Our Stone Paternal Lineage


Our Descent from Early Humans

In the human evolutionary tree, we belong to the genus Homo, which appeared perhaps a little more than 2.5 million years ago, at roughly the beginning of the current ice age (the Quaternary or Pleistocene glaciation) and a little after the time when stone tools began to be used. Homo erectus ("upright man"), who evolved in Africa (or perhaps in Asia) from earlier Homo species, eventually populated much of Africa, Europe and Asia; these were hunter-gatherers who used stone tools and weapons and who learned to control fire. (This entire period is part of the Stone Age.) Homo erectus was the ancestor of Homo heidelbergensis, who is ancestral to several extinct species such as Homo neanderthalensis but also to our species Homo sapiens
("wise man") and to our subspecies Homo sapiens sapiens (anatomically modern humans), who emerged around 200,000 years ago.

   Stone hand ax

Homo erectus stone hand axe.

Great Rift Valley, East Africa,
1 million to 400,000 years before present. 
From the collection of Don Stone.

Migration Out of Africa

The most popular theory until early 2016 was that some Homo sapiens migrated from East Africa to Asia 60,000 or more years ago, arriving in Australia some 50,000 years ago, and that around 50,000 years ago another Homo sapiens migration out of Africa occurred, this time to the Middle East, from which place they spread (for example) to Europe, where they encountered other species (such as Homo neanderthalensis) and apparently interbred with them. However, an analysis of the mitochondrial DNA in the bones or teeth of 55 European modern human remains dating from around 35,000 years ago (Late Pleistocene) to 7,000 years ago (early Holocene) supports the theory that there was a single major migration out of Africa (somewhat more recent than 55,000 years ago) which led to modern humans settling in both Australasia and Eurasia (Cosimo Posth et al., "Pleistocene Mitochondrial Genomes Suggest a Single Major Dispersal...," Current Biology, published online Feb. 4, 2016). This proposed single major migration would probably have taken place when the climate was more mild and moist in Arabia than in northeast Africa.

  For some details, see the brief discussion below of this hypothesized single major dispersal out of Africa.
  (If needed, some minimal genetics background is available above the dispersal discussion.)

It has been most widely assumed that our ancestors were confined to refugia in southern Europe (e.g., in the Balkans or middle Danube basin) during the Last Glacial Maximum (roughly from 26,500 to 19,000 years ago) but were able to migrate north as the ice receded. However, Posth and his colleagues propose that the people in these refugia were largely replaced by immigrants from elsewhere, and these immigrants and their descendants were the ones who actually traveled north as the ice receded.

Relatively Recent Innovations: Agriculture, Metal-working, Writing

Agriculture arose independently in several different places beginning about 12,000 years ago. It provided people with a greater quantity of food, though for quite a while the food had less variety and nutritional value than the earlier hunter-gatherer diet. The development of agriculture, with its sedentary rather than nomadic lifestyle, is a dominant feature of the last part of the Stone Age (called the Neolithic Age, i.e., the New Stone Age). Yuval Noah Harari makes the point in Sapiens that rather than viewing humans as domesticating wheat we could view wheat as domesticating humans, leading them to clear fields for its benefit and then to plow, plant, irrigate, fertilize, and weed the fields as well as to protect them by fencing. As a result, the amount of wheat on the earth multiplied probably more rapidly than the amount of people on the earth.

Several thousand years later people developed metal-working skills, producing copper or alloy tools, cups, jewelry, etc.; the most common alloy was bronze (copper plus, usually, tin).

Around this time, various number systems were developed for record keeping (e.g., for trade), the simplest being tally systems (one mark corresponds to one item). Not long afterwards proto-writing was developed, allowing the representation of not only the quantity but also what was being counted.

The Bronze Age was followed (at different times in different places) by the Iron Age. It was in the Iron Age that written language developed and alphabetic characters were introduced.

  Cuneiform tablet

Terracotta cuneiform tablet section from temple archives, relating to perishable goods, beer and reeds, and including some personal names.

Sumer, Third Dynasty of Ur,
ca. 2112 – ca. 2004 B.C.   From the collection of Don Stone.

Migration to Britain

Our ancestors arrived in northern Europe several thousand years ago, but their precise migration path and timeline are uncertain. Our haplogroup I-Z63 is believed to have arisen roughly 4,700 years ago, perhaps in or near what is now Denmark (based in part on the current distribution of this haplogroup). Our later paternal ancestors were certainly in what is now England by the time the Plantagenets began to rule, and perhaps long before this. There are at least three possible routes our ancestors may have taken from the general area of Denmark to England:

  1. From Denmark (at that time basically Jutland and Anglia) or northwestern Germany or the Netherlands (the Saxon or Frisian coast of the North Sea) to England as Jutes, Angles, Saxons, or Frisians;
  2. From Scandinavia to England as Vikings;
  3. From Scandinavia to Normandy as Vikings and later to England as Normans.

It is currently difficult to know how likely these possibilities are, though they have probably been listed in order of decreasing probability. Note that all of our Stone ancestors for whom we have records in England lived in Essex, i.e., in the old kingdom of the East Saxons.

Our Recent Paternal History

Roughly 55 miles northeast of London, in Tendring Hundred in the northeast part of the county of Essex, our Stone ancestors lived for many generations in three adjacent rural parishes: Little Bentley, Ardleigh, and Great Bromley. (The "ley" or "leigh" at the end of these parish names is Anglo-Saxon for "meadow" or "pasture".)

Widespread adoption of hereditary surnames in southern England and East Anglia began around 1250 and achieved considerable momentum during the reign of King Edward I (1272-1307). The early appearances of our surname in Tendring Hundred have the form "atte Stone", i.e., "at the Stone", indicating that the original bearer lived near a prominent stone. Since there are no natural stone formations of any significant size in this area, the stone was probably a road or boundary marker.

The first known use of the surname Stone in Tendring Hundred occurs in 1302 when Philip atte Stone, late servant of Robert de Vere, Earl of Oxford, was accused with others of forcibly entering the park of the said earl at Great Bentley and hunting therein against his will. It would not be surprising if Philip or his father was the first in his family to use the surname "atte Stone".

Walter atte Stone of Little Bentley appears in subsidy rolls (tax lists) for 1320 and 1327. (It is possible that he is a son of the above Philip atte Stone.) In 1398 William atte Stone appears in Ardleigh (see top of chart to right), and since he had a son named Walter, it is likely that he is descended from the above Walter atte Stone of Little Bentley in 1320 and 1327.

Seven generations after William atte Stone the brothers Simon and Gregory Stone migrated to Massachusetts in 1635 to escape persecution as Puritans in England. Puritans wanted to purify the established Church of England (removing any vestiges of non-biblical Roman Catholic theology or practice), and they rejected the established church's hierarchy of authority, believing instead that individuals could interpret the bible for themselves and that congregations had the right to conduct their own affairs.

Our Early Paternal Genetic History

The preceding discussion of migration out of Africa shows how genetic data can help us learn about the migrations of early humans (both the routes and their timelines). Let's focus now on our early paternal genetic history, as revealed in part by genetic testing of living individuals.
  If needed, some minimal genetics background is supplied below. 

Using the current Y-Chromosome phylogenetic tree, with Y-Chromosomal Adam at the top, our inital sequence of mutations corresponds to the following haplogroups:  A0-T (our first deviation from Y-Adam), A1, A1b, BT, CT, CF, and F. (Note that these mutations are cumulative; members of haplogroup F also have the mutations defining CF, CT, etc. Incidentally, these mutations are often called SNPs, SNP being an acronym for their formal name: single-nucleotide polymorphism. A different type of mutation is useful for relatively modern genealogy: insertions or deletions within short tandem repeats or STRs.) The field of genetic genealogy has advanced surprisingly quickly, correcting and adding detail to the Y-Chromosome phylogenetic tree as more living people have been tested (and tests have become more detailed, sophisticated and cheaper) and as more ancient DNA samples have become accessible. We can illustrate this progress with two views of haplogroup F and the later haplogroups I and J.

  See haplogroup F example below. 

Our More Recent Paternal Genetic History

The following table continues the story from haplogroup IJ to the most recent mutation currently detected for me; the data comes from YFull: http://www.yfull.com/tree/IJ/ and http://www.yfull.com/tree/I1/. Their statistical approach to dating, based on derivation of the SNP mutation rate from a large quantity of Big Y and FGC data together with Y-chromosome sequences for three ancient DNA samples, is explained in http://www.yfull.com/faq/what-yfulls-age-estimation-methodology/ and http://www.yfull.com/faq/how-does-yfull-determine-formed-age-tmrca-and-ci/. Dates in the table are expressed in years before present or ybp.

YFull DNA Data
Haplogroup Date haplogroup
was formed
[by the appear-
ance of a new mutation],
in ybp
Date of Most Recent
Common Ancestor
in ybp
Proposed geographic origin of haplogroup Significant events in human development
[Sources: Jared Diamond's
Guns, Germs, and Steel
Yuval Noah Harari's Sapiens: A Brief
History of Humankind
Anthony Adolph's In Search of Our
Ancient Ancestors
. . . . . . . . . . . .    
IJ 46,400 42,400 West Asia    
I [= I-M170] 42,400 27,300 Europe    
I1 [= I-M253] 27,300 4,700 Europe 13,000 ybp: beginnings of village life in a few places
12,000 ybp:

origin of agriculture (cultivation of crops, domestication of animals)
before 5,000 ybp: invention of writing, perhaps in Sumer
(located in what is now modern Iraq)
I-DF29 4,700 4,700 Europe    
I-Z63 4,700 4,200 In or near modern Denmark 4,250 ybp: first empire (Akkadian Empire of Sargon)
. . . . . . . . . . . .    
I-Y3979 4,100 4,000      
I-Y3969 4,000 1,900   2,500 ybp: invention of coinage
I-Y3969* 1,900        

Note that the dates given above are actually approximate midpoints of intervals. For example, the age of haplogroup IJ is estimated by YFull to be between 48,900 ybp and 43,800 ybp (for a confidence interval of 95%; a narrower range could be specified, though with less confidence that the actual formation date was in that range); the age of IJ given in the table, 46,400 ybp, is the (rounded) midpoint of this interval.

The date of the MRCA in the table is the approximate date of the most recent ancestor in the given haplogroup, prior to the mutation that defines the "child" haplogroup. So we had a sequence of ancestors in haplogroup IJ from about 46,400 ybp to about 42,400 ybp. Then the mutation M170 occurred, defining haplogroup I, which thus has the formation date of about 42,400 ybp.

Our Haplogroup I1 was founded during the last glacial period (ice age), shortly before the Last Glacial Maximum (LGM). Northern Europe was covered by ice during the roughly 7,000 years of the LGM, but then as the glaciers receded, I1 hunter-gatherers were able to migrate north, eventually reaching what is now northern Germany, Scandinavia, and probably even Doggerland, the area (now submerged beneath the North Sea) which connected England with continental Europe.

Maciamo Hay says (http://www.eupedia.com/europe/Haplogroup_I1_Y-DNA.shtml#origins):

The I1 branch is estimated to have split away from the rest of haplogroup I some 20,000 years ago. I1 is defined by at least 25 unique mutations, which indicates that this lineage experienced a serious population bottleneck. Men belonging to this haplogroup all descend from a single ancestor who lived between 10,000 and 8,000 years ago.
  (See bottleneck reasoning below for details.) 

More recently, YFull estimated the time back to this single I1 ancestor (given in the table above as the date of the MRCA for I1) as 4,700 ybp, significantly more recent than 10,000–8,000 ybp. The difference between these two estimates is likely due to different assumed or computed mutation rates. (Note that YFull estimates that the formation of I1 occurred around 27,300 ybp, significantly earlier than the estimate of 20,000 ybp by Maciamo Hay.)

In the above YFull table of successive haplogroups, I have omitted several haplogroups which came in close succession after I-Z63 and before I-Y3979. The next-to-last line in the table is for haplogroup I-Y3969 (also known as I1a3a1a1b1b). I and two other people who took the Family Tree DNA Big Y test and forwarded the results to YFull were found to have the mutation (SNP) Y3969. Further mutations were found for the other two (who are close relatives of each other), dated to about 1,900 ybp, but the same or similar mutations were not found for me. The asterisk (*) in the final line of the table indicates that haplogroup I-Y3969 is the most detailed haplogroup we can currently assign for my DNA. Hence I am in a position similar to the later sons of the haplogroup-X father introduced in the Genetics Background (immediately below): there are one or more mutations that some have but I don't have. (However, I most likely do have some mutations from I-Y3969 that were not caught by the Big Y test).

  Top of chart
Middle of chart
Bottom of chart

Genetics Background (for Migration Out of Africa or Our Early Paternal Genetic History above)

Human DNA is located in two places in cells: in the nucleus and in the mitochondria (which convert chemical energy from food into a more usable form). Most nuclear DNA is inherited from both parents via recombination (a process by which DNA is exchanged between the maternal and paternal chromosomes). However, Y-chromosome DNA is inherited only from the father and only by sons. Mitochondrial DNA is inherited only from the mother.

Looking first at the patrilineal situation, the Y chromosome is usually inherited unchanged but occasionally has one or possibly more mutations. When there is a mutation in a son's Y-DNA, this son is the founder of a new Y-chromosome haplogroup or clade (defined and characterized by this mutation); this new haplogroup will be a subgroup of the father's haplogroup. Male-line descendants of this son will inherit this mutation and belong to the same new haplogroup, as well as to all the older and larger haplogroups which are ancestral to the new one in the Y-chromosome phylogenetic tree. To continue this example, let's suppose that the father has several sons, the oldest son having the mutation and all the other sons having the same Y-DNA as their father (these sons will be members of the same haplogroup as their father).

However, a male-line descendant of one of these non-mutation sons (or of one of their agnatic cousins, uncles, etc.) may have a different mutation (the chances are very small that it will be the same mutation as the oldest son had), and this different mutation will define a different haplogroup. Let's call the father's haplogroup X, the oldest son's haplogroup X1, and the later descendant's haplogroup X2. Since X1 and X2 both split off from X, they are in a sense "children" of X, and these "children" will have other "children" as further mutations occur. Hence, we have a tree somewhat like a standard tree of descendants in genealogy, but this phylogenetic tree shows the evolution of the human Y chromosome—it contains haplotypes (Y-DNA data) rather than individuals. The notation used for the phylogenetic tree is somewhat like the Burke's Peerage style of presenting descendants: children are listed indented under their parent. The tree for the above example would look like this:

 └ X

At the top of the Y-chromosome phylogenetic tree is the haplogroup of Y-chromosomal Adam, the most recent common ancestor patrilineally of all living humans.

Similar comments can be made about the matrilineal situation, involving mitochondrial DNA (mtDNA). At the top of the mtDNA phylogenetic tree is the mtDNA haplogroup of Mitochondrial Eve, the most recent common ancestor matrilineally of all living humans. Each mtDNA mutation adds a branch to this tree.

Single Major Dispersal Out of Africa (some details not given in Migration Out of Africa above)

The mtDNA haplogroup M has been found in modern Asians, Australasians, and Native Americans, but not in modern Europeans, and this information has been considered evidence of two separate dispersals out of Africa (since the mutation defining M could likely have arisen in Asia in someone who was part of the first dispersal). But Posth et al. discovered that haplogroup M was present in the newly-sequenced mtDNA from three hunter-gatherers of Pleistocene Europe, suggesting that the M mutation arose in Africa and that there was a single major migration out of Africa (but that M became extinct in Europe presumably during the stressful circumstances of the Last Glacial Maximum).


Haplogroup F Example (from Our Early Paternal Genetic History above)

Here are snapshots of our understanding of haplogroup F at two different times:

  This is the section of the 2005 Y-Chromosome Phylogenetic Tree (distributed as a poster by Family Tree DNA) that includes haplogroup F and its children G, H, I, J, and K:

 └ F

(Note that the five haplogroups G through K were placed as children
of F in part because no better information was then available.)
  In contrast, this is the section of the 2015 Y-Chromosome Phylogenetic Tree that includes haplogroup F and its "descendants" G, H, I, J, and K:

 └ F

To summarize, at the beginning of 2005 it was thought that haplogroups G, H, I, J, and K all split off directly from haplogroup F; from 2005 to 2015 many new mutations and thus haplogroups were discovered, some of which were intermediate haplogroups between F and G, H, I, J, or K. The first such intermediate haplogroup is named GHIJK to show the haplogroups which will eventually come from it; G splits off from GHIJK as does another intermediate haplogroup, HIJK. Looking further down in this tree, around the end of 2005 haplogroups I and J were discovered to have split off from an intermediate haplogroup IJ. This discovery was made independently by more than one scientist. One discoverer was Dr. James F. Wilson, associated with the company Ethnoancestry; Dr. Wilson discovered a mutation which was given the name S22 (the initial S in the name is a code indicating that the mutation was discovered by Dr. Wilson). The same mutation was also discovered by Dr. Peter Underhill at Stanford University and given the name M429. I was an early customer of Ethnoancestry, and in January 2006 I received email from its president Dr. David Faux informing me that in addition to performing the tests I had ordered, they took the liberty of testing me for the recently discovered mutation S22, and the presence of that mutation in my DNA and in the DNA of a member of haplogroup J (and in no members of haplogroups other than I and J) showed that there was a new earlier haplogroup, IJ, from which I and J developed. So my personal DNA helped revise this early part of the Y-Chromosome Phylogenetic Tree.


Bottleneck Reasoning (behind bottleneck comment of Maciamo Hays)

A population bottleneck (or genetic bottleneck) is a dramatic reduction in genetic diversity that accompanies a dramatic reduction in population size, due to environmental events (e.g., earthquake, climate change) or human activities (e.g., war). Why do we suspect an I1 bottleneck? Let's assume (somewhat arbitrarily) that M253 was the first of these 25 or more unique mutations defining I1. Then any one of the other unique mutations would define a new haplogroup if there were some members of I1 who had it (and had descendants) and some who didn't have it (but had descendants).  This new haplogroup would be a "child" of I1 in the phylogenetic tree.  However, we don't currently know of any members of I1 who have just some of this set of unique mutations; if a person has M253, then he has all the other unique mutations.  There certainly were many men long ago who had some of these unique mutations but not others, but their line of descendants died out.  Hence the proposal that all later I1 men are descended from a single I1 ancestor who lived thousands of years after the founding of I1.


Prepared by Don C. Stone, Jan.–Apr. 2016.

This document is licensed under a
Creative Commons Attribution-ShareAlike 3.0 Unported License