DNA Genealogy


The Milligan/Milligan DNA Project (formerly MACS) aims to generate an interest in the study of DNA Genealogy amongst those who share the variant surnames Millican, Milligan, Millikan, Milliken, Millikin, Mulliken, Mullikin, many of whom are in the R-M222 Haplogroup. DNA testing has proved to be one of the fastest growing areas in genealogical research and the reason for its popularity is simple. Where traditional methods of research become exhausted and a family lineage can be taken no further, DNA testing can often link people to distant cousins or branches, particular with those individuals who have a genealogical paper trail traced to Ireland, Scotland or England.

Y chromosome

Two basic DNA tests are available to family historians: the Y chromosome test and the mitochondrial test.  Y chromosome testing is usually the preferred option in Clan/Surname Projects: as a tool it can be used to predicate how close two male individuals or groups of male with the same surname are related.  In a DNA sequence called Short Tandem Repeats (STRs), relatedness is quantified by the number of mutations that occur at certain loci or marker (location) on the Y chromosome . At each marker, the number of repeats, called alleles (pronounced AL-eels), varies between individuals and it is the sum that makes up a person’s unique DNA profile, called the Haplotype. The loci or marker is usually notated as DYS (DNA Y chromosome Segment) and followed by a number meaning at a position, for example, DYS 393.

In DNA Genealogy, the number of alleles at a given marker can be analysed by comparing them with individuals who are in the same Haplogroup or ‘super-family’, defined by a single nucleotide polymorphism (SNP).  It is the number of varying alleles in a person’s haplotype then that are analysed to determine the number of generations two or more examined Y chromosomes are from the most recent common ancestor. The closer the match the higher the probability two individuals might share a common ancestor, which is calculated in terms of genetic distance based on the rates at which Y chromosome genetic markers mutate or change over time. The rates of mutation are the subject of ongoing research and can be studied in more detail in Charles F. Kerchner’s article on DNA Mutation Rates. Estimated rates of mutation should be treated with caution as mutations are random and can occur in multiples at anytime.  Consequently, as genetic markers can suddenly mutate for no apparent reason and some can mutate faster than others, it is important to identify patterns of mutation specific to our own Project and to ensure where possible, that there is a solid genealogical paper trail to support each participant’s DNA result.

Milligan/Milliken DNA Studies

Since 2002, when I first became involved in DNA Genealogy, the number of Milligans, Millikens etc, joining the DNA Project has steadily grown; today there are now over 50 individual DNA tests.  In December 2002, Paul Millican from Austrialia also launched his Millican DNA website with a particular emphasis on the Millican families in England.  A long with others, we had forged a mutual interest in the study of DNA Genealogy with the aim of supporting all who carry the surnames of Millican, Milligan, Millikan, Milliken, Millikin, Mulliken, Mullikin. Work on another Surname, Grierson, which is closely linked to the Amuliganes in Nithsdale, lead to further collaborative research with David Grierson also from Australia. There is now evidence to show the Grierson lairds of Lag near Dunscore in Nithsdale, share a common ancestor with the Milligans/Millikens and that one branch of Milligans share a more recent ancestor.   Estimated dates to the most recent Milligan-Grierson common ancestor (MRCA) range from 600 to 900 years before present (2012).  Future work in this area would aim to narrow this timeframe and trace the ancient origins of the R-M222 surnames in Nithsdale and southern Scotland as a whole.  

DNA testing has now identified two primary Milligan/Milligan modal haplotypes within the R-M222 Haplogroup and at least two smaller clusters. Haplotypes The R-M222 Haplogroup of the Human Y-DNA tree is SNP called M222 and is associated with many individuals whose roots lie in northwest Ireland, Ulster and Scotland. A modal haplotype is the haplotype of a group of related men which is certain to have been the haplotype or DNA signature of their common ancestor. This modal haplotype usually contains mutations shared by all the descendants of their ancestor, passed from father to son (called a transmission event), which can be used to differential between other branches of a shared surname. The identification of two modal haplotypes, one sharing a set of genetic markers indicative of the chief line of the Mullikine/Amuligane Clan/Surname in Scotland, has only been made possible through DNA Genealogy.

For the purpose of this article, the two modal haplotypes are called modals-1 & 2 of the Mullikine/Amuligane Clan/Surname; both modals have their roots in Mid Nithsdale in Dumfriesshire. Neither, however, are likely to have shared a common ancestor within the last 800 years.  Modal-1, which was previously modal 2 under the MACS, now appears to represent the lineage of McRath Amuligane, called in early documents Macrath ap Molegan or Makerathe Molgan.  He was one of a number of Scots landowners from Dumfriesshire, who rendered homage to Edward I (1272-1307), king of England, for his land at Berwick-on-Tweed on August 28, 1298. McRath’s land appears to have been forfeited, for soon afterwards, King Edward issued a writ, dated September 3, 1298, directing the sheriff of Dumfries to restore to him his land in return for homage and feudal service. McRath’s surname is derived from the personal name Molegan, the eponymous ancestor the Mullikine/Amuligane lairds of Blackmyre in Nithsdale, whose name is first recorded about 1210, when he witnessed a charter of Edgar son of Dovenald, lord of Nithsdale. After almost 700 years, however, it is impossible for us to know with any certainty the exact allele values of Molegan’s DNA signature, but we can predict them through the observed mutations in Modal 1. It is defined by the following string of genetic markers, each with a set value of alleles, extending to 111 markers.





The numbers highlighted in red are key genetic markers called Off-Modal markers: DYS 389/2=30, GATA-H4=12, 557=17, 534=15, 710=33, GATA-A10=12 and 461=13. These are mutations which are common to groups of related men and can be observed in the Milligan/Milligan Results Page. For example, if you look under the section headed DYS 389-2 increased, you will observe all the people in this group (Modal 1) share the allele value of 30. Within this group, two further subclades can be observed by comparing the genealogies of known family histories.  These subgroups can be predicted using markers DYS 449 & 441 and are the subject of a separate article. In summary, one group is composed of descendants who share a close genetic tie with the Milligans of Dempsterton near the village of Dunscore in Mid Nithsdale. One participant (kit no. 10045) is directly descended from the last of the Milligans of Dempsterton.  The second group appears to be composed of descendants with collateral ties with the lairds of Blackmyre in the parish of Penpont near Thornhill, who also held lands in Kirkcudbrightshire and Ayrshire (the Milligans of Dempsterton may have held land in Ayrshire).  This subgroup contains a paper trail linked to Major James Milliken of Milliken Estate, who was allowed the Mullikin coat of arms in 1741.

The second Milligan/Milligan modal haplotype is composed of a more varied set of values, which have fewer paper trails compared with the first group; but like the first, it is supported by a direct paper trail to Mid Nithsdale. There are some interesting permutations in this group and it is very likely the next significant cluster defining another subgroup will be identified here. It is defined by the highlighted markers, DYS 389/2=29, GATA H4=11, 557=16, 534=16, 710=36, GATA-A10=13 and 461=12.





This group is still a work in progress with DYS 458=17 posing the most interesting paradox. The value 17 seems an older genetic marker value and yet comparative studies suggest DYS 458 mutates faster and in this case, may well be a one step back mutation.  At DYS 458, the participant at kit no. 191000, who descends from James Miligan (1772-1832), mason of Thornhill in Mid Nithsdale, shares the value of 17 with kit no. 12068 and another testee, whose DNA results are not on the Milligan/Milliken Project website.  Yet, all share the value of 17 at DYS 464c, a key Grierson marker, not found in Modal-1. To better understand the DNA composite of Modal-2, it is important to draw a direct link with the DNA research compiled by David Grierson in his Introduction To Grierson DNA Research.  The Griersons and Milligan/Millikens are related through John McRath of Laight, a kinsman of Gilbert Grierson of Lag.  David’s chart has been more or less arranged from the oldest to the youngest haplotypes and has been differentiated by markers 389-1, 576 and CDYb.  The Grierson R-M222 modal is found on line 47 of the Grier Chart 1d dated July 2011 and is defined as follows:





It is evident, the Off-Modal markers in Modal-2 are a nearer match to the Grierson modal and in particular, those Grierson markers that are thought to represent the Griersons of Lag. Marker DYS 389-1 is revealing.  The predominate value at this marker is 14, except at those results with the surname Grierson, which have the value 13, a consistent feature in both Modal-1 & Modal-2. The link here is significant, as the Grierson DYS 578=18 is differentiated by one mutation at Modal-2 DYS 578=17. The combined values of DYS 389/2=29, GATA H4=11, 557=16, 534=16, 710=36, GATA-A10=13 and 461=12, indicates a deep shared ancestry in Nithsdale, descended from the lineage of an unnamed ancestor rather than Molegan. The surname Grierson shares an equivalent in Mac style with McCrere, which is also found in Dumfriesshire and Galloway in the 1400s and may indicate the presences of an earlier style.  It seems to have been the practice within the Grierson kindred to drop the suffix ‘son’ to form the surname Grier or Greer. I would suggest this might well have been reflected in the surname McCrere. If the case, it might account for the numerous references to the surname Greer and Grier found in Dumfriesshire and Galloway by the 1600s. The practice of dropping the elements ‘son’ or ‘mac’ can be found in other surnames, such as, the prefix ‘mac’ in McCleland or McClellan to form Cleland or Clellan, and Hewison or Howison without the suffix ‘son’ in the surname Howie.

Within the Milligan/Milliken DNA Project, it was known for some time that there were two major M222 branches, which share a common ancestor pre-dating Molegan of Nithsdale. In effect, it was realised only one of these two sub-groups, called Exploratory R-M222 subgroup A and B, could represent the original genetic line traced from Malgon, the eponym of the lineage name Amuligane.   With that in mind, one of the Projects aims has been to establish which of the two sub-groups is directly descended from Molegan and the Amuligane lairds of Blackmyre.  In July 2014, after testing with FTDNA’s Big Y, the project had its first major breakthrough when two members from ‘sub-group A’, Milligan (kit no. 135550) and Milligan (12068), were assigned a SNP named FGC4133. A few months later in October, 2014, the author, Milliken (23702) from Sub-group B was confirmed A223 that is assessed parallel to FGC4133 (consider them as brothers). Since then other members have been tested, which has resulted in further branching discoveries and a new Haplotree is now being developed.  To date, all the FGC4133 Milligans and Milliken’s tested are in Exploratory R-M222 subgroup A, and those assigned to A223 are all found in Exploratory R-M222 subgroup B.  Both the FGC4133 and A223 Amuligane branches have paper trails going back to Nithsdale and both share a long and established history with the Griersons of Aird in the parish of Tynron and of Lagg in the parish of Dunscore in Nithsdale. Significantly, since then several Grierson researchers have also been confirmed FGC4133.

THORNHILL in Nithsdale, Dumfriesshire

Kit No. 191000 is descended directly from James Milligan and Margaret Hutchinson in Thornhill, whose headstone stands upright in Dalgarnock Churchyard next to Kirkbog near Thornhill . The headstone at Dalgarnock records, James Milligan died on 13th January, 1832, aged 60 years and was a stonemason in Thornhill. Margaret’s death took place on 19th November, 1839, at the age of 65 years. James’s approximate birth date can be calculated by his age at the time of his death, which gives him an approximate year to 1772 with an error margin between 1771 and 1772.  He is more than likely the same James Milligan, whose baptism is recorded on 21st July, 1771, and whose parents are given as ‘James Milligane’ and ‘Mary Halliday’ in Thornhill.  Family tradition in Canada makes James Milligan the eldest son of Thomas Milligan of Thornhill. I have searched the records in Nithsdale and I have been unable to identify a Thomas Milligan, thought to be the father of a James Milligan. It seems this claim was probably transmitted in error.

 In Memory of

James Milligan, Mason

Thornhill, who died 13th Janry

1832 Aged 60 years.

And of Margaret Hutchison

His Spouse who died 19th Novr

1839 Aged 65 years.

Also 5 of their children, 3

Sons and 2 daughters, who

Died in infancy


Minister of Russittown Flats, North

 America, died at Mountreal 7th

Febry 1855 Aged 42 years.

Much regretted by his Flock.

For God is our defence

And he to us doth safely bring

The Holy One of Israel

Is our almighty King

Psalm LXXXIX 18th

A.D. 1843

Erected by James and Archibald

MILLIGAN their sons.

In 1881, James Milligan’s grandson, also called James (he had emigrated to Brunswick in Canada with his father Robert Milligan in 1842), made what must have been his last visit to Thornhill, the town of his birth and childhood memories. On his return to Canada, he published an account of his trip to Scotland in a local newspaper and the following extract, is a personal testimony to what he did and how he was welcomed home.

A Tour Through Scotland – James MILLIGAN recounts the experience of his recent visit: -

“... From Newmarket we crossed the Tweed and stopped at Dumfries ... There is a beautiful statue of Burns cut in stone representing him standing at the plough. Burns died and was buried at Dumfries. An elegant mausoleum was erected some years ago over his grave. In this connection it might be interesting to know that the builder of this beautiful tomb lived in St. John for some years. He died here and is buried in the old burial ground. His name was John MILLIGAN and his grave is marked with a large tablet and is on Central Avenue .... My native place is Thornhill about 14 miles distant and we went there next ... I stopped at the Queensbury Arms overnight and in the morning I walked out. On the streets I met a number of old men who were young men and lads when I left Scotland. I said to them, one after another, ‘Do ye ken me?’ and the answer always came, ‘I ken ye weel’. All were glad to see me and the officers of the Masonic Lodge presented me with a history of the lodge of which my grandfather and father were both past masters. I found in the graveyards the names of ancestors of mine as far back as 1619”.

It is unfortunate James Milligan from Brunswick in Canada never mentioned the names of his ancestors, whose graves dated from as far back as 1619. The oldest extant memorial in Dalgarnock Churchyard dates from 1607 and is inscribed to the memory of John Smith in Barnhill, who died aged 80 years. The Milligan tradition in Canada identifies James Milligan with three other siblings, Margaret who married Samuel Kerr, possibly of Sanquhar in Upper Nithsdale, and John and Thomas neither of whom had children. James Milligan and Mary Halliday in Thornhill also had children called Margaret and Thomas, along with George and Robert Milligan.

     Children of James Milligane and Mary Halliday in Thornhill:

      James Milligane baptised on July 21, 1771.                             

      George Milligane baptised on March 20, 1774.

      Margaret Milligane baptised on March 22, 1776.

      Robert Milligane baptised on June 22, 1778.

      Thomas Milligane baptised on October 29, 1780.

The early history of the Milligans in Thornhill can be traced through several sources; Morton Parish Kirk Session minutes and the registers of baptisms and marriages, and several early rentals. Some of this information can be viewed on this link.  Dalgarnock Churchyard appears to have been the ancestral burial ground of this family and the oldest Milligan memorial in Scotland (see above) is located in this churchyard and dates from 1640. Although, the medieval church of Dalgarnock has long disappeared, the Milligans, originally spelt Amuligane, have lived in area since as early as the 1400s. However, the Milligans do not appear in Thornhill until 1607, when “John Muligane in Thornhill” witnessed the last will and testament of Jean Douglas, widow of John Kirkpatrick in Laught in the parish of Morton. Could John Muligane be the man buried in Dalgarnock?

The town of Thornhill is located in the parish of Morton and was once known as New Dalgarnock, the name given to it by William Douglas, earl of Queensberry, in 1610. New Dalgarnock is now the "auld toun" portion of Thornhill. In 1619, William Douglas, friar of Coshogle, granted to “John Amuligane” in Thornhill a tack for a house and yard in the town, which he was to hold for eight years from Whitsunday 1619 for the payment of a “reikhen” at Fasting Seven yearly. In the earliest extant Rent Roll of 1660-1671 relating to lands belonging to the earl of Queensberry in the parish of Morton, the names of the following Milligans appear in Thornhill: John Milligan in Mid Taylor in Thornhill, Patrick Milligan, Gilbert Milligan, James Milligan and William Milligan in Thornhill. The names of most of these men appear in the list of parishioners in 1684 and the Hearth Tax lists of 1691.  

From the Kirk Session minutes and the register of baptisms and marriages, we can with reasonable certainty follow the history of the Milligans in Thornhill down to James Milligan’s father, James, who married Mary Halliday. In the last decade of the 1600s only one James Milligan appears in the Kirk records, James Milligane in Thornhill, husband of Jean Edgar. He and his wife lived in New Dalgarnock (the west part of Thornhill) in 1684 and 1691, and had a son called James Milligan baptised on January 4, 1694.  It seems very likely James is the same James summon to the Kirk Session in 1715 to confess to the sin of excessive drunkenness!  If not, it must have been his son, James Milligane, who married Nicolas Edgar and also lived in Thornhill in 1715, when the first of the children was baptised.

Known children of James Milligane and Nicolas Edgar in Thornhill:

1. Jannet Milligane baptised on March 6, 1715.

2. Mary Milligane baptised on September 2, 1716.

3. Jean Milligane baptised on September 13, 1719.

4. Isabel Milligane baptised on January 24, 1723.

5. James Milligane baptised on December 26, 1725.

Known children of James Milligane and Mary Edgar in Morton Castle.

1. John Milligane born in Morton Castle and baptised on February 5, 1744.

2. William Milligane born in Morton Castle and baptised on May 22, 1746.

3. John Milligane born in Hallgill and baptised on May 8, 1749.

There is an interesting document in Adam Percy’s A History of the Douglas family of Morton, which lists a number of tenants in the baronies of Morton and Lochrannie in 1761.  It lists several Milligans: George Milligane in Whitefauld, now part of Burn, John and John Milligane in Laught and James Milligane servant to Margaret Lookup in Thornhill (wrongly given as in Moniaive). So, who was this James? He could be identified with James Milligane spouse of Margaret Lukup or Lookup, but then, why would he be called her servant?  Perhaps, he is the same James Milligane in Thornhill, who married Margaret Boar and had two known children baptised by the Rev. Robert Aitken, minister of Morton: John Milligane on October 2, 1765, and Agnes Milligane on July 9, 1767. The identity of James Milligane is less certain, but it seems, he might well be identified with James Milligane younger in Thornhill, aged twenty eight years and unmarried, purged of malice by the Kirk Session in 1755.

There is another Milligan couple of interest to this search, James Milligane and his spouse Mary Edgar, who for a short time lived at the old castle of Morton.  It had been abandoned by the Douglas family of Morton in or about 1714, but still seems to have been occupied or at least part of it, by tenants or cottars as late as 1761. The marriage of James Milligane and Mary Edgar is still extant and is recorded in the marriage register of Closeburn. It records “James Mulligain” in this parish and “Mary Edgar” in the parish of Keir married on July 9, 1734. Later, we find the baptism of their son, James, on April 19, 1741. In the register, “James Millegan” and “Mary Eggor” lived in Auchencairn, a small farm east of Kirkpatrick in Closeburn parish.