After the episode at Glen Fruin between clans Gregor and Colquhoun in 1603, western Dumbartonshire slowly became more "settled" or peaceful. The MacGregors ceased to exist as a clan and the resident clans of MacAulay, MacFarlane, and Buchanan became less powerful as their lands slowly passed into the hands of strangers. In 1614, Angus Og MacDonald of Dunyvaig seized Dunyvaig Castle, which had been held by the Bishop of the Isles. Sir Aulay MacAulay of Ardincaple, with twenty of his men, accompanied the Bishop to Islay to demand the surrender of the castle.
On 26 March 1639, Covenanters captured Dumbarton Castle to prevent it from being used as a Royalist base in the event of an invasion from Ireland. Once secured, the Earl of Argyll placed Walter MacAulay, Laird of Ardincaple, as keeper of the castle with a garrison of forty men. In 1648, the parish of Row (modern Rhu) was created at the instigation of Aulay MacAulay, Laird of Ardincaple, who wanted to separate from the parish of Rosneath on the opposite side of the Gare Loch. He built the first parish kirk a year later and provided land for the kirk, minster's manse, and garden.
The Glorious Revolution of 1688 saw the overthrow of the Roman Catholic, James II of England, in favour of the Protestant, William III of Orange. Though most of the English accepted William, Jacobites within Ireland and Scotland opposed him in favour of the deposed James. In 1689, the Earl of Argyll's offer to raise a regiment of 600 men in aid of William was accepted. Argyll's regiment was to consist of 10 companies of about 60 men each. That same year, Archibald MacAulay of Ardincaple raised a company of fencibles in aid of William. William and his wife Mary were crowned King and Queen of Scotland as William II and Mary II on 5 November 1689. In 1690, "Ardencaple's Company" within the Earl of Argyll's Regiment was commanded by Captain Archibald MacAulay of Ardencaple, Lieutenant John Lindsay, and Ensign Robert MacAulay "Anshent" (ancient). Later in 1694, Archibald's younger brother, Robert, is listed as Captain Robert MacAulay in the Earl of Argyll's Regiment of Foot. Even after the revolution had succeeded there was still a fear of invasion in Dumbartonshire by adherents to the expelled Jacobite king. Local parishes were required to muster their men. An example of the size of one particular muster around 1693 is as follows: in Kilmaronock, fifty men and ten guns; in Gleneagles, seventy-four men and three-score swords; in Luss, seventy men "with arms conforme"; in Cardross, one hundred men and thirty stand of arms; and in Rhu, there were eighty-men and fifty-six firelocks. At first the individual parishes selected their own officers, but at general musters they were divided into two companies—one containing those above Leven, and those living below in the other. At a shire mustering at Kilpatrick in 1696, MacAulay of Ardincaple was selected as Captain of the company above Leven, with Noble of Ferme, Lieutenant, and Dugald MacFarlane of Tullibintall, Ensign.
At the beginning of the 18th century, a group of MacAulays migrated to the former counties of Caithness and Sutherland. William Buchanan of Auchmar's 18th century account of the surname MacAulay stated that a group of MacAulays in Caithness claimed to descend from the MacAulays of Ardincaple.
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