SNPs, STRs and the ancestral tree of I-Y33765

The I-Y33765 mutation is found within the "non-recombining" portion of the human Y chromosome.  Depending on the version of the Genome Reference Consortium (GRC, 2007) Human Reference sequence which is used (at present this will be either 37 [aka Human Genome Assembly hg19] or 38 [aka Human Genome Assembly hg38]) the numeric position of the SNP (single nucleotide polymorphism) on the Y chromosome is either 16276363 [hg19] or 14164483 [hg38] (see image below).  The reference sequences record a guanine (G) molecule at the respective position which is replaced or substituted in the mutated form by a cytosine (C) molecule.  The G, reference form, is termed "ancestral" or "negative" while the C, mutation form, is termed "derived" or "positive".

This mutation or "base substitution" was first identified in 2017 by YFull, Moscow, Russian Federation in a comparison of two FamilyTreeDNA Big Y-500 test BAM files.  YFull named the mutation Y33765; the letter Y indicating that it was first identified in their analysis and 33765 being the next available integer in their company's numeric sequence. 

Unlike the DNA in other chromosomes of the human genome, which is "shuffled" in a process known as "cross-over" when the egg or sperm are formed (hence at each generation) in order to create genetic diversity in a population, the majority of DNA in the Y chromosome is within the "non-recombining region" that remains largely unchanged.  This means that it's genetic sequence is generally "conserved" or stable and at each generation passes from father to son with only occasional small random changes.  

The genetic evolution of this non-recombining part of the Y chromosome is classified into groups termed "haplogroups" that each contain large numbers of these mutations  each of which is termed a single nucleotide polymorphism (SNP).  The haplogroups are themselves each defined by a particular SNP [aka mutation or base substitution].  These major haplogroups are identified by a letter; the oldest male haplogroup designated A and the youngest R.  Because of the generally stable conserved nature of the Y chromosome, together with the occasional random SNP changes, it has been possible for geneticists to construct an ancestral tree for male Homo sapiens.  The Y33765 SNP is a very recent mutation within the I haplogroup.  It seems very probable that the first male Homo sapiens to enter Europe belonged to this I haplogroup. 

 

More precisely the I-Y33765 SNP is within the extensive subclade or branch of haplogroup I termed I2a1a which is itself defined by the SNP P37.2.   This major branch of the I haplogroup is estimated to have formed (circa 18,400ybp) during the last glacial maximum somewhere in southern Europe.  There are at least six phylogenetically significant SNPs in the ancestral tree of Y33765 between it and P37.2 as shown in the simplified table below.

 

From the table it is easy to understand that SNPs are very useful tools that can be used to determine a mans deep ancestry on a scale of many thousands of years.  In Scandinavia and the Baltic region the I2 male ancestral lineage is associated with hunter-gather populations.  In central southern Sweden male ancient DNA samples from skeletal remains excavated at Motala (Mathieson et al.,2009) have been characterised as belonging to this haplogroup.  The Motala hunter-gather encampment has been dated to the Mesolithic period.  In Lithuania the skeletal remains of a man buried near a supposed shamanic ritual site has produced Y-DNA with an I-L233 haplogroup (Butrimas, 1992; Mittnik et al.,2018) .  Radiocarbon dating has estimated he was alive during the late mesolithic/early neolithic. 

If two chaps are each derived for a given SNP then they must be related through a shared or common male ancestor.  If they are each derived for a SNP that formed very recently, such as I-Y33765, then their common ancestor must have lived at some time after the original formation of that SNP.  By comparing the SNPs that are shared by several men it is possible to draw a phylogenetic tree that maps their genetic relationship.

While the presence or absence of a combination of SNPs is the definitive test used to confirm a mans haplogroup and hence his genetic relationships, SNPs are not the only form of alteration within the Y chromosome that can provide this information.  STR's (short tandem repeats) are another form of Y-chromosome marker which can be used to discover such information.  Unlike SNPs, that involve just a single base change in the DNA sequence, STRs are areas of the DNA molecule that contain repeat sequences of from two to perhaps a dozen or more bases.  The number of repeats of these short series of bases at a particular site or "loci" can vary between individuals as a result of random mutation.   Not all STR sites mutate at the same rate.  So, by using a combination of STR markers, that mutate with differing speeds, it is possible to determine a chaps STR profile or "haplotype".  A mans STR haplotype can be used to predict his haplogroup (what SNPs he is likely to be derived or positive for) and to compare his genetic relationship with other men. 

FamilyTreeDNA (Houstton, USA) and YSeq (Berlin, FRG) sell a range of STR test "panels" that contain from 12 to 111STR markers.  While a 12STR panel test can be used to predict a mans haplogroup it is unlikely to allow his relatedness to other chaps to be judged with any precision.  By using more STR marker panels the precision is improved.  By testing with the 111STR panel it is possible to differentiate genetic relationships between closely related men.  As a consequence STR comparison is particularly useful to assess relatedness within the genealogical time-frame equivalent to the last 500 years or so.   

From the comments above it follows that by using 111STR markers it should be possible to predict if a man will be derived for a relatively recent SNP like I-Y33765.  This is most effectively done if his STR haplotype is compared to the mode (the value most likely to be sampled) haplotype obtained from the STR results of men who have been confirmed as derived for I-Y33765 by SNP testing.  The following table gives the I-Y33765 mode STR values based on results from six men. 

References

 
Butrimas, A., (1992) Spigino Mezolito Kapai, Lietuvas Archeologia, 8, 4

GRC., (2007) The GRC is a collaboration between the The Wellcome Sanger Institute, the McDonnell Genome Institute at Washington University, the European Bioinformatics Institute and the The National Center for Biotechnology Information

Mathieson, I,Lazardis, I,Rohland N, et al., (2015) Genome-wide patterns of selection in 230 ancient Eurasians, Nature 528 499

Mittnik, A., Wang, C., Pfrengle, S. et al. (2018) The genetic prehistory of the Baltic Sea region. Nat Commun 9, 442 

I-Y33765, Cnut the Great and "the Dane" in Domesday

Three, apparently unrelated, male lines sharing the Clement surname (see map below: 236748 & 282009; IN82043; YS32054), each with documented eighteenth century genealogy in the rural hinterland surrounding the port city of Bristol have been shown by Y-DNA testing to be derived for the I-Y33765 SNP.  This may indicate that this part of south west England represents an early locus of the SNP in the British Isles.  As the present working hypothesis is that I-Y33765 arrived in England with the Danish armies of Sweyn Forkbeard and Cnut the Great it is natural to ask if there is any evidence for settlement by these invaders at specific locations in south Gloucestershire and north Somerset?

Recent studies (Prior et al, 2010; Lewis, 2016) have used the work of Norman tax gatherers in 1086, as recorded in Domesday Book, to estimate the land owned in 1066 by descendants of King Cnut’s Danish followers in south west England and specifically in the Anglo-Saxon kingdom of Wessex.  In a detailed analysis Lewis (2016) has shown that eighty-one individuals with Danish names were landowners in Wessex on the eve of the Norman invasion and he considered “they represent scores of families at all levels of landed society which either were Danish or identified themselves as such” and “Most of the Wessex Danes of 1066 were probably Real Danes of the second generation, the sons of men who first acquired land under Cnut.”  Further his judgement is that “Wessex landowners with the strongest claim to be considered new settlers from Denmark” are those who ”bore the explicit byname ‘the Dane’ “ in Domesday Book.  

With these comments in mind, the Domesday record contains four “Real Danes” who together held eight Wessex manors, of which over 70% are within a 20km radius of the English I-Y33765 ancestral localities (see Figure 1).    All these manors are in the north of the county of Somerset with the main group of six clustered close to the Severn Estuary (Figures 1 & 2).   

Figure 1: Manors owned in 1066 by men described as “the Dane” in Domesday Book (blue circles) and the eighteenth century ancestral locality (red disc with white cross) of men who are derived (+) for the I-Y33765 single nucleotide polymorphism (SNP)

According to the classification adopted by Lewis two of these Danes are “great landowners”, one a “greater thegn” and the other a “lesser thegn”.  Their holdings vary significantly in extent and value but together must represent a community of newcomers from Scandinavia who had been living in Somerset for less than half a century in 1066.  Lewis considers these “Danes who came to Wessex after 1016 probably mostly acquired land by peaceful means, principally through marriage into English families and clientage from Cnut and Earl Godwin” and so for many Scandinavian newcomers we may conjecture that the manner by which they obtained their estates, that is marriage with Anglo-Saxon women, may also have implicitly ensured their Y-DNA entered the English genetic pool.

Table 2: Eleventh century Scandinavian landownership close to the eighteenth century home locations of I-Y33765 English men

The main group of six manors owned by these four “Real Danes” form a single contiguous Scandinavian land holding which stretched about 10km inland from the shore of the Severn Estuary at Clevedon (Figure 2).  It seems possible that this concentration of Scandinavian influence would attract compatriot “northmen” to this part of Wessex and may consequently have facilitated the establishment of further “visiting” Swedish Y-DNA in the area

Figure 2: Six manors owned by “Real Danes” (pink) form a contiguous Scandinavian estate in north-west Somerset

Lewis also speculates that as “Tickenham is only 5 miles from Bristol” and “Tholf’s acquisition of interests near Bristol…may well have been deliberate policy and the manors may have been associated with urban property which was simply not recorded in Domesday Book”.  Similar logic might be applied to Thorkel’s manor at Backwell which is even closer to the important town and port of Bristol.  Indeed each of the manors, with the exception of Clewer, might be considered to be within the hinterland of the port at Bristol and hence their owners might have property or other commercial interests in that town.  In the eleventh century Bristol was probably the second largest urban centre in the western half of Wessex (after Exeter) and had significant trade links with Dublin and the Viking trade routes along the west coast of the British Isles.  Writing circa 1125, so about a century after Cnut became king of England, William of Malmesbury described Bristol as “a port which is a commodious and safe harbour for all vessels, into which come ships from Ireland and Norway and from other lands beyond the seas” (Bettey,1996).  So the commercial trade of nearby Bristol may also have facilitated the arrival of Scandinavian Y-DNA at the manors of north-west Somerset.

While most of the Scandinavian owned manors are 12 to 24 km away from the eighteenth century ancestral locations of those English men who are derived for I-Y33765, the manor of Clutton, owned by “Thorkel the Dane” in 1066, is particularly close to the ancestral locality of the IN82043 individual within the parish of Chew Magna (Figure 3).  Between 1750 and 1850 ancestors of IN82043 are recorded in baptismal, marriage and burial registers in several parishes within the valley of the River Chew (Figure 3, pale green) and one of these parishes, Stowey, directly abuts Clutton parish which itself approximates to the area of the Manor of Clutton (Figure 3, olive green) as recorded in Domesday Book. There is no reason to think this geographic proximity is evidence that the I-Y33765 mutation had been circulating in the Chew Valley area since the latter years of Anglo-Saxon England but at the very least it is a noteworthy coincidence.

Figure 3: “Thorkel the Dane” was Lord of the Manor of Clutton in 1066.  The parish of Clutton (olive green) which approximates to that medieval manor directly abuts the parish of Stowey and is very close to several other parishes (pale green)where ancestors of IN82043 are recorded in church registers during the period 1750-1850. 

With respect to an average distance between the Scandinavian owned manors and the ancestral homes of I-Y33765 men we have an estimate of about 19km (Table 2). Also we can assume there would be approximately 25 generations spanning the seven hundred years between the Norman Conquest and the mid eighteenth century.  Using these numbers the rate of movement required, to account for the observed distribution of I-Y33765 in the 1750’s relative to a supposed locus for the SNP’s English origin from one of these pre-Conquest Scandinavian owned manors (Figure 1), would be less than one kilometre per generation. 

Hence, based on the present evidence, it seems quite feasible to speculate that, a man born in, or with ancestry from, south east Sweden, who was associated during the eleventh century with one or more of these Scandinavian owned Somerset manors, could be the patriarch of modern men whose ancestry is from south Gloucestershire and north west Somerset and who are derived for the I-Y33765 mutation.

References

Bettey, J., (1996) St Augustine’s Abbey, Bristol, Bristol Branch of the Historical Association, The University, Bristol. 28pp

Lewis, C.P., (2016) Danish Landowners in Wessex in 1066, p172-211, In: Danes in Wessex. The Scandinavian impact on Southern England c800-c1100, Eds, Ryan Lavelle & Simon Roffey, Oxbow Books

Prior, S.,Roberts, T. & Twinn, P., (2010) In Search of Vikings in South West England, p103-124, In: Early Medieval Enquiries, The Proceedings of the Clifton Antiquarian Club, V 9, Eds, Abby George, Donovan Hawley, George Nash, John Swann, Laurie Waite, Clifton Antiquarian Club, Bristol