The Origins and Evolution of Clans
Though most clans consider they have a distinguished lineage - in many cases claiming to be "a royal race" - few are prepared to recognise the implication of having previously belonged to a parent kindred that may in fact be a clan still in existence, or one from which came other present-day clans. The desire for an immaculate conception is particularly strong for those names struggling to assert themselves as independent clans in the face of claims by others that they are merely a sept of an existing clan; but refusal to accept links to paternal kindreds - whether present day clans or not - defies the meaning of the word clann (children or descendants - i.e. "family") and ignores the realities of kindred history in the Scottish Highlands.
That reality is best understood by looking at the history of the most well documented kindred in the Highlands: Clan Donald. Donald the progenitor of the MacDonalds was a grandson of Somerled mac Ghillebrigte, and therefore a member of Clann Somerhairlie; and Somerled was a descendant of the 9th century warrior who appears in medieval chronicles as "Gofraidh mac Fearghus, toiseach Oirgiall" (Godfrey son of Fergus, chief in Argyll), and therefore a member of Clann Gofraidh - a kindred name that was still applied to MacDonalds and their cousins as late as the 16th century. Those cousins included the MacDougalls whose progenitor was a son of Somerled, and the MacAlisters who were descended from a son of Donald himself - and the MacAlisters have never felt that acknowledging a descent from the progenitor of another clan in any way derogates from their existence as an independent clan in their own right.
Just as the father of a modern family is born into an existing family, so the namefather - or as he's sometimes called, the "eponymous" - of a clan is born into an existing clan; and since in most cases the fame required to have a clan named after them required success as a warrior leader or a politician, and only the sons of kings or chiefs had a chance to attain such positions in the middle ages, it follows that most new clans sprang from important existing clans (though there may be little if any record left of the parent kindred as such). The process of the birth and growing-up of potential new clans continued into more modern times and can be seen in the survival of the much-debated concept of septs, and in the fact that as late as the early 19th century many in the Highlands had in effect a choice of surnames; the old parent kindred or the newly emerging clan (see separate pages on Septs and Surnames).
Unfortunately very few clans are as well documented as the MacDonalds and their cousins, but the survival of some medieval clan pedigrees - such as the early 15th century collection known as MS.1467 - clearly show how some other clans share a common ancestry that has sometimes been denied in more recent centuries. The matter is complicated however by deliberate attempts on behalf of some clans to claim other sorts of ancestry which were thought at the time to enhance their reputations - such as the fake FitzGerald origin invented for the Mackenzies in the 17th century by the then Earl of Cromartie. The whole issue of "Pedigree-Making and Pedigree-Faking" has been admirably dealt with by David Sellar, a recent Lord Lyon, in his article "Highland Family Origins" in The Middle Ages in the Highlands, ed. Lorraine Maclean (Inverness, 1981).
Much of the modern idea of a clan comes from the institution as it was, or appeared to be, in the 18th century - before the catastrophes of Culloden and the Clearances. Many of the features of the classic clan of the 18th century are themselves however either mythical or confined to that era, and bear little resemblance to the clan as it evolved in earlier times. In most of the larger clans only a minority of clansmen were in fact descended in the male line from the chief whose surname they would use (if and when surnames were required), and many of those chiefs were not themselves descended in an unbroken male line from the progenitor of the clan remembered in the surname they so proudly bore. Few clans had always lived on the lands they so fiercely defended; and some, maybe many, of the smaller clans that did were no longer the lairds-in-chief of those lands in the 18th century - having been conquered, absorbed, or taken under the protection of incoming greater chiefs from elsewhere in the country.
Though clan histories of the 17th and 18th centuries proudly pointed to a succession of elder sons or nearest male heirs succeeding as chiefs in accordance with the principles of primogeniture, right back to the eponymous of the clan - i.e. to the concept of a "rightful heir" and any challengers as usurpers - in fact the old Celtic system of succession (sometime called "tanistry") survived at least into the 16th century in many clans. It allowed for the succession of qualified cousins to the chiefship if they could convince the leading men of the clan that they were the most suitable candidate for the job. Thus it is that most clan genealogies - based on accounts written down in the late medieval or early modern periods at the behest of the chiefs who established the principle of primogeniture in their clan - are highly misleading, even if not actually faked in the way previously mentioned.
Histories and Genealogies of Clans
The Family History Room in the Highland Archive and Registration Centre probably has the largest collection of clan and family histories relating to the Highlands - all of which should also be found in the National Library of Scotland, whose catalogue may show many more: www.nls.uk/catalogues.
The two standard reference works listing clan histories, which are both now badly out of date, are:
Margaret Stuart & Sir James Balfour Paul, Scottish Family History (Edinburgh, 1930)
Joan P. S. Ferguson, Scottish Family Histories (Edinburgh, 1968 & 1986).
Highland Roots has produced a more up-to-date listing:
Graeme M. Mackenzie, Highland Clan and Family Histories: A Guide to Published Histories, Genealogies, Family Trees ... (Inverness, 2015), details of which can be found here.
A map showing roughly where in the Highlands each clan was at one time located can be accessed here.