In the 1880s, the crofters rebelled and won a considerable measure of security.