I was happy to see this question not only because I think it's a very thoughtful and interesting one, but also because, despite its complexity, it's one we can answer with considerable authority. For this we must point directly to the work of Allan Macinnes, whose seminal and extremely relevant Clanship, Commerce and the House of Stuart 1603-1788, does much of the heavy lifting for us.

As part of this his study of the Gàidhealtachd, or the largely Gaelic-speaking region of Scotland, Macinnes undertakes a broad survey of the fifty primary Highland clans to chart the strains of both their confessional inclinations and their political loyalties through the Jacobite era. This is discussed to some degree within the body of his text but is explicitly depicted in an appendix (pp. 247-249) wherein general confessional and political categories are listed out. Some time ago I had taken the liberty of transposing this data into a living spreadsheet that offers a bit of flexibility for the sake of visualization. That sheet is available here and Macinnes's original data can now be searched, sorted, filtered, and grouped according to one's needs. I recommend grouping by era to follow the trends most germane to your enquiry.

I shall leave it to you to view his conclusions, but I will summarize the gist and add in a couple of contextual notes to address your question appropriately.

The most important point here is to understand that most aspects of 'clanship' were neither static nor cleanly delineated, and that like any complex society over a century-long period of time, the Gàidhealtachd was in constant transition. Our modern perceptions of Highland rigidity with regard to sept and surname hardly mattered in the long eighteenth century, and the same goes for faith, loyalty, and practices. All of these cultural and societal facets transcended 'artificial boundaries' of specific clans and in fact consistently diffused between them.

As it pertains to faith, you're correct that the Gàidhealtachd was a mixture of different confessional traditions. To summarize Macinnes's findings, by 1745 and the last Jacobite rising, only twelve of the fifty primary Highland clans represented a significant Catholic population (24%) and half of those were divided or mixed between other confessional traditions.

How this informed the tendency for a given clan to subscribe to Jacobite ideologies or to actively participate in the risings is difficult to assess. What these facts make utterly clear, though, is that Jacobitism was decidedly not ultimately determined by locale (Highland versus Lowland) or by faith (Catholic versus Protestant). A perfect example of this latter point is that Donald Cameron of Lochiel brought three chaplains along with his regiment in the last rising, representing Catholic, non-juring Episcopal, and Presbyterian traditions – which undoubtedly was done to cover the varied tenets of his tenants.

Macinnes makes it clear that defense or assertion of faith was simply not a primary motivating factor when considering clan-wide directives undertaken by a chief or fine (elites). As I add in my doctoral thesis, shared religious beliefs 'provided a bond of common sentiment only so far as to organise action within a much larger opposition movement' (p. 61). Ironically in the case of the Forty-five, it was the non-juring Episcopalian communities in Scotland's North-eastern Lowlands that not only considered themselves duty-bound by confessional doctrine to restore the Stuarts to the throne of the Three Kingdoms, but that turned out in even larger numbers than the Highlanders who are falsely but firmly lodged in popular memory as the only 'true' Jacobites.

I hope this goes some way to sufficiently answering your question in a general sense. Plenty of further reading on this subject is available, and I would specifically recommend the following to you:

• Allan Macinnes, Clanship, Commerce and the House of Stuart, 1603-1788 (1996).

• Alasdair Roberts, '‘Roman Catholicism in the Highlands’ in James Kirk, ed., The Church in the Highlands (1998).

• Bruce Lenman, ‘The Scottish Episcopal Clergy and the Ideology of Jacobitism’ in Eveline Cruickshanks, ed., Ideology and Conspiracy: Aspects of Jacobitism, 1689-1759 (1982).

• Thomas McInally, ‘Missionaries or Soldiers for the Jacobite Cause? The Conflict of Loyalties for Scottish Catholic Clergy’ in Allan Macinnes and Douglas J. Hamilton, eds., Jacobitism, Enlightenment and Empire, 1680-1820 (2014).

I'd also like to recommend this fantastic free online course about the history and transformation of the Highland clans hosted by the brilliant Dr Andrew Mackillop and the University of Glasgow. I found it to be a near-perfect introduction to the early modern Gàidhealtachd.

With best wishes,

Dr Darren S. Layne
Creator and Curator
The Jacobite Database of 1745
Research Blog: Little Rebellions